Devendra Kumar Yadava

Harsh Kumar Dikshit

Gyan Prakash Mishra
Shailesh Tripathi Editors

Fundamentals
of Field Crop
Breeding
Fundamentals of Field Crop Breeding
Devendra Kumar Yadava •
Harsh Kumar Dikshit •
Gyan Prakash Mishra • Shailesh Tripathi
Editors

Fundamentals of Field
Crop Breeding
Editors
Devendra Kumar Yadava Harsh Kumar Dikshit
Crop Science Division Division of Genetics
Indian Council of Agricultural Research Indian Agricultural Research Institute
Delhi, India Delhi, India

Gyan Prakash Mishra Shailesh Tripathi

Division of Genetics Division of Genetics
Indian Agricultural Research Institute Indian Agricultural Research Institute
Delhi, India Delhi, India

ISBN 978-981-16-9256-7 ISBN 978-981-16-9257-4 (eBook)

https://doi.org/10.1007/978-981-16-9257-4

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Foreword

The book “Fundamentals of Field Crop Breeding” describes fundamental concepts

and also the advances in plant-breeding practices including developments in crop
genomics. The book covers origin, reproduction biology, genetic principles, plant-
breeding procedures and techniques and tools used in the improvement of major field
crops. The chapters are structured well to describe breeding procedures starting from
conventional breeding methods to modern molecular tools including several new
developments. In addition, the information on status of crop improvement and
conservation has added value to the publication. The book bridges the knowledge
gap with regard to modern breeding tools for developing high yielding, climate-
resilient and micronutrient-dense varieties of different field crops.
I congratulate the editors Drs. Devendra Kumar Yadava, Harsh Kumar Dikshit,
Gyan Prakash Mishra and Shailesh Tripathi along with all the contributors of
different chapters for bringing out this publication. I hope that the book would
greatly benefit students, research scholars, scientists and others having interest in
crop breeding.

Department of Agricultural Research and Education T. Mohapatra

Indian Council of Agricultural Research
New Delhi, Delhi, India
26 November 2021

v
Preface

The current global population of 7.5 billion is expected to reach 9.3 billion by the
year 2050. To meet the food requirements of this burgeoning population, food
production has to be enhanced by nearly 60%. Such a huge enhancement in global
food production needs an increase in the productivity of nearly all the crops. In
addition, more nutritious crops are required to tackle the micronutrient deficiency
problem in changing climate. In the present scenario, climate change,
biofortification, mitigation of biotic and abiotic stresses are the major challenges
before the plant breeders in achieving the required food production in times to come.
The book entitled “Fundamentals of Field Crop Breeding” compiles crop-based
breeding procedures for the major crop plants and is an advanced textbook and a
reference book for the post-graduate plant-breeding students and also for the plant
breeders. Twenty-six chapters covering various aspects of field crop breeding have
been included in this book. This book covers details of cereals, commercial crops,
oilseeds and pulse crops. Besides, overall progress made in various field crops,
efficient breeding in the crops using modern tools and the maintenance breeding in
different crops are also suitably covered. In addition, this book consolidates the
fundamental concepts and the latest advances in plant breeding of different crop
plants. The latest developments in the breeding of crops using both conventional and
molecular approaches including genomics are also included. Sincere efforts have
been made by the authors to include most of the relevant latest developments about
breeding of field crops. The book is expected to expose the students and researchers
to modern breeding tools and advanced concepts in the breeding of field crops.
The editors are hopeful that compiled information will serve as a basic resource
material for students, teachers and researchers which will be of help in improving the
production and productivity of various field crops. The crop-wise information has
been compiled by most experienced plant breeders. The editors are extremely
thankful to all the authors for their cooperation and contribution.

Delhi, India Devendra Kumar Yadava

Harsh Kumar Dikshit
Gyan Prakash Mishra
Shailesh Tripathi

vii
Contents

1 Breeding Field Crops: History, Current Status and

Introspections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
K. K. Vinod, S. Gopala Krishnan, Manoranjan Senapati,
and Ashok Kumar Singh
2 Wheat Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Gopalareddy Krishnappa, Bhudeva Singh Tyagi, Vikas Gupta,
Arun Gupta, Karnam Venkatesh, Umesh R. Kamble, Sendhil R,
Gyanendra Singh, and Gyanendra Pratap Singh
3 Rice Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
S. Gopala Krishnan, K. K. Vinod, Prolay K. Bhowmick,
Haritha Bollinedi, Ranjth K. Ellur, Rakesh Seth, and A. K. Singh
4 Maize Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Firoz Hossain, Vignesh Muthusamy, Jayant S. Bhat,
Rajkumar U. Zunjare, Santosh Kumar, Nitish R. Prakash,
and Brijesh K. Mehta
5 Barley Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Santosh Kumar Bishnoi, Madhu Patial, Chuni Lal,
and Ramesh Pal Singh Verma
6 Pearl Millet Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
C. Tara Satyavathi, S. Mukesh Sankar, Sumer Pal Singh,
Chandan Kapoor, S. L. Soumya, and Tripti Singhal
7 Sorghum Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
Prabhakar, R. Madhusudhana, and C. Aruna
8 Small Millets Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 449
Vilas A. Tonapi, K. N. Ganapathy, K. Hariprasanna,
B. Venkatesh Bhat, B. Amasiddha, S. Avinash, and C. Deepika
9 Sugarcane Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499
Bakshi Ram, R. Karuppaiyan, and G. Hemaprabha

ix
x Contents

10 Jute Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571

C. S. Kar, Pratik Satya, and Gouranga Kar
11 Cotton Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 609
Vijay N. Waghmare
12 Maintenance Breeding of Pusa Basmati Varieties . . . . . . . . . . . . . 677
Rakesh Seth, A. K. Singh, and S. Gopala Krishnan
13 Maintenance Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 703
R. N. Yadav, Priya Ranjan Kumar, Zakir Hussain, Sangita Yadav,
Sandeep K. Lal, Atul Kumar, P. K. Singh, Amit Bera,
and Shiv K. Yadav
14 Efficient Breeding of Crop Plants . . . . . . . . . . . . . . . . . . . . . . . . . . 745
Pawan L. Kulwal, Reyazul Rouf Mir, and Rajeev K. Varshney
15 Brassica Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 779
Devendra Kumar Yadava, Yashpal, Navinder Saini, Joghee
Nanjundan, and Sujata Vasudev
16 Groundnut Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 837
T. Radhakrishnan, Praveen Kona, B. C. Ajay, and Narendra Kumar
17 Soybean Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 907
Anita Rani and Vineet Kumar
18 Castor Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 945
S. Senthilvel, T. Manjunatha, and C. Lavanya
19 Sunflower Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 971
H. P. Meena and M. Sujatha
20 Chickpea Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1009
G. P. Dixit, A. K. Srivastava, V. Jayalakshmi, Shayla Bindra,
and Sarvjeet Singh
21 Pigeonpea Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1063
S. J. Satheesh Naik, Abhishek Bohra, Indra Prakash Singh,
and Abha Tiwari
22 Mungbean Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1097
Gyan Prakash Mishra, Harsh Kumar Dikshit, Kuldeep Tripathi,
Muraleedhar S. Aski, Aditya Pratap, Uttarayan Dasgupta,
Ramakrishnan M. Nair, and Sanjeev Gupta
23 Urdbean Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1151
Debjyoti Sen Gupta, Jitendra Kumar, Ashok Kumar Parihar,
Anup Chandra, G. K. Sujayanand, and Sanjeev Gupta
Contents xi

24 Lentil Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1181

Harsh Kumar Dikshit, Gyan Prakash Mishra, Muraleedhar S. Aski,
Akanksha Singh, Kuldeep Tripathi, Ruchi Bansal, Aditya Pratap,
Sanjeev Gupta, and Shiv Kumar
25 Field Pea Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1237
A. K. Parihar, Rajesh Yadav, Amrit Lamichaney, R. K. Mishra,
Anup Chandra, D. S. Gupta, Kuldeep Tripathi, K. K. Hazra,
and G. P. Dixit
26 Lathyrus Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1323
A. K. Parihar, S. Barpete, Arpita Das, Amrit Lamichaney,
and Sanjeev Gupta
About the Editors

Devendra Kumar Yadava is serving as ADG Seeds, Indian Council of Agricul-

tural Research, New Delhi. Breeder for the last 25 years including 19 years at Indian
Agricultural Research Institute (IARI), contributed in the development and release of
21 varieties (mustard 18; pulses 3) including early maturing mustard varieties, viz.
Pusa Mustard 25, 27, 28, 26 and RGN 145 which have provided greater choice to
farmers under changing climatic scenario. Bred six low erucic acid varieties, viz.
Pusa Mustard 21, 22, 24, 29, 30 and 32 and two Canola quality varieties Pusa
Double Zero Mustard 31 and 33. He is Fellow of National Academy of Agricultural
Sciences (NAAS) since 2015 and recipient of many awards like Rafi Ahmed Kidwai
Award 2017, ICAR, New Delhi; Dr. B.P. Pal Memorial Award, 2012, IARI, New
Delhi; NAAS Recognition Award 2018; Dr. P.R. Kumar Brassica Outstanding
Scientist Award 2017, SRMR, Directorate of Rapeseed Mustard Research,
Bharatpur. He has guided three M.Sc. and five Ph.D. students as Chairman and
presently guiding four Ph.D. students and published 90 research papers in high
impact factor journals.

Harsh Kumar Dikshit is serving as Principal Scientist at ICAR-Indian Agricul-

tural Research Institute, New Delhi (India). He is working on genetic improvement
of grain legumes through conventional and molecular approaches. He has developed
15 varieties of different grain legumes (lentil, mungbean and dry beans) for cultiva-
tion in India. He is involved in the development of leading mungbean varieties IPM
99-125, IPM 02-3, IPM 02-17 and Pusa 1431 and lentil varieties L 4717 and L 4727.
His present focus is on basic and applied research on early maturity, biofortification
and biotic stresses of lentil and mungbean. He is faculty of Division of Genetics and
is involved in teaching different courses and thesis research guidance to post-
graduate students. He has done his Master’s and PhD in Plant Breeding from G.B.
P.U.A. & T. Pantnagar (India). He is Fellow of ISGPB and ISRPD and recipient of
several awards including ICAR-Dr. Rajendra Prasad Award 2020.

Gyan Prakash Mishra is currently working as Principal Scientist at ICAR-Indian

Agricultural Research Institute, New Delhi (India). Before that he has worked at
DRDO-Defence Institute of High Altitude Research, Leh (India) as Scientist “C”,

xiii
xiv About the Editors

ICAR-Directorate of Groundnut Research, Junagadh (India) and ICAR-Indian Insti-

tute of Vegetable Research, Varanasi (India) as Senior Scientist. His major research
interest includes crop improvement through conventional, molecular and transgenics
approaches. He has done his Master’s and PhD in Genetics from Indian Agricultural
Research Institute, New Delhi (India) and postdoc from University of California,
Riverside and Purdue University, USA as BOYSCAST-Fellow. As a faculty of
Division of Genetics, he is involved in teaching of different courses and also guiding
the post-graduate students. He is the recipient of various prestigious awards includ-
ing NAAS Associate 2018, NASI-Membership 2018, IARI-Merit Medal and Best
Student Award 2001, ISCA-Pran Vohra Award 2012, DRDO-National Science Day
Award 2009 and ICAR-Dr. Rajendra Prasad Award 2020.

Shailesh Tripathi is currently working as Principal Scientist at ICAR-Indian Agri-

cultural Research Institute, New Delhi (India). Prior to joining IARI, he served as
Scientist at International Crops Research Institute for the Semi-Arid Tropics
(ICRISAT), Hyderabad. He obtained his Ph.D. in Plant Breeding and Genetics in
2004 from G. B. Pant University of Agriculture and Technology, Pantnagar. He was
involved in transfer of “QTL hotspot” containing quantitative trait loci for several
root and drought tolerance traits into popular chickpea varieties of IARI resulting in
the release of drought-tolerant chickpea varieties. He also developed chickpea
suitable for machine harvesting and extra-large seeded kabuli chickpea. He has
published over 45 research papers in peer-reviewed journals. He is actively involved
in teaching post-graduate students as Faculty of Genetics at IARI.
Breeding Field Crops: History, Current
Status and Introspections 1
K. K. Vinod, S. Gopala Krishnan, Manoranjan Senapati,
and Ashok Kumar Singh

Abstract

Agriculture is the fundamental basis of human evolution and has evolved itself as
the civilisations progressed. Crop breeding is a process in which the most chosen
plant is selected for further cultivation. The science behind the genetics has paved
the way to trait-based breeding, wherein desirable traits were selected over the
undesired ones. The breeding work in India began mainly with the widespread
evaluation of wheat genotypes for the improvement of grain, straw and rust
resistance. This was followed by breeding for a number of crops including
tobacco, sisal hemp, barley, flax and a few fruit tree species. In the year 1955,
All India Coordinated Research Project (AICRP) was launched which has
transformed the cultivar evaluation system and release in India. Even at the
international level, there was an upsurge in the establishment of a number of
crop-based non-profit research institutions. International Rice Research Institute
(IRRI) was the first such institute which was opened in the year 1960 at
Philippines. Breeding efforts in India is yet to venture deep into the genomics-
assisted breeding including genomic selection and gene editing in majority of the
field crops, although the research in this direction is progressing. Recent efforts
towards the integration of technologies to translate breeding success into genetic
gain are also discussed. With this backdrop, this chapter gives a brief about the
key developments in the breeding history of field crops, particularly in India,
during the last few decades. Also discussed are the future perspectives.

Crop improvement by breeding is a continuous process. Those who are engaged in this vital task
have a hand in crop plant evolution and enjoy the pride and privilege of fighting the war against
hunger - Anonymous.

K. K. Vinod · S. Gopala Krishnan · M. Senapati · A. K. Singh (*)

Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1

Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_1
2 K. K. Vinod et al.

Keywords

Breeding methods · Green revolution · Marker-assisted selection · Genomic

selection · Genetic gain

1.1 Introduction

Agriculture is a tradition as old as human civilisation. Since time immemorial,

agriculture was a gatherers’ pursuit wherein the grains, roots, fruits and nuts were
collected by the early hunters. Evidence for the use of cereal seeds such as sorghum
grasses dating back to 0.11 million years in the Late Pleistocene was seen from the
starch granule assembly on the surface of middel stone age tools (Mercader 2009).
Humans started organised agriculture much later in the Holocene, about
10,000 years ago, with the collective domestication of several grain species such
as wheat, rice, barley and chickpea (Eckardt 2010; Willcox et al. 2009; Zuo et al.
2017). However, the crop improvement by breeding began only in the late nine-
teenth century with the rediscovery of Mendel’s research findings. In breeding, selec-
tion is the crucial step that requires a multitude of factors and methods to achieve the
breeding objective. Starting from intuitive selection to genomic selection, the pro-
cess requires diversity to choose from. Therefore, generating new varibility is crucial
in crop breeding.
All the methods, be it for generating variability and/or for deciding to select, are
fundamentally anchored to the science of genetics. Breeding crop varieties revolves
around two elemental phenotypic dimensions, namely, quantitative and qualitative.
Quantitatively, the need ‘for producing more to feed more’, is the primary dimension
that safeguards the food security for the growing world population; while the second
defines how well the crop produce serves as the food and feed. All other breeding
objectives such as adaptation, tolerance to stresses, and resilience can be mapped
onto these basic dimensions.
Unlike, during the early Holocene when agriculture was mainly in the subsistence
mode, in the Anthropecene era, it has metamorphosised into an industry. Thereby
another dimension of ‘commercial’ has been sandwiched between the two basic
dimensions of crop breeding. This had brought in a dramatic evolution in agricul-
tural research globally, particularly in crop breeding. The most historical outcome of
this evolutionary transformation was the ‘green revolution’, which brought in a
paradigm shift in the way modern cultivars are bred.
Since the onset of the twentieth century, there have been consistent efforts to
control and understand the pattern of plant evolution. The contemporary birth of the
new sceince of genetics has spearheaded artificial hybridisations resulting in
identifying a better variant on a continuous scale facilitated by combining more
than one desirable trait at a time. This has led to the refinement of the selection
process in breeding. Besides, a weightage was attached to some traits such as yield
1 Breeding Field Crops: History, Current Status and Introspections 3

over the other, during the selection process. The breeding process has become more
systematic, thanks to the laws of inheritance by Gregor J. Mendel, who demonstrated
the possibility of predicting the occurrence of variation in a breeding population.
Later into the century, heredity has seen its molecular definition through the discov-
ery of deoxyribonucleic acid (DNA) structure by Watson and Crick in 1953. A
parallel development in mathematical and statistical predictions, invented by
R.A. Fisher, in combination with landmark genetic discoveries of T.H. Morgan, A.
H. Sturtvent, W. Bateson, G.W. Beadle, E.L. Tautum, O.T. Avery, C.M. MacLeod,
M. McArty, S. Benzer, J.B.S. Haldane, J. Lush, etc., laid out the foundation for the
architecture of modern plant breeding.
Humans use only 0.03% of the total flowering species for food. Among the
347,298 known species of vascular plants worldwide (WCVP 2020; Cheek et al.
2020), 50,000 are edible, but only ~120 are cultivated for food (FAO 1996). Among
these, just three crops, namely, rice, wheat and corn, supply more than 60% of the
world’s dietary energy. In addition, oilseeds, legumes and millets contribute more
than 15% of the calories (Loftas 1995). These crops, collectively known as field
crops form the backbone of global food security. Majority of the field crops are
annuals that produce staple grains in human food. They are cultivated in vast areas
and occupy lands all around the world. Among the various species humans have
domesticated, no other group of crops have undergone rigorous breeding efforts like
that of field crops leading to significant changes in the trait forms making them
amenable for intensive cultivation.

1.2 Chronicling Breeding for Improvement of Field Crops in

India

The breeding efforts in food staples have been tremendous during the last century.
Current estimates indicate that food demand will go up by 36–56% from the period
between 2010 to 2050 and, meanwhile the people at risk of hunger will shift sharply
from 91% to 8% (van Dijk et al. 2021). Crop breeding needs to be continuously
impressive as it was, in the coming decades too to meet such a formidable challenge.
This is highly relevant to India, which at present harbours 17.7% of the world human
population with a meagre 2.4% land share (Kumar 2011), and having an alarming
annual population growth rate of 1.0%. At the current rate, one per cent of the Indian
population is about 14 million, more than half the size of the population in Australia,
which means India adds more than one Australia every two years. Historically, India
has always been at the forefront of agricultural development worldwide. A subcon-
tinent that has been struggling to sustain agriculture since the beginning of the
twentieth century with continuous famines and crop failures, India was almost
absent in the world agricultural map at the beginning of the twentieth century.
Follwing the recommendations of Famine Commission of 1980, the Department
of Agriculture under the Goverment of India was revived, alongwith setting up of
several provincial agricultural departments. In 1903, the British Indian Government
decided to establish a Central Agricultural Research Institute under the Department
4 K. K. Vinod et al.

of Agriculture to introduce scientific agriculture in India. Consequent inauguration

of the Agricultural Research Institute and College in 1905 at Pusa in Bihar marked
the beginning of organised agricultural research in India (Howard and Howard
1929). Breeding research at the Agricultural Research Institute began with the
extensive evaluation of wheat cultures, with a main emphasis on hybridisation to
improve grain, straw and rust resistance. Breeding for other crops such as tobacco,
sisal hemp, barley, flax and a few fruit trees was also taken up (ARIC 1909).
Agricultural Research Institute and College was later renamed as Imperial Agricul-
tural Research Institute in 1919, and then as Indian Agricultural Research Institute
(IARI).
Contemporarily, rice breeding research was initiated in Bengal and Madras
provinces with the setting up of several research stations. The Royal Commission
of Agriculture in 1928 proposed to scale up and coordinate the agricultural research
pan India, by establishing an Imperial Council of Agricultural Research (GoI 1928).
The Imperial Council of Agricultural Research established in 1929 was rechristened
as Indian Council of Agricultural Research (ICAR), and provided with extensive
mandate on different crops. Understanding the immediacy of independent research,
ICAR had established several crop-specific research institutes at different locations
at different time (Table 1.1).
Among the crops, rice pioneered in setting up of research establishments in
India. Although the rice research had begun during the 1911–12 period, only Bengal
and Madras provinces were endowed with research, until the establishment of ICAR.
Further, several research stations were established, and by 1950, there were
82 research stations spread across 14 states (Ghose et al. 1960). The launch of the
All India Coordinated Research Project (AICRP) in 1955 reformed the cultivar
evaluation system and release in India. The major mandate of AICRP was to
coordinate applied research on national and regional issues and to develop
location-specific varieties and technologies in various crops. The first crop-based
project was started for maize in 1957, and was named All India Co-ordinated Maize
Improvement Project (AICMIP). Subsequently, the All India Coordinated Rice
Improvement Project (AICRIP) was established in 1965. Later on, several crop-
based coordination projects were initiated by ICAR at different crop research
institutes. These institutes were provided with regional research stations covering
all major production zones of the respective crops. Currently, every field crop has an
independent AICRP system, that links several agricultural universities, institutes and
private research organisations, who are involved in varietal/ technological develop-
ment, evaluation and release. As a whole, AICRP has grown to be the single largest
varietal evaluation and release system in the world. Additionally, to make agriculture
support countrywide, state governments have opened several agricultural
universities and research stations to cater for the need of local farmers and to provide
agricultural education. Crop improvement by breeding is one of the major mandates
of all crop-based research institutions.
1 Breeding Field Crops: History, Current Status and Introspections 5

Table 1.1 Establishment of major field crop-specific institutes in India under ICAR
Year Institute Location Mandate Crop(s)
1905 Agricultural Research Institute and Collegea Pusa Wheat, barley, tobacco
etc.
1937 Indian Agricultural Research Instituteb New Delhi Wheat, barley, rice,
legumes, Brassica,
horticultural crops
1946 Central Rice Research Institute (presently Cuttack Rice
National Rice Research Institute)
1976 Central Institute for Cotton Research Nagpur Cotton
1977 Directorate of Oilseeds Researchc (presently Hyderabad Oil crops
Indian Institute of Oilseed Research)
1978 Directorate of Wheat Researchc (presently New Delhi Wheat
Indian Institute of Wheat and Barley
Research)
1979 Directorate of Groundnut Researchc Junagadh Groundnut
1983 Directorate of Rice Researchc (presently Hyderabad Rice
Indian Institute of Rice Research)
1984 Directorate of Pulses Researchc (presently Kanpur Grain legumes
Indian Institute of Pulses Research)
1987 National Research Centre for Sorghumc Hyderabad Sorghum
(presently Indian Institute of Millets
Research)
1993 National Research Centre on Bharatpur Brassica
Rapeseed and Mustard (presently
Directorate of Rapeseed-Mustard Research)
1994 Directorate of Maize Researchc (presently New Delhi Maize
Indian Institute of Maize Research,
Ludhiana)
a
Renamed as Imperial Agricultural Research Institute in 1919
b
Shifted to New Delhi following the destruction of IARI at Pusa in Bihar earthquake of 1935
c
Instituted as AICRP, and later given independent research status

1.3 Role of International Centres in Strengthening

the Breeding Efforts

Contemporary to the inception of agricultural research institutions in India, globally,

there was a rise in installations of crop-based non-profit international research
institutions. The first among these, the International Rice Research Institute (IRRI)
was opened in 1960 at Los Baños, Laguna, in the Philippines. Subsequently,
International Maize and Wheat Improvement Centre (CIMMYT) came into being
in 1966, as a scientific and educational institution exclusively involved in wheat and
maize research. The year 1967 saw the opening of two more institutions, the
International Institute for Tropical Agriculture (IITA) in Nigeria and the Interna-
tional Centre for Tropical Agriculture (CIAT) in Columbia. Instituted in 1971 at
6 K. K. Vinod et al.

Montpellier in France, the Consultative Group of International Agricultural

Research (CGIAR) brought the international institutions under its governance.
Currently, there are 15 research centres under CGIAR, of which seven works on
tropical field crops. The major activity of these centres is breeding, besides other
allied technological development.
As per the 2020 performance report of the CGIAR, 78% of its innovations were
genetic with 66% impact directed to alleviate poverty and 15% directed to nutritional
security (CGIAR 2020). Sixty years into existence, international research
organisations could transform agricultural research worldwide sowing the
foundations of the green revolution in major cereals such as wheat and rice. The
noble efforts of Dr. Norman E. Borlaug in developing high yielding, semi-dwarf and
disease-resistant wheat varieties, which ensured food security in countries like India,
Mexico and Pakistan have earned him the popular title of ‘father of green revolution’
as well as a Nobel peace prize in 1970 (Swaminathan 2009), besides several others.
Aided by Dr. Norman Borlaug in wheat and IRRI in rice, Dr. M. S. Swaminathan
spearheaded transformative research in India from the fields of IARI in 1966. The
results were remarkable, a quantum jump of 42% increase in wheat production could
be achieved in one year. Three genes governing plant height, namely, rht1 and rht2
from Norin 10 in wheat and sd1 from Dee-Geo-Woo-Gen (DGWG) in rice, were
responsible for this phenomenal achievement in the history of crop evolution. This
gave an impetus to the breeding research in India and breeders geared up this
momentum to deliver scores of improved cultivars in the ensuing decades in all
the field crops.

1.4 Breeding Research on Field Crops

Until the beginning of the twentieth century, no organised breeding efforts had taken
place in field crops, anywhere in the world. The breeding research in India also
evolved simultaneously with similar efforts across the globe. Drawing parallel to the
developments in the science of genetics, different breeding methods dominated the
landscape of field crop improvement from time to time in India. In Fig. 1.1, we have
taken rice as the model crop to demonstrate the evolutionary pattern of breeding
methods, because rice was not only genetically rich in India but also had undergone
all the breeding methods developed so far. We would, therefore, be focussing our
discussions in this chapter based on Indian experience on breeding methodologies
during the past century and their evolution, establishment and impact made on
improving different field crops. Also, elaborate details of individual crops will not
be covered except for the key landmarks, keeping in mind that such details would be
following in subsequent chapters dealing with different field crops.
In the early twentieth century, the indigenous cultivars in India were of geneti-
cally admixed populations. Admixed populations had extreme variability within,
because of the significant proportion of wild alleles they carried. Since these
populations did not undergo serious selection for yield, the wild alleles were more
aligned to adaptation, rather than productivity. Because of these, the cultivars were
1 Breeding Field Crops: History, Current Status and Introspections 7

Introduction

Pureline selection

Hybridisation and selection

Mutation breeding

Hybrid breeding
Green revolution
Molecular breeding

1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020

Fig. 1.1 Evolution of breeding methodologies in rice improvement. Unlike in rice, introduction of
elite genetic materials had begun in other field crops much earlier (denoted by the dotted lines).
Introduction in rice has been comparatively intermittent

tall, prone to lodging, hardy, less yielding, photosensitive and took longer time to
yield. Although selections were carried out among these populations in the early
years, only marginal yield improvement could be realised initially. However, begin-
ning from the 1960s breeding research has started to become more organised, with
the plans of pan India integration of varietal release systems and institutional
research. This movement in research organisation paid off with the development
and release of newer cultivars and invigorated research systems sowing the seeds of
the green revolution in the coutry. A glance at the productivity spectrum of major
field crops (Fig. 1.2) reveals that all the crops have experienced a yield gain of at
least by a minimum of 107% as in red gram to 539% in maize in the next 70 years.
The next highest yield increase was in wheat (516%), followed by cotton (513%),
pearl millet (475%) and rice (405%).

1.4.1 Introduction

The initial part of the organisational plant breeding efforts in India was laden with
scores of introductions of crop varieties from abroad. Owing to its rich indigenous
diversity, introductions in rice were intermittent, but in other field crops such as
wheat and maize, a considerable number of genotypes were introduced, particularly
through international centres. Several direct introductions happened during the
pre-green revolution period. The activity was so intense and programmed, a separate
Division of Plant Introduction for coordinating the imports from abroad was started
at IARI in 1961 (Pal 1962). The Division later became the current National Bureau
of Plant Genetic Resources (NBPGR) in 1976. Among the most notable field crop
introductions in IARI were Ridley from Australia; Lerma Rojo 64, Sonora 64 and
PV18 from Mexico in wheat; LSB2 and Dolma from the USA; Clipper from
8 K. K. Vinod et al.

Fig. 1.2 Productivity of major field crops in India, between 1950 and 2020. Except for three crops,
productivity increase was more than 200% during this period. *Crops such as sunflower, lentil and
soybean were later introductions and their base data is of 1970. ¶Sugarcane yield is given in quintals
and not in kilograms. (Data source: GoI 2020)

Australia in barley; IR8, IR20, IR36, IR50 and IR64 from the Philippines in rice;
Peredovik and Aramvirikij from USSR in sunflower; Asiriya Mwitunde from
Tanganyika (a territory in present Tanzania); Rehovot 33–1 from Israel; M13 from
the USA in groundnut; Bragg and Lee, and Improved Pelican from the USA in
soybean; and Improved Ghana from Ghana in pearl millet (Singh 1991). Several of
these introductions were directly absorbed into the breeding pipelines, while excep-
tional widely adapted genotypes were released as varieties. One of the most noted
introductions was the first rice variety officially released worldwide by IRRI in 1966,
IR 8 (Peng et al. 1999).

1.4.2 Pureline Selection

Besides the introduction, initial efforts were also focussed on selection in crops, with
or without hybridisation. Before the green revolution in the mid-1960s, pureline
selection was the common way of cultivar development in self-pollinated species
like rice. Mostly involving local landraces and exotic introductions, there were
hundreds of pureline rice varieties released across India. Among the success of
pureline selection in India, GEB24 was a milestone rice cultivar. A selection from
Konamani, also known as Athur Kichli Samba, a local landrace, GEB24 was
considered as a spontaneous mutant. With its fine grain and high quality, GEB24
was officially released for cultivation in 1921 and is considered one of the first
officially released crop varieties in India. GEB24 also served as one of the major
parental lines in generating the initial breeding materials in IRRI, after its
1 Breeding Field Crops: History, Current Status and Introspections 9

establishment in 1960. By the end of 1965, there were 66 pureline selected

rice varieties released in Tamil Nadu alone, out of 445 rice varieties released across
India. Among these, outstanding releases were Dular, Latisail, Manoharsali, MTU
15 and Nagina 22, to name a few (Mishra 2002). There were also noteworthy
advancements in quality rice breeding, such as Type 3 (selection for Dehradooni
Basmati), Basmati 370 and N105 (selection for Hansraj) and Type 9 (selection from
Duniapat).
Unlike in rice, pureline selection in wheat did not sustain for a longer time in
India, instead, hybridisation followed by pedigree selection was adopted as early as
1907 in Pusa (Howard 1909). The first 20 years of Imperial Agricultural Research
Institute witnessed the release of a few pureline selected wheat varieties such as NP4,
NP6, NP12, Pb8, K13, K53, AO13, AO85, Motia, Bansi, Gulab, Arnej 206, etc.
(Nagarajan and Singh 1997). Although several of these lines were tested and grown
in other countries, NP4 remained one of the most outstanding wheat varieties across
the world for its grain quality. NP4 was selected from Mundia, an awnless landrace
that had shown remarkable adaptability to varying environments in addition to its
exceptional quality (Tomar et al. 2004). Within no time NP4 became the landmark
contribution of IARI in its early history.

1.4.3 Recombination Breeding

Hybridisation and selection remained the most adopted breeding strategy among the
field crops around the world. Among the early success of hybridisation in India, the
most remarkable achievement was the ‘nobilization of canes’. In sugarcane, inter-
specific hybridisation between Saccharum officinarum with S. spontaneum followed
by backcrossing and selection could lead to the development of superior canes called
‘noble canes’ with high yield and sugar content (Barber 1915). Subsequently, the
improved canes coud revolutionize the sugar industry in India. In 1949, a most
ambitious intersubspecific hybridisation programme was launched in rice under the
aegis of the Food and Agricultural Organization (FAO), to combine the fertiliser
responsiveness and hardiness of japonica with quality and adaptation of indica.
Although the programme was not a great success, two popular varieties were
evolved, namely, Mahsuri in Malaysia and ADT27 in India. Additionally, two
more varieties, Malinja in Malaysia and Circna in Australia, were also released for
cultivation under this programme.
The most important landmark in rice breeding came through the development of
semi-dwarf varieties aided by the identification and introgression of sd1 gene. In
1961, Peter Jennings, a young agronomist from the USA was recruited to IRRI by
the Rockefeller Foundation to investigate the dwarf rice. He came across a
Taiwanese rice variety, Taichung Native 1 (TN1), that was widely grown. Semi-
dwarf in nature, TN1 resembled its parent, Dee-geo-woo-gen (DGWG) for the plant
height. Jennings made the first 38 crosses at IRRI, with 11 of them using DGWG or
TN1 as one of the parents (Hargrove and Coffman 2006). The inheritance of semi-
dwarfism was identified as single gene controlled. Later in 1963, Dr. Henry Beachell
10 K. K. Vinod et al.

made a selection of a line, IR8–288-3 from the F4 generation of the Jennings’ eighth
cross, between Peta and DGWG. IR8–288-3, later became the ‘miracle rice’, IR
8. Introduced into India in the same year, IR8 was released for cultivation in the same
name. IR8 could help boost the rice productivity by a whopping 150–200% in its
first year of introduction, beginning to transform the face of agriculture itself from
poverty-ridden to self-sufficiency.
The development of IR8 remains the most remarkable contribution of IRRI to the
world. IR8 could cast the same magic spell worldwide, saving millions from poverty
all across the major rice consuming countries like Bangladesh, Vietnam and India.
Almost at the same time, a similar story was unfolding in wheat breeding too,
wherein the dwarfing genes from a Japanese variety, Norin10 were utilised to
develop semi-dwarf varieties. In the early 1960s, Dr. Norman E Borlaug in
CIMMYT was striving to improve wheat yields in Mexico by using the semi-
dwarfing trait. A series of crosses followed, and Dr. Borlaug could get exceptional
success in his 8156th cross between Penjamo 62 and Gabo 55. Named as Ciete
Cerros, 8156 was remarkably high yielding and could transform the wheat produc-
tion scenario in Mexico by 1962. By the mid-1960s, Mexico became self-sufficient
in wheat production. Introduced into Pakistan as Mexipak and Kalyan Sona in India,
this variety scripted another chapter in the history of green revolution.
Although there were few hybridisation-based varieties released in rice before the
1960s, majority of the post-green revolution era varieties, both in India and else-
where in the world were developed through hybridisation and selection. Among the
nine hybridisation-based varieties released in Tamil Nadu before 1960, CO14 was
the first variety released in 1940. As per the compiled information from the Direc-
torate of Rice Development in India, there were 814 rice varieties released between
1969 to 2012, of which 89% came from pedigree breeding. Despite the huge number
of varietal releases in India, only a handful went onto become ‘mega varieties’,
having been grown in larger areas and for long time. The first mega variety released
in India was Jaya, developed by crossing TN1 with Type 141.
Released in November 1968, Jaya soon replaced IR8 and TN1 that were ruling
the rice production in the country. There was another variety, Padma (CR 28–25)
released along with Jaya, and both became the torchbearers of the indigenously bred
Indian rice under the AICRIP system (Hopper and Freeman 1969). Later on, other
megavarieties were released, Swarna (MTU7029) in 1980, Savitri (CR1009) in
1983, Samba Mahsuri (BPT5204) and Pusa Basmati 1 in 1989 (Fig. 1.3a), Pusa
44 in 1994, Cotton Dora Sannalu (MTU1010) in 2000, Pusa Basmati 1121
(Fig. 1.3b) in 2005 and Pusa Basmati 1509 in 2013. The AICRIP system in India
steadfastly increased the rice varietal output with an average upward trend (Fig. 1.4).
Although there were intermittent years with several releases such as 1978 and 2008,
the average trend increased from 1–2 varieties per year during 1969 to 26 per year in
2012.
In the case of wheat, the initial focus of the erstwhile Imperial Agricultural
Research Institute was to improve Indian varieties, which were of excellent grain
quality. India majorly grows spring wheat and not winter wheat. One of the major
problems with the local cultivars was the tall stature of the plants, which made them
1 Breeding Field Crops: History, Current Status and Introspections 11

Fig. 1.3 Some of the landmark varieties released from ICAR-IARI, New Delhi. (a) to (c): Pusa
Basmati 1, the first semi-dwarf Basmati cultivar; Pusa Basmati 1121, a mega Basmati rice variety
with maximum cultivation extent; Pusa RH 10, the first aromatic rice hybrid; (d) to (e): Two wheat
mega varieties, HD2967 and HD3086 with remarkable scale of adoption; (f) Vivek QPM
9 Improved, the first QPM hybrid enriched with Pro-vitamin A; (g) Pusa 23, a pearl millet hybrid
with A1 cytoplasm; (h) Pusa 10216, MAS-derived chickpea variety with drought tolerance
12 K. K. Vinod et al.

55

52
48
43
42
41

36

36
34
31
29

27

26
22

22
20

20

20

19
16

16
15
15

15

14
13
13

12

12
11
11

8
0
1
0
5

0
4
0

1
1969
1971
1973
1975
1977
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
2009
2011
Fig. 1.4 Number of rice varieties released per year between 1969 and 2012 in India, mostly
channelled through the AICRIP system. Dotted line indicates 10 years moving average. (Data
source: Directorate of Rice Development, Patna)

prone to lodging. An additional problem was the rust disease. Therefore, the initial
breeding emphasis was to improve rust resistance, and due to this, the grain yield of
Indian wheat varieties relatively remained below 2.0 tons/ha until the beginning of
the 1960s. Although the wheat hybridisation at Pusa had started as early as 1907, it
did not make the expected success. Contrary to the expectations, an earlier attempt of
direct introduction was also met a dead end. Pal and Ramanujam (1944) observed
that during the first 40 years of IARI, the 40% increase in wheat area had come with a
reduction in productivity. Until the import of semi-dwarf wheat from Mexico having
Norin 10 lineage, the situation did not improve.
The inception of the All India Coordinated Wheat Improvement Project
(AICWIP) in 1965 was a gamechanger in the wheat history of India. The first set
of varietal introductions from CIMMYT included Sonora 63, Sonora 64, Mayo
64 and Lerma Rojo 64. Introduced into cultivation, these varieties helped to double
the wheat production within two years, ending the 60 years’ drought for high-
yielding varieties. It was so coincidental that the green revolution in the major staple
crops, rice and wheat, happened at the same time, orchestrated by three genes, Sd1 in
rice and Rht1 and Rht2 in wheat, all controlling the same trait, semi-dwarfism.
Borlaug’s 8156 became the first wheat megavariety in India, in the name of Kalyan
Sona. Kalyan Sona had both the Rht genes. The post-green revolution era in wheat
witnessed a cascade of new varieties as happened in rice, with IARI playing a
flagship role. Starting from UP301 released in 1969, varieties were evolved contin-
uously, all with Mexican lines as one of the parents. Cultivars such as Hira, Moti,
Janak etc., followed, finding niches in the timely sown, high fertility conditions. As
the years advanced, newer wheat varieties sharing complex pedigrees began to show
up. Further, high yielding varieties such as HD2189, HD2204 etc. were also got
released in neighbouring countries, Nepal, Bangladesh and Pakistan. Since then,
1 Breeding Field Crops: History, Current Status and Introspections 13

with the latest editions of high yielding cultivars such as HD2967, HD3086,
HD3226 and HD3249, wheat varieties have often helped to touch the surplus
production marks in India. Released in 2014, HD2967 and HD3086 (Fig. 1.3d, e)
together currently occupy more than 50% of the wheat area in India (Mishra et al.
2020). The role of CIMMYT derived wheat lines in cultivar release in India is
immense, and several high yielding varieties such as the recently released variety,
DBW222 are direct introductions.
Introduced into India in the seventeenth century, maize was not the crop of choice
of the Indian population as its staple cereal, unlike that of rice and wheat. At the
beginning of the twentieth century, maize was in cultivation as a primitive cereal,
in the north-eastern and sub-Himalayan India. Besides, there were other landraces
too, but very limited in number and acreage. By the turn of the twenty-first century,
however, there was a marked shift in the priority of maize in India’s staple food
spectrum, by becoming the third major food staple after rice and wheat (Yadav et al.
2014).
Elsewhere in the world too, maize cultivation was not as advanced as today
during the beginning of the last century. In the USA for instance, yield lingered
around 1.5 tons/ha during the 1900s to around 2 tons/ha until 1950, with the world
average touching 1.9 tones/ha by 1960 (Duvick 2005). Maize yield began to rise
sharply since the 1950s, however, there was no single cause that can be attributed to
the yield boom, as that in the case of rice and wheat. However, the availability of
nitrogenous fertilisers and concerted efforts in hybrid breeding could be considered
as the prominent reasons for improved maize yields. Introduced during the 1930s in
the USA, inbred-based hybrids made a dramatic shift in maize production, with the
yield levels climbing from 2 tons/ha to 4 tons/ha by 1945, while the hybrid area
expanded from 1 to 99% by 1960. Yield continued to climb with the introduction of
lines from other countries, deriving new combinations. Population improvement
became a routine breeding practice this time around, having the name ‘recurrent
selection’ introduced by George Frederick Sprague in 1952, to distinguish it from
pedigree breeding (Hallauer 2000).
In India, maize breeding got an impetus with the launch of the All India
Co-ordinated Maize Improvement Project (AICMIP) in 1957, the first of its kind
in the country. In the 1950s, average maize yield was around 600 kg/ha,
predominated with tall flint type low yielding varieties and primitive lines. Realising
the potential of maize as an alternate cereal with wide uses as food and feed, ICAR
launched its first coordinated research programme in maize ahead of the staple
cereals, rice and wheat. By the time AICMIP was launched, several introductions
of exotic lines were facilitated by Rockefeller Foundation. AICMIP took the further
initiative to bolster exotic genetic base subsequently with the help of CIMMYT,
starting from the year of its inception in 1966. The initial launch of hybrids from
AICMIP included Ganga 1, Ganga 101, Ranjit and Deccan by 1961 (Yadav et al.
2015). Presently, all the high yielding maize cultivars in the country share the lineage
with the introduced germplasm, which had both yield potential and adaptability in
varying degrees under Indian conditions.
14 K. K. Vinod et al.

Population improvement played a significant role in maize improvement in India

until the 1980s, beyond which hybrids have taken over the horizon. Currently, maize
breeding has taken a major reorientation towards grain quality improvement and
product diversification. With the introduction of quality protein maize (QPM) from
CIMMYT, another milestone laid by Dr. Surinder K Vasal and Dr. Evangelina
Villegas, India released its own QPM hybrid ‘Sakthiman 1’ in 1981. The role of
IARI in recent maize improvement in India is noteworthy, with the release of several
improved hybrids such as Pusa HQPM 5 Improved, Pusa HQPM 7 Improved, Pusa
Vivek QPM 9 Improved (Fig. 1.3f) combining high pro-vitamin A together with
increased lysine and tryptophan fractions. Pusa Vivek QPM 9 Improved is the
world’s first QPM hybrid combining pro-vitamin A.
Population improvement in other major cereals such as sorghum and pearl
millet also drew parallels to the success in major cereals. Established in 1972, the
International Crop Research Institute for Semi-Arid Tropics (ICRISAT) had a
mission to reduce poverty, hunger, malnutrition and environmental degradation in
the dryland tropics. All the five mandate crops of ICRISAT were field crops, two
cereals—sorghum and pearl millet, and three legumes—chickpea, pigeon pea and
groundnut, marked to provide a balanced nutrition of carbohydrates, protein and fat.
Prior to this, ICAR launched a coordinated programme ‘All India Coordinated Millet
Improvement Project’ in 1965 with IARI as its headquarters. Pearl millet was
included in the project initially, and in 1969 sorghum was added. Later, with
the substantial development, both the crops were separated into independent
co-ordinating units, pearl millet in 1985 and sorghum in 1987.
With all the research systems in place, the breeding outturn in these crops was
tremendous, with ICRISAT playing a major role in bringing in exotic germplasm.
The results were commendable, pearl millet yields went up from 300 kg/ha to
1250 kg/ha under minimal input and harsh tropical conditions, within 70 years.
Currently, there are about 175 hybrids released in pearl millet through the coordi-
nated varietal evaluation system. Unlike that in maize, sorghum variability in India
was tremendous, and the population improvement had begun as early as the 1930s.
Sorghum improvement in India, as a whole, is not much celebrated in the later years
of the twentieth century. Although yield potential improved, the area declined
drastically since the 1990s, bringing down the total production along with.

1.4.4 Mutation Breeding

Another major method employed in the field crop breeding was induced mutagene-
sis, which became very popular after the 1960s. Established as a method for barley
breeding (Freisleben and Lein 1942), mutation breeding soon became very popular
in all the crops, particularly in field crops, due to the ease of mutation process.
Although physical mutagens like X-rays were used in the early stages, chemical
mutagenesis soon became the most popular choice. By the 1960s, use of gamma rays
was introduced as a follow-up of peaceful use of ionising radiation after world war II
(Micke et al. 1990). A gamma garden was established in IARI in the year 1960, the
1 Breeding Field Crops: History, Current Status and Introspections 15

second in India, after the first one was established at the Bose Institute, Calcutta in
1959 (Pal 1962). By 1990, several mutant varieties were released around the world
totalling 519 among the field crops such as rice, wheat, maize, sorghum, pearl millet,
chickpea, pigeon pea, soybean, Brassica and cotton (Micke et al. 1990). Among
these, 251 varieties (48.4%) were from rice, followed by 104 (20.0%) from wheat.
The early introductions of Mexican wheat such as Sonora 64 and Lerma Rojo
64A had red grains not preferred by Indian people. Mutation works on these varieties
at IARI, resulted in the release of Sharbati Sonora and Pusa Lerma both with amber
coloured grains. Although several mutants were developed in wheat through muta-
tion breeding, only a few traits such as grain colour, disease resistance and plant
height had notable improvement. Comparing to other methods of breeding, induced
mutations were random and often produced relatively less success when compared to
the number of mutagenic attempts. Further, the research accomplishments published
on mutation breeding across crops were more academic and described similar
mutagenic effects, camouflaging the actual success stories. Notwithstanding, the
recent experience in identifying a novel herbicide-tolerant AHAS mutant of rice,
‘Robin’, reinforces the faith in mutation breeding (Shoba et al. 2017).

1.4.5 Hybrid Breeding

Hybrid vigour, or the superiority of progenies over their parents, has been observed
by several naturalists much before Mendel, including him, but with marginal
attention (Mather 1955). Darwin was convinced of the phenomenon and reported
it in 1876 (Darwin 1876). A century later, the phenomenon has become one of the
most accomplished breeding methods in crop plants, ensuring food security to
millions of humans and livestock. Hybrid development in each of the major field
crops has a story to narrate, except in wheat which is still being explored to strike a
convincing advantage for yield. The conviction that hybrid vigour can be used for
crop improvement came much earlier, which saw the birth of the term ‘heterosis’ by
G H Shull in 1914 (Shull 1914) and after his extensive work on maize (Shull 1946).
But a major bottleneck remained – controlled pollination. Especially in crops like
maize, every grain in a cob used to be a different hybrid due to open pollination.
Shull could initially create several inbreds by inbreeding but could not control the
deterioration in certain lines (Shull 1908).
Nevertheless, mechanical emasculation in maize was possible through
detasselling, a laborious task, but hybrids could be produced. By the 1930s,
commercial-scale maize hybrids were available in the USA. At this time around,
the Texas Agricultural Experiment Station (TAES) at College Station was bustling
with research activities on male sterility systems and hybrid vigour in crop plants. In
the 1950s, came the phenomenal discovery of cytoplasmic genetic male sterility
(CMS) in maize with the identification of Texas cytoplasm (cms-T). The cms-T was
first described in the line ‘Golden June’ in 1952 (Rogers and Edwardson 1952) and
became one of the most studied CMS systems in crop plants. Since cms-T was
proved to be a perfect CMS system, soon several hybrids started appearing at
16 K. K. Vinod et al.

commercial scale. It was strikingly popular that by 1970, 85% of the US maize
hybrids possessed cms-T cytoplasm. Within the two years spanning 1969 and 1970,
15% of the hybrids were wiped out by the outbreak of southern corn leaf blight
incited by Bipolaris maydis race T. The T toxin produced by the pathogen had a
specific binding site on the T-urf13 protein produced by the cms-T. The devastation
was so severe that by 1972, most of the hybrids with cms-T were withdrawn
(Levings III 1990).
There were other cytoplasms available in maize (Beckett 1971), that can be
broadly grouped into C (Charrua) and S (USDA), that saved the hybrid maize
industry (Weider et al. 2009). Use of these CMS systems has since been moved to
other countries. In India, use of CMS systems for hybrid production is not commonly
practised, because the process of detasselling is not as expensive as elsewhere.
Further, the manual detasselling does not warrant any specific maintenance breeding
as that in the case of male sterility systems. One of the major problems for CMS
systems is the maintenance of parental lines. Maintenance breeding of three lines, A,
B and R, particularly A-line is an arduous task with isolation distances and con-
trolled pollination, which is expensive than detasselling. Moreover, contaminated
A-lines are difficult to purify. Therefore, almost all of the commercial maize hybrids
in India has normal cytoplasm. Nevertheless, most recently in IARI, a baby corn
hybrid has been developed using cms-T which is currently in the advanced stages of
variety release. Compared to other CMS, cms-T remains most stable in Indian
conditions.
Although there were various reports of CMS discovery in rice, the breaking news
of commercial hybrids came from China (Virmani and Edwards 1983). In the
autumn of 1970, Li Bi Hu of the Hunan Academy of Agricultural Sciences
(HAAS) identified a natural male sterile line among the weedy rice (Oryza sativa
f. spontanea) populations in Hainan island. Named as ‘wild abortive (WA)’,
Dr. Yuan Long Ping of HAAS made several crosses with this WA line to produce
several MS lines. One of the first MS lines developed was Er-jiu-nan 1A, which was
later used extensively in hybrid rice production (Lin and Yuan 1980). Er-jiu-nan 1A
was developed from the early maturing variety 6044, by four backcrosses. Other
male sterile lines were also developed subsequently such as Zhen Shan 97A, V20A
and several others. The first set of WA-based hybrids was released soon, and by
1978, about five million ha was under hybrid rice in China. The first set of hybrids
were named after their female parents. Those derived from Er-jiu-nan 1A were
named as ‘Nan-You’, hybrids, those from Zhen Shan 97A were known as ‘Shan-
You’ and those from V20A were named with the prefix ‘Wei You’. In the initial
years of development, there were two other male-sterile systems used in China, Boro
and Hong-Lien, which showed practical prominence.
Boro cytoplasm was initially described by Shinjyo (1969) when the cross
between Chinsurah Boro 2 was made with Taichung 65. However, efficient transfer
of Boro type met with difficulties in indica rice, leaving WA as the only source of
viable CMS in rice. The restorer genes, Rf1 and Rf2 were identified for Boro type,
while Rf3 and Rf4 restored fertility in WA CMS system. Obtained from China
through IRRI, WA cytoplasm and its derived lines spread throughout the world
1 Breeding Field Crops: History, Current Status and Introspections 17

with a new hope. By 1980, IRRI began full-fledged research of hybrid rice with WA
cytoplasm as the pivot. Several, hybrids were developed, however, the resulting
heterosis was not as prominent as reported in China. This slowed down the initial
thrust a bit, but still, the works continued in several countries. In India, hybrid rice
research had begun in 1980 with the collaboration of IRRI as the major knowledge
and resource partner (Jachuck et al. 1986).
By 1981, Er-jiu-nan 1A, Zhen Shan 97 A and V20A were introduced into India
along with their maintainers. Initial hybrid development was done using the
introduced lines directly, however, there was a significant issue of grain quality
among the hybrids developed under Indian conditions. Moreover, they showed
increased susceptibility to pests and diseases. Conversion of Indian lines into male
sterile lines was felt indispensable. By 1989, a national programme on hybrid rice
was launched. The efforts bore fruit, the first set of hybrid rice was released in India
in 1994, comprising four of them, APRH1, APRH2, MGR1 and KRH1. At the initial
stage, all the successful hybrids were developed using only one A-line, IR58025A.
This line, IR58025A, was developed by Dr. Sant Singh Virmani, the hybrid rice
breeder at IRRI in 1988. When the conversion of Indian lines took momentum, in
IARI, the same was replicated using lines under Basmati lineage. Two lines were
identified as maintainers of WA cytoplasm, Pusa 167–120–3–2 and Pusa 150–21–
1–1, both with exceptional grain quality, long slender grains and agronomic features.
Among these, Pusa 167–12–3–2 was derived from the cross of Type 3/Ratna.
IR48483A, a male sterile line developed at IRRI by crossing Zhen Shan 97A/
MR365, was backcrossed to Pusa 167–12–3–2, and after six backcrosses
IR58025A was developed. As a result, this line possessed long slender grains with
aroma. IR58025A was further crossed to Pusa 150–21–1–1 to develop Pusa 6A after
six backcrosses. By 2001, Pusa 6A became the parent of the first superfine grain
aromatic rice hybrid in the world, Pusa RH 10 (Fig. 1.3c). Before the development of
indigenously derived male sterile lines with better combining ability and grain
quality, IR58025A was the major A-line used in hybrid rice development in India.
Among the 127 rice hybrids released as of today, at least 15% have been developed
using IR58025A as female parent.
Besides the involvement in hybrid development, IR58025A stands as a major
contributor to the male sterile line development in India. One of the major drawbacks
of using IR58025A was the aroma it imparted in the hybrids, which was an undesired
feature in the non-aromatic grain sector. However, this problem has now been
overcome in the latest array of male-sterile lines. At the beginning of the 1990s,
hybrid rice in India was restricted to the public sector institutions, as there were few
private sector companies involoved. This sitiation soon changed, and during the
10 years between 2000 and 2009, 44% of the rice hybrids released were from the
private sector. After 2010, the scenario completely changed with private sector
hybrid contribution going up to 91%. Only seven public sector hybrids were released
between 2010 to 2021.
In wheat, unlike in maize and rice, hybrid development has always been a
dubious challenge. The existence of male sterility driven by cytoplasmic factors in
wheat was known before that in rice, when Kihara (1951) reported it for the first
18 K. K. Vinod et al.

time. Ten years later, a usable version was identified when Triticum timopheevi
cytoplasm was found to induce sterility by interaction with T. aestivum nucleus
(Wilson and Ross 1962). By this time, several reports of male sterility manifestation
were pouring out of laboratories worldwide. From India, Rana and Swaminathan
(1968) reported T. zhukovskyi as a source of MS cytoplasm. But there was a common
problem. The availability of restorer genes was scarce. For timopheevi cytoplasm, Rf
genes were sourced from T. timpheevi itself. It was the only system that looked
viable. The first male sterile line ‘Bison’ was developed (Wilson and Ross 1962),
and it could be successfully used to generate fertile hybrids (Schmidt et al. 1962).
Other than the restorer gene scarcity, another major bottleneck existed in wheat
for diversifying cytoplasm in the form of undesirable nuclear-cytoplasmic
interactions. Here again, timopheevi cytoplasm showed an exception, as no such
interaction was reported (Virmani and Edwards 1983). Additionally, hybrids based
on male sterility systems often showed less yield heterosis than the hand-pollinated
hybrids. In the meantime, some commercial hybrids were released, but with little
impact. All over the world, enthusiasm for hybrid wheat was dying down, until in the
1990s the efforts took another turn with the advent of chemical hybridisation agents
(CHA). CHAs are growth-regulating chemicals that can selectively interfere with
pollen production (McRae 1985; Duvick 1999). With renewed hope, the global area
under hybrid wheat has begun to rise, but at a slow pace. Altogether, in Europe and
America more than 60 hybrids were released (Gupta et al. 2019). In India, no wheat
hybrids are released for commercial cultivation, except for two CMS-based hybrids,
Pratham 7070 and Pratham 7272. However, they could not compete with the high
yielding pure line cultivars.
A significant level of hybrid developments had happened in two other field crops,
pearl millet and sorghum. Hybrid production in the early years of pearl millet
improvement used the protogynous flowering behaviour as a mode of effecting
cross-pollination. However, this method was not failproof, as any human error
could result in reduced hybrid seed set. With the discovery of the CMS system
‘Tift 23A’ (Burton 1965a), the hybrid production scenario was set for a change in
pearl millet. Tift 23A was developed by Glenn W. Burton in 1965 at Tifton, Georgia,
in the USA after several years of research on male sterility systems. Tift23A carried
A1 cytoplasm, which was stable enough to promote hybrid seed production. Along
with Tift23A, there was another line, Tift18A developed by Burton (Burton 1965b).
Introduced into India, two parallel programmes progressed, one for diversification
and the other for hybrid development. IARI and Punjab Agricultural University
(PAU) were the pioneers of pearl millet breeding in India (Srivastava et al. 2020).
The first hybrid, Hybrid Bajra 1 (HB1) was released by PAU in 1965. HB1 was
developed from Tift23A by crossing to BilB3 (Athwal 1966). Subsequently, several
other cytoplasms were reported, but A1 cytoplasm remained the major source of
female lines for hybrid production in India (Kumar and Andrews 1984; Srivastava
et al. 2020). One of the IARI developed hybrids, Pusa 23 using A1 cytoplasm, has
become widely adopted in the northern plains (Fig. 1.3g). The major issue with
hybrid pearl millet was increased susceptibility to diseases, particularly downey
mildew. Diversification of parental base hence has become a major strategy for
1 Breeding Field Crops: History, Current Status and Introspections 19

developing newer hybrids in pearl millet, an effort continuing in different institutions

of India.
In the case of Sorghum too, hybrid breeding research before the pre-green
revolution period was negligible. The preliminary report of the heterosis in sorghum
came from the Lubbock substation of TAES in 1927 (Conner and Karper 1927).
Twenty-seven years later, Stephens and Holland (1954) reported a novel CMS
cytoplasm ‘Milo’, from a cross between Double Dwarf Yellow sooner Milo and
Texas Blackhull kafir at TAES. They identified the possibility of using the system
for commercial hybrid production and developed Combine Kafir (CK) lines since
kafir nuclear genes could restore the sterility induced by milo. Some of these lines
were introduced to India, after the inception of AICMIP. Coordinated research
efforts under the project on sorghum resulted in the release of the first hybrid,
CSH1 or Coordinated Sorghum Hybrid 1 in 1964. Its parents were CK60A and
IS84 (IS84-SA7529-55-1-1-1-1 from the Texas Durra Caudatum race) were both
introduced from Texas. The second hybrid, CSH2 followed next year from the cross,
CK60A/IS 3691. Initially, at least six hybrids were released with the directly
introduced parents or from the lines selected within them. In the meantime, launch
of ICRISAT has accelerated the hybrid breeding activities in sorghum, with an
increasing number of conversions taking place using local germplasm. Starting
with CSH1, as many as 26 Kharif sorghum hybrids have been released in India,
until 2016.
Hybrid breeding in other field crops has not been much accomplished as that in
cereals, particularly using male sterility systems. Notwithstanding, several commer-
cial hybrids using conventional methods such as hand pollination has been released
in sunflower, safflower, Brassica and groundnut claiming different levels of heterosis
realisation. Notable exceptions are pigeon pea and Brassica, wherein extensive
research on male sterility was done. First reported male sterility in pigeon pea was
genetic male sterility (GMS) in 1978 (Reddy et al. 1978). Although few other GMS
systems were identified, maintenance of male sterility was the major bottleneck in
the commercialisation of this technology. Search for alternate systems such as CMS
was begun, with the particular objective of wide hybridisation. First report came in
1995, with Ariyanayagam et al. (1995) identifying Cajanun sericeus cytoplasm
induced male sterility in C. cajan. The sericeus system was denoted as A1 cyto-
plasm, followed by the discovery of A2 cytoplasm from C. scarabaeoidus (Chauhan
et al. 2004).
Dalvi et al. (2010) provided a comprehensive review on the male sterility systems
in pigeon pea. So far, two hybrids are released, ICPH 3762 in 2010 and ICPH 2740
in 2015, but the breakthrough in yield and other desirable traits are yet to be realised.
In Brassica also, the CMS systems such as tour, trachy and mori were used for
hybrid development. The first CMS-based hybrid in India was released in Punjab,
PGSH 51, based on tour cytoplasm. Later, CMS-based hybrids such as NRCHB
506, DMH 1 and Coral 432 (PAC 432) were released (Chauhan et al. 2011). Hybrid
breeding in Brassica has another accomplishment. In 2008, a transgenic hybrid,
DMH 11 was developed by Delhi University which became India’s first transgenic
hybrid (Jagannath et al. 2002). Recent developments in hybrid Brassica have
20 K. K. Vinod et al.

attracted private sector researchers too (Yadava et al. 2012). There were also
attempts to develop male sterility systems in chickpea and groundnut which remain
unresolved at the commercial level.

1.4.6 Genomics-Assisted Breeding

By the end of the 1980s, genomics-based breeding began to take shape in field crops,
pioneering from the development of DNA based markers in rice. Contemporarily,
tissue culture techniques were also found extensive development, but the initial
enthusiasm soon died as the expected returns eluded the researchers. The promise
offered by genetic engineering for targeted crop improvement has faced hurdles in
commercial deployment due to anti-genetically modified organisms (GMO) activ-
ism. Interest in this field was so enormous, several laboratories for agricultural
biotechnology research have come up all over the world. Notwithstanding the set-
back in transgenic plants, techniques such as the development of linkage maps and
mapping of loci, targeting both qualitative and quantitative traits, were invigorating
the scientists with a ray of hope of success. During the 1990s, there was a quantum
leap in molecular techniques, thanks to the Human Genome Project (HGP), a
worldwide consortium. Began in 1990 and concluded in 2003 (www.genome.
gov), HGP provided several cutting-edge technologies that has parallelly been
translated to crop genomes. The first attempt to sequence a cultivated crop genome
began in 1998 with the inception of the International Rice Genome Sequencing
Project (IRGSP) in the same mode as that of HGP.
The genome of the japonica cultivar, Nipponbare, was completely decoded by
2005 (IRGSP and Sasaki 2005). The availability of the genome information was
soon made public. Parallelly, with the help of several bioinformatic tools supported
by the modern computing platforms, the whole rice genome was annotated under a
different project, Rice Genome Annotation Project (RGAP) beginning from 2004.
Several databases have been created and made publically available. All these
developments have completely reinvented the way trait-based breeding was done.
Similar developments in other field crops had seen the unfolding of many crop
genomes. Almost at the same period, the publications of the first linkage map of rice
(McCouch 1990; McCouch et al. 1988) based on restriction fragment length poly-
morphism (RFLP) and microsatellite markers (Temnykh et al. 2001; McCouch et al.
2002) were made. Microsatellites, also known as simple sequence repeats (SSR)
found abundantly in the genome particularly dispersed within the non-coding
regions and widely distributed, could generate high density linkage maps due to
their enormity in the rice genome.
All this was possible by the Nobel winning invention of Kary Banks Mullis, who
described a lab-based method to amplify DNA in vitro using an enzymatic reaction
(Mullis et al. 1986) known as polymerase chain reaction (PCR). This method was
simple and very effective in the targeted amplification of DNA. PCR spurred a series
of discoveries of different molecular markers, but none prevailed as that of SSRs. By
the beginning of the twenty-first century, SSRs have been widely recruited as the
1 Breeding Field Crops: History, Current Status and Introspections 21

molecular tool targeting various genetic studies such as diversity, linkage and
quantitative trait locus (QTL) mapping. Most of the QTLs, mapped earlier using
other marker systems such as RFLP were remapped using SSRs. Since SSR profiles
were highly reproducible across genotypes, they found their way into the breeder’s
kit – as an indispensable selection tool.
To use any marker for selection, it must establish a close linkage with the gene of
interest. Stronger the linkage more efficient the marker becomes in selection. Several
QTLs have also been reported at the same time, flanked between two adjacent SSRs.
The abundance of SSRs helped the researchers to narrow down to the gene by
recruiting SSRs within the flanks. This way, most of the major QTLs have been fine
mapped. Integrating the sequencing techniques of the amplified fragments, the target
gene could be easily identified using an annotation database constructed from model
species such as Arabidopsis and rice. Now gene-based/functional markers are also
available for targeted selection.

1.4.7 Marker-Assisted Selection in Breeding

Marker assisted selection (MAS) denotes employing molecular markers in the

selection process. Since they are based on the DNA itself, their usefulness becomes
definitive in the selection process. Moreover, the whole process allows several
progenies to be looked into, even when they are young, which adds to the
throughputness of the MAS. Although MAS can be integrated into several breeding
methods, it has been particularly successfull in backcross breeding for rectifying
specific defects in already popular crop varieties. Currently, marker-assisted back-
cross breeding (MABB) is being widely used in field crops in India. MABB targets
to augment the selection process to reduce the turnaround time for varietal develop-
ment, most economically. After identifying the target gene/QTL, MABB allows
them to be transferred to an elite/popular varietal background where specific traits
need improvement. Additionally, integration of desired traits by pyramiding the
target genes/QTLs can also be undertaken under MABB programmes.
During the last 10 years, MABB has undergone several refinements in the
protocols targeting precision and economy. One of the major changes was the
integration of a rigorous phenotypic selection along with foreground and back-
ground selection, particularly in the early generations (Singh et al. 2011). This has
not only helped recovery of the recurrent parent phenome to its near totality but also
aided in accelerating the breeding process. Integration of phenotypic selection in
MAB has been a crucial factor in Basmati breeding, because of the exclusive grain
quality of this group of rice. Often when a non-Basmati source is used as the gene/
QTL donor, severe impairment of Basmati quality is experienced requiring further
refinements (Babu et al. 2017). In the preliminary protocols of MABB, only fore-
ground and background selection were included (Liu et al. 2003) with the idea that
recovery of maximum recurrent parent genome (RPG) would recover the phenome
also. However, in practice, this does not seem to occur due to several undetected
regions of the donor genome lying latently in the progenies. While this can be
22 K. K. Vinod et al.

attributed to the limited number of background markers, scaling them to a high-

density coverage can make the entire selection process expensive and time-
consuming (Ellur et al. 2016), jeopardising the fundamental objective of accelerated
breeding. However, the early generation phenotypic selection could address this
issue effortlessly. Yet another improvement was the reductive screening in back-
ground selection, in which the completely recovered background markers were
progressively eliminated from the selection process (Sagar et al. 2020). This could
not only economise the selection by reducing the time but also could aid in
conserving the resources.
Recently, postponing the entire background selection to a later generation was
also attempted, relying initially on phenotypic selection along with foreground
selection. The results were dramatic, as the final selections could accumulate as
much RPG recovery as possible along with the phenome recovery, ultimately saving
a lot of time and money, along with aiding the initial screening of a large number of
progenies (Oo et al. 2021). Cultivar releases using MAS in India has taken off in
2007, with the release of Improved Pusa Basamti 1 and immediately followed by
Improved Samba Mashsuri. Since then, several improved varieties have been
released for commercial cultivation (Table 1.2). Among the institutions, IARI has
the maximum share of 36% among the releases, covering three crops, rice, maize and
chickpea. All of the rice cultivars released using MABB, targets bacterial blight
and/or blast resistance, while in maize hybrids focus was on developing QPM
hybrids, with or without pro-vitamin A enrichment. In chickpea, two MAS derived
cultivars were released, Super Annigeri 1 and Pusa Chickpea 10,216 (Fig. 1.3g)
having fusarium wilt resistance and drought tolerance, respectively. There are four
Indian rice cultivars improved by IRRI, directly released for cultivation in India such
as Swarna Sub1, Samba Sub1, CR1009 Sub1 and IR64 Drt1 (DRR Dhan 42).

1.4.8 Genomic Selection (GS)

GS is the contemporary buzzword in genomic assisted breeding. If MAS is used for

individualistic improvement, especially targeting elite cultivars, GS envisions popu-
lation improvement even for self-pollinated crops. Similar to MAS, GS also weighs
on the availability of desired alleles and amasses them into a set of individuals
through a series of breeding steps. However, there are fundamental differences in the
approaches that are followed. MAS requires mapping of the target alleles before their
use in the introgression or pyramiding programmes, whereas GS does not require
mapping individual target alleles. While MAS requires donor and recipient (recur-
rent) parents, GS typically needs training and testing (breeding) populations. Funda-
mentally, GS operates on a closed breeding system, which means it starts with a set
of diverse founders that are known to harbour different allelic combinations of target
loci. Thus, founders in the GS programme are elite genotypes with high breeding
values, that are interbred to develop a large number of biparental populations. Bred
to near homozygosity, the progenies of these crosses are divided into two, a training
set and a testing set. Training set undergoes a low- or mid-density SNP genotyping
 1

Table 1.2 MAS derived varieties of field crops released and notified in India
Sl. Markers Year of
No. Crop Improved Variety Trait Genes incorporated used release Developer
1 Rice Improved Pusa Basmati 1 Bacterial blight xa13, Xa21 CAPS, 2007 IARI
STS
2 Rice Improved Samba Mahsuri Bacterial blight xa5, xa13, Xa21 SSR 2008 IARI
3 Rice Swarna Sub1 Submergence tolerance Sub1 InDel 2009 IRRI
4 Rice Samba Sub1 Submergence tolerance Sub1 InDel 2011 IRRI
5 Rice Improved Lalat Bacterial blight Xa4, xa5, xa13, Xa21 STS 2012 NRRI
6 Rice Improved Tapaswini Bacterial blight Xa4, xa5, xa13, Xa21 STS 2012 NRRI
7 Rice PR122 Bacterial blight Xa4, xa13, Xa21 SSR 2013 PAU
8 Rice PR121 Bacterial blight Xa4, xa13, Xa21 SSR 2013 PAU
9 Rice Pusa 6 (Pusa 1612) Blast Pi2, Pi54 SSR 2013 IARI
10 Rice CR1009 Sub1 Submergence tolerance Sub1 InDel 2013 IRRI
11 Rice PR123 Bacterial blight Xa4, xa13, Xa21 SSR 2014 PAU
12 Rice IR64 Drt1 (DRR Dhan Drought tolerance qDTY2.2, qDTY4.1 SSR 2014 IRRI
42)
13 Rice Pusa 1592 Bacterial blight xa13, Xa21 SSR, STS 2015 IARI
14 Rice PR124 Bacterial blight Xa4, xa13 SSR 2015 PAU
15 Rice Pusa Basmati 1609 Blast Pi2, Pi54 SSR 2015 IARI
Breeding Field Crops: History, Current Status and Introspections

16 Rice Pusa Basmati 1728 Bacterial blight xa13, Xa21 SSR, STS 2016 IARI
17 Rice Punjab Basmati 3 Bacterial blight xa13, Xa21 SSR 2016 PAU
18 Rice CR Dhan 800 Bacterial blight xa5, xa13, Xa21 STS 2016 CRRI
19 Rice Pusa Basmati 1637 Blast Pi9 SSR 2016 IARI
20 Rice Ranjit Sub1 Submergence tolerance Sub1 InDel 2016 AAU
21 Rice Bahadur Sub1 Submergence tolerance Sub1 InDel 2016 AAU
22 Rice Pusa Basmati 1718 Bacterial blight xa13, Xa21 SSR, STS 2017 IARI
23 Rice Punjab Basmati 4 Bacterial blight xa13, Xa21 SSR 2017 PAU
23

(continued)
 24

Table 1.2 (continued)

Sl. Markers Year of
No. Crop Improved Variety Trait Genes incorporated used release Developer
24 Rice Punjab Basmati 5 Bacterial blight xa13, Xa21 SSR 2017 PAU
25 Rice PR127 Bacterial blight Xa45(t) STS 2018 PAU
26 Rice DRR Dhan 51 Blast Pi2 SSR 2018 IIRR
27 Rice Pusa Samba 1850 Blast Pi1, Pi54, Pita SSR, STS 2018 IARI
28 Rice CO43 Sub1 Submergence tolerance Sub1 InDel 2018 TNAU
29 Rice DRR Dhan 50 Submergence, drought qSub1, qDTY2.1, qDTY3.1 SSR 2018 IIRR
tolerance
30 Rice CR Dhan 801 Submergence, drought qSub1, qDTY1.1, qDTY2.1, SSR 2018 NRRI
tolerance qDTY3.1
31 Rice CR Dhan 802 (subhash) Submergence, drought qSub1, qDTY1.1, qDTY2.1 SSR 2018 NRRI
tolerance
32 Wheat PBW723 (Unnat Stripe and leaf rust Yr17, Yr40, Lr37, Lr57 SSR, 2017 PAU
PBW343) resistance CAPS
33 Wheat PBW761 (Unnat Stripe rust resistance Yr15 SSR 2019 PAU
PBW550)
34 Wheat PBW752 Stripe rust resistance Yr10 SSR 2019 PAU
35 Wheat PBW757 Stripe rust resistance Yr15 SSR 2019 PAU
36 Wheat PBW771 Stripe and leaf rust Yr40, Lr57 CAPS, 2020 PAU
resistance SSR
37 Maize Vivek QPM9 Lysine and tryptophan opaque2 SSR 2008 VPKS
38 Maize Pusa HM4 improved Lysine and tryptophan opaque2 SSR 2017 IARI
39 Maize Pusa HM8 improved Lysine and tryptophan opaque2 SSR 2017 IARI
40 Maize Pusa HM9 improved Lysine and tryptophan opaque2 SSR 2017 IARI
41 Maize Pusa Vivek QPM9 Provitamin-A crtRB1 InDel 2017 IARI
improved
42 Maize Provitamin-A crtRB1 InDel 2020 IARI
K. K. Vinod et al.
 1

Pusa Vivek hybrid

27 improved
43 Maize Pusa HQPM5 improved Provitamin-A crtRB1 InDel 2020 IARI
44 Maize Pusa HQPM7 improved Provitamin-A crtRB1 InDel 2020 IARI
45 Chickpea Super Annigeri 1 Fusarium wilt resistance Foc4 SSR 2019 IARI
46 Chickpea Pusa chickpea 10216 Drought tolerance QTL hotspot on LG4 SSR 2019 IARI
47 Pearl HHB67 improved Downy mildew resistance QRsg1, QRsg4 RFLP 2005 ICRISAT
millet
48 Soybean NRC127 KTI free Null allele of KTi3 SSR 2018 IISR
49 Soybean NRC142 KTI + lipoxygenase free Null allele of KTi3 SSR 2019 IISR
IARI ICAR-Indian Agricultural Research Institute, New Delhi, ICRISAT International Crops Research Institute for Semi-Arid Tropics, Patancheru, IIRR
ICAR-Indian Institute of Rice Research, Hyderabad, IISR ICAR-Indian Institute of Soybean Research, Indore, IRRI International Rice Research Institute, Los
Banos, NRRI ICAR-National Rice Research Institute, Cuttack, PAU Punjab Agricultural University, Ludhiana, TNAU Tamil Nadu Agricultural University,
Coimbatore, VPKAS ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora
Breeding Field Crops: History, Current Status and Introspections
25
26 K. K. Vinod et al.

covering the whole genome, as well as a multi-location evaluation within the target
population of environment (TPE). The data is used for generating a valid model that
connects genotypic and phenotypic data. This model is then used for predicting the
genomic estimated breeding values (GEBVs) of the testing panel. Since the training
data involves multi-location data, the element of genotype-by-environment interac-
tion is inbuilt in the GS model.
A minimum of three locations is required, and not more than two replications to
improve heritability. There are several statistical approaches to modelling, however,
two methods, genomic best linear unbiased predictor (gBLUP) and ridge regression
BLUP (rrBLUP) are adjudged to be the best methods in model building (Meuwissen
et al. 2001). Further, a large population is desirable because the GS models attempt
to capture total additive genetic variance for predicting GEBVs. A larger population
requires robust experimental designs such as augmented, spatial, partially replicated
(p-rep) or sparse testing. The selected lines based on the GEBVs form the Stage
1 cohort, which can either be recycled for the next breeding cycle or be advanced for
varietal development. Selection intensity needs to be high to capture maximum
number of allelic combinations. Further, accelerated breeding cycle improves the
effectiveness of GS in crop breeding programmes.

1.5 An Overview of Breeding Research in the Last Decade

In the decades past 1960s, the green revolution has cast its magical spell to a
significant extent on the field crops. All the crops experienced an emulated version
of the yield increase as that happened in the three prime cereals. Strong scientific
intervention on varietal development, along with improved cultural practices and
calculated fertilisation, has all contributed to increased productivity. In the last
10 years, two remarkable shifts have occurred; for the first time, use of marker-
assisted breeding has resulted in the release of 46 cultivars, and a quantum increase
in the release of cultivars bred by the private sector. In rice alone, 29 cultivars were
released by marker-assisted breeding, with notable improvement in disease resis-
tance targeting both bacterial blight and blast, either singly or in combination
(Table 1.2). In rice, about 90% (68 out of 75) of the hybrids released during the
last decade has come from the private sector (Fig. 1.5). This is a welcome change, as
several private producers are coming forward in seed production and marketing,
making the seed availability to farmers unlimited. Furthermore, private-sector
research organisations are looking for higher yield and grain quality besides stress
resilience as the major breeding targets to sustain competition among themselves as
well as with the public sector institutions. This major shift towards commercial
agriculture is not for rice alone. Currently, the hybrid sector in field crops is
dominated by private organisations and are giving stiff competition to public sector
organisations. The exception is wheat, wherein private seed suppliers produce and
market high yielding pure line varieties to a considerable extent.
Another noteworthy development in the breeding research in India comes from
the varietal turnover, particularly from the non-hybrid sector. So far, this sector
1 Breeding Field Crops: History, Current Status and Introspections 27

16
Public Private
14

12

10

4
*
2

Fig. 1.5 Pattern of release of rice hybrids in India between 1994 and 2021. There is a marked shift
in private sector hybrids during the last ten years. The dotted lines indicate three year moving
average. *Data for 2021 is incomplete

remains the mainstay for the public sector institutions. The varietal release system in
India takes two routes, national varietal release and provincial varietal release.
National release follows rigorous nationwide testing and widely adapted cultivars
are only passed through this system, ultimately released and notified by the Central
Sub-committee on Crop Standards, Notification and Release of Varieties for Agri-
cultural Crops (CVRC). Most of the specifically adapted cultivars are approved
through provincial bodies such as State Varietal Release Committees (SVRCs).
Examining the varietal release during the last 10 years, in 14 field crops, which
included both hybrid and non-hybrid cultivars, one could see a marked difference in
the pattern of release. The most striking feature is the number of releases, 743 under
SVRC, a 34% increase over the CVRC releases totalling 554 cultivars (Fig. 1.6).
However, CVRC releases looked relatively more balanced than the SVRC releases.
Although rice dominated the number of releases, an equally good number of varietal
releases happened in maize, wheat and cotton under CVRC, while a predominance
of rice cultivar release was seen under SVRC.
In rice, SVRC release was three times more than that in CVRC. This pattern raises
more concerns than comfort because indiscriminate release of varieties that are
specifically adapted would render them less adopted, leaving the varieties mostly
to the breeder than the ultimate stakeholder, the farmer. This also would slow down
the dissemination of widely adapted cultivars, which need to find its adoption against
the flash flood of narrowly adapted varieties. Another dimension to this problem is
the performance evaluation system of the breeder’s service under public funded
organisations. Often, the number of cultivars released than the number adopted is the
28 K. K. Vinod et al.

Fig. 1.6 Varietal release pattern among 14 field crops between 2011 and 2021. The CVRC releases
were relatively more balanced among the major crops, while SVRC releases were mostly dominated
by rice cultivars

criteria followed for assessing a breeder. This leads to unhealthy practices and
competitions, thwarting the very basic objective of crop improvement.
Notwithstanding, the breeding efforts during the first two decades of the twenty-
first century has been eventful. Several high yielding varieties have seen remarkable
adoption within a short period of time from release. Varieties such as HD2967 and
HD3086 in wheat, Pusa Basmati 1121 and Pusa Basmati 1509 in rice, etc. have
grown into megavarietal proportions. Another important dimension is the focus shift
towards grain quality, as well as climate resilience. With the technological
advancements, breeding efforts in India is yet to venture into genomics assisted
breeding. Modern tools such as genomic selection and gene editing have not been
used in improving field crops in India. Although the research in this direction is
progressing, the looming threat of anti-GMO campaigns shadows the future of gene-
edited breeding lines, although all of them do not fall under the category of GMOs.
Recently, efforts are also underway to integrate technologies to translate breeding
success into genetic gain.

1.6 Towards Improving Genetic Gain

Genetic gain, the advantage accrued every generation within a unit of time, by
genetic improvement of crops has been a pivot of discussion for a long time.
Hazel and Lush (1942) defined genetic gain as the average improvement in geno-
typic/ phenotypic value within a population as a consequence of selection. In the
practical sense, this means a perpetual increase in productivity, described more
comprehensively as an ‘evergreen revolution’ by Prof. M. S. Swaminathan
1 Breeding Field Crops: History, Current Status and Introspections 29

(Swaminathan 1996). The dimensions of the evergreen revolution are multifaceted

and subsume ecological, economical and sustainable components (Swaminathan
2006). Genetic gain is an ultimate translation of trait advantage as a result of the
accrual of beneficial alleles. Therefore, the gain can happen in any trait individually
or in combination resulting in an overall advantage to the selected population. The
combining of multiple traits for selection can be realised through the use of appro-
priate selection indices. One of the primary requirements to achieve gain is herita-
bility. We know that heritability increases in several ways, the most common route is
through the accumulation of favourable alleles which cumulatively improves the
trait expressivity. Breeding interventions such as selecting a large set of genotypes
increases the probability of accumulating more variants, and more variants provide
the opportunity of generating several allelic combinations. Several allelic
combinations allow the steady accumulation of them, a perpetual increase leading
to the evergreen revolution.
Encapsulating all these components into a mathematical expression, Jay Laurence
Lush (1937) made the famous breeder’s equation, which would help to predict the
expected genetic gain in generations under selection. Breeder’s equation primarily
has three components, the selection intensity (i), heritability (h2) and additive
variance (σ2A), the product of which will help us to predict the gain. As discussed
above, i allows drawing the maximum number possible from a spectrum of alleles
(σ2A), with h2 translating the effect into the gain. Later a fourth component was
added as a denominator to the equation, the cycle time (L), which is the average time
per generation (Eberhart 1970), which has more relevance today than during the time
of Lush. Probably, Lush could not have imagined having this component added as
the original equation was framed for animal breeding, and it was not relevant to
animal breeding as reducing the gestation period in animals was impractical. Having
several generations squeezed within a time frame allows more opportunities for
accrual of alleles, therefore lower the cycle time increases the gain phenomenally.
For instance, keeping all the genetic factors constant, but having two generations a
year than the regular one, alone can double the gain. But directly applying the
equation to the public sector plant breeding has a catch. Mostly, the public sec-
tor plant breeding has been random, which means parents are selected at random and
progenies are also selected at random which leads to the breeding success also
becoming random. Breeder’s equation does not work with this randomness but
requires a closed system rather than an open one. A closed system means the
founders of the population should breed and the progenies must interbreed, recycled
through the selection process, accumulating the gain. The conundrum of random
breeding therefore cannot provide an actual assessment of genetic gain in the true
sense. However, assuming the whole breeding population within a species as the
breeding population, we can make a rough estimate of gain through era trials.
Era trials, evaluation of representative cultivars of different breeding eras, can
help us in indirectly estimating the realised genetic gain approximately (Rutkoski
2019a, b). Era trials have been used to estimate the genetic gain in maize hybrids
(Meghji et al. 1984), which was later extended to later eras as well (Duvick 2005).
There are other cautions too, era trials cannot compare the effect of breeding
30 K. K. Vinod et al.

2.5 0.040

0.035
2.0
0.030

0.025
1.5

0.020

1.0
0.015

0.010
0.5
0.005

0.0 0.000
0 10 20 30 40 50 60 70 80 90 100

Differential Gain

Fig. 1.7 A hypothetical relationship between realised yield and genetic gain in a crop for
100 years. The yield differential is calculated with respect to the base value at the beginning of
the breeding. Progressive genetic gain is calculated per year. Once the yield plateaus gain starts to
decay significantly

programmes, such as genetic gains by hybrids vs pure line varieties, because the
breeding itself is an outcome of a random set of parents and the pattern of yield
increase is not linear between eras. Further, the random representative(s) of each era
may not be truly representative. However, era trials can depict an overall picture of
where the breeding system stands currently. Another factor that decays the genetic
gain is the yield plateauing. In a hypothetical system as given in Fig. 1.7, the yield
plateauing can result in decay in genetic gain significantly if no breeding interven-
tion is made to uplift the yield levels, a situation currently being faced by several
field crops.
Realised genetic gains in field crops in India, show varying trends. It is not
surprising because, the quantum genetic gain for the evergreen revolution in differ-
ent crops should differ, based on their importance in the food chain as well as on the
base yield potential. It is proposed that a genetic gain of 1.3% per annum is required
to sustain food production in wheat (Rosegrant and Agcaoili 2010). Currently, data
are being generated to quantify realised genetic gains through era trials in major field
crops. In a recent exploration of yield and related traits in wheat, Yadav et al. (2020)
examined wheat yield from 1905 to 2016 by mining the historical data and found
that average genetic gain ranged from 0.54% per year to 0.82% per year (over the
first released variety, NP4). This estimate comes closer to the estimates made by
Lopes et al. (2012) using CIMMYT lines within a window of 30 years, in which a
gain of 0.9% among high yielding, 0.7% among intermediate and 0.5% among low
yielding cultivars have been reported. However, considering the wide window used
by Yadav et al. (2020), (no methods were found to explain how the estimates were
1 Breeding Field Crops: History, Current Status and Introspections 31

made) the yield gain in India could have been much larger, if we consider the decay
in genetic gain over the periods of intermittent yield stagnation.
Throwing light into this assumption, the preliminary trend from the era trials in
wheat indicates improved gain (unpublished data). The wheat yield improvement in
India could be attributed to parallel genetic gain in biomass, grain number per spike
and reduced duration. Examining the genetic gain in rice, with a specific focus on
rainfed environments, Kumar et al. (2021) report rather a short-term genetic gain in
rice, for a 10-year window between 2005 and 2014. They found an annual genetic
gain of 0.68% among irrigated checks, which increased to 0.87% under moderate
reproductive stage drought stress, while 1.9% gain could be achieved under severe
drought conditions. Although these figures cannot be scaled to rice breeding in
general, but indicates that trait targeted breeding still offers opportunities to improve
gain in crops like rice. In another such study in pearl millet, Yadav et al. (2021)
report achievement of 4% genetic gain per year during the last 30 years, primarily
attributable to hybrids. There was a marked gain in ear length and ear diameter, and
they are rated as the major components of yield gain. In chickpea too, the prelimi-
nary reports from era trials indicate significant genetic gain for the last 60 years
(unpublished data). Presently, efforts are underway to accelerate genetic gain in crop
breeding systems involving field crops.
One of the global movements towards accelerating the genetic gain is to employ
GS in a strict sense that oversees all the components of genetic gain. In India,
recently a pilot programme has been launched with selected field crops and involv-
ing several national and international institutions to start GS-based crop improve-
ment with the help of organisations such as Bill and Melinda Gates Foundation
(BMGF), Excellence in Breeding (EiB) and Breeding programme assessment tool
(BPAT). The major objective of this project is to generate crop product profiles for
TPEs, breeding programme optimisation, implementing GS and data digitalisation
through breeding management system (BMS).

1.7 Threats and Opportunities

In this section, we concisely present the prospects of crop breeding in India. This is
not particular to field crops alone. For several parts of the last 120 years, owing to
various factors, crop breeding in India has progressed through leaps and bounds.
Except for few milestones, public sector plant breeding has not been much eventful
before the 1950s. Restructuring of breeding research was the main highlight of the
pre-green revolution phase, which could successfully prepare the grounds for green
revolution. Yadav et al. (2019), while examining the production and productivity
pattern of major cereals, reveal that the phase immediately following the green
revolution was more productive than the green revolution itself. Although the threat
of yield stagnation is lingering, as seen occurring in wheat yield in Europe (Brisson
et al. 2010), the current situation in India shows a more comfortable scenario.
However, with unpredictable phenomena such as climate change on the horizon,
time is ripe to have another reorientation of breeding research in India to sustain an
32 K. K. Vinod et al.

evergreen revolution. With the caveats of climate change around, it is estimated that
as many as 30% of the world population would be at risk of hunger by 2050.
Events related to climate change are currently being reported around the world,
and in India, a tropical country, the threat is more formidable. Major challenges are
drought, flood, soil salinisation, submergence, temperature fluctuations, low
nutrients besides biological threats from pests, diseases and weeds. Besides, physio-
logical disorders can also emerge under shifting environments. Therefore, future
breeding should reorient towards precision agriculture with added resilience in crops
to face unexpected adverse events. This means the future belongs to widely adapted
cultivars than specifically adapted ones. It is time to recycle specifically adapted
cultivars through breeding to evolve wide adapted ones.
Agriculture is the largest industry in the world with the lowest capital input. This
is particularly relevant to countries like India, where crop breeding happens
unorganised. Comparing to other nations, Indian agriculture has a long way to go
in harnessing crop productivity in key crops. The most single reason for this is the
lack of adequate support. Despite having human and genetic resources, crop breed-
ing development in India has been heavily dependent on international inputs. Several
genes that are being used today are discovered in Indian landraces but the discoveries
have been made abroad. Unless increased focus is given with sufficient institutional
and financial support, future of plant breeding in India will be challenging. The
reorientation of agricultural research that happened in the post-1950s came with
futuristic investments such as AICRP and research institutions. Since its inception,
the AICRP system has not undergone serious restructuring, and still follows out-
dated protocols. A total reorientation of breeding with product profile and TPE
oriented system attached with state of the art infrastructure, standard operating
protocols, a modernised AICRP system and a renewed futuristic plan is the need
of the hour from the policy intervention front.
The technologic front in crop breeding has been transformative in the last three
decades. Particularly, developments in genome biology have changed the landscape
of trait-based breeding. With accurate interventions such as MABB, now we have
the capability to transfer a target allele to an elite background, where a particular
allele is lacking. Besides, techniques for large scale mining of alleles are also
available. With the high-end computational capabilities and high throughput
genotyping and phenotyping platforms breeding time is set to reduce considerably
in the future. Accurate predictions are taking over phenology-based selections.
Besides, accelerated generation turnover technologies such as doubled haploids,
rapid generation advancement and speed breeding are going to augment genomics
assisted breeding for better realisation of genetic gain. Additionally, genome editing
techniques are also getting ready for manipulation of individual genes to generate
novel traits that are hitherto lacking. In the twenty-first century, technological
options are unlimited for breeding modernisation. However, rational use of these
techniques is warranted for which appropriate human resource development is
essential.
The natural reserves of enormous genetic diversity and the availability of the best
human resources in the world are the primary opportunities we are bestowed with.
1 Breeding Field Crops: History, Current Status and Introspections 33

Compared to the global scenario, several genetic resources in India remain

underutilised. Currently, a megaproject is in operation to characterise and utilise
15,000 Indian rice landraces that are conserved in the National Gene Bank, for allele
mining, gene and trait discovery targeting several biotic and abiotic stress tolerance,
physiological and quality parameters. This project is expected to offer various novel
solutions hitherto not utilised in rice breeding. One of the major problems
concerning human resources has been the insufficient number of highly trained
personnel in research. Brain drain in agriculture research needs to be plugged,
particularly in crop improvement, for which strategic integration of genetic
resources, institutions, infrastructure, human resources, technology and market is
to be made.
We need to build a globally competitive research and education system in India.
Further, the research should be strictly oriented to meet the challenge of future food
needs for our growing population. With his futuristic vision, Prof. Swaminathan
wrote while introducing the concept of the evergreen revolution, ‘Countries like
India, China, and Bangladesh have to produce more and more food and other farm
commodities from diminishing per capita arable land and irrigation water resources.
Therefore, productivity enhancement is the only pathway available to us to produce
more to feed the growing population. This is why an Evergreen Revolution approach
is exceedingly important. An Evergreen Revolution needs the integration of frontier
technologies like biotechnology and information communication technology with
traditional ecological prudence’ (Swaminathan 2006).

1.8 Conclusion

In the present chapter, we have chronicled the breeding research in India, particularly
keeping field crops in focus, while introspecting the achievements made. More
discussions happened around the major field crops, but without critical details as
there are specific chapters to follow for those crops. However, we have tried to
narrate the milestones in the history of breeding wherever appropriate, while keeping
the future course in mind. No specific dealing of stress tolerance and quality
improvement has been made in this chapter, as that would be redundant. From the
modest beginning with the inception of IARI to commence the organised research in
agriculture, then through ICAR, modern breeding has transformed India from a ‘ship
to mouth’ economy to a self-reliant economy. We have also discussed the
opportunities of utilising modern technologies in fast-forwarding breeding and
thereby genetic gain.

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Wheat Breeding
2
Gopalareddy Krishnappa, Bhudeva Singh Tyagi, Vikas Gupta,
Arun Gupta, Karnam Venkatesh, Umesh R. Kamble, Sendhil R,
Gyanendra Singh, and Gyanendra Pratap Singh

Abstract

Wheat (Triticum spp.) is a major staple rabi cereal contributing about 20%
calories to the human diet and important cereal for ensuring food and nutritional
security in many parts of the world. Burgeoning population and diversification of
food habits involving more of wheat-based products have increased the demand
for wheat. Therefore, integration of modern crop tools with conventional
approaches is necessary to develop the future genotypes that not only will be
climate resilient and input responsive but also have higher yield per unit time and
space so as to meet the growing demand. It deals with the wheat crop in a holistic
manner focussing on a wide range of topics including origin, evolution, taxon-
omy, genetics, breeding, quality, stresses, high throughput phenotyping, genomic
selection, genome editing, speed breeding and new plant breeding techniques
(NPBT). This chapter also covers Indian approaches of wheat varietal develop-
ment and testing under co-ordinated system as a case study, and thus would be a
valuable reading material for students, researchers, academicians and policy
makers.

Keywords
Wheat · Genetics · Quality · Stresses · Genome editing · New breeding techniques

G. Krishnappa (*) · B. S. Tyagi · V. Gupta · A. Gupta · K. Venkatesh · U. R. Kamble · Sendhil R ·

G. Singh · G. P. Singh
ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
e-mail: gopalareddy.k@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 39

Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_2
40 G. Krishnappa et al.

2.1 Introduction

Wheat (Triticum spp.) is a major cereal crop contributing about 20% calories to the
diet and is a staple crop of many countries including India. Wheat-based multiple
products for the end users have increased the demand for wheat. Apart from major
source of starch and energy, it also provides variable amounts of a different
components which are essential or beneficial for health including protein, vitamins,
minerals, and phytochemicals. Wheat being a major source of cereal dietary fibre, its
consumption reduces the risk of cardio-vascular disease, type 2 diabetes, and certain
forms of cancer. Compound annual growth rate in production was much higher at
national level with 2.07% as compared to 1.35% at global level; attributed to India’s
positive growth in productivity (1.23%), followed by crop acreage (0.84%). The
level of global and national wheat productivity is broadly similar, although global
trends are slightly higher side on year-to-year basis, with the exception of 2000,
2002, 2012 and 2020 production years. It is important to state that in India, we
cultivate only spring wheat genotypes with maturity duration of ~140 days as
compared to the global scenario that includes a major portion of winter wheats
(close to 300 plus days for maturity) and this clearly indicates that our per day
productivity is much higher.

2.1.1 Importance of Crop and Progress Made in the Past 25 Years

The last 25 years of global and national trends on wheat area, production and
productivity are analysed and presented in Table 2.1 and Fig. 2.1 (FAOSTAT
2020). In India, wheat area under cultivation increased by 6.35 million hectares
(25.38%), i.e. from 25.01 million hectares during 1996 to 31.36 million hectares
during 2020. Contrary to the national scenario, global wheat area reduced by 2.73
million hectares (
1.21%), i.e. from 224.58 million hectares to 221.85 million
hectares during the same period. India’s wheat production increased from 62.10

Table 2.1 Dynamics in wheat area, production and productivity for India vis-à-vis in the world
Change
Parameter CAGR (%) CV (%) Quantum %
Period: 1996–2020
A. India
Area (mha) 0.84 6.99 6.35 25.38
Production (mt) 2.07 16.41 45.76 73.69
Productivity (kg/ha) 1.23 10.52 1015.51 40.90
B. World
Area (mha) 0.01 2.12
2.73
1.21
Production (mt) 1.35 10.69 197.48 34.13
Productivity (kg/ha) 1.32 10.11 862.91 33.49
CAGR is compound annual growth rate and CV is coefficient of variation
2 Wheat Breeding 41

250
World India
Area (million hecatres)

200

150

100

50

2006

2018
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005

2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017

2019
2020
900
Production (million tonnes)

800
World India
700
600
500
400
300
200
100
0

2018
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017

2019
2020
4000
3500
India World
Yield (kg/ha)

3000
2500
2000
1500
1000
500
0
2018
2019
2020
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017

Fig. 2.1 Trend in wheat area, production and productivity for India vis-à-vis the world

million tons during 1996 to a record production of 107.86 million tons during 2020
with a quantum jump of 45.76 million tons. Similar trends at global level were also
observed for the wheat production. However, India’s performance with respect to
percentage change (73.69%) for production was more than double as compared to
the world’s wheat production (34.13%). Our national wheat productivity increased
from 2483 kg/ha during 1996 to 3498 kg/ha during 2020. A similar trend was
observed for global wheat yield; however, again percentage change was much higher
at national level (40.90%) compared to global (33.49%). Overall, during the past
25 years, wheat area increased at national level but it has marginally decreased at
global level.
42 G. Krishnappa et al.

2.2 Origin, Evolution and Distribution of Species and Forms:

Wild Relatives

Wheat is a classic example for understanding the evolutionary theory of allopoly-

ploid, speciation, adaptation and domestication in plants (Gustafson et al. 2009).
Origin and evolutionary pattern of wheat are presented in Fig. 2.2. The cytogenetic
and genomic studies indicated that the mutation, polyploidy in the form of amphi-
ploidy and inter-generic hybridisations are the major factors responsible for the
evolution of present-day wheat. The wheat species can be broadly classified into
three groups, namely diploid, tetraploid and hexaploid, based on the number of
chromosome in the reproductive cell, i.e. n ¼ 7, 14, 21, respectively. Cytogenetic
studies revealed that four different genomes (ABD and G) representing four different
sets of seven chromosome contributed to the origin of tetraploid and hexaploid
wheats. The hexaploid wheat consists of two evolutionary lineages. The most
known and grown T. aestivum (AABBDD) comprises one lineage while
T. zhukovskyi (genome AAAAGG) comprises another lineage.
The earliest cultivated forms were diploid (genome AA) and believed to be
domesticated in south-eastern Turkey (Heun et al. 1997). During the process of

Fig. 2.2 Origin and evolutionary pattern of wheat. Solid arrows indicate hybridisation followed by
chromosome doubling. Dashed arrows indicate domestication or direct selection within a species.
Boxes indicate cultivated taxa
2 Wheat Breeding 43

domestication major emphasis was given on two traits, i.e. non-brittle rachis or tough
rachis and the hull-less grains or free threshing grains. The source of A genome of
tetraploid and hexaploid wheats was related to two diploid species,
i.e. T. monococcum and T. urartu. Earlier studies by Kihara (1944) indicate that
AA genomes were contributed by T. monococcum. However, on the basis of
repeated nucleotide sequences in the phylogeny of polyploidy species of wheat,
Dvorak et al. (1993) concluded that AA genomes in the tetraploid and hexaploid
wheats are more related to AA genomes of T. urartu. The BB genomes of the
tetraploid and hexaploid wheats are closely related to Sitopsis section of Aegilops
with Ae. speltoides being the closest species. The SS genomes of Ae. speltoides is
also closest to the GG genomes of T. timopheevi. The AABBDD genomes are
thought to be arisen through hybridisation of T. turgidum with Aegilops tauschii.
Petersen et al. (2006) re-sequenced two single copy nuclear genes DMC1 and EF-G
isolated from each of the three genomes in hexaploid wheat (BBAADD) and two
genomes of the tetraploid wheat (BBAA) using a sophisticated extension of PCR
technique, and on the basis of phylogenetic analysis with diploid species, they
suggested that the DD genomes of wheat was derived from Ae. taushcii. The D
genome contributed significantly to the wheat flour properties that make bread wheat
so valuable in bread making (Morris and Sears 1967).
The diploid wheats include two species, viz., T. monococcum and T. urartu. The
sterility in the hybrids of monococcum and urartu (Johnson and Dhaliwal 1976)
indicate that they are valid species. Reproductive barrier is not essential but one of
the important criteria for recognising the species and natural hybridisation between
diploid species is a rare phenomenon. The cultivated einkorn T. monococcum ssp.
monococcum is the domesticated form of wild einkorn T. monococcum ssp.
aegilopoides. The cultivated ssp. of monococcum differs from ssp. aegilopoides in
having slightly large kernel and less brittle rachis. It is believed to be domesticated in
‘Fertile Crescent’ of Near East, which encompasses the eastern Mediterranean,
south-eastern Turkey, northern and western Iraq and its neighbouring regions of
Transcaucasia (Matsuoka 2011). The wild diploid species T. urartu also found in
Fertile Crescent though it has never been domesticated. The tetraploid wheat
(2n ¼ 4x ¼ 28) originated as a result of natural crossing between T. urartu and
Aegilops speltoides. This resulted in origin of both the tetraploid species, namely
T. turgidum (AABB genome) and T. timopheevi (AAGG genome).
The wild form of T. turgidum ssp. dicoccoides with brittle spike is reported from
the Fertile Crescent. The non-brittle spikes with tough rachis among the wild form
were selected by farmers. From there it spread to the other parts of world. Durum
wheat is said to be derived from T. dicoccum (Damania 1998). The emmer wheat
underwent further diversification in response to the agro-ecological conditions and
gave rise to free threshing tetraploid wheats, namely rivet wheat (T. turgidum ssp.
turgidum), polish wheat (T. turgidum ssp. polonicum) and khorasan wheat
(T. turgidum ssp. turanicum). Interploidy introgression in hybrid swarms is thought
to be contributed to further diversification of the turgidum wheat by giving rise to
two sub-species T. turgidum ssp. paleocolchicum and T. turgidum ssp. carthlicum.
McFadden and Sears (1946) created an artificial spelta (hexaploid wheat) from a
44 G. Krishnappa et al.

hybrid of T. dicoccum and Ae. Tauschii, followed by chromosome doubling with

colchicine. Therefore it was inferred that spontaneous hybridisation between emmer
wheat (T. dicoccum) and goatgrass produce an early spelta (T. spelta 2n ¼ 6x ¼ 42
genome AABBDD). Later more easily free threshing bread wheat was evolved
through natural mutation and selection. Hexaploid T. zhukovskyi originated recently
by interspecific hybridisation of cultivated T. timopheevii with cultivated
T. monococcum (Dvorak and Luo 2001).

2.3 Taxonomic Position of Genus Triticum

In botanical classification, wheat is a member of the grass family Poaceae (also

called Graminae), the subfamily Pooideae and the tribe Triticeae. Beside wheat,
many agricultural important crop species like barley, rye, and several forage species
belongs to the tribe triticeae. The tribe is mainly distributed in the east Mediterranean
and central Asiatic regions. Linnaeus (1753) describes five genera, namely Secale,
Triticum, Hordeum, Aegilops and Elymus, in this tribe, whereas Clayton and
Renvoize (1986) recognised 18 genera in the tribe triticeae. Later on van Slageren
(1994) added Ambylopyrum genus in the tribe. All these genera were classified into
two sub-tribes, namely Hordeineae (barley lineage with nine genera (Elymus,
Hystrix, Sitanion, Leymus, Psathyrostachys, Hordelymus, Hordeum, Taeniatherum,
Crithopsis)) and Triticineae (wheat lineage with nine genera (Agropyron,
Eremopyrum, Heteranthellium, Secale, Dasypyrum, Triticum, Ambylopyrum,
Aegilops, Henrardia)) (Feldman and Levy 2015). The genus Brachypodium was
earlier included in this tribe but later on excluded from this tribe (Hasterok et al.
2004). Bowden (1959) advocated that there is no need to treat Aegilops as a separate
genus from Triticum, however van Slageren (1994) considered Aegilops and
Triticum are closely related but separate genera.
Several species of genus Secale and Aegilops serve as primary genepool based on
crossability with Triticum species, while several species of genera Elymus, Leymus,
Psathyrostachys, Dasypyrum are capable of being hybridised with wheat (Wang
2011), and considered as secondary and tertiary genepool of wheat. The taxonomy
of genus Triticum is always debatable. In recent years, Mac Key (1966 and 1977)
and Dorofeev et al. (1979) illustrated the system of classification of genus Triticum,
while van Slageren (1994) revised the classification provided by Mac Key (1966).
Goncharov (2011) reviewed the taxonomic history of genus Triticum and differences
between various classifications of genus Triticum. van Slageren (1994) classified the
genus Triticum into 3 sections and 6 species. These 6 species were further divided
into 4 autonym and 13 non-typical subspecies, while Dorofeev et al. (1979)
recognised 27 species in the genus Triticum (Table 2.2). van Slageren (1994)
considered T. sinskajae a free threshing mutant of T. monococcum, T. jakubzineri
a form of T. turgidum, T. militinae a free threshing mutant selected from single
specimen of cultivated T. timopheevi, T. petropavlovskyi mutated form of
T. polonicum, T. aethiopicum free threshing emmer selected from T. dicoccon,
T. isphanicum as a form of T. polonicum due to more standard glume morphology.
 2

Table 2.2 Overview of Triticum species

Van Slageren (1994) Dorofeev et al. (1979) Chr. Genomic
Sect Species and Sub-species Sect Species No. Common name constitution
Monococcon T. monococcum L Monococcon T. monococcum L 14 Cultivated Einkorn AbAb
ssp. monococcum L T. sinskajae A. F ilatet Kurk 14 Naked einkorn AbAb
Wheat Breeding

ssp. aegilopoides (Link) Thell T. boeoticum (Boiss) 14 Wild einkorn AbAb

T. urartu Thumanian ex Gandilyan Urartu T. urartu Thumanian ex 14 Wild form AuAu
Gandilyan
Dicoccoidea T. turgidum L Dicoccoidea
ssp. dicoccoides (Korn. Ex Asch. & T. dicoccoides (Korn. Ex Asch. & 28 Wild emmer wehat AuAu BB
Graebn.) Thell Graebn.) Thell
ssp. dicoccon (Schrank) Thell T. dicoccum (Schrank) Schuebl 28 Emmer wheat AuAu BB
ssp. paleocolchicum (Menabde) A T. karamyschevii Nevski 28 Georgian wheat AuAu BB
love and D. Love
T. ispahanicum Heslot 28 Emmer wheat AuAu BB
ssp. turgidum L Triticum T. turgidum L 28 Rivet, cone or AuAu BB
pollard wheat
ssp. durum (Desf) Husn T. durum Desf 28 Macaroni wheat AuAu BB
ssp. carthlicum (Nevski) A. Love & T. carthlicum Nevski 28 Persian wheat AuAu BB
D. Love (syn. T. persicum Vav.)
ssp. turanicum (Jakubz.) A love and T. turanicum Jakubz 28 Khorassan wheat AuAu BB
D. Love
ssp. polonicum (L.) Thell T. polonicum L 28 Polish wheat AuAu BB
T. jakubzineri Udacz. et Schachm 28 Naked tetraploid AuAu BB
T. aethiopicum Jakubz 28 Ethiopian wheat AuAu BB
T. timopheevi (Zhuk.) Zhuk
ssp. timopheevi (Zhuk) Zhuk Timopheevii T. timopheevii (Zhuk.) Zhuk 28 Zanduri wheat AbAb GG
ssp. armeniacum (Jakubz.) Zhuk T. araraticum Jakubz 28 Wild Zanduri AbAb GG
syn T. ararticum
45

(continued)
 46

Table 2.2 (continued)

Van Slageren (1994) Dorofeev et al. (1979) Chr. Genomic
Sect Species and Sub-species Sect Species No. Common name constitution
T. militinae Zhuk. et Migusch 28 Naked tetraploid AbAb
Triticum T. aestivum L. Triticum
ssp aestivum L T. aestivum L 42 Bread wheat AuAuBBDD
ssp. compactum (Host) Mackey T. compactum Host 42 Club wheat AuAuBBDD
ssp. sphaerococcum (Percival) T.sphaerococcum Perciv 42 Indian dwarf wheat AuAuBBDD
Mackey
T. petropavlovskyi Udacz. et 42 Rice-head wheat AuAuBBDD
Migusch
ssp macha (Dekapr and Menabde) Spelt T. macha Dekapr. et Menabde 42 Macha wheat AuAuBBDD
Mackey
ssp. spelta (L.) Thell T. spelta L 42 Dinkel wheat AuAuBBDD
T. vavilovii (Thum.) Jakubz 42 Yunanense Wheat AuAuBBGG
Kiharae T. kiharae Dorof. et Migusch 42 AbAbGGDD
T. zhukovskyi Menabde & Ericz Timopheevii T. zhukovskyi Menabde et Erizjan 42 Zhukovsky’s AbAbAuAuGG
wheat
G. Krishnappa et al.
2 Wheat Breeding 47

These were not considered as separate taxa at species or sub-species level by van
Slageren (1994).

2.4 Spike Morphology and Pollination System

The wheat inflorescence commonly known as ear and in botany called as terminal
distichous compound spike. In spike, the spikelets are arranged on the alternate side
of the zig-zag rachis (Fig. 2.3). In a majority of tetraploid and hexaploid species of
Triticum, the rachis is tough and resists disarticulation. However, T. dicoccoides and
T. dicoccon disarticulate easily when mature. Each spikelet is subtended by two
sterile or empty glumes. These glumes are arranged alternately on opposite side of
the short central axis called rachilla. In a majority of Triticum species the glumes are
shorter than the spikelet. The glumes are glabrous or pubescent. In some of the
Triticum species, the glumes are keeled throughout, while in some species lower
portion of glume is rounded. The shape of glume apex differs significantly in
different species of Triticum. In T. aestivum, each spikelet consists of 3–6 florets
attached alternately on rachilla. Each floret has its own lemma and two nerved palea.
The tip of lemma may or may not be extended to awn. Based on the length of awn,
the wheat is classified as long medium, short or awnless. The wheat flower is
hypogynous and simple in structure consisting of whorl of three stamens and a
single carpel. The uppermost floret of spikelet is imperfect (Percival 1921).
Wheat is usually self-pollinated species and anthesis starts from the middle third
of the spike and proceeds upwards rapidly and downwards little slower. In spikelet,
the basal flower is first to open then the secondary florets (de Vries 1971). The
receptivity of stigma depends on weather conditions. The anther dehiscence begins
with elongation of filament and is completed after the anther is pushed out of floret
due to lodicules swelling. Parts of the pollen fall on their own stigma and fertilise the
ovary. The wheat pollen is short lived and the viability of pollen depends on the
weather conditions. Generally, pollen remains viable upto 30 to 40 min after pollen
shedding. The florets close again due to collapse of lodicules. In case ovary remains

Fig. 2.3 Wheat inflorescence. (a) Spike of wheat. (b) Spikelet of wheat 4. (c) Floret of wheat 8
48 G. Krishnappa et al.

unfertilised, Okada et al. (2018) reported the second opening of flowers in wheat
within a few days of post-anthesis. In the second opening there is a significant
enlargement of ovary and forces the lemma end to be apart. Despite cleistogamous
flower, less than 1% out crossing is reported in the wheat.

2.5 Gene Banks and Conservation of Genetic Resources

The key to success in any crop breeding programme depends on tapping the genetic
variability of existing plant genetic resources in hybridisation programme. The
extent of diversity present in the gene bank still remain untapped and may contain
many useful traits that can be used in accelerating the rate of genetic gain in wheat
breeding. The wheat genetic resources conserved in various gene banks also stored
much useful information on passport and evaluation data. The gene bank serves as a
focal point for providing information on plant genetic resources. The basic purpose
of collating such information is to enable the plant breeders to make more thorough
use of plant genetic resources. Significant progress has been made in various modern
biotechnology tools such as recombinant DNA technology, cell biology and allied
disciplines in recent years. Such tools should be targeted to mine genetic diversity as
part of pre-breeding programmes for efficient integration with conventional breeding
programme so as to achieve better and faster breeding outcomes.
Conservation of wheat genetic resources is a global concern. The in-situ conser-
vation is one of the way of conservation of biodiversity, especially crop wild
relatives. Damania (1996) advocated the need to safeguard the natural ecosystem
as it is highly dynamic and understanding it’s components in short notice is unreal-
istic. Various countries, like Armenia, Russia, Syria, and Turkey, are involved in
in-situ conservation of wild relatives of wheat crop (Meilleur and Hodgkin 2004).
However, ex-situ conservation of wheat genetic resources had contributed a lot to the
improvement of wheat yield, disease resistance and nutritional quality. Around
856,168 germplasm accessions are being conserved in various national and interna-
tional organisations. Our global partner, CIMMYT has made significant contribution
in conserving, improving and distributing wheat germplasm particularly to develop-
ing countries. CIMMYT’s wheat programme has a focus on development of new
germplasm and their distribution in the form of various international trials and
nurseries. In the gene bank of CIMMYT, around 110,281 accessions of wheat are
conserved (Table 2.3). These are nearly 13% of total wheat germplasm conserved in
various gene banks. The introduction of Norin 10 genes in the CIMMYT programme
revolutionised the wheat production in many parts of the world. Pavon, Veery,
Bobwhite, Attila and Kauz are some of the CIMMYT lines, which have been used
extensively in the breeding programme. The National Small Grain Collection at
USA also safeguards the important global collection. Over the years, India and
China have also developed sound scientific management for ex situ conservation
of wheat genetic resources.
2 Wheat Breeding 49

Table 2.3 Germplasm holding of wheat in various gene banks

Name of the institute Accessions
CIMMYT, Mexico 110,281
National Small Grain Collection, USDA 57,348
Institute of Crop Germplasm Resources, Chinese Academy of Agricultural 43,039
Sciences, China
National Bureau of Plant Genetic Resources, India 35,889
International Center for Agricultural Research in the Dry Areas (ICARDA), Syria 34,951
National Institute of Agrobiological Sciences, Japan 34,652
N.I. Vavilov Research Institute of Plant Industry, Russia 34,253
Instituto di Genetica Vegetale (IGV), Bari, Italy 32,751
Leibniz Institute of Plant Genetics and Crops Plant Research (IPK), Gatersleben, 26,842
Germany
Australian Winter Cereals Collection, Agricultural Research Centre, Tamworth, 23,811
Australia
National Plant Gene Bank of Iran, Iran 18,442
Kazakh Research Institute of Agriculture and Plant Growing 18,000
Others 385,909
Total 8,56,168
Source: FAO (2010)

2.6 Molecular Cytogenetics and Breeding

Wheat cytogenetics started with the discovery of chromosome number of durum

wheat (2n ¼ 28) by Karl Sax in 1918, followed by the reporting of chromosome
number of eight wheat species, viz. T. monococcum (2n ¼ 14), T. dicoccum
(2n ¼ 28), T. durum (2n ¼ 28), T. turgidum (2n ¼ 28), T. polonicum (2n ¼ 28),
T. spelta (2n ¼ 42), T. compactum (2n ¼ 42) and T. vulgare (2n ¼ 42), with the basic
chromosome number of x ¼ 7 by Sakamura in Japan (Sakamura 1918). These
chromosomes numbers of identified species were later confirmed by Kihara and
Sax in 1919 and 1922. Kihara used genomic analysis to study the evolutionary
relationship among different Triticum species as earlier successfully demonstrated in
genus Drosera by Rosenberg (1909). Genomic analysis involves the crossing of
allopolyploids with their presumed diploid ancestral species to study pairing pattern
of their triploid hybrids. In the hybrids, if there is occurrence of basic number of
bivalents, it is taken as a sign of genomic homology of the diploid parent with one of
the genomes present in allopolyploid species.
Genomic homology becomes confusing when there is presence of higher order of
pairing like trivalents, tetravalents and pentavalents, indicating some degree of
differentiation of otherwise identical genomes. Kihara (1919) analysed chromosome
pairing behaviour in the crosses between tetraploids and hexaploids, and observed
14II and 7I in the pollen mother cells. Similarly, Sax in 1922 observed 7II and 7I in
the pollen mother cells of hybrids generated from tetraploid and diploid crosses.
Whereas, in crosses of T. vulagre and Ae. cylindrica (CCDD) giving F1 hybrid
50 G. Krishnappa et al.

Fig. 2.4 Genomic analysis based on pairing behaviour among diploid and tetra and allohexaploids
as described by Kihara (1919)

having 7II + 21I (ABCDD) as well as in reciprocal crosses in the pollen mother cells
as earlier reported by Kihara. Based on these studies as well as other studies as
depicted in Fig. 2.4, it was concluded that the genus Triticum had three different
genomes having 7 chromosomes each and these genomes were designated by Kihara
as A, B, C and D. It has been concluded that the hexaploid wheat genomes A and D
have been contributed from T. uratru and Ae. Taushii (not from Ae. Caudata and
designated as D).
The exact donor of B genome of present-day hexaploid and diploid bread wheat is
still lacking, although many related diploid species exhibited partial homology and
chromosome pairing but not to the extent observed for the A and D genome donors.
Currently, Ae. speltoides (2n ¼ 14, BB) species considered as the probable B
genome donor (Dvorak et al. 1973). However, there are studies against the general
acceptance including Kimber (1974), the study suggest that T. speltoides is probably
homologous to the G genome of T. timopheevii and B genome donor to T. turgidum
or T. aestivum is unrecognised. The C-banding technique helps in the identification
of heterochromatin (dark-staining regions) and euchromatin (light-staining regions)
on the chromosome axis. Within a homoeologous group, there was no similarity for
the C-banding of chromosomes except for fifth group. C-banding comparisons of the
diploid species T. monococcum, T. speltoides, and T. tauschii with that of the A, B,
and D genomes, respectively, in hexaploid wheat confirmed that T. speltoides could
not be the donor of the B genome to wheat and that T. monococcum and T. tauschii
are the probable donors of the A and D genomes, respectively (for details see Gill
and Kimber 1974).
2 Wheat Breeding 51

2.6.1 Structure of Wheat Chromosomes

There are 21 pair of chromosomes identified cytologically having a primary con-

striction/centromere with secondary constrictions on two pairs of chromosomes
indicating sites for ribosomal RNA genes. According to the observations of Sears
(1954), the length of chromosomes at metaphase is on average 5.6 μm enclosed in
the nucleus having a total volume of 1700 μm3 in which about 36.2 pg of DNA is
accommodated. The total DNA length is about 11.2 m with a volume of 35 μm3 and
is divided into 42 chromosomes. The DNA is coiled extensively and the first level of
compaction is the nucleosome as revealed under electron microscope and by par-
tially digestion of DNA with micrococcal nucleases. A haploid nuclear genome of
hexaploid bread wheat has 16.72  109 bp (17.325 pg) of DNA, distributed on
42 chromosome 0.682 pg on 1DL to 2.475 pg on 3BL. The DNA contents in the A,
B and D sub-genomes are found in the ratio 1.16:1.2:1.0 (Gupta 1991). It has been
shown through reassociation kinetics that F75% of this DNA is repetitive (Mitra and
Bhatia 1973).
Another 20% of DNA constitutes non-coding unique sequences. In addition, 30%
of cytosine residues in this DNA are highly methylated regulating the expression of
genes (Moore et al. 1993). Only 1% of this DNA is known to take part in protein
synthesis; in this 1% DNA, F1, 000 genes have already been recognised, some of
them representing multigene families (Lagudah et al. 2001; McIntosh et al. 1998).
With the advancements in banding techniques, Sears (1954) identified individual
wheat chromosomes through monatomic analysis and made some morphological
observations, although cytologically most chromosomes were indistinguishable.
Furthermore, Sears and Sears (1978) expedite the chromosome identification
through isolation of marker telocentric chromosomes. Gill and Kimber (1974)
identified individual wheat chromosomes, and wheat ideogram was constructed
using C bands, which was facilitated by the telocentric chromosomes to recognise
individual chromosomes.

2.6.1.1 Cytogenetic Stocks in Wheat

Wheat Aneuploids
Aneuploids in wheat have been developed by ER Sears, using cytogenetics
techniques in the Chinese spring cultivars. These stocks are possible because
wheat genome is polyploidy and can tolerate aneuploidy (Sears 1954, 1966a).
During the 1930s, ER Sears was able to identify a few haploid plants, resulting
from the cross between Chinese Spring with rye, which formed the basis of devel-
opment of aneuploid stocks. In total, 220 lines were isolated, which comprised the
stocks: 21 Monosomics (2000 + 100 ); 7 Monoisosomic (2000 + i”); 21 Trisomics
(20“+1’“); 38 Nullisomic–tetrasomic (20”+100 “); 4 Monosomic–tetrasomic
(20“+1’+1’“‘); 8 Nullisomic (20”); 20 Double monosomic (19“+1’+1’);
Ditelosomic (20”+t“), 21; 20 Double-ditelosomic (20”+tS” + tL”) and 41 Ditelo-
monotelosomic (2000 + t” + t’). But the maintenance of these stocks is very difficult as
52 G. Krishnappa et al.

it is necessary to characterise the progeny of each aneuploid for ascertaining the

chromosome number.
These aneuploidy stocks have a great potential for localisation of genes to specific
chromosomes/chromosomal arms (McIntosh 1988). A unique genetic system for
production of deletion stocks systematically with variable sized terminal deletions in
individual chromosome arms was reported by Endo (1988). He suggested that
presence of certain chromosome from Aegilops cylindrica in Chinese spring in the
monosomic condition, it induces chromosomal breaks in the gametes lacking
A. Cylindrica chromosome and results in generation of various chromosomal
aberrations, including deletions. The broken chromosome ends, if not fused to
other broken ends, are stabilised by the rapid gain of telomere structure (Werner
et al. 1992). Such deletions in plants without the A. cylindrica chromosome are
transmitted regularly to the offspring, and they identified 436 deletions by
C-banding.

Alien Addition and Substitution Lines

Development of alien addition and substitution lines started during the late 1950s by
producing amphiploids through crosses between hexaploid wheat and any diploid
alien species, whose chromosomes were to be added or substituted. An amphiploid
having 2n ¼ 56 was first crossed with hexaploid wheat, giving a heptaploid
(2n ¼ 49), which on selfing would produce progenies having different chromosome
numbers including monosomic addition lines, which could then be selfed to obtain
disomic alien addition lines. Such alien addition lines (including wheat-rye addition
lines) were developed in the USA and Canada. These alien addition lines can be
crossed with monosomics, and on selfing will give progenies having disomic
substitution lines.
The aneuploid stocks offer great benefit as the cytogenetic markers identified on
each of the 21 chromosomes will help in identification of each chromosome and
chromosome arm. Because of the nulli-tetrasomic lines, Sears (1966b) was able to
place the 21 wheat chromosomes into 3 genomes and 7 homeologous groups. For
locating genes on to individual chromosomes, monosomic and telosomic have been
used (McIntosh et al. 1995; Sears 1966c). These deletion stocks have been used to
place the EST markers onto specific deletion bins for precisely map genes of interest
(Qi et al. 2004). In addition, the deletion stocks were crucial in relating genetic maps
to physical maps of chromosomes, map-based cloning of genes (Simons et al. 2006;
Yan et al. 2003), and studying the distribution of genes (Gill et al. 1996) and
recombination frequency along the chromosomes (Akhunov et al. 2003). The
whole genome sequencing project of wheat has been made possible by the use of
the ditelosomic stocks for isolating individual chromosome arm through flow sorting
for the construction of arm-specific BAC libraries (Safar et al. 2004).

Diploidising System
Bread wheat contains three closely related genomes therefore; loss of any chromo-
some of a homeologous group can be compensated by the homeologous group
chromosomes because of which monosomics have been possibly developed. Despite
2 Wheat Breeding 53

closely related chromosomes, homeologous group chromosomes strictly follow

diploid type behaviour and form 21 bivalents. The genetic control of chromosome
pairing in wheat is dependent on a series of promoters and suppressing pairing
homologues genes (Sears 1976). The strongest effect on pairing is associated with a
gene on chromosome 5BL known as Ph1 locus, which prevents homoeologous
chromosomes to pair at meiosis. Apart from Ph1 locus, two more suppressors
have been identified Ph2 on 3DS and another suppressor on chromosome 3AS.
This feature of Ph1 locus was utilised for transfer of desirable genes from alien
species to wheat, because in wheat plants deficient for 5B or those carrying a
mutation for Ph1 locus (Sears 1977) pairing between wheat chromosomes and the
corresponding homoeologous alien chromosomes would occur. This will allow
transfer of alien genes on to wheat chromosomes through recombination.

Alien Introgressions
Development of new plant varieties requires genetic variability, which can be
created by crossing the available germplasm in the primary gene pool. Modern
plant breeding, although increased crop productivity world-wide, however, it also
eroded the genetic variability of the crops (Gill et al. 2011; Hoisington et al. 1999).
Alien introgression of different gene(s) for tolerance to biotic/abiotic stress tolerance
in wheat is presented in Table 2.4. To introduce new variability, use of secondary
and tertiary gene pools is required and is generally referred as ‘wide hybridisation’.
Many wheat varieties have been released around the world carrying alien

Table 2.4 Alien introgression of different gene(s) for tolerance to biotic/abiotic stress tolerance in
wheat
Source Gene/trait Reference
T. monococcum Sr21, Sr22, Sr35 The (1973), Kerber and Dyck (1973), McIntosh
et al. (1984), Rouse and Jin (2011)
T. dicoccum Sr9 Knott and Anderson (1956)
T. turgidum var. Sr2 McFadden (1930)
dicoccoides
T. turgidum var. Sr11, Sr12 Knott and Anderson (1956), Sheen and Snyder
durum (1964)
T. dicoccoides Lr64, Pm16, Pm 26, Kolmer et al. (2010), Reader and Miller (1991)
Pm 30, Pm31
T. timopheevii Sr36, Sr 37 McIntosh (1988), McIntosh and Gyarfas (1971)
Th. Salt tolerance Colmer et al. (2006)
bessarabicum
and
Th. elongatum
Ae. ventricosa 2 ns blast resistance, Maia (1967), Helguera et al. (2003), Williamson
nematode resistance, et al. (2013)
Rkn3
54 G. Krishnappa et al.

chromosomal introgression from related wild species. About 110 leaf rust (Lr),
86 stem rust (Sr), and 83 stripe rust (Yr) resistance genes have been identified in
wheat or wild relatives, most conferring race-specific resistance to these rust
pathogens (Bhatta et al. 2019; Cox et al. 1992; Huerta-Espino et al. 2011; Ram
et al. 2005; Singh et al. 2015).
Using ionising radiation, Sears (1956) transferred a leaf rust resistance gene from
Aegilops umbellulata to chromosome 6B of bread wheat. The classical example of
alien introgression T1BL1RS resulted from the breakage of wheat chromosome
1BL1BS at the centromere, and the 1BS arm of wheat was replaced by the 1RS arm
of rye. This introgressed chromosomal segment carried group of resistance genes to
leaf rust (Lr26), stem rust (Sr31), stripe rust (Yr9), powdery mildew (Pm8) (Friebe
et al. 1996), along with robust drought-tolerant root system (Sharma et al. 2011).
Similarly, powdery mildew resistance gene Pm 21 (T6AL6VS) was introgressed
from Dasyprum villosum (L.) Candargy had other important genes for resistance to
wheat curl mite, stripe rust and Fusarium head scab (De Pace et al. 2011). Transfer of
Ae. Umbellulata-derived leaf and stripe rust resistance to hexaploid wheat has been
demonstrated by Chhuneja et al. (2008) and Bansal et al. (2017). Direct cross
between wheat and Ae. kotschyi have been used to develop amphiploids with high
grain iron and zinc and flag leaf iron and zinc concentrations as that of the Ae.
kotschyi parent (Rawat et al. 2009). CIMMYT had developed about 1300 primary
SHW, and have been confirmed to possess valuable traits for better performance
under biotic and abiotic stresses, along with yield potential (Mujeeb-Kazi et al. 2008;
Yumurtaci 2015). Dyck and Kerber (1970) transferred first leaf rust resistance gene,
Lr21, from Ae. squarrosa var. strangulata ‘R.L.5271’ to Canthatch and Thatcher
wheat cultivars through direct hybridisation. Lr42 has been one of the most effective
Lr genes introduced from Ae. tauschii accession TA2450 for further utilisation in
hexaploid wheat breeding (Gill et al. 2019).

2.7 Genetic Studies of Qualitative and Quantitative Traits

Improvement in any crop requires the presence of genetic variation and also the
exploitation/manipulation of that variation for developing improved genotypes.
Selection is generally practised for selecting desirable plants within the population,
which is based only on identification phenotypically superior plants. Phenotype is
composed of both heritable and non-heritable variation. The heritable component is
governed by the gene(s) present in the genome of the plant, whereas the unexplained
variation (environmental influence) affecting the expression of trait is non-heritable.
In order to select the plants, understanding of fundamental laws of inheritance and
genetics of different traits is necessary. Some characters are governed by one or few
genes and are also less influenced by environmental variation and are referred as
oligogenic/qualitative traits. These traits produce specific effect, and population can
be classified into distinct classes. Some traits are controlled by several genes having
small effect are referred to as polygenic/quantitative traits. These traits are largely
affected by environmental factors, and population shows continuous variation and
2 Wheat Breeding 55

cannot be classified into distinct classes as in case of oligogenic traits. The earliest
examples of genetics studies in wheat for presence of awns and glume hairiness were
reported to be governed by genes, which were monogenically inherited.
However later studies indicated more complex inheritance. Based on chromo-
some substitution lines genes conditioning earliness were reported to be present on
seven chromosomes (Kuspira and Unrau 1957). Similarly, genetics have been
worked out by different workers for different wheat traits, like biotic stresses
(rusts, powdery mildew, Karnal bunt, Spot blotch, Tan spot, etc.), abiotic stresses
(heat, drought, waterlogging, salinity, PHST, etc.), agro-morphological traits, viz.
earliness, tillering, lodging, plant height, spike density, 1000-kernel weight, grain
number and yield using conventional inheritance studies as well as using cytogenetic
stocks to identify chromosomal regions governing these traits. The qualitative
inheritance have been reported mainly for biotic stresses, particularly rust and
powdery mildew resistance, whereas the quantitative inheritance have been reported
for spot blotch, Karnal bunt, Septoria, head scab, heat and drought tolerance and
most of the yield contributing traits. Grain yield being a complex trait generally
associated with different yield contributing traits, which are also polygenically
inherited. Selection for oligogenic traits can be practised early in generation as
they are having high heritability. The quantitative traits like grain yield are having
low heritability and are also influenced by environmental factors, so selection will be
better if practised later in generations as it gives opportunity for combing several
component traits to be selected upon. Therefore knowledge of trait genetics is of
utmost importance for wheat breeding.

2.8 Breeding Objectives

2.8.1 Grain Yield: The Ultimate Aim

Breeding for higher yield is one of the primary objectives of wheat improvement to
meet the ever increasing demand for wheat-based diets across the globe. Breeders of
autogenous crops aim to develop inbred varieties through selection and accumula-
tion of desirable alleles with additive effects on desirable traits, including yield.
During the initial 3 decades of green revolution, the global wheat yield was around
3% per annum, whereas, the following two decades witnessed the growth of merely
1.4% (FAO 2020). The quantum jump in wheat yields across the globe started in the
1960s, with the continuous effort of Nobel Laureate Norman E. Borlaug with his
crossing programme including Norin-10/Brevor cross that introduced the Rht-B1
and Rht-D1 dwarfing alleles, which led to the development and release of input
responsive semi-dwarf varieties led to Green Revolution.
Historically, chromosomal translocation of 1RS-1BL between wheat and rye was
one of the most landmark introgression till date in wheat improvement, which
increased the wheat yield potential and tolerance to biotic and abiotic stresses.
56 G. Krishnappa et al.

This landmark segment is still present in many of the important wheat cultivars,
currently cultivated across the globe (Schlegel 1997). The contribution of E.R. Sears
deserves a special mention for his great contribution to this field. Development of
synthetic wheat is another important strategy by repeating the interspecific crosses
that occurred in nature that led to the formation of hexaploid wheat. Different
accessions of the hexaploid wheat progenitors T. monococcum, T. turgidum, and
Ae. tauschii used for the formation of new genetic constitutions of wheat, greatly
increasing the genetic variability of the primary gene pool (Mujeeb-Kazi et al. 2008).
Numerous synthetic wheat germplasm pools have been developed by CIMMYT,
Mexico.

2.8.1.1 Trait-based Breeding to Increase the Yield Gain

Selection of wheat genotypes based on yield components will help in the cultivar
improvement along with yield per se selection, since yield is a complex trait and
influenced by several component traits. Introgression of multiple traits for better
agronomic and physiological performance into a single variety could help in the
genetic progress of grain yield. Some of the yield components that have been
successfully utilised for cultivar development with improved grain yield in different
wheat breeding programmes are discussed below.

Early Flowering and Maturity

Development of new high yielding wheat cultivars having early flowering and
maturity is one of the important breeding objectives. The main focus of breeding
programmes is to develop genotypes, which mature early as an adaptive mechanism
for terminal heat and drought stress experiencing environments. Most of the present
wheat cultivars incorporated vernalisation and photoperiod insensitive genes to
promote early flowering and maturity (Chen et al. 2016). Vernalisation genes Vrn-
A1, Vrn-B1, and Vrn-D1 control flowering and maturity in wheat. Wheat workers
developed cultivars combining vernalisation to promote early maturity and improve
grain yield potential. Photoperiod sensitive genes including Ppd-D1a, Ppd-B1, and
Ppd-A1 control photoperiod sensitivity, regulating flowering and maturation times in
wheat (Gomez et al. 2014). High yielding with early maturing genotypes suitable for
diverse growing conditions have been developed in different breeding programmes
across the globe by incorporating the vernalisation, photoperiod, and dwarfing genes
(Royo et al. 2018). By articulating wheat phenology, breeding for high yielding and
early-maturing wheat genotypes can be achieved due to negative correlations
between flowering and yield (Mondal et al. 2016). Such cultivars should have faster
growth rates to accumulate sufficient biomass in shorter duration to increase grain
yield potential.

Plant Height
Global wheat productivity has significantly increased due to the development of
semi-dwarf wheat cultivars. Dwarfing/height reduction genes like Rht1 (Rht-B1b),
Rht2 (Rht-D1b), Rht-D1c, and Rht8 have been extensively utilised for cultivar
development by many breeding programmes across the globe (Zhang et al. 2016).
2 Wheat Breeding 57

Dwarfing genes reduce the coleoptile and internode length resulting in the reduction
of plant height, thereby increasing assimilate partitioning to the ear, which results in
higher HI and lodging resistance. Although numerous dwarfing genes are available,
only a few genes have been extensively utilised for wheat yield improvement (Chen
and Hao 2015). Therefore, integration of less explored dwarfing genes, such as Rht4,
Rht5, Rht11, Rht12, and Rht24 with the commonly used dwarfing genes (i.e. Rht1,
Rht2, Rht8), would further help in improving the yield and lodging resistance
(Rebetzke et al. 2012a,b). Some studies including Shearman et al. (2005) suggested
that the plant height has reached its theoretical limit of around 70–80 cm in wheat,
indicating that little progress will be achieved through further reduction in plant
height. Further reduction of plant height will have effect on biomass and yield (Berry
et al. 2015). Therefore, strategic breeding that combines both plant height and grain
yield to maximise yield potential and lodging resistance has been suggested (Gao
et al. 2017).

Harvest Index
Harvest index (HI) is one of the important physiological traits; it has considerable
effect on grain yield. Despite significant improvement in HI, the trait has not been
exploited to its full potential, and the trait has remained at approximately 0.55, which
is below a theoretical limit of 0.62 (Gaju et al. 2009). Positive and linear relationship
was observed between HI with grain yield over time suggesting that HI can improve
yield gains even further (Zheng et al. 2011).

Biomass
Total biomass has a definitive role in wheat grain yield improvement. Physiologi-
cally, increase in biomass has been largely attributed to higher photosynthetic rate,
stomatal conductance, leaf chlorophyll content and improved radiation-use effi-
ciency (Bustos et al. 2013). It has been suggested that further improvements in
grain yield can be achieved by increasing photosynthetic capacity by optimising
biomass production, while maintaining lodging resistance (Beche et al. 2014). They
suggested that by increasing photosynthetic capacity through optimisation of bio-
mass production, while maintaining lodging resistance will further improve the grain
yield.

Kernel Weight
Grain yield improvement has been associated with increased thousand kernel weight
(TKW). TKW is reported nearly linear with moderate to high correlation with grain
yield (Gao et al. 2017), suggesting selection of bolder grains could be highly
effective for improving wheat yield. As a result, increasing grain weight potential
at specific positions within the spikelet has been suggested (Calderini and Reynolds
2000), rather than breeding for higher TKW.
58 G. Krishnappa et al.

2.8.2 Quality

There are about 46 technological parameters that can be used to judge the quality of
wheat grain and its physical and chemical constituents. Among the physical
characters, virtuousness, kernel hardness and hectolitre or test weight are the most
studied. Among the chemical parameters, starch and proteins are most predominant
constituents of wheat grain, which play a vital role in determining its quality. Mainly
two approaches are being followed in various breeding programmes across the globe
to improve the wheat quality, i.e. testing of fixed lines at F6/F7 generations or testing
from F2 onwards. In most of the breeding programmes, testing of fixed lines for
various quality parameters is the common practice due to various practical
challenges. But for maximum genetic gain selection, easily measurable quality traits
like sedimentation value, protein content, iron and zinc are preferable at early
generation breeding material. Since age old, the main focus of breeding programmes
across the globe is to enhance the productivity per se to feed the increasing the
population. After reaching the self-sufficiency of food grains, now breeding for
better quality is one of the prime research areas across the globe. Breeding for
quality is a tedious, cost intensive and time consuming process, which makes
breeding for quality a slow and protracted. Wheat quality has historically been the
last to utilise new technology for breeding.

2.8.2.1 Genetic Resources: A Valuable Donor for Quality Improvement

Genetic resources including wild relatives, synthetic wheats and landraces have been
reported to contribute to enhance wheat grain quality (Ogbonnaya et al. 2013).
Enormous diversity associated with landraces makes them a good source of bread-
making related alleles such as wbm (Sanchez-Garcia et al. 2015). Landraces are one
of the most important sources of wheat biofortification, as a collection of Sicilian
landraces found to contain high levels of micronutrients (Rasheed et al. 2019).
Conventional breeding approaches have been successfully used to incorporate
several novel alleles for grain zinc content into elite breeding material by crossing
high yielding elite wheat lines with Ae. tauschii-based synthetic hexaploid wheats or
T. spelta accessions (Velu et al. 2018). Pre-breeding is an important approach in
plant breeding and is practiced when desired variations are exhausted in the routine
germplasm lines and cultivars. It is an important step wherein one harnesses diver-
sity arising from wild relatives/wild germplasm/unexploited or other unimproved
materials. It refers to all activities designed to identify desirable traits and/or genes
from unadapted germplasm or materials that cannot be used directly in breeding
programme. These traits can be bred to an intermediate set of materials that can be
further utilised for producing new varieties for farmers.
Promising sources of high Zn and Fe in wheat are wild emmer (T. dicoccoides),
einkorn (T. monococcum), diploid progenitors of hexaploid wheat (such as Aegilops
tauschii), T. spelta, T. polonicum, and landraces of T. aestivum. Genetic variability
in cultivated hexaploid and tetraploid wheat is low, but wild and primitive wheats are
promising genetic resources. Fe and Zn content in wild relatives were 50% higher
2 Wheat Breeding 59

than in the modern cultivated wheat, and the highest concentrations were upto twice
than that of modern cultivars. Among wild wheats, the collections of wild emmer
wheat, Triticum turgidum ssp. dicoccoides, showed greater genetic variation with as
high as 14 to 190 mg/kg of grain Zn concentrations (Cakmak et al. 2004). In a study
consisting of different recombinant substitution lines derived from Triticum
dicoccoides, a Gpc-B1 locus has been identified on the short arm of 6B chromosome
and that locus affects both wheat grain protein and Zn concentrations (Distelfeld
et al. 2007). The grain Fe and Zn concentration of Aegilops kotschyi and A. tauschii
showed that the S and D genome species accumulate significantly higher Fe and Zn
than the cultivated wheats.

2.8.2.2 Genetic Improvement of Grain Industrial Quality

The definition of wheat quality varies across stakeholders in the wheat chain. The
grading system to classify wheat grain into different classes varies considerably
among countries. End product appeal and organoleptic properties are the most
important attribute of wheat quality for small and marginal farmers with subsistence
farming practices as they generally mill and process the wheat grain to feed their
families. On the other hand, commercial farmers consider wheat quality
characteristics that allow the sale of their grain at the best possible price. Miller’s
primary interest is the higher flour/semolina recovery of suitable quality with low
milling cost. Therefore, grain size, density, hardness, and roundness are the most
important traits for miller’s quality (Edwards et al. 2010). Millers are also interested
in the production of suitable flour for processing industry (the ability of a flour or
semolina to be processed at minimum cost and to give a uniform product). To
produce the flour with the desired characteristics for processing industry, very
often millers blend and combine different types of grain differing in quality traits.
Grain hardness, gluten extensibility and strength are the most important for
processing industry. Grain hardness and dough visco-elastic properties to be consid-
ered while breeding wheat genotypes for industrial grain quality, which includes
milling, processing and end-use quality. At global market, generally wheat grains are
classified as soft, hard or very hard (durum wheat), sometimes locally as medium
hard wheat. Genetically, presence of two small proteins called puroindolines
encoded by the Pina-D1 and Pinb-D1genes determines the grain hardness. Presence
of both the puroindolines makes the grain texture soft, but if either one is mutated or
altered then it makes the grain texture hard. Durum wheat is hard as both the
puroindolines are absent due to the lack of the D genome durum wheat species.
Grain hardness affects the water absorption, flour particle size, and milling process
and partly defines end-use quality like hard grain flour for bread and soft grain flour
for cookies and pastries. In contrast, gluten content and composition defines the
dough visco-elastic properties including gluten extensibility and elasticity.
Gluten is mainly formed by the glutenins and gliadines, further glutenins are
divided into high and low molecular weight. Generally, glutenins are associated with
gluten strength or elasticity and gliadins with viscosity and extensibility. The most
important genes controlling these proteins are Glu-1, Glu-3 and Gli-2, and it is well
known that their different alleles have been associated to gluten quality
60 G. Krishnappa et al.

characteristics. Other less explored but important quality traits such as starch
properties and enzymatic activities are in their infancy to utilise them in breeding
programmes. Therefore, breeding programmes need to develop a holistic breeding
approach, to ensure suitable gluten quality with diverse levels of gluten strength
combined with the required extensibility along with medium protein content in hard
to semi-hard grain texture genotypes. On the other hand, the overall strategy for
durum wheat has been to develop genotypes with suitable quality to be accepted by
the pasta-making industry across the globe. Durum wheat genotypes with large
kernel size, medium to low gluten strength, and with high yellow pigment content
are preferred.

2.8.2.3 Genetic Improvement of Nutritional Quality

Nutritional quality can be defined as the ability of a food to provide enough nutrients
for a correct physical and mental development for a healthy life of human beings
(Guzman et al. 2019). Recently, development of nutri-dense crops is one of the
important research priorities and breeding objectives, particularly for the staple crops
including wheat that represent a major proportion of the food and calories in
developing and under developed countries. Wheat is a potential source of different
micronutrients and other bioactive components, but the levels of some of these are
not high enough to meet the daily requirements of people in countries where wheat
represents the main source of calories.

2.8.2.4 Biofortification: A Promising Strategy to Contain Malnutrition

Nutrition (protein, vitamins and minerals) deficiency is one of the most important
public health issues across the globe, particularly in developing and underdeveloped
countries. Biofortification is a process to improve the nutritional value of crop plants
through plant breeding, agronomic and transgenic approaches. Consumption of
biofortified staple crops will help in the alleviation of malnutrition, thereby it
improves the human health condition. Presently, development of nutrient dense
staple food crops is one of the prime research areas for the scientific community.
Biofortification has been recognised as an economical and sustainable strategy that
can be useful as a complementary solution to the problem of malnutrition. Staple
crops often exhibit genetic variation in essential nutrient contents, which enable
breeders to develop nutrient dense high yielding genotypes through conventional or
molecular breeding approaches. Development of nutrient dense crops through con-
ventional/molecular breeding approaches is both economical and does not have any
effect on consumer acceptance, unlike transgenic approaches.
With the aim of developing bread wheat cultivars with 40% higher Zn concen-
tration over the current commercial cultivars in the target regions of South Asia,
CIMMYT is leading the partnership-based global effort within the HarvestPlus
project (Velu et al. 2011). Millions of resource-poor wheat consumers in South
Asia and Africa are prone to Zn deficiency, making Zinc to be the primary target
nutrient for wheat under the HarvestPlus project. Large genetic variability has been
identified for zinc in the wheat genetic resources, which enables to develop high
yielding wheat cultivars with elevated levels of zinc through various breeding
2 Wheat Breeding 61

approaches. Currently, CIMMYT breeding programme mainly focused on transfer-

ring genes governing higher Fe and Zn from Triticum dicoccon and Triticum spelta-
based synthetics, landraces, and others reported high Zn and Fe sources in to the high
yielding elite wheat backgrounds.
Synthetic hexaploids and other donor parents with significantly higher Fe and Zn
concentrations were used as donor parents for a limited-backcross breeding approach
onto adapted CIMMYT wheat parents (Velu et al. 2011). Energy-dispersive X-ray
fluorescence spectrometry is used for rapid estimation of grain iron and zinc
centration in biofortification programmes (Paltridge et al. 2012). Five biofortified
wheat varieties have been released in different countries with elevated levels of Zn
(Bari Gom 33 in Bangladesh, Zinc Shakti (Chitra), WB02 and HPBW-01 in India,
and Zincol 2016 in Pakistan (Velu et al. 2015). In India, a project entitled Consortia
for Research Platform (CRP) in ‘Biofortification in wheat for nutritional security’ is
undergoing under the umbrella of ICAR.

2.8.3 Biotic Stresses

2.8.3.1 Rusts
Historically, the rust diseases have been one of the major biotic production
constraints for wheat production. Globally, yellow rust (Puccinia striiformis f. sp.
tritici), stem rust (Puccinia graminis f. sp. tritici), and leaf rust (Puccinia triticina)
are the most damaging diseases of wheat (Roelfs et al. 1992). Historically, yellow
rust has caused and is presently causing significant and severe losses on susceptible
wheat cultivars worldwide. Moreover, detection of the widely virulent race Ug99 in
Uganda in 1998 challenged the misconception that stem rust was a conquered
disease. Now, upto 90% of world’s wheat cultivars are considered stem rust suscep-
tible (Singh et al. 2006), and the disease is threatening 20% of the world’s wheat in
Central and North Africa, the Middle East and Asia.
Leaf rust of wheat, caused by the fungus Puccini tritici, can cause heavy yield
losses in wheat. Symptoms are small, round-to-oval, raised, orange-red, dusty
pustules that are scattered mostly on the upper surface of the leaves and leaf sheaths
of infected plants. Leaf rust frequently starts on the lower leaves and gradually
progresses up the plant to the flag leaf. As the season progresses, the pustules
become more and more numerous until more of the total leaf area is destroyed.
Such severely infected leaves usually shrivel and die prematurely. Leaf rust
decreases the yield, grain quality and forage value, and in most wheat producing
regions the use of susceptible cultivars has resulted in yield losses of 10%–70%.
Stripe rust caused by Puccinia striiformis f. sp. Tritici continues to be a dominant
factor, limiting yield potential in wheat. Pustules coalesce to produce long yellow
stripes between veins of the leaf and sheath and so are also known as yellow rust.
Small yellow, linear lesions occur on floral bracts. These pustules are filled with
spores of the fungus. The stem rust disease caused by fungus Puccinia graminis f. sp.
Tritici, appears as elongate blister like pustules, or uredinia, most frequently on the
leaf sheaths of the wheat plant, but also on stem tissues, leaves, glumes and awns.
62 G. Krishnappa et al.

Stem rust pustules on leaves develop mostly on the lower side, but may penetrate and
make limited sporulation on the upper side. As infected plants mature, uredinia
change into telia, altering colour from red into dark brown to black, thus the disease
is also called black rust. Severe infection of stems interrupts nutrient flow to the
developing heads, resulting in shrivelled grains and stems weakened by rust infec-
tion are prone to lodging (Roelfs et al. 1992). Severe wheat yield losses due to stem
rust ranged from 9 to 33% in Scandinavia in 1951 and 5–20% in eastern and central
Europe in 1932 (Zadoks 1961).

2.8.3.2 Powdery Mildew

Powdery mildew of wheat is caused by an obligate, biotrophic ascomycetous fungus
Blumeria graminis sp. Tritici during the late winter and early spring. Powdery
mildew is a wind-borne disease favoured by the presence of disease in the preceding
season. Disease infection can start during early crop growth when conditions are
cool and wet. As the temperature rises and the humidity falls, the incidence and
severity tend to diminish. The disease is preferred by mild temperatures (10–22  C),
and 100% relative humidity (RH) favours the conidium germination. Prolonged
cloudy weather fastens the disease development. During winter, spores survive in the
host tissue after infection and may come from earlier infections within the field or
from fields farther away. The disease is most common in dense early sown crops
with high nitrogen fertility and rapid plant growth. Cultivation of disease-resistant
cultivars/varieties is an efficient method for commercial breeding and disease control
by the introgression of resistance genes which enhance the durability of the variety.
Host resistance is more likely to be durable when two or more resistance genes are
pyramided in a single wheat variety. Information about the genetic diversity and
distribution of Pm genes in a set of wheat varieties is required for the pyramiding of
resistance genes. Until now, nearly 73 Pm genes/alleles have been identified in
60 loci from common wheat and its wild relatives.

2.8.3.3 Loose Smut, Karnal Bunt, Common Bunt and Tan Spot
Loose smut (Ustilago tritici) is a disease that affects wheat all over the world. This
seed borne fungus survives from crop to crop in the embryo and is disseminated with
the grain, making it spread easily but difficult to control. The fungus is protected
within the seed and grows with the growing point of the wheat plant, therefore not
only is it protected from being cleaned from the seed, it is also protected from contact
(protectant) fungicides. Karnal bunt (KB) is a fungal disease caused by Tilletia
indica (Mitra). The incidence of KB varies considerably from year to year,
depending on the variability in favourable weather during heading stage of wheat
crop. The importance of KB lies in the fact that the disease is prevalent only in a few
countries around the world, and the pathogen being seed, soil and airborne is difficult
to manage once introduced in an area. Therefore, wheat importing countries have
imposed strict quarantine measures and insist on zero tolerance limits on shipment of
wheat from KB prone regions.
Common bunt (CB) caused by Tilletia caries, is the world’s most destructive
wheat disease. Instead of spikes filled with healthy wheat seeds present at crop
2 Wheat Breeding 63

maturity, the fungus produces kernels filled with bunt balls of spores that possess a
fishy odour. The bunt spores then adhere to healthy wheat seeds during harvest. Tan
spot is a foliar spotting disease caused by the fungus Pyrenophora tritici repentis
also known as yellow spot or yellow leaf blotch and occurs in all the major wheat-
growing areas worldwide. Intensified wheat production, changes in cultural practices
involving adoption of conservation agriculture practices, including shifts from
conventional tillage and stubble burning to reduced or zero tillage practices with
residue retention, and shorter crop rotations contributed to the development of tan
spot in epidemic proportions worldwide.

2.8.3.4 Head Blight/Head Scab

Fusarium head blight (FHB), also called ear blight or head scab, is caused by
Fusarium spp. and is one of the most destructive diseases of wheat (Triticum
aestivum). FHB occurs primarily in warm and humid climatic conditions during
the flowering stage. The most common species causing FHB is Fusarium
graminearum (sexual stage Gibberella zeae). This fungus is also associated with
stalk rot of corn. Another Fusarium species that causes FHB is Fusarium culmorum.

2.8.3.5 Septoria Blotch

Septoria of wheat is a disease complex caused by three pathogens: Mycosphaerella
graminicola, Phaeosphaeria nodorum and P. avenaria triticae. Nowadays the name
for the disease caused by Mycosphaerella graminicola usually is referred to as
Septoria tritici blotch (STB) or simply Septoria blotch, while that caused by
P. avenaria and P. nodorum is called Stagonospora blotch. Losses to Stagonospora
blotch caused by S. nodorum typically are much lower, but can reach 15% or more
(King et al. 1983). Both pathogens can reduce grain test weight in addition to yield,
and also reduce the quality of the grain produced. Losses to STB can range from
30 to 50% during severe epidemics (Eyal and Levy 1987) but typically are much
lower. Epidemics of STB are most severe in areas with extended periods of cool, wet
weather, particularly northern North America, northern Europe and areas with a
Mediterranean climate such as North Africa, South Africa, parts of South America
and western North America.

2.8.3.6 Viral Diseases

The economically most important wheat infecting viruses are the soil-borne viruses
either belonging to the genus Furovirus (family Potyviridae), i.e. soil-borne wheat
mosaic virus (SBWMV) and soil-borne cereal mosaic virus (SBCMV), or belonging
to the genus Bymovirus, i.e. wheat spindle streak mosaic virus (WSSMV) and wheat
yellow mosaic virus (WYMV). All these viruses are transmitted by the soil-borne
plasmodiophorid Polymyxa graminis Ledingham.

2.8.3.7 Nematode Disease

Plant parasitic nematodes are recognised as one of the major constraints in wheat
production with nearly 17 important nematode species, the majority of them belong-
ing to three genera, namely Heterodera, Pratylenchus and Meloidogyne.
64 G. Krishnappa et al.

2.8.3.8 Wheat Blast: A New Threat

Wheat blast, caused by Magnaporthe oryzae pathotype triticum (MoT), was discov-
ered in Parana state of Brazil in 1985, and since then spreading to an area of about
3.0 mha, causing losses of 10–100% depending on years, genotypes, planting date
and environment. Later the wheat blast disease reported in central and south
low-lying areas of Santa Cruz region of Bolivia, south and south-east Paraguay,
and north east Argentina. Resistance genes for wheat blast disease are presented in
Table 2.5. Most recently it was observed in Bangladesh in 2016, eight districts with
upto 25–30% yield loss. Wheat blast is a seed and airborne disease, till date
resistance sources are identified but there was limited knowledge on its genetics
available. MoT population is very diverse and exhibits many pathotypes that could
cross-infect different hosts and overcome resistance. Fungicide schemes are partially
effective under low to medium WB pressure. Pathogen has the ability to develop
fungicide resistance. The wheat blast pathogen an attack any aerial parts of wheat
plant but disease is seen mainly on spikes. The pathogen spread is favoured by warm
and humid weather due to rainy days and temperature of 18–25  C, during flowering
followed by hot, sunny and humid days. Minimum temperature for the infection is
10  C and maximum is 32  C with optimum between 25 and 30  C.
India has proactively been involved in stopping the spread of wheat blast further
from the neighbouring country Bangladesh. After the Bangladesh outbreak, India,
the world’s second largest wheat producer, all of sudden became vulnerable to WB
although as of the cropping season pertaining to the year 2020, this deadly disease
has been successfully averted to gain an entry into the country (Goddard et al. 2020).
The major wheat growing regions of North Eastern Plain Zone (NEPZ) and the
Central Zone (CZ) could probably be vulnerable based on pathogen climate
requirements. Even the country’s main wheat-producing region, i.e. North Western
Plain Zone (NWPZ), is also vulnerable to blast winters and becomes humid and
warm (Cardoso et al. 2008). The Government of India (GOI) enforced wheat
holidays in Nadia and Murshidabad districts of West Bengal and created wheat-
free zones of 5 kilometres from the Bangladesh border. ICAR-Indian Institute of
Wheat and Barley Research conducts regular survey and surveillance for monitoring

Table 2.5 Resistance Resistance Genes Reference

genes for wheat blast
Rmg1 (Rwt4) Takabayashi et al. (2002)
disease
Rmg2 and Rmg3 (7A and 6B) Zhan et al. (2008)
Rmg4 and Rmg5 (4A and 6D) Nga et al. (2009)
Rmg6 (1D) Vy et al. (2014)
RmgTd (t) Cumagun et al. (2014)
Rmg7 (2A in T. dicoccum) Tagle et al. (2015)
Rmg8 (2B) Anh et al. (2015)
RmgGR119 Wang et al. (2019)
2NS translocation (Ae. ventricosa) Cruz et al. (2016)
2 Wheat Breeding 65

and mitigating the blast threat. Blast-resistant varieties like DBW 187, HD 3249 and
DBW 352 were recommended to grow in the disease-prone areas of NEPZ.

2.8.4 Abiotic Stress

Abiotic factors are one of the major yield-limiting factors for crop plants including
wheat. Temperature extremes, drought, flooding, salinity and heavy metal stress,
among others, affect the growth and yield of crop plants. Abiotic stresses at a given
growth phase are likely to affect the organs development and so yield components
set at that phase, leading to a reduction in yield potential. Drought and heat are the
two major abiotic factors limiting the wheat crop productivity; the problem is further
complexed by climate change. Wheat is particularly vulnerable to high temperatures
and every single degree raise in average temperature during reproductive period may
lead to significant yield losses (Yu et al. 2014).
Rising of every 1–2  C temperature reduces the time taken for grain filling and
also affects the survivability of the productive tillers around 15.38%, which ulti-
mately affects the grain yield (53.57%) (Nahar et al. 2010). Even a short spell of heat
waves during grain filling may result in substantial grain yield loss (Mason et al.
2010). Although frost injury to wheat is relatively less compared to heat stress
situations, mountainous and sub-mountainous region are experiencing cold or frost
injury due to sudden temperature fall. Sodicity or salinity is another abiotic stress
which significantly affects crop growth and yield. Globally one-fifth of the irrigated
land and 2% of the dry land agriculture is affected by salt stress. In India, about 6.73
mha land is salt affected, out of which a 3.77 mha is sodic while the remaining 2.96
mha is under salinity affected (Mythili and Goedecke 2016).
Another major and highly unpredictable abiotic stress is lodging. Inadequate root
anchorage, poor stem structure and strength, and adverse weather disturbances like
excess wind velocity, rain, hailstorm along with topography, soil type, crop man-
agement practices and disease collectively may result in lodging (Mulsanti et al.
2018). It is a global problem as many parts of the world have been recorded with
significant percent of yield reduction caused due to crop lodging. Along with these,
other abiotic stresses like pre-harvest sprouting and water logging are further
exacerbating the yield loss in wheat (Abhinandan et al. 2018).
Breeding for abiotic stress prone environments has been the major focus area
from decades, but the advancements are far below the expectation due to its complex
nature. Advancement in developing stress tolerant germplasm relies heavily on the
efficient breeding programmes and phenotyping approaches. Phenotyping includes
identification, induction and categorisation of desired target environment, stress
management and complete characterisation of experimental material. Phenotyping
is mainly required to understand the complexity of genotype-phenotype interaction
and to accelerate plant breeding through deeper understanding of plant phenology
and physiology. Recent scenario of the agricultural research strongly favours the
adoption of a ‘trait-based’ crop improvement approach for increasing productivity
under changing climatic conditions. Identification and selection of right traits allow
66 G. Krishnappa et al.

the plants to uptake more resources under stress condition and also to use them more
efficiently. Physiological traits linked to abiotic stress adaptation are the best avail-
able opportunities for genetic improvement of wheat, as they involve a combination
of favourable alleles (Reynolds et al. 2009).

2.8.4.1 Role of Phytohormones Under Abiotic Stress

Hormones play an important role in plants adaptation to adverse environmental
conditions. Cross-talk in hormone signalling reflects plant ability to integrate differ-
ent inputs and respond appropriately. There are six main groups of hormones,
namely auxin, cytokinin(CK), gibberellic acid (GA), abscisic acid(ABA), ethylene
and brassinosteroids. Among all plant hormones ABA is most critical and hence
termed as ‘stress hormone’. Stress-induced senescence and abscission are the char-
acteristic features of ABA. Under water-deficit conditions, ABA-modified root
architecture contributes for the development of deeper root system along with
enhancing hydraulic conductivity of plant and maintenance of cell turgor, which
will finally contribute towards desiccation tolerance. Other hormones such as auxin,
ethylene and cytokinins (CKs), may alter the effect and biosynthesis of ABA.
Under water and temperature stress, ethylene can regulate root growth and
development by limiting organ expansion. A significant positive correlation was
observed between rate of grain filling and ABA content. The higher grain ABA
concentration might result from autosynthesis within the grain and partly by the
translocation from leaves and roots during soil drying. ABA increased the endoge-
nous content of proline under drought conditions. CK plays a supportive role during
water deficit conditions by stimulating osmotic adjustment. Brassinosteroids
increase the tolerance to high temperature in wheat leaves and brome grass. The
tolerance in plants to high temperature due to application of brassinosteroids is
associated with induction of de novo polypeptide (heat shock protein) synthesis. In
a dwarf wheat variety, high temperature-induced decrease in cytokinin content was
found to be responsible for reduced kernel filling and its dry weight.

2.8.4.2 Wheat Improvement for Waterlogging Tolerance

Frequent occurrence of climatic extremes such as heavy rainfalls, reduction in
freshwater availability and saline water intrusion close to the coastal area adversely
affect agricultural production worldwide. Waterlogging adversely affects bread
wheat production in about 4.5 million hectares in irrigated soils of the Indo-Gangetic
Plains of Northern India and some other parts of the country. Under high soil
salinity, leaf area index, leaf area, maturity duration and dry matter accumulation
in spikes are also reduced. The combined salt and waterlogging stresses significantly
reduce wheat yield by reduction in effective tiller number grain weight, length of
spike and spikelets number, and also show more adverse effect than salt alone stress
in case of compacted soils. The soil where water stands on the soil surface for a
prolonged period of time or the available water fraction in the soil surface layer is at
least 20% higher than the field water capacity, is defined as waterlogged soil.
Tolerance to waterlogging by plants defined as the capability to maintain high
rates of growth coupled with greater source to sink accumulation and eventually
2 Wheat Breeding 67

higher grain yield under adverse climatic conditions. Due to the increased frequency
of extreme climate events, waterlogging has become an important constraint to crop
production globally.

2.8.4.3 Pre-harvest Sprouting Tolerance in Wheat

Among abiotic stresses, pre-harvest sprouting (PHS) is a major concern for wheat
cultivation in eastern and far-eastern parts of the country due to untimely rains
around maturity time. The PHS in wheat is characterised by premature germination
of kernels in a mature spike prior to harvest (usually under wet and humid
conditions) due to early breakage of seed dormancy usually the result of moist
weather conditions that persist after physiological maturity. It causes yield loss
due to decrease in thousand grain weight and also affects end product quality.
Besides, wheat flour made from the sprouted wheat loses its thickening power
and bread baked from sprouted wheat grain shows smaller volume and a compact
interior. This decrease in quality is mainly due to early α-amylase activity, which can
be characterised by Hagberg falling number. Either too low or high seed dormancy is
undesirable, allowing pre-harvest sprouting after seed maturity or delaying germina-
tion after seed sowing. Therefore, development of wheat genotypes with a balanced
degree of seed dormancy is needed to grow wheat in such areas where temperature
and moisture during grain development adversely affects the expression of dor-
mancy and pre-harvest sprouting resistance. PHS tolerance is a complex trait and its
genetics need to be dissected using modern methods of QTL analysis.

2.8.5 Heterosis and Hybrid Development

Hybrid wheat is considered to be one of the possibilities for increasing wheat yield
potential. Despite over 45 years of research primarily on development of hybrid
wheat through cytoplasmic genetic male sterility-fertility restoration system, only
limited success could be achieved. The reasons for its limited success are limited
heterotic advantage; their lack of agronomic quality or diverse resistance advantage,
high cost of seed production and fixing in polyploid with the result no advantage
over pure lines was observed. Few reports indicate that hybrid cultivars have also
been released through the use of chemical hybridising agents (CHA) in some
countries. Though the prospects of exploiting of hybrid vigour in wheat were
recognised as early as 1962 and work on hybrid wheat started the world over
including India, due to the advent of high-yielding varieties utilising Rht gene
(s) the emphasis was shifted. In the post Green Revolution era, it was felt that the
northwestern plains of the country comprising Punjab, Haryana, western Uttar
Pradesh, plains of Jammu and Uttarakhand and northern Rajasthan, which were
considered as the seat of the Green revolution and contributed most to the wheat
basket, have reached a sort of saturation level. To keep the productivity growth rate
in tune to the future demand, it is needed to explore new innovative approaches to
break the yield barriers and make wheat cultivation more remunerative. In this
context, exploiting hybrid vigour at commercial level through development of
68 G. Krishnappa et al.

hybrid wheat is considered promising that offer a significant means of overcoming

food shortages because of yield heterosis.
Although the heterosis was reported in wheat in the early periods of the twentieth
century, the discovery of an effective cytoplasmic male sterility (CMS) and pollen
fertility restoration systems in wheat in 1951 by Kihara opened up new avenues for
commercial hybrid seed production. After search of the male sterility system in
wheat, the efforts were made in India to explore the basic facts for development of
hybrid wheat. The levels of heterosis were explored through hand pollination, and
reports have provided ample evidence of significant and positive heterobeltiosis
(heterosis over better parent) for yield ranging from 0 to 100% in wheat, but most of
these results are based on space planted and small plot trials. Harvest index was
noticed as an important indicator of source to sink relationship, and therefore, the
possibility of increasing yield potential through better harvest index was advocated
during the 1990s. Under the field conditions, the minimum accepted standard
heterosis for yield was established at 20% level for commercial exploitation of a
hybrid and studies indicated significant standard heterosis of more than 20% for
yield and yield traits under drill sown conditions.
As floral biology of wheat is key factor in order to understand the outcrossing
behaviour, the extent of natural outcrossing up to 1.82% in cultivated varieties of
wheat was observed. It was reported that wheat has mixed chasmogamous/cleistog-
amous type of flowering and autogamous/allogamous mode of pollination. Impor-
tant floral traits that influence outcrossing in wheat are stigma size, anther size,
anther extrusion, pollen number and pollen viability. The stigma length of wheat
genotypes has been noted to be 1.84–3.75 mm, whereas anther length was observed
from 2.87 mm to 5.07 mm. Anther extrusion has been observed from 8.7 to 87.4%.
Phenotypic differences among wheat cultivars for days to heading, anthesis, anther
size, pollen grain size, pollen viability, duration of floral opening and openness of
florets were also observed, and it was suggested that the selection for long anthers,
high rate of anther extrusion and more openness of florets may be effective in
promoting natural cross pollination.
The pollen viability in wheat ranged from 83.4 to 98.4%. The largest separation
angle between the glumes of the first two florets of spikelet was found to be 11.50–
35.80, and it was observed that wheat florets get closed within 8.7–40.3 min of floral
opening. All the viable pollen grains that have access to the stigma surface germinate
as soon as they come in contact with the stigma. There is a positive association
between anther size and the quantity of pollen produced /anther. A significant
association of anther length with stigma length and anther extrusion with duration
of floral opening was observed, and it was suggested that the selection for the traits
that promote outcrossing may result in the genotypes with more open pollination
ability and these may be utilised as parents to improve yielding ability through
enhanced heterozygosity.

2.8.5.1 Male Sterility and Fertility Restoration

Male sterility and fertility restoration are two most important components in cyto-
plasmic genetic male sterility system. A number of studies have been conducted for
2 Wheat Breeding 69

utilisation of cytoplasmic male sterility system for hybrid production in wheat. In the
investigations on basic aspects of male sterility system, the effect of timopheevii
cytoplasm was reported on level of hybrid vigour, and it was observed that restora-
tion of male sterility in the F1 was genetically complex, incomplete and affected by
genetic background. Investigations on genetic male sterility were also carried out,
and a specific type of male sterility ‘S738’ caused by the interaction of three
recessive genes was reported for the first time that had an additive effect occurring
in F2 population of a composite cross received from Mexico. In this system, degree
of male sterility was dependent upon ms gene number (the lesser the number, the
lesser is the expression of male sterility). Thus, the genotypes having one, two and
three ms genes exhibited 36–49, 47–68 and 73–97% male sterility, respectively. This
expression was found to be influenced by environment and by modifying genes. The
application of genetic male sterility in recurrent selection schemes was also
advocated.

2.8.5.2 The CMS System

Systematic investigations revealed that T. timopheevii and T. araraticum cytoplasm
(G type) induced complete male sterility and there are genes restoring fertility for G
type cytoplasm. At Indian Agricultural Research Institute (IARI), New Delhi, ten
CMS lines, namely Lok-1KMS 9A, 2009KMS 9A, 2038 A, 2046KMS 9A, 2041
KMS 9A, 2022 A, 2042 A, 2046 KMS A, 2019KMS 9A and 2160A having
cytoplasm from T. timopheevii, T. araraticum, T. zhukovskyi, Aegilops speltoides
and Ae. caudata, have been developed. Three cytoplasmic male sterile lines, namely
2041 KMS 9A, 2046 KMS 9A and 2338 KMS 20A carrying T. araraticum cyto-
plasm, were characterised. Cytoplasmic male sterile lines carrying cytoplasm from
Aegilops umbellulata, Ae. comosa, Ae. caudata and Ae. speltoides have also been
produced.
However gene(s) restoring fertility in these cytoplasms have not yet been
identified. No apparent adverse effects on morphology by T. araraticum and
Ae. speltoides have been noticed. About eighty CMS lines including those of
T. araraticum, T. timopheevii, Ae. speltoides, Ae. kotschyii and Ae. Variabilis were
backcrossed with respective maintainers for diversification. Two exotic genetic
stocks registered as PWR 4099 and PWR 4101 indicated complete fertility restora-
tion in T. timopheevii-based CMS lines. Genetic studies revealed that there are
duplicate dominant genes involved in restoring complete fertility in T. araraticum
cytoplasm and that one out of two genes restored fertility with greater degree than the
other. In order to enhance variability among alloplasmic lines, agronomically supe-
rior genotypes maintaining male sterility have been utilised. Although there is no
significant result for heterosis for yield in totality, few hybrids showed heterosis for
yield components, viz. spikelet number, spike length and tillers/plant.

2.8.5.3 Genetic Male Sterility

Although genetic male sterility has been reported in wheat, there is no report
available showing development of any hybrid wheat. The reason could be the
non-availability of appropriate kind of genetic male sterility system. A number of
70 G. Krishnappa et al.

male sterile plants were isolated from crosses involving Selection 212 and other
hexaploid wheats including Selection 82. These were isolated from F3 progenies
derived from a cross involving Selection 212 and HD 2009. In Selection 82, male
sterility is caused by the modification of anthers into fully fertile ovaries. This
modification of anther into ovaries takes place in 85 to 90% of the florets per
spike. Breeding behaviour of genetic male sterile plants was studied for
8 generations, which showed consistency of hpg-mst trait. During this period, selfed
hpg-mst spikes produced 6.06 seeds per spike, which was much lower than Selection
212 (40.4 seeds per spike). In terms of sterility, hpg-mst plants exhibited 85 to 100%
male sterility and 100% female fertility. The inheritance of hpg-mst traits was
studied by crossing with cultivar Kundan. All the Fl hybrids produced 45 seeds
per spike amounting to full fertility, indicating the dominance of fertility trait over
the sterility.
A segregation ratio of 3 fertile: 1 sterile plants in the F2 generation clearly
revealed the monogenic recessive control of hpg-mst trait. The hpg-mst system has
few advantages as the hpg-mst plants produce 10–12% seeds (selfed or left open);
therefore, it is most economical to maintain it in homozygous condition and it
enhances the chances of out crossing (female fertility) because of the presence of
multiple ovaries in the florets of hpg-mst plants. Selection 82 was used for develop-
ing wheat hybrids involving ten different genotypes. In one combination where
pollinator was Agra Local, 53 hybrid plants produced 3240 grams of grain yield in
3 m2 area. On the other hand, it has disadvantages also as hpg-mst seeds in crossing
block may give rise to 10–12% male sterile plants that lower the production per unit
area. The genotype possessing hpg-mst are slightly tall (about 110 cm), and there-
fore, not suited to favourable environments. However, diversification of genetic
male sterility system to dwarf genotypes is needed to exploit the system to its fullest
extent.

2.8.5.4 Chemical Hybridising Agents

The chemicals were used as a tool to create male sterility in wheat; and more than
40 chemicals have been patented as potential chemical hybridising agents (CHAs)
world over. In the 1970s, the use of CHAs as pollen suppressant began to get serious
thought, and maleic hydrazide (MH) was identified as potential chemical in 1960 at
IARI, New Delhi. The technique of inducing male gametic sterility looked
promising as it does not require restorer parents and large quantity of seed can be
produced using CHA. Some of the growth regulators like ethrel and herbicide
daltapon, which expectedly have strong phytotoxic response, were also tried. Results
indicated that these chemicals induced partial male sterility.
The successful utilisation of anilates as chemical hybridising agents in rice
inspired the synthesis and screening of some oxanilates and inalonani lates at
premeiotic stage on few varieties during 1997. Systematic investigation helped in
identification of most effective fluoro-anilates inducing male sterility without having
any adverse effect on different growth and yield parameters including female
fertility. In the 1990s, comparative studies were made to study the effect of etherel
and MH, two most widely used CHAs, and it was observed that the etherel was more
2 Wheat Breeding 71

effective towards reduction in seed set. The appropriate stage for higher efficacy of
CHA was reported from spike length of 7–8 mm to early boot stage. Further, the late
sown crop was found more responsive to CHA than normal sown crop. Deficiency of
copper was also reported to induce male sterility in wheat. In the private sector, the
Maharashtra Hybrid Seed Company (MAHYCO) in collaboration with Monsanto of
USA is the only company, which has commercialised hybrid wheat based on CMS
approach and has released three varieties Pratham 7050, Pratham 7070 and New
gold for the Central and Eastern zone of India.

2.8.5.5 Bottlenecks in Research

The insufficient levels of heterosis, low seed multiplication rate and complexity of
the hybridisation systems were explored as major limiting factors for hybrid wheat
development. The self-pollinated nature of wheat with occasional outcrossing of
usually less than 1% makes the selection for floral characters, which enable sufficient
cross fertilisation like more open flowering habit, duration of flower opening,
improved anther extrusion in the male parent and stigma receptivity in the female
parent more crucial for successful development of hybrids. These traits need to be
investigated properly to identify the parents that can be put under conversion to male
sterility system and fertility restoration.
The discovery of an effective cytoplasmic male sterility and pollen fertility
restoration systems in wheat using Ae. caudata cytoplasm opened up new avenues
for commercial hybrid seed production, but the stability of male sterility across the
locations is another bottleneck in the direction of development of hybrids, which
restricts the hybrid lines to the location specificity. T. timopheevii seems to be the
most suitable one for commercial production of hybrid seed. The inclusion of yield
potential in the bread wheat is also an important issue. As wheat in natural polyploid
(allohexaploid), the transfer of donor traits from related species takes in more
negative traits than the positive components. This needs strengthening of the pre-
breeding activities for improving parental lines. The economics of hybrid seed
production is of major concern for successful hybrid technology. The contributing
factors such as the plant population, male and female row ratios, plant spacings and
input managements should be optimised for getting maximum hybrid seed at lower
costs.

2.9 Breeding Approaches: Conventional and Molecular

Including Use of Genomic Tools

Bread wheat is one of the most important food crops improved by mankind over the
past 8000 to 10,000 years when the species first arose in the world. The wheat
domestication coincides with the beginning of agriculture, and since then it has been
constantly under selection by humans sometimes with accidental and also applying
intentional but empirical selective pressures. With the advancement in scientific
breeding methods, the focus of breeding programmes on yield potential, resis-
tance/tolerance to biotic and abiotic stresses and quality have been prioritised.
72 G. Krishnappa et al.

Additionally efforts have been made to introgress new variability from alien species
which otherwise was not available in the primary gene pool. With the development
of molecular genetics, tools like molecular markers, genome sequencing, better
understanding of the complex traits are also progressing. New approaches like
transgenic, gene editing, speed breeding and high-throughput phenotyping are
emerging and have shown promise to improve and enhance the efficiency in crop
breeding.

2.9.1 Conventional Breeding Methods

2.9.1.1 Mass Selection

From a variable population, seeds are collected from phenotypically desirable
individuals in a population, and next generation is planted from the selected mixed
seed. Mass selection has been practised by local conservators/farming communities
to improve old varieties/land races. A variant of this method is progeny selection, in
which best plants are harvested separately and their progenies are grown separately
and compared for their performance. The better performing progenies are selected
and the rest are rejected based not only on phenotypic selection but also on progeny
performance.

2.9.1.2 Pure-Line Selection

From a genetically variable population, several phenotypically superior plants are
selected and individual plant progenies are grown and evaluated over a period of
several years. The homozygous progenies are bulk harvested separately, and yield
trials are undertaken to ascertain the yield performance of selected progenies. Any
progeny performing superior to varieties under cultivation is then released as a new
‘pure-line’ variety.

2.9.1.3 Hybridisation-Based Methods

Breeding methods employing hybridisation have the objective of combining supe-
rior gene/gene combinations from diverse parents to produce homozygous progenies
in self-pollinated crops. Genes, however, are always in the company of other genes
in a collection called a genotype. Different methods like pedigree, bulk and back-
cross breeding methods are in practice.

Pedigree Method
Pedigree method involves crossing of two genotypes differing in a few traits but
possessing traits, which are absent, in each one of them followed by selfing and
selection in successive segregating generations. The unique feature of this method is
that the record is maintained for parent-progeny relationship in all the segregating
generations until homozygosity is achieved. From every F2 plant individual, F3
progeny is planted separately and a few plants are selected based on desirable
features to constitute the next generation followed up to F5–6. At this stage, each
phenotypically superior progeny is harvested in bulk to obtain large seed for further
2 Wheat Breeding 73

evaluation in yield trials. These lines are evaluated for yield, disease resistance,
quality features, etc.

Bulk Method
Bulk method of breeding does not require the record keeping of parent-progeny as in
case of pedigree method and also in handling of segregating generations. In bulk
method of breeding, the F2 onwards seed is harvested in bulk and used for raising the
next generation, and both natural selection and artificial selection are practised. After
several cycles of selfing, single plants are selected and evaluated just like in the
pedigree method.

Back Cross Method

Backcross method is generally applied in situations when an outstanding variety
becomes susceptible to major diseases or it lacks some important character. In this
method the outstanding variety lacking few traits is crossed with donor having that
trait followed by four to six backcrosses with the outstanding variety to recover
recurrent parent genome. At the end of backcrossing cycles, selfing is done to
recover the homozygous progenies having the target trait in the recurrent parent
genome.

Hybrid Breeding
Hybrids are generally referred to a specific cross between two good combiners in a
particular cross and the superior performance of hybrids over parents is referred to as
hybrid vigour (a separate section in this chapter provides further details).

2.9.2 Non-Conventional Breeding Methods

Till the 1980s, genetic enhancement of crop plants was primarily based on conven-
tional plant breeding approaches. Although conventional breeding has continued to
be the breeder’s choice, faster genetic gain is hampered particularly for complex
traits (Tuberosa 2012). Selection of desirable traits by indirect selection through
closely linked molecular markers was conceived as an alternative to solve the
limitations of conventional breeding (Collard and Mackill 2008). Since the 1990s,
marker assisted selection (MAS) has been used in plant breeding programmes
through tagging of the major genes, which enabled in the development of many
varieties in different crop plants. Initially, both public and private sector
organisations funded large number of marker assisted backcross breeding (MABB)
projects across the globe; later the focus was shifted towards only foreground
selection due to faster varietal replacement ratio. Later, marker assisted recurrent
selection (MARS) being used as an effective tool to accumulate the alleles for the
trait of interest (Rai et al. 2018). Nevertheless, MAS (Collard and Mackill 2008;
Servin et al. 2004) and MARS (Crossa et al. 2010) are still the breeder’s choice to
rectify the drawbacks associated with widely adapted cultivars through gene
pyramiding and further incorporate novel gene(s) into desirable parents. Recently,
74 G. Krishnappa et al.

genomic selection (GS) and speed breeding have emerged as the most promising
breeding strategies to accelerate genetic gain in crop plants. GS has a clear-cut
advantage over pedigree breeding and MAS to enhance genetic gains for complex
traits (Crossa et al. 2017). Integrated approach of genomic selection and speed
breeding could fast-track gene bank mining for rapid genetic gain (Li et al. 2018).

2.10 Precise and High Throughput Phenotyping Protocols

2.10.1 Physiological Techniques for Abiotic Stresses

2.10.1.1 Normalised Difference Vegetation Index (NDVI)

Canopy health in terms of canopy greenness indicating canopy growth or early
vigour is a crucial characteristic of a high yielding cultivar and therefore is largely
used as a proxy trait for abiotic stress tolerance. Canopy greenness is measured by
green seeker or NDVI (Normalised Difference Vegetation Index), which is also used
to estimate the nitrogen levels in many agricultural crops (Lawal et al. 2018). Several
studies indicated significant linear relationship between NDVI values and seedling
vigour, growth rate and senescence patterns in wheat (Lopes and Reynolds 2012).

2.10.1.2 Canopy Temperature (CT)

The genotypes with low canopy temperature are able to regulate stomatal function-
ing efficiently along with extraction of water from deeper layer of soil. Plant canopy
emit long wave infrared radiation, which are sensed by infrared thermometer and
displayed as temperature. Several studies demonstrated CT as a promising trait for
screening large population under low moisture with multiple complementary traits
like, deep root, stomatal conductance and finally better water use (Balota et al. 2008).
However, CT is affected by various factors such as soil moisture, solar radiation,
wind speed, temperature and relative humidity. Water stress was imposed between
tillering and anthesis stages in wheat (Rashid et al. 1999), and mean canopy
temperatures were used as a selection trait. These CT variations among genotypes
were significantly correlated with yield.

2.10.1.3 Water Use Efficiency (WUE)

In general, efficient user is expected to be a higher producer, and hence higher water
use efficiency is a preferred trait. Schulz et al. (2021) pursued WUE as a crucial
factor for determining the final yield as it is directly related to the stomatal evapora-
tive rate and the biomass produced. However, management practices also play an
important role for WUE but at plant level, stomata are the key players. WUE is
highly dependent on the carboxylation pathway, and compared to C3 and C4 plants
CAM plants have a higher WUE because of unique carboxylation pattern (Hatfield
and Dold 2019). WUE can be used as a key trait to screen large segregating
population and significantly correlated with lower stomatal conductance. The impor-
tance of selecting crop cultivars with higher WUE which can produce higher or at
2 Wheat Breeding 75

par yield under limited or reduced irrigation has been previously reported (Meena
et al. 2019).
There is a necessity for designing specialised experiments aimed at identification
and development of germplasm with true genetic ability with increased WUE.
Physiological trait-based identification of drought adaptive genotypes have been
earlier reported by Fletcher et al. (2018) and Nakhforoosh et al. (2016). These
studies had a few limitations in the form of screening a very few genotypes initially
and that too under pot culture conditions, such results are often difficult to translate
to field conditions (Meena et al. 2019). Few planned wheat breeding efforts by
screening large set of germplasm lines leading to identification of cultivars with
enhanced WUE at global level were reported earlier (Meena et al. 2019).

2.10.1.4 Transpiration Efficiency (TE)

The balance between transpiration (H2O) and gas exchange (CO2) helps to maintain
optimum leaf temperature and photo-respiratory activity for better productivity, and
hence TE used as an alternate trait for WUE (Farooq et al. 2009; Pietragalla and
Vega 2012). So, under moisture deficit condition genotypes that reduce water loss
through efficient transpiration should be identified and selected. TE is an important
representative selection trait for light interception, leaf transpiration, gas exchange
and photosynthetic ability (Steduto et al. 2007). However, it is also directly or
indirectly dependent on the carboxylation efficiency of genotype (Ludlow and
Muchow 1990) and higher for C4 plants (maize and sorghum), compared to C3
plants (wheat, oats, cotton). The cereal crops have higher TE than the legumes due to
higher energy requirements of N fixation. For wheat, wide variations in TE has been
found and correlated well with carbon isotope discrimination. Transpiration effi-
ciency has a significantly negative association with carbon isotope discrimination
(CID). The relationship between CID and TE was confirmed in many C3 crops
(Richards et al. 2010). Rebetzke et al. (2002) concluded that low 13C/12C discrimi-
nation along with low stomatal conductance helps wheat to improve water use
efficiently to improve harvest index.

2.10.1.5 Stomatal Conductance (SC)

For an active soil–plant–atmosphere continuum, stomata are the key controller.
Under the variable soil–atmosphere moisture, stomatal alterations help to maintain
plant internal water status by restricting the CO2: H2O movement between leaf and
atmosphere. The significance of SC as an early response to water stress has been
documented extensively for drought conditions (Damour et al. 2010; Ennahli and
Earl 2005). Many studies have found a significant positive correlation between SC
and crop yield, but still for field selection SC is not given much importance in
breeding programmes (Roche 2015). Changhai et al. (2010) showed that the transpi-
ration efficiency was more affected than the photosynthetic efficiency in wheat under
drought stress. The major role to maintain transpiration efficiency was played by
stomatal conductance and more precisely by stomatal pores. In a drought experi-
ment, Liu et al. (2005) highlighted a significant reduction in stomatal conductance in
water-stressed potato plants at tuber initiation and tuber bulking stages after 48 h and
76 G. Krishnappa et al.

24 h of withholding of irrigation, respectively. Studies have shown that partially

stomatal closure is an adaptive strategy under drought stress to reduce SC and loss of
water (Zait et al. 2019). However, the exact mechanism of stomatal closure is not
well understood, but root hydraulic conductance and abscisic acid (a signalling
molecule) are reported as the main determinant of SC. Under well irrigated
conditions, higher stomatal conductance will maximise photosynthetic rates and
hence the yield, but when the water is limiting then sustained SC accompany drought
avoidance in plants to maintain adequate yield.

2.10.1.6 Relative Water Content (RWC)

RWC is a regularly used parameter to identify the variation in plant water status
among genotypes and to quantify the extent of dehydration under abiotic stress (Guo
et al. 2010). The RWC value ranges between 95 and 98% for a tolerant genotype or
under normal conditions and ~ 40% under severe stress condition.

2.10.1.7 Leaf Chlorophyll Content

The crop canopy greenness contributed mainly by the photosynthetic pigment;
chlorophyll is another trait of importance to screen germplasm for heat tolerance
in germplasm lines. The chlorophyll pigment reflects only the green fraction of
the light after absorbing all other colour fractions and hence it is green in colour. The
canopy greenness is directly related to photosynthetic efficiency of the plants. The
chlorophyll content of the leaf can be estimated by a destructive lab-based DMSO:
acetone extraction method and by using an instrument called chlorophyll meter,
which is non-destructive and optical method. The measurement by optical method
using different types of chlorophyll meters is found to be more relevant than DMSO
method under field conditions (Dwyer et al. 1991). The chlorophyll content
measured through chlorophyll meters is in the form of an index called chlorophyll
content index (CCI). The CCI ranges from 0 to 99.9, and with the increase in the
level of heat stress the CCI decreases and CCI of healthy plant ranges from 40 to 60.
As optical method is based on leaf reflectance, it is influenced by time of day in terms
of light (Mamrutha et al. 2017). Care should be taken to measure chlorophyll content
at uniform time and in specific leaf across the genotypes under field (Mamrutha et al.
2017).

2.10.1.8 Canopy Greenness/Stay Green Habit

Prolonged maintenance of canopy greenness also referred to as stay-green nature is a
physiological adaptation mechanism by plants under heat stress and drought
environments. Lim et al. (2007) described stay greenness as ‘leaf senescence is
characterized initially by structural changes in the chloroplast, followed by a con-
trolled vacuolar collapse, and a final loss of integrity of plasma membrane and
disruption of cellular homeostasis’. Stay green trait in tolerant genotypes helps in
withstanding chlorophyll loss and maintains photosynthesis levels under high tem-
perature stress. Association of stay green habit with sustained yield levels under heat
stress has been earlier reported, and QTL regions regulating this have been identified
(Vijayalakshmi et al. 2010). There are mainly two types of stay green types. One is
2 Wheat Breeding 77

productive type, where in the stay green plant parts actually contribute for sink/grain
filling. Another is cosmetic stay green type, where in greenness in these plants will
not contribute for grain filling. Hence, identification of true and productive stay
green types are also a challenge and can be done by considering other traits like
water soluble carbohydrates in stem, peduncle, etc.
The canopy greenness can be measured by an instrument known as normalized
difference vegetation index (NDVI) sensor. Spectral reflectance-based NDVI values
are highly correlated with yield under temperature stress (Lopes and Reynolds
2012). NDVI values range from 0 to 1. Zero represents no greenness and one
represents maximum greenness (Mamrutha et al. 2017). Stay green habit can also
be measured by other instruments such as canopy analyser (Licor) or porometer,
which measures leaf area index and green area index (GAI). Many other techniques
like the digital photography of the canopy can also be taken from same height from
the ground level, and pictures can be analysed with different softwares (Adobe
photoshop CS3 extended or later version) to assess the early ground cover (Mullan
and Reynolds 2010).

2.10.1.9 Earliness Per Se in Wheat

Earliness (earliness per se) in wheat is an adaptation strategy characterised by early
heading, followed by early maturity of genotypes under high temperature stress
environments. Earliness helps genotypes to complete the essential plant growth
stages, such as seed setting and grain filling under favourable temperatures, thereby
avoiding the occurrence of terminal/late heat stress. Mondal et al. (2013) reported
that the early heading entries performed well in areas affected from terminal heat
stress as earliness helps them to escape high temperatures during grain filling stages.
In addition to helping them escape the terminal heat stress, earliness also resulted in
achieving >10% higher yield compared to the local check varieties under high
temperature stress environments. High grain filling rate in early maturing genotypes
was also reported to be promoting heat stress tolerance in durum wheat (Al-Karaki
2012). Tewolde et al. (2006) reported that earliness helped cultivars adapt to high
temperature stress as they had longer post-heading period resulting in longer grain
filling duration. Therefore, earliness was also suggested as a key trait in breeding for
high temperature stress tolerance (Joshi et al. 2007).

2.10.1.10 Photosynthetic Efficiency

The differential rate of photosynthesis expressed as photosynthetic efficiency is
again a very essential component trait contributing to tolerance under high tempera-
ture stress. Stable photosynthetic rates over longer duration in heat tolerant
genotypes contributed to higher grain weight, higher harvest index under stress
showing the positive association of rate of photosynthesis with yield parameters
under heat (Al-Khatib and Paulsen 1990). Looking at the major role played by
photosynthesis in determining yield under heat stress, it is also pertinent to have
phenotyping techniques to help breeders to select for genotypes with higher photo-
synthetic efficiency. The relative photosynthetic efficiency can be indirectly
predicted using the chlorophyll content index, however there are instruments
78 G. Krishnappa et al.

available which can measure the photosynthesis exactly. Infra-red gas analyser
(IRGA) is used to measure the photosynthesis on a real time basis when stress
period is available or stress is imposed under experimental conditions. IRGA
measures the amount of CO2 fixed during photosynthesis by estimating the differ-
ence in amount of CO2 pumped in and moving out of closed leaf chamber (Nataraja
and Jacob 1999).

2.10.1.11 Cell Membrane Thermal Stability

Under high temperature conditions, the cell membrane becomes weak and tends to
rupture, leading to leakage of electrolytes. Membrane thermal stability is being
repeatedly used as a measure of electrolyte diffusion resulting from heat induced
cell membrane leakage. Increased level of electrolyte leachates diffused from cells is
measured here. Heat tolerant genotypes are identified by measuring electrical con-
ductivity as an index to indirectly measure membrane thermal stability (Blum and
Ebercon 1981). Greater amount of electrical conductivity said to be indicating better
heat-stress tolerance (Saadalla et al. 1990). Presence of high genetic heritability of
membrane stability in wheat was seen to be an advantage for its use in breeding for
heat tolerance (Fokar et al. 1998).

2.10.1.12 Root Studies

Based on the hypothesis that under water-stress conditions root biomass contributes
significantly towards higher yields, Jain et al. (2014) conducted an experiment to
identify the most stable wheat variety under water-deficit environment for root dry
matter and root volume. They also calculated the stress tolerance index (STI), which
indicates the tolerance to moisture stress. Tomar et al. (2016) studied a set of
158 wheat genotypes after screening in polyvinyl chloride (PVC) pipes for root
architecture traits. The visible evaluation of root images using WinRhizo root
scanner of HW2004 (water stress tolerant) indicated compact root system with
longer depth, while HD2877 (water stress sensitive) exhibited higher horizontal
root spread and less depth at reproductive stage. The importance of water is much
more in the crops requiring higher water input, like rice and semi-irrigated aerobic
cultivation of rice is recommended as a water saver strategy.

2.10.2 Other Screening Methods

2.10.2.1 Index-Based Field Screening

For large scale screening in open field conditions, we do not have a standardised
methodology as we don’t have any hold over the indirect water sources available like
rain, dew, etc. Hence, we could only screen the same if there is no rain fall during the
crop period. Under such scenario we use physiological indices like Drought Sensi-
tivity Index (DSI). The formula for DSI calculation is as given below:
2 Wheat Breeding 79

DSI ¼ ð1
Y D =Y i Þ=ð1
X D =X i Þ:

where YD is the grain yield for each genotype under drought condition, Yi is the grain
yield for each genotype under irrigated condition, XD is the mean of genotypes grain
yield under drought condition, Xi is the mean of genotypes grain yield under irrigated
condition, DSI less than 1 is desirable for water moisture stress-tolerant genotypes.
The lower value of DSI represents better tolerance under water stress.

2.10.2.2 High Throughput Screening Platforms

Under controlled conditions screening could be done with high-throughput
phenotyping (HTP). High-throughput phenotyping is a remote sensing technology,
which may meet the requirements for the phenotyping of large number of genotypes
grown in plots in less time. Use of active and passive spectral sensing systems for
drought and high yield was described by Becker and Schmidhalter (2017) is also a
high-throughput technology used to evaluate the drought tolerance of winter wheat.
Wheat crop was grown under drought conditions for 2 years, to estimate the moisture
stress tolerance of 20 wheat cultivars by using high-throughput measurements.
Thermometric measurements showed a strong linear relationship to drought-related
parameters (RLWC and CID of leaf and grain) and grain yield under drought stress,
and demonstrated a significantly high suitability for high-throughput measurements.
Additionally, four spectral reflectance sensors, including a hyperspectral passive
sensor, an active flash sensor, the Crop Circle and the GreenSeeker were utilised to
evaluate drought stress related destructive and non-destructive morpho-physiologi-
cal characteristics. The experimental results emphasised that precision phenotyping
supported the incorporation of plant traits in breeding programmes for effective
phenotyping to screen drought-tolerant genotypes.
In addition to using spectral reflectance measurements, novel facilities such as
temperature-controlled phenotyping facility (TCPF) has been employed to precisely
phenotype genotypes for abiotic stresses such as heat (Sharma et al. 2018, 2019)
(Fig. 2.5). In a study involving 75 genotypes from a recombinant inbred line
population, they screened against heat stress using TCPF, the authors reported that

Fig. 2.5 Temperature-controlled phenotyping facility (TCPF) at ICAR-IIWBR, Karnal

80 G. Krishnappa et al.

greater precision in differentiating high-temperature responses in the TCPF was

evident from the repeatability in terms of growth, physiology and productivity.

2.11 Emerging Challenges at National and International Level

Wheat is one of the widely grown staple food crops for feeding the global human
population. Suitability of wheat for making infinite and diverse end products has
made it a popular cereal over other crops. As per the WHO estimates, the world
would need almost 60% higher wheat by 2050 from its current production level of
732 million tons in 2018–19 (FAO 2021); more specifically South Asia and
Sub-Saharan Africa are expected to double their wheat production to meet the then
population load (Fig. 2.6). The survey report of FAO also estimates that North
African, Middle East’s, Sub-Saharan Africa’s, Indonesia’s, Philippines and
Brazilian wheat imports would soar by 2050 due to population growth rate and
wheat consumption per capita growth rate. The world’s significant wheat exporters,
viz., USA, Canada, Australia, the Black Sea Region, Europe and Argentina, are
expected to see minimal, or even negative, population growth towards 2050. In
contrast, population growth will be strongest in the countries of the tropic and
subtropical regions where little wheat is grown. It is believed that, even without
projecting large imports by China, the world wheat trade will likely double by 2050,
to 240 MMT or more.
Thus, realising that wheat already accounts for one-third of all global grain
traded. Such a large expansion of trade will have major implications for all segments
of the industry, including buyers, shippers, handlers, and especially the producers in
those countries that will supply the increased exports, including the USA. To meet

Fig. 2.6 Comparative wheat yield (t/ha)—India vis-à-vis other countries during 2019
2 Wheat Breeding 81

this demand, developing countries should increase their wheat production by 77%,
and more than 80% of demand should come from vertical expansion. The production
target is not very high, however, it has to be achieved when productivity growth
(genetic gain per annum) in wheat is hovering around 0.9%. Besides, there is an
urgent need for enhancing productivity through agronomic (water, nutrients, weed
management, etc.), genetic and physiological interventions along with resource
conservation technologies.
Providing an adequate supply of food, however, seems to be achieved at present
for the current global population, sustaining this to future will be very challenging in
view of steadily increasing population, increasing purchasing power and continuous
diminishing of available fertile cultivable land and water for agriculture. The chal-
lenge is expected to make even more difficult by the projected changes in climate,
particularly higher temperatures and changes in rainfall distribution and amount
(Parry et al. 2010). Food supply will need to grow by 2–3% each year to meet the
projected demand; but in the past decade the yields of the major cereals, rice, maize
and wheat have increased at less than half this rate. Apart from that, a majority of the
population in the developing countries is facing the challenge of malnutrition
because of the consumption of cereals-based diets for meeting their energy demand.
HarvestPlus have initiated bio-fortification programme prioritising different
nutrients for different countries in different crops. Zinc is target micronutrient for
which bio-fortification programme on wheat is underway in India.
The AICRP on Wheat and Barley is successful in releasing the bio-fortified
varieties for cultivation in different zones of the country. WB 02 is the first
bio-fortified variety released for cultivation in the country having a fair amount of
grain iron and zinc contents (Chatrath et al. 2018). The climate predictions by the
Intergovernmental Panel on Climate Change (IPCC) indicated that the mean atmo-
spheric temperatures are expected to increase between 1.8 and 5.8  C by the end of
this century (IPCC 2007). The increase in frequency of hot days and greater
variability in temperatures in the future is also predicted as an effect of climate
change (Pittock et al. 2003; Team et al. 2014). Important crops like maize and wheat
are more prone to be affected as they produce less grain at temperatures above 30  C.
The impacts of climate change on food systems are expected to be widespread,
complex, geographically and temporally variable, and profoundly influenced by the
socio-economic conditions (Vermeulen et al. 2012). The projected rise in tempera-
ture of 0.5  C to 1.2  C will be the major cause of grain yield reduction in most areas
of South Asia. Higher temperatures are likely to affect around seven million hectares
of wheat area in developing countries and around 36 million hectares in temperate
wheat production countries. The Asia-Pacific region is likely to face the worst
impacts on cereal crop yields. Loss in yields of wheat, rice and maize are estimated
in the vicinity of 50, 17 and 6% respectively by 2050 (IFPRI 2009). This yield loss
will threaten the food security of at least 1.6 billion people in South Asia. Warmer
temperatures resulted in an annual wheat yield reduction to the tune of 19 million
tons, amounting to a monetary loss of $2.6 billion between 1981 and 2002 (Lobell
and Field 2007).
82 G. Krishnappa et al.

In India, it has been predicted that with every rise in 1  C temperature, the wheat
production will decline by 4–six million tons (Ramadas et al. 2019). Approximately,
three million ha wheat area in north eastern and north western plain zones is exposed
to terminal/reproductive heat stress (Gupta et al. 2013). Another report by Joshi et al.
(2007) stated that around 13.5 million ha wheat area in India is vulnerable to heat
stress. Temperatures above 34  C in northern Indian plains leading to significant
yield loss was reported (Lobell et al. 2012). India is considered to be the second
largest producer of wheat. The Northern Indian states such as Uttar Pradesh, Punjab
and Haryana are some of the major wheat producing states, where the crop is more
vulnerable at a 1  C rise in temperature resulting in reduction wheat yield. In South
Asia, higher night temperatures during February and March impacted subsequent
wheat production and would likely to endanger food security (Janjua et al. 2010;
Paymard et al. 2019; de Lima et al. 2020). High temperature stress affects wheat crop
at germination, early establishment stages, dry matter partitioning, reproductive
organ development and reproductive processes leading to decrease germination,
poor seedling emergence leading to abnormal seedlings, poor vigour, reduced
overall growth of developing seedlings, decreased seed set and low grain number
(Kumar et al. 2021; Prasad and Djanaguiraman 2014; Sehgal et al. 2018).
Climate change also affects the cropping patterns and crop rotations and
influences the emergence of new biotypes/pathoypes. The outbreak of Ug99 stem
rust causing major upheaval in Ug99, as it has overcome the resistance in most wheat
cultivars. An estimated 80–90% of all global wheat cultivars growing in farmer’s
fields are now susceptible to Ug99 or variants (Joshi et al. 2008). Similarly, Yr9
virulence first reported in East Africa and then migrated to South Asia through
Middle East and West Asia over 10 years and caused heavy yield losses, and this
virulence was reported in 1996, in North Western India (Nayar et al. 1996). Now, for
the first time, Bangladesh reported wheat blast in early 2016, a deadly disease which
otherwise confined to Latin America. Now the wheat blast disease was also reported
from Zambia (Tembo et al. 2020). This disease results in complete crop loss in case
of severe infection as it attacks the rachis and may completely hamper the grain
filling. There are a few reported sources of resistance, which confers moderate level
of resistance to the wheat crop (Urashima et al. 2004 and 2005). In China, sharp eye
spot disease caused by Rhizoctonia cerealis is an emerging problem in high intensity
cropping systems, and during 2003, this disease was also reported from Egypt
(Hammouda 2003). Similarly, the prevalent pathogens and pests may evolve due
to selection pressure posed by resistance gene deployment as well as due to climate
change.
With the introduction and adoption of semi-dwarfing high yielding varieties of
wheat for cultivation during and after green revolution, the soil fertility status have
been depleted. Micronutrient deficiency and organic carbon content have gone
down. There is an urgent need to address this issue by following addition of green
manuring crops in the cropping system, residue retention and farm yard manure.
Further the use of high doses of fertilisers and excess use of irrigation led to the
depletion and deterioration of soil health and water. Half of the applied fertilisers are
lost in one way or the other. There is an urgent need to breed for efficient genotypes,
2 Wheat Breeding 83

which are both efficient in utilisation of fertiliser and also give optimum yield under
limited or reduced irrigation. With the adoption of conservation agriculture practices
in high intensive cropping systems, the foliar diseases of wheat like septorea, tan
spot and Fusarium head blight are more frequently affecting the crops due to the
hemi-biotrophic nature of pathogens (Sharma and Duveiller 2003).
In the humid subtropics of South Asia, there is evidence of stress conditions,
which favour foliar blight (Dubin and Bimb 1994). Factors such as minimum tillage
or surface seeding, irrigation, late planting or low soil fertility may be responsible for
higher foliar blight severity in the wheat-based cropping systems of the Indo-
Gangetic plains. Keeping in view the present and future challenges, researchers
need to look for new variability in cultivated as well as secondary and tertiary pools
and keep on continuously churning that into the breeding programmes to develop
climate resilient, nutrient rich and efficient genotypes in terms of nutrient, water and
radiation use.

2.12 Breeding Progress and Varietal Development

2.12.1 Conventional Breeding

In India three wheat species, namely T. aestivum (bread wheat), T. durum (Kathia or
Macaroni wheat) and T. dicoccum (Khapli or Emmer wheat), are commercially
cultivated in different parts of the country. The wheat growing farmers have played
a significant role in preserving enormous variability in blend of land races, compris-
ing of variable grain traits and morphological characteristics. The systematic wheat
improvement work started with the establishment of the Imperial Agricultural
Research Institute at Pusa in Bihar by Howard and Howard in 1905. Land races
were subjected to pure-line selection for developing better yielding NP Series of
wheat varieties. Among these, special mention can be made of NP 4, which won
several national and international awards for its grain quality. In the next phase, the
wheat improvement was carried out through recombination breeding involving
selected pure lines in hybridisation process at number of government agricultural
colleges came up at Kanpur, Lyallpur, Pune and Sabour. Also, the contemporary
wheat researchers took up massive hybridisation work at Shimla, Powarkheda,
Niphad and some other places, which led to develop large number of improved
wheat varieties bearing initials like NP, K, C, Pb, Pbc, AO, Hyb, RS, Niphad,
Kenphad, etc.
Later the focus shifted towards resistance breeding and in this pursuit, success
was achieved in the development of a classical variety NP 809, the first Indian wheat
variety resistant to all the three rust and loose smut diseases. Later on NP 824 was the
first variety developed for the good management conditions. Among large number of
varieties developed during this period prior to 1965, the notable varieties like Pbc
518, Pbc 591, NP 52, NP 165, K 13, K 46, K 65, K 68, Pbc 228, C 273, C 281, C
519, Niphad 4, AO 113, AO 115, Hyb 23, Hyb 38, RS 31–1, Kenphad 28, etc.
played important role in augmenting wheat production to some extent. During 1947,
84 G. Krishnappa et al.

the wheat production of the country was 5.6 million tons, which was increased to the
extent of 12.3 million tons in 1965 but was far below to meet the demand which was
mainly due to the tall growing habit as well as proneness to lodging under high
fertility conditions. A famine-like situation was predicted by Paddok brothers in
India by the year of 1975. In fact it was a do or die situation, and there was no
immediate solution in sight to bail out the country from such precarious situation. At
this juncture when no other approach proved fruitful, a dwarf Korean wheat land
race ‘Daruma’ showed a ray of hope. The Japanese researchers developed the well-
known ‘Norin-10’ dwarf wheat genotype by crossing with Daruma.
Later on after the Second World War was over, the Norin-10 was picked up by
U.S. biologist SD Salmon. In USA., Orville Vogel recombined the dwarfing trait of
Norin-10 in the winter wheat background and successfully developed the first high
yielding dwarf winter wheat variety known as ‘Gains’ in the early 1950s. It was
Norman Ernest Borlaug who for the first time in the latter half of the 1950s
transferred the Norin-10 dwarfing genes (Rht1, Rht2) in to the spring wheat back-
ground, while working in Mexico. The Indian wheat scientists took note of these
dwarf Mexican wheat in the international nurseries received from Borlaug and
grown at Indian Agricultural Research Institute (IARI), New Delhi, during
1961–62. From this point onwards what had happened in the field of wheat research
in India is a history. It was a turning point for achieving a spectacular change in the
production and productivity of wheat in the country. A food deficit country not only
became self-sufficient in wheat production but also joined the elite group of wheat
exporting countries in the world. Due to the coordinated efforts made by the
multidisciplinary team of scientists with the progressive support of able
administrators and hard work of farmers under the banner of the All India Coordi-
nated Wheat Improvement Project (AICWIP) initiated by the Indian Council of
Agricultural Research (ICAR) in 1965.
It could be a sheer coincidence that the advent of dwarf wheats and initiation of
AICWIP took place simultaneously in India, in 1965. Considering the encouraging
results obtained from the preliminary trials on dwarf wheats, the Indian Scientists
visited Mexico to take on the spot stock of large number of dwarf wheat strains being
grown there. In the beginning, the seed of four varieties, namely Lerma Rojo 64A,
Sonora 63, Sonora 64 and Mayo 64 along with 613 advance generation progenies
exhibiting segregation for rust resistance, plant height, maturity duration, grain
attributes and phenomenon of grain shattering were introduced. After conducting
the multilocational field trials, Lerma Rojo 64A and Sonora 64 were released for the
first time as dwarf wheats for commercial cultivation in the country. However, the
consumers did not like them because of their red grains and poor Chapati making
quality.
For seeking answer to this drawback, the segregating generations of 613 progenies
introduced from Mexico were subjected to rigorous selection by the breeders
working at IARI, New Delhi; Punjab Agricultural University (PAU), Ludhiana;
Govind Ballabh Pant University of Agriculture & Technology (GBPUA&T),
Pantnagar; Government Agriculture College, Kanpur and Chaudhary Charan
Singh Hisar Agricultural University (CCSHAU), Hisar. Number of amber-seeded
2 Wheat Breeding 85

Area, Producon and Producvity in India

120
Production and Productivity

Producon (107.86 mt)

100
80
60
Producvity (34.39 Q/ha)
40
20 Area (31.36 mha)
0

2000-01

2008-09
1964- 65
1966-67
1968-69
1970-71
1972-73
1974-75
1976-77
1978-79
1980-81
1982-83
1984-85
1986-87
1988-89
1990-91
1992-93
1994-95
1996-97
1998-99

2002-03
2004-05
2006-07

2009-10
2011-12
2013-14
2015-16
2017-18
2019-20
Fig. 2.7 Trend of area, production and productivity of wheat in India

genotypes exhibiting rust resistance, semi-dwarf plant type and appropriate maturity
duration were developed at these centres for yield evaluations. Based on their yield
performance in multilocational coordinated trials and National demonstrations, four
amber-seeded improvement dwarf varieties, namely Kalyansona, Sonalika, Safed
Lerma and Chhoti Lerma were released in 1967. The commercial success of these
varieties acted like a catalyst, which not only brought revolution in the wheat
production but also encouraged the breeders to work with more vigour and dedica-
tion. Very soon, Kalyansona and Sonalika became most popular varieties among the
farmers and both these varieties occupied larger area in the country.
The area under wheat has increased from 12.84 million hectares in 1966–1967 to
20.92 million hectares in 1976–1977, but the production jumped tremendously from
11.4 million tons to a record level of 29 million tons during the corresponding
period. In this way, an era of ‘Green Revolution’ was actually ushered in India. A
massive hybridisation programme was initiated by Indian breeders, involving the
dwarf wheat germplasm received from the International Centre for Maize and Wheat
Research (CIMMYT), Mexico and indigenous cultivars/land races. This strategy of
breeding led to develop better wheat varieties year after year to suit to varying
production conditions of different wheat growing zones of the country. The wheat
production progressively scaled new heights year after year. The phenomenon
increase in area, production and productivity established new to newer records
(Fig. 2.7).
The AICRP on Wheat and Barley have been successful in releasing more than
480 high yielding wheat varieties, which are notified for the different agro-ecological
regions of the country. Of which, 311 wheat varieties have been released and notified
by the CVRC, while 169 wheat varieties released by the SVRC. So far, 405 bread
wheat varieties, 64 durum wheat, and 7 dicoccum wheat besides 4 triticale varieties
have been notified. Among these, the land mark varieties like Kalyansona, Sonalika,
C 306, WL 711, UP 262, WH 147, HD 2189, HD 2009, Lok 1, HUW 234, HD 2329,
VL 616, HD 2285, GW 496, HI 8498, GW 322, WH 542, PBW 343, UP 2338, HD
2733, DBW 17, HD 2967, HD 3086 and DBW 187, etc. dominated and occupied
larger area for seasons of wider adaptability, high yield potential, disease resistance,
86 G. Krishnappa et al.

better grain quality, etc. At present, good choice of improved varieties is available
for farmers for growing under different production conditions (Table 2.6).
Two new bread wheat varieties namely, DBW 187 and DBW 303 have been
released recently for cultivation in the North Western Plains zones, the country
having high yield potential and are adoptable for early sown high productive
environments (Table 2.7). The extent of genetic gain in grain yield achieved in the
Indo-Gangetic plains can be seen from the yield potential of wheat varieties, which
rose from 33.7 quintal per hectare in 1965 to 61.3 quintal per hectare in 2020
(Fig. 2.8). The released varieties have been identified for making various products
like bread, biscuit, chapatis, pasta products, etc. (Table 2.8).
In addition to improved varieties, 247 wheat genetic stocks were registered by the
Plant Germplasm Registration Committee of NBPGR, New Delhi. Of them,
140 genetic stocks are for biotic stresses, 42 for quality components and 23 for
abiotic stresses. These genetic stocks are continuously shared with the researchers in
the country for use in their breeding programmes. A single genotype HD 2160 has
played important role in the development of as many as 18 improved wheat varieties
(HD 2987, HD 2967, HD 2501, HD 2428, HD 2402, HD 2327, HD 2307, HD 2281,
DL 788-2, PBW 54, PBW 120, PBW 154, PBW 175, PBW 222, K 9465, K 8962, K
8434 and Raj 1972). In the same context, a single cross number 8156 performed in
the 1950s at Mexico proved most productive, giving rise to well-known varieties like
Kalyansona, Mexi-Pak, Super X, etc., which led the foundation of wheat revolution
in the developing countries of Indian sub-continent.
India is producing enough wheat, and now the country is exporting wheat to
several countries. Besides production, breeding programmes are focusing to develop
nutrient rich wheat for consumption to mitigate wide spread micronutrient malnutri-
tion. WB 02 is the first biofortified bread wheat variety released for cultivation in
North India, which is rich in zinc (42.0 ppm) and iron (40.0 ppm) developed by the
ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana. Besides this
a few other wheat varieties like HPBW 01 (iron 40.0 ppm and zinc 40.6 ppm), Pusa
Tejas (HI 8759) durum wheat variety (12%protein, 42.1 ppm iron and 42.8 ppm
zinc), Pusa Ujala (HI 1605) (high protein 13%, iron 43 ppm and zinc 35 ppm),
MACS 4028 (d) (14.7% protein 46.1 ppm iron and 40.3 ppm zinc) have been
released during the last 5 years. The Indian wheat breeding programme has made
tremendous achievements in terms of developing high yielding varieties and making
India not only self-sufficient but also exporter of wheat.

2.12.2 Genomics Assisted Breeding

At national level, a few varieties developed using marker-assisted selection have

been released for cultivation. PBW723 (Unnat PBW343) is the first variety using
modified marker assisted back cross breeding (MABB) and released at the national
level having five resistant genes introgressed into it. Based on APR against individ-
ual pathotypes, PBW723 possesses resistance against all predominant pathotypes of
yellow and brown rusts. PBW723 also has enhanced resistance to Karnal bunt
2 Wheat Breeding 87

Table 2.6 Wheat varieties for different zones and production conditions in India
Production
Zone condition Varieties
Northern Hills Zone ES-RF-low HS 542, HPW 251, VL 829
(NHZ) fertility
TS-RF-low HS 562, HPW 349, HS 507, VL 907, VL 804
fertility
TS-IR-high HS 562, HPW 349, HS 507, VL 907, VL 804
fertility
LS-RI VL 892, HS 490, HS 420
High altitude VL 832, HS 375
areas
North Western ES-IR-high DBW 303, DBW 187, WH 1270
Plains Zone fertility
(NWPZ) TS-IR-high DBW 222, DBW 187, HD 3226, PBW 723, HPBW
fertility 01, WB 2, DBW 88, HD 3086, WH 1105, HD 2967,
WHD 943(d), PDW 314 (d), PDW 291(d)
LS-IR-medium HD 3298, PBW 771, HI 1621(VLS), HD 3271(VLS),
fertility PBW 752, PBW 757(VLS), DBW 173, DBW 90, WH
1124, DBW 71, HD 3059, PBW 590, WH 1021, DBW
16, WR 544 (VLS), RAJ 3765
TS-RF-low HI 1628, NIAW 3170, HD 3237, HI 1620, PBW
fertility/RI 660, WH 1142, PBW 644, WH 1080, HD 3043, PBW
396
North Eastern TS-IR-high HD 3249, DBW 187, NW 5054, K 1006, HD 2967,
Plains Zone (NEPZ) fertility DBW 39, CBW 38, Raj 4120, K 307, HD 2824, HD
2733, PBW 443, HUW 468, K 9107
LS-IR-medium HI 1621(VLS), HD 3271(VLS), DBW 107, HD 3118,
fertility HD 2985, HI 1563, NW 2036, DBW 14, NW 1014,
HD 2643
TS-RF/RI HD 3293, DBW 252, HI 1612, K 1317, HD 3171, HD
2888, K 8027, C 306
Central Zone (CZ) TS-IR-high HI 1544, GW 366, GW 322, GW 273, HI 8759(d), HI
fertility 8737(d), HD 4728(d), HI 8713 (d), MPO 1215 (d), HI
8498(d)
LS-IR HI 1634, CG 1029, MP 3336, MP 1203, HD 2932, HD
2864, MP 4010
TS-RF-low Raj 4238, DBW 110, MP 3288, MP 3173, HI 1531, HI
fertility/RI 1500, DDW 47(d), UAS 466(d), HD 4672(d), HW
2004 (Amar)
Peninsular Zone TS-IR-high DBW 168, MACS 6478, UAS 304, MACS 6222,
(PZ) fertility NIAW 917, Raj 4037, GW 322, DDW48, MACS 3949
(d), UAS 428 (d), UAS 415 (d), MACS 2971(dic),
DDK 1029 (dic), DDK 1025(dic)
LS-IR HI 1633, HD 3090, AKAW 4627, HD 2932, Raj 4083,
HD 2833
TS-RF-low NIAW 3170, UAS 375, HI 1605, UAS 347, DBW
fertility/RI 93, NIDW 1149 (d), MACS 4058(d), GW 1346(d),
(continued)
88 G. Krishnappa et al.

Table 2.6 (continued)

Production
Zone condition Varieties
HI8805(d), HI 8802(d), HI 8777(d), UAS 446 (d),
NIAW 1415, HD 2987, HD 2781, AKDW 2997–16(d)
Southern Hills Zone TS-RI-medium HW 5216, COW (W) -1, HW 2044, HW 1098 (dic)
(SHZ) fertility
Marginal areas Salinity- KRL 210, KRL 213, KRL 19
alkalinity
condition
Resistant to WB NEPZ DBW 187, HD 3293, HD 3249, HD 2967, DBW
252, HD 3171
NWPZ DBW 303, DBW 222, WB 02, WH 1105, DBW
88, DBW 173, HD 3043
Where ES, TS, LS, VLS early, timely, late and very late sown; IR, RF, RI irrigated, rainfed, restricted
irrigation; (d), dic. Trit durum, dicoccum and triticale

Table 2.7 Landmark varieties of wheat in India and their yielding ability
Yield Yield
S. Year of potential S. Year of potential
No. Variety release (q/ha) No. Variety release (q/ha)
1 S 227 1965 33.7 14 UP 1990 51.3
2338
2 C 306 1965 36.0 15 WH 1992 61.5
542
3 Sonalika 1967 45.5 16 Raj 1995 48.9
3765
4 Kalyan 1970 46.0 17 PBW 1995 63.0
Sona 343
5 WL 711 1975 46.8 18 HD 1999 62.9
2687
6 UP 262 1977 44.0 19 HD 2001 61.5
2733
7 WH 147 1977 45.1 20 GW 2002 61.0
322
8 HD 2189 1979 45.7 21 DBW 2006 64.1
17
9 HD 2009 1980 45.8 22 HD 2011 66.0
2967
10 Lok 1 1981 45.4 23 HD 2014 71.1
3086
11 HUW 1984 35.3 24 DBW 2019 96.6
234 187
12 HD 2285 1985 42.5 25 DBW 2020 82.1
222
13 HD 2329 1985 47.1 26 DBW 2021 97.4
303
Note: DBW 187 and DBW 303 are recommended for early high fertility condition
2 Wheat Breeding 89

70

60
DBW187

CPAN DBW17 HD3086

50 3004 PBW343
HD2687 HD2967
WL711 HD2329 UP2338
Yield (q/ha)

HD2009
40
K.Sona
S227
30

20

10

0
1965 1970 1975 1980 1985 1990 1994 1995 2000 2005 2010 2015 2020
Genetic gain in yield in NWPZ

Fig. 2.8 Landmark varieties of wheat in India

Table 2.8 Promising genotypes for specific end product quality

Quality product Promising genotypes
Chapatti C 306, LOK 1, SUJATA, RAJ 3765, HD 2285, PBW 373, PBW
(Score > 8.0/10) 533, HUW 234, K 9107, MACS 6145, MACS 6164, NW 1014, HI
1500, UP 262, HW 2004, DL 788–2, GW 273, GW 322, HD 2833, GW
173
Bread HI 977, HS 240, VL 738, HD 2285, HD 2733, LOK 1, GW 120, GW
(>575 ml bread loaf 173, GW 190, HD 2189, MACS 2496, NI 5439, K 9107, HD 2733 and
volume) NIAW 917
Biscuit Sonalika, UP 2425, WH 542, HD 2687, Raj 3765, PBW 373,
(>7.5 biscuit spread and DBW 16
factor)
Pasta PDW 233, WH 896, HI 8498, HD 4672, RAJ 1555, A-9-30-1, MACS
2846, DDK 1009 and NP 200

compared to recipient variety PBW343. Post release, the variety PBW723 has made
its way to farmer’s field and is being grown in Punjab at an average yield of 55–60
qtls/ha. More than 11,000 quintals seed have been produced since the last 2 years
(Sharma et al. 2021).
Another variety, Unnat PBW550 possesses gene Yr15 in PBW550 background
and provides complete foliage resistance to rusts. Gene Lr57/Yr40 has been
introgressed in DBW17 background and the variety PBW771 has been released
and recommended for cultivation under late sown conditions of Indo Gangetic
Plains. Similarly, another cultivar, PBW752 having Yr10 gene has been released
and recommended for NWPZ for late sown irrigated conditions. PBW757, a short
90 G. Krishnappa et al.

duration cultivar released by PAU for cultivation under very late sown conditions
having Yr36 gene in PBW550 background. A spectrum of wheat varieties having
one or more resistant genes are available for cultivation under almost all target
environments of the region and are the outcomes of systematic resistance breeding
efforts.

2.13 Modernisation of Crop Improvement Programme

Several new tools and techniques have been constantly invented and are being used
to facilitate breeding of new improved crop varieties including wheat. Although the
field of New Plant Breeding Techniques (NPBTs) is young, it reveals a great
potential and offers several advantages over conventional breeding techniques.

2.13.1 New Plant Breeding Techniques

2.13.1.1 Targeted Mutagenesis: ODM, ZFN, MGN, TALEN

Targeted mutagenesis aims in the creation of small mutations in the plant DNA at the
pre-determined specific sites, and sometimes it is also known as ‘site-specific
mutagenesis’. Conventionally, plant cells are exposed to chemical or physical
mutagens to obtain random mutations. Whereas, in the targeted mutagenesis minor
mutations occur at pre-decided sites, usually to inactivate a target gene of interest or
to restore the function of a mutated gene. However, precise knowledge of the
targeted gene is an essential pre-requisite in targeted mutagenesis compared to
conventional mutagenesis. Several targeted mutagenesis techniques developed in
the past decade can be employed in plants, including ZFN (Zinc Finger Nuclease)
techniques, ODM (Oligonucleotide Directed Mutagenesis), MGN (Meganuclease)
techniques and TALEN (Transcriptional Activator like Effector—Nuclease)
technique.
ODM is mainly based on the use of oligonucleotides for the induction of targeted
mutations in the plant genome. Approximately, 20–100 long oligonucleotides
chemically synthesised in order to share homology with the target sequence except
nucleotides to be modified in the host genome. ZFNs are custom-designed proteins
to cut at specific DNA sequences. They consist of a ‘zinc finger’ domain
(recognising specific DNA sequences in the genome of the plant) and a nuclease
that cuts double-stranded DNA. ZFN techniques in plant breeding are the novel tools
for the introduction of site-specific mutations in the plant genome or the site-specific
integration of genes (Osakabe et al. 2010). MGNs are very specific restriction
enzymes that recognise 12–30 base pairs of DNA sequences and create a double
strand break (DSB) that activates repair mechanisms and DNA recombination.
MGNs are a very broad group of proteins expressed by several different organisms.
Among them, the family group of LAGLIDAGD MGNs is commonly used for
targeted mutagenesis. TALENs are artificial restriction enzymes that are custom-
designed to cut at specific DNA sequences like ZFN.
2 Wheat Breeding 91

2.13.1.2 Techniques Resulting in ‘Negative Segregants’: Reverse

Breeding, RdDM
This group of techniques also called ‘transgenic construct-driven breeding
techniques’ (Lusser et al. 2012) has a common feature of transgenesis only in an
intermediate step of the breeding process. The transgene used is subsequently
eliminated by crossing and selection and is therefore not present in the final products,
and for this reason it is called ‘negative (for the absence of the transgene)
segregants’.

2.13.1.3 Variants of Plant Transformation Techniques: Cisgenesis

and Intragenesis
As against transgenesis which can be used to insert genes from any organism, both
eukaryotic and prokaryotic, into plant genomes, cisgenesis and intragenesis are
terms recently created by scientists to describe the restriction of transgenesis to
DNA fragments from the species itself or from a cross-compatible species. In the
case of cisgenesis, the inserted genes, associated introns and regulatory elements are
contiguous and unchanged. In the case of intragenesis, the inserted DNA can be a
new combination of DNA fragments from the species itself or from a cross-
compatible species (Rommens 2007; Schouten and Jacobsen 2008).

2.13.2 Speed Breeding: Faster and Better Phenotyping

Speed breeding is a recent technique that involves the manipulation of environmen-

tal conditions under which crop genotypes are grown, aiming to accelerate flowering
and seed set, to advance to the next breeding generation as quickly as possible.
Speed breeding (SB) techniques have now been developed for wheat by accelerating
plant growth, flowering, seed set and maturation using supplemental lighting under
controlled growth conditions. Consequently, the generation time of crop plants is
reduced significantly as compared to the field or normal glasshouse conditions. The
method saves breeding time and resources through rapid generation advancement.
Watson et al. (2018) could get upto 6 generations of spring wheat (Triticum
aestivum), durum wheat (T. durum) in a year with supplemental lighting using
LED lights in environment controlled growth chambers and single seed descent
(SSD) method, compared to 2–3 under glasshouse conditions and one generation
under field conditions. As a result, speed breeding offers opportunities to rapidly
develop homozygous and stable genotypes, and to facilitate rapid generation
advancement, resulting in accelerated development and release of new cultivars
(Watson et al. 2018). Also, speed breeding technology fits well with MAS and
high-throughput phenotyping methodologies for multiple trait selection.
92 G. Krishnappa et al.

2.13.3 Genome Editing

The second generation genome editing tool CRISPR (clustered regularly interspaced
short pal-indromic repeats)/associated nuclease Cas9 (CRISPR/Cas9) system is
gaining momentum over the ZFN and TALEN genome editing strategies (Upadhyay
et al. 2013). Just like other nucleases, CRISPR/Cas9 involves RNA-guided Cas9
nuclease from bacteria or archaea to generate targeted double-stranded breaks that
are repaired by NHEJ or HDR for efficient genome editing in eukaryotes (Horvath
and Barrangou 2010). Genome editing technologies can accelerate wheat breeding
by allowing the introduction of precise and predictable modifications directly in an
elite varietal background. Recently, the International Wheat Genome Sequencing
Consortium (IWGSC; https://www.wheatgenome.org) released the fully annotated
high quality reference genome of bread wheat variety ‘Chinese Spring’. This will
provide more novel target genes responsive to various biotic, abiotic, quality and
agronomical traits improvement through CRISPR/Cas9 system. CRISPR technology
is useful both in precise enhancing the activity of positive-regulator genes and in
eliminating the negative-regulator genes that affect the trait of interest.
However, there are only few reports available for validation of CRISPR technique
in wheat compared to other crops like rice. Most of these genes are targeted by wheat
researchers to address the major abiotic and biotic stresses, along with improving
agronomic traits in wheat. The first demonstrations of the CRISPR/Cas9 system in
wheat were used to knockout TaMLO locus (Shan et al. 2013), TaPDS and TaINOX
(Upadhyay et al. 2013). In subsequent research, simultaneous knockout of the three
TaMLO homoeoalleles has been established to confer resistance to powdery mildew
in bread wheat (Wang et al. 2014). Shan et al. (2014) also validated the CRISPR/
Cas9 system by targeting TaLOX2 by expressing the sgRNA under the transcrip-
tional control of TaU6 promoter in wheat. Recently, Wang et al. (2019) showed
multiplexed genome editing through CRISPR in hexaploid wheat by targeting three
different genes, viz. TaGW2, TaLpx-1 and TaMLO.

2.13.4 Genomic Selection: Rapid Genetic Gain

Recently, GS and speed breeding have emerged as the most promising breeding
strategies to accelerate genetic gain in crop plants. An integrated approach of GS and
speed breeding could fast-track gene bank mining for rapid genetic gain in crop
plants (Li et al. 2018). GS could be a promising strategy to accelerate genetic gain
per unit time and cost, especially for traits governed by small and cumulative effect
genes. However, the optimal integration of GS in active breeding programmes faces
several challenges. Nevertheless, GS has a clear-cut advantage over other breeding
techniques to enhance genetic gains for complex traits (Crossa et al. 2017). During
the last one decade number of empirical GS studies reported in different crop plants,
highest number of GS studies reported in wheat, followed by maize and rice, which
together make upto 75% of all the studies (Krishnappa et al. 2021). Various studies
suggest that GS is becoming a substantial component of modern crop breeding
2 Wheat Breeding 93

programmes due to rapid increase of genetic gain (Gorjanc et al. 2018). But there are
very limited reports on the actual impact of GS on realised performance improve-
ment (Voss-Fels et al. 2019) in different breeding programmes. Maize is an excep-
tion; drought-tolerant high-yielding commercial maize referred to as ‘AQUAmax’
hybrids were developed by the private sector through precision phenotyping and
crop growth models in genomic prediction frameworks in the USA (Cooper et al.
2014).

2.14 Status Varietal Development and Maintenance Breeding

During the recent decades, India has observed a remarkable advancement in agricul-
tural production and productivity owing to development of high yielding varieties by
the National Agricultural Research System. The strides made in varietal develop-
ment programme would not have been possible without concurrent advancement of
institutional system for crop breeding research and quality seed production. Crop
improvement research was initiated at various Indian Council of Agricultural
Research (ICAR) institutes and State Agricultural Universities (SAU’s) and further
strengthened with initiation of All India Coordinated Improvement Projects during
the 1960s. The system of varietal release, farm verification trials and maintenance
breeding are very well developed and standardised in wheat. There are precise
guidelines for conducting All-India Coordinated Trials in a uniform way, which
ensures quality breeding material/potential entries are promoted further for release.
Once the variety is identified, seeds of the variety are to be deposited with the
NBPGR for conservation in gene bank. After obtaining the acknowledgment with IC
No. from the NBPGR, the release and notification proposal of the variety/hybrid
needs to be submitted to the Central Sub-Committee on Crop Standards, Notification
and Release of Varieties.
The AICWIP was initiated during 1965 at the Indian Agricultural Research
Institute (IARI), New Delhi, and under this project several high-yielding wheat
varieties were developed. Varieties developed by AICWIP were quickly adopted
by farmers due to their high yield potential and wider adaptability (Singh et al.
2019). During 2017, the erstwhile AICWIP project was reconstituted as the All India
Coordinated Research Project (AICRP) on Wheat and Barley under the
ICAR-Indian Institute of Wheat and Barley Research (ICAR-IIWBR) at Karnal
(Haryana). ICAR-IIWBR through its network of cooperating centres engaged in
coordinating the multidisciplinary and multi-location testing of varieties across the
different ecosystems for enhancing and sustaining the wheat production.
Breeder seed indents are reflections of demand of variety at national level and
extent of adoption of particular variety by the farmers. As breeder seeds are produced
by the ICAR institutes/SAUs and further supplied to the various indenting agencies,
viz. National Seed Corporation, State Seed Corporations, State Department of
Agriculture, Private Seed Companies for multiplication into foundation and certified
seed. During the past 5 years, among various wheat varieties, HD- 2967 developed
by the ICAR-IARI, New Delhi, remained as a top indented variety; however, during
94 G. Krishnappa et al.

2021-22, HD-3086 released during 2014 by the ICAR-IARI, New Delhi, took over
the top slot. Further, two latest varieties, viz. DBW- 187 (2019) and DBW-222
(2020) developed by the ICAR-IIWBR, Karnal, rapidly adopted by the farmers and
demand for breeder seed production has increased within a short span of time to
1617.4 q and 506.3 q during 2021–22, respectively. All the below mentioned
varieties (Table 2.9) are outcome of the concentrated efforts of scientist engaged
in the varietal development programme through (AICRP) on Wheat and Barley.
The new varieties developed by the plant breeder needs to be genetically pure,
uniform and free from any seed borne disease. The purity of basic seed/breeder seed
is the most critical aspect, which determines the success of entire seed multiplication
chain. Genetically impure seed may lead to high cost of rogueing and eventually may
lead to even rejection of foundation and certified seed plots. In order to maintain
highest genetic purity, utmost care needs to be taken while production of nucleus and
breeder seed under the strict supervision of concerned breeder (Chakarabrty and
Sharma 2018).

2.14.1 Maintenance Breeding

2.14.1.1 Selection of Earhead

In a plot of advanced generation seed multiplication at second year of AVT Trial,
more than 350 years may be selected randomly based upon diagnostic characters of
variety. In case of released varieties, ear heads may be collected from uniform seed
multiplication filed. These selected ears are threshed separately and are examined for
their colour, shape and size, and ear heads which are not true to type are rejected.

2.14.1.2 Nucleus Seed Multiplication: Stage 1 (Ear to Row Method)

Seeds of selected ear heads are sown in three-meter row (six) for each variety, hence
known as ear to row method. The individual rows are periodically examined
throughout the growing season. All the segregating and lines containing off types
are rejected. Ear rows which show the typical characters of variety and show
uniformity are harvested and threshed individually. The harvested seed if bulked
and used for planting of breeder seed plot, then called as nucleus seed. Around
300–500 ear to rows are grown, considering the demand of breeder seed of particular
variety. Generally, five-meter isolation distance is maintained to avoid any contami-
nation from other source.

2.14.1.3 Nucleus Seed Multiplication: Stage II (Ear to Row Progeny Plot)

In case of varieties having very large area under cultivation, breeder seed require-
ment is higher. Therefore, in such cases, another cycle of nucleus seed production is
followed, which involves sowing of seeds of each selected ear row separately. The
plots sown from seed of each selected ear row is known as ‘Ear to Row Progeny
Plot’. These plots are examined for the essential diagnostic characters of the varieties
at different stages as in the nucleus seed multiplication stage. In this method,
six-meter length of rows are sown in six rows having spacing of 20 cm each, further
 2

Table 2.9 Year-wise breeder seed production of highest indented varieties of wheat in India (in quintals)
Wheat Breeding

S. 2017–18 2018–19 2019–20 2020–21 2021–22

No. Variety Ind. Variety Ind. Variety Ind. Variety Ind. Variety Ind.
1 HD-2967 3079.9 HD- 2967 2893.8 HD-2967 2972.9 HD-2967 2467.3 HD- 3086 1700.6
2 WH 1105 1367.0 HD-3086 1327.6 HD-3086 1936.3 HD- 3086 1731.7 HD-2967 1659.0
3 HD 1347.2 RAJ 1119.5 PBW 1569.4 PBW 1148.8 DBW 187 1617.4
3086 4238 723 723
4 LOK-1 916.0 WH 1105 847.9 RAJ-4238 955.0 WH 1105 583.0 HD-3226 1151.3
5 Raj 887.9 LOK-1 810.4 PBW 746.2 RAJ 560.8 HI 8759 846.2
4079 725 4238
6 GW-366 766.0 Raj-4079 716.0 LOK-1 600.0 PBW-725 439.4 RAJ 676.4
4238
7 RAJ 756.0 GW-322 564.2 HI 8713 462.2 WB-2 358.8 PBW 593.0
4238 723
8 GW-322 745.8 PBW-725 557.2 GW-366 445.0 HI 8759 356.4 DBW 222 506.3
9 DPW 621–50 522.8 HI 549.9 HI 1544 398.8 HD 354.1 HD 352.1
1544 2851 2851
10 HI 480.1 PBW 468.0 GW-322 386.6 GW-366 335.2 JW-3382 298.4
1544 723
Source: Seed net India Portal
95
96 G. Krishnappa et al.

these plots are isolated with minimum of five-meter length for any other varieties to
avoid contamination in NSS-II.

2.14.1.4 Breeder Seed Production

Breeder seed is produced as per the allocation of indents by the Department of
Agriculture Cooperation and Farmers Welfare, Government of India to the
concerned institute. The breeder seed is produced from the nucleus seed (stage I or
II) under the supervision of a qualified plant breeder. The isolation of three meter is
recommended from other wheat variety and needs to ensure that the breeder seed
plot is 150 meter isolated from loose smut infected wheat plots. At the time of
sowing, care must be taken to keep one row blank after every eight rows for easy
inspection and roguing. All plants which are not typical of the variety are considered
as offtypes, and it is very essential to rogue out these offtypes from breeder seed
plots to maintain purity of foundation and certified seeds. Breeder seed plots are
monitored by team of experts consist of breeder of the variety, the concerned Project
Director or his/her nominee, representative of the National Seed Corporation or seed
certification agency and based on the monitoring report of team (BSP III), breeder
seed is harvested and made available to the varied indenting agencies for further
multiplication.
Varietal improvement/development programme is the backbone of food security
of India. Wheat improvement programme over the years have developed varied high
yielding, multiple stress tolerant and bio-fortified varieties catering the needs of
farmers. Further, vigorous efforts are being made to make available quality seeds of
such varieties at farmer’s doorstep, which is reflected in terms of higher varietal
replacement rate (74.0% for varieties which are less than 10 years old) and seed
replacement rate (40.30%) in wheat in India.

2.15 Coordinated System of Testing

In India, the systematic wheat research started about 100 years ago after joining of
Sir Howards as the Imperial Botanist at Pusa (Bihar) in 1905. Later on, after
establishment of the Indian Council of Agricultural Research (ICAR) in 1935, it
became the main funding agency and promoter of wheat research in India. An
important milestone in this process was the establishment of the All India Coordi-
nated Wheat Improvement Project (AICWIP) in the year 1965, by the ICAR. Then
AICWIP was elevated to the status of the Directorate of Wheat Research (DWR) in
the year 1978, and in 1991, it moved from IARI, New Delhi, to its present location at
Karnal, along with two regional stations (Flowerdale, Shimla and Dalang Maidan).
In 2014, it became an institute, ICAR-Indian Institute of Wheat and Barley Research.
In India, wheat is grown on an area of about 30 million hectares, and the cultivation
extends from 90N (Palni hills) to above 350N (Srinagar valley of J & K), thus the
wheat crop is exposed to a wide range of agro-climatic changes such as humidity,
temperature, photoperiod during crop season, soil types, altitudes, latitudes and
cropping systems. From wheat research and coordination point of view and based
2 Wheat Breeding 97

Table 2.10 Five major zones and states covered under each zone in the country
Zone Area covered
Northern Hills Zone Western Himalayan regions of J&K (except Jammu and
(NHZ) Kathuadistt.); H.P. (except Una and PaontaValley); Uttarakhand
(except Tarai area); Sikkim and hills of West Bengal and N.E.States
North Western Plains Punjab, Haryana, Delhi, Rajasthan (except Kota and Udaipur
Zone (NWPZ) divisions) and Western UP (except Jhansi division), parts of J&K
(Jammu and Kathua distt.) and parts of HP (Una dist. And Paonta
valley) and Uttarakhand (Tarai region)
North Eastern Plains Eastern UP, Bihar, Jharkhand, Orissa, West Bengal, Assam and
Zone (NEPZ) plains of NE States
Central Zone (CZ) Madhya Pradesh, Chhattisgarh, Gujarat, Kota and Udaipur divisions
of Rajasthan and Jhansi division of Uttar Pradesh
Peninsular Zone (PZ) Maharashtra, Karnataka, Andhra Pradesh, Goa, plains of Tamil
Nadu

on land use planning, the country is divided into following five major zones:
(1) Northern Hills Zone (NHZ), (2) North Western Plains Zone (NWPZ),
(3) North Eastern Plains Zone (NEPZ), (4) Central Zone (CZ) and (5) Peninsular
Zone (PZ) as described below Table 2.10.
Through coordinated research efforts, many high yielding wheat varieties suited
to different agro-ecological conditions and growing situations have been released.
These genotypes were very successfully helped in increasing the wheat production
from a mere 12.5 million tons in 1964 to 108.75 million tons during 2020–2021. The
wheat crop in India is menaced by a number of diseases. The survey and surveillance
activity has helped to monitor the dynamics of important wheat diseases, particularly
the three rust diseases. Through this mechanism, the occurrence/evolution of new
pathotypes is made known before crossing the threshold limit of disease infestation,
in the meantime, the genetic resistance is created against the new virulence in form of
resistant varieties. Large number of donors lines carrying ‘R-genes’ conferring
resistance against different rust races have been identified for utilisation in breeding
programmes. The coordinated research through the AICRP on Wheat and Barley
caters to the needs of cooperating centres by streamlining the research efforts and
facilitating the evaluation and screening of the breeding materials. Every year
national and international nurseries are supplied to different centres across various
wheat growing zones, with an aim of screening the lines at hotspots and assessing the
resistances across locations and environments.
Multi-disciplinary approach of variety testing in AICRP on Wheat and Barley:
The Crop Improvement Division is primarily involved in coordination activities of
the AICRP on Wheat and Barley, wherein the multilocation evaluation of wheat
varietal trials and nurseries are undertaken. In addition to breeding work, pathologi-
cal, agronomical and quality programmes also support in variety of development and
testing approach of wheat in India. The wheat coordinated varietal evaluation
programme entails a huge multilocation testing programme, which is undertaken
98 G. Krishnappa et al.

Table 2.11 Different National initial varietal trials (NIVTs) under coordinated system of testing
NIVT Cultural conditions Zones
NIVT-1A&1B Timely sown, irrigated condition (T. aestivum) NWPZ & NEPZ
NIVT-2 Timely sown irrigated condition (T. aestivum) CZ & PZ
NIVT-3A Late sown irrigated condition (T. aestivum) NWPZ, NEPZ
NIVT-3B Late sown irrigated condition (T. aestivum) CZ, PZ
NIVT-4 Timely sown irrigated (T. durum) CZ and PZ
NIVT-5A Timely sown, restricted irrigation (T. aestivum) NWPZ, NEPZ
NIVT-5B Timely sown, restricted irrigation (T. aestivum & durum) CZ and PZ

with the cooperation of 29 funded and 95 voluntary centres spread across 5 wheat
growing zones in the country.
Initially, the system of varietal evaluation was confined to the specific zones
including initial varietal trials and advance varietal trials for different production
conditions. Under this system flow material from one zone to another zone was not
done, and the adaptability of genotypes was limited to specific zones. Realising this
problem and widening the testing environments and to have free flow material of
material across zones, the system of testing was re-structured with the incorporation
of National Initial Varietal Trials (NIVTs) and their details along with production
conditions and zones are presented below Table 2.11.
However, in NHZ separate zone specific Initial Variety Trials (IVTs) in place of
NIVTs are conducted. This way, the Indian wheat programme is unique regarding
the multi-location testing of new genotypes through different trials. The procedure of
evaluation system was re-structured in such a way that the materials from different
centres are pooled and tested at different levels, namely station trials, national initial
varietal trials (NIVT) and advance varietal trials (AVTs) to sort out superior germ-
plasm with respect to yield, disease resistance and quality in the following manner.
After 1 year of testing in IVTs, deserving genotypes are promoted to AVTs in NHZ
at zonal level. However, in case of remaining four zones, deserving genotypes come
from NIVTs for advance testing in each of four AVTs of NWPZ, NEPZ, CZ and PZ
(Table 2.12 and Fig. 2.9).
The impact of wheat varieties is immense in Indian agriculture and helped
country to increase ten-fold wheat production from 9.5 million tons in 1963–64 to
108.75 million tons in 2021–21. Thus, it has contributed in un-precedential growth
in wheat production could have been possible because of continuous replacement of
old varieties with high yielding improved varieties (Table 2.4) as a result of
concerted efforts of wheat researchers and a systematic and effective seed replace-
ment mechanism. In nut shell, this system is very unique and un-parallel that has
been very effective for development and deployment of high yielding, rust resistant
and end product specific quality wheat meet food and nutritional security of the
country. The importance of this system of evaluation in different trials and nurseries
in India’s wheat improvement programme is reflected in the effective management
of Wheat and Barley rusts in India through the deployment of diverse rust resistant
wheat varieties based on the pathotype distribution in different areas.
2 Wheat Breeding 99

Table 2.12 Trial series and criterion for promotion of different trials in coordinated system
Materials are evaluated for one year in station trials for yield potential and for disease reactions in
IPPSN before entering national testing system under AICRP
#
One year inter zonal test
Trial series Criteria of promotion/retention
Respective NIVT (NIVT-1A, NIVT-1B, Yield potential, disease reactions and quality
NIVT-2, NIVT-3A, NIVT-3B, NIVT-4, parameters are taken into account for promoting
NIVT-5A, NIVT-5B materials into various zonal level AVTs
#
AVT-I (first year)
One year zonal test
AVT-IR-TS-TAS/TAD/TDM Yield potential, disease reactions and quality
AVT-IR-LS-TAS/TAD parameters are taken into account for retaining
AVT-RIR-TS-TAD materials in AVT-II
#
AVT-II (final year)
One year zonal test
AVT-IR-TS-TAS/TAD/TDM Yield potential, disease reactions, quality
AVT-IR-LS-TAS/TAD parameters and agronomical evaluations are
AVT-RIR-TS-TAD performed on final year entries

Fig. 2.9 Flow chart showing varietal testing system in AICRP on wheat and Barley
100 G. Krishnappa et al.

2.16 Conclusions

Breeding programmes in India have made significant progress, and achievements are
reflected in terms of record wheat production of 108.75 million tons during 2021 as
compared to 12.3 million tons in 1965. Deployment of high yielding, resistant
varieties through the use of both cultivated and wild germplasm have led to signifi-
cant improvement in yield potential, and breeding programme have been able to
contain the losses caused by biotic and abiotic stresses. Nutrient rich varieties have
been developed and released to minimise the micronutrient malnutrition. Varieties
having specific traits which are required for industrial products like Chapatti, bread,
biscuit, pasta, macaroni, noodles, etc. have been released. The wheat crop is also
facing challenges of abiotic stresses particularly heat and drought. Although several
heat tolerant varieties have been released but needs further improvements in the traits
to breed better climate resilience. The natural resources like land and water are
shrinking due to urbanisation and depletion of ground water due to excessive use.
Varieties having high nutrient, water and radiation use efficiency, and productivity
needs to be targeted so that same or higher production levels can be achieved with
minimum use of these resources. The varietal replacement rate with the deployment
of new varieties has been improved in the recent decade in comparison to the past.
Many high yielding and disease resistant varieties have been released for different
zones of the country but the life span of varieties is usually considered to be
3–5 years due to the breakdown of deployed resistance. The recent advances in
genomics like GWAS, genomic selection, speed breeding and phenotyping
platforms need to be adopted in the breeding programmes for better understanding
and dissecting of complex traits. These technologies can assist the conventional
breeding approaches to breed high yielding, nutrient rich and climate resilient
varieties with a higher precision. Besides record production the country achieved,
there is a continuous need to sustain and further improve the productivity in India to
feed the growing population.

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https://www.fao.org/faostat/en/#home
https://www.fao.org/news/archive/news-by-date/2020/en/
https://www.fao.org/news/archive/news-by-date/2021/en/
Rice Breeding
3
S. Gopala Krishnan, K. K. Vinod, Prolay K. Bhowmick,
Haritha Bollinedi, Ranjth K. Ellur, Rakesh Seth, and A. K. Singh

Abstract

Rice (Oryza sativa L.) belongs to Poaceae family and serves as food for more than
half of the global population. Domesticated from O. preperennis about 10,000
years ago, it is cultivated in a wide range of ecosystems right from below the sea
level to high mountain regions. Genetic improvement in India has helped in
improving average productivity from 0.67 tons/ha in 1950–1951 to 2.74 t/ha
during 2020–2021. Development of research infrastructure along with basic
research helped in gaining understanding of the genetic nature of economically
important traits. The major breakthrough in yield improvement was achieved
through utilisation of sd1 in developing semi-dwarf high yielding varieties with
sturdy stem, spurring the green revolution. Hybrid rice further enhanced rice
productivity. Deciphering rice genome and advances in genomics helped in
functional characterisation of
2800 economically important genes governing
yield, resistance to major biotic and abiotic stresses, grain and nutritional quality,
which enabled the integration of molecular markers in breeding. Thirty-six
MAS-derived varieties with resistance to biotic and/or abiotic stress and
12 varieties with enhanced Zn and/or protein content have been released in
India. Advances in genetics, breeding, genomics and phenomics, have enabled
population improvement through genomic selection, while genome-editing has
helped in creating novel alleles for useful genes. Aided by an evolving system for
multi-location evaluation of elite genotypes under the All India Coordinated Rice
Improvement Programme and a robust system of seed supply chain for dissemi-
nation of improved rice varieties, higher adoption by farmers has helped in
improving and sustaining rice productivity. However, sustaining it in the face

S. Gopala Krishnan (*) · K. K. Vinod · P. K. Bhowmick · H. Bollinedi · R. K. Ellur · R. Seth ·

A. K. Singh
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 113
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_3
114 S. Gopala Krishnan et al.

of climate change is a major challenge. Adoption of advanced tools and

techniques can help rapid and precise breeding of improved rice varieties suited
to changing human needs.

Keywords

Breeding · Genome-editing · Gene pool · Genomic selection · Heterosis ·

Phenomics · Rice · Yield · Biotic and abiotic stress · Grain and nutritional quality

3.1 Introduction

Rice (Oryza sativa L.) is the most important staple-food crop feeding more than half
of the world’s population. Currently, rice is cultivated in an area of 192.02 million
hectares (mha) with an estimated annual production of 966.88 mt of paddy (644.91
mt of milled rice equivalent) and an average productivity of 4.06 t/ha of paddy across
the world. India has the world’s largest area under rice and the second highest
production in the world (Table 3.1). Only about 31 million tonnes of rice is traded
through the international market. Leading rice exporting countries are India,
Thailand, Vietnam, the USA and Pakistan. India has surpassed Thailand to become
the first among the rice exporting countries in 2012 with the export of more than ten
million tonnes and is still the top exporter of rice. Rice export contributes to nearly
25% of total agricultural exports from the country.
Rice is the staple food for ~800 million (65%) population of India. Rice research
in India has helped in the production of 121.46 million tonnes of milled rice from an
area of 43.78 mha at an average productivity of 2.77 t/ha during 2020–2021 as
compared to merely 20.60 million tons of milled rice from an area of 30.8 mha with
average rice productivity of 0.67 tons/ha in 1950–1951. The crop is grown in highly

Table 3.1 Area, production and productivity of rice in top ten rice producing countries across the
globe
Rank Country Area (mha) Production (mt) Productivity (t/ha)
1 India 43.78 191.91 (121.46) 4.38
2 China 29.96 211.41 (141.01) 7.06
3 Bangladesh 11.52 54.59 (36.41) 4.74
4 Indonesia 10.68 54.60 (36.42) 5.11
5 Thailand 9.72 28.36 (18.91) 2.92
6 Viet Nam 7.47 43.45 (28.98) 5.82
7 Myanmar 6.92 26.27 (17.52) 3.8
8 Nigeria 5.28 8.44 (5.63) 1.6
9 Philippines 4.65 18.81 (12.55) 4.04
10 Pakistan 3.03 11.12 (7.41) 3.66
World 192.02 966.88 (644.91) 4.06
Figures in parentheses are milled rice equivalent
Source: FAOSTAT, http://www.fao.org/faostat/en/#data/QCL accessed on 29/08/2021
3 Rice Breeding 115

Fig. 3.1 Trends in area, production and productivity of rice in India

diverse conditions ranging from hills to coasts. Primarily a Kharif crop, it is

cultivated round the year in one or the other parts of the country. The area under
rice has remained almost unchanged over the years, but production has increased
more than five times (Fig. 3.1).
The average productivity of rice in India is 2.77 t/ha, which is less than the global
average rice productivity and is significantly lower as compared to China which
produces 141.01 mt from an area of only 29.96 mha with average productivity of
4.71 t/ha of milled rice. India contributes 21% of global rice production. The year
2020–2021 recorded the highest rice production of 121.46 mt. The annual area,
production and productivity of rice during the last two and half decades is presented
in Table 3.2. Currently, out of the total area of 43.78 mha, 24 mha is under irrigated
rice in eight states, namely Punjab, Haryana, Uttar Pradesh, West Bengal, Bihar,
Odisha parts of Andhra Pradesh and Tamil Nadu. About 17.2 mha is under the
rainfed ecosystem with more than 70% in eastern India. Around 85% of the total rice
production is contributed by the favourable ecologies of irrigated and shallow-
lowland ecosystems. Rice is one of the most resource intensive crops among all
the crops, and annually it uses about 200 km3 of irrigation water, 6.5 mt of fertilisers,
17% of total pesticides used in Indian agriculture and emits 3.5 mt of methane
(Pathak et al. 2018).
Future projections indicate that the current levels of production may not be
sufficient to feed the ever-increasing population of our country. To meet the food
demands for the future, it is projected that India should produce about 137.3 million
tons of rice by the year 2050, i.e. it needs to produce about 0.56 million tons
additional rice every year. This increased production has to necessarily come from
116 S. Gopala Krishnan et al.

Table 3.2 Annual area, production and productivity of rice in India during the last 25 years
Year Area (mha) Production (mt) Productivity (kg/ha)
1995–1996 42.84 76.98 1797
1996–1997 43.43 81.73 1882
1997–1998 43.45 82.54 1900
1998–1999 44.80 86.08 1921
1999–2000 45.16 89.68 1986
2000–2001 44.71 84.98 1901
2001–2002 44.90 93.34 2079
2002–2003 41.18 71.82 1744
2003–2004 42.59 88.53 2077
2004–2005 41.91 85.13 1984
2005–2006 43.66 91.79 2102
2006–2007 43.81 93.35 2131
2007–2008 43.91 96.69 2202
2008–2009 45.54 99.18 2178
2009–2010 41.92 89.09 2125
2010–2011 42.86 95.98 2239
2011–2012 44.01 105.3 2393
2012–2013 42.75 105.24 2462
2013–2014 44.14 106.54 2416
2014–2015 44.11 105.48 2391
2015–2016 43.39 104.41 2404
2016–2017 43.99 109.70 2494
2017–2018 43.77 112.76 2576
2018–2019 43.79 116.42 2658
2019–2020 43.66 118.87 2723
2020–2021 43.79 121.46 2774

increased productivity rather than an increase in area under rice and that too under
declining soil, water and other natural resources.

3.2 Origin, Evolution and Distribution of Oryza Gene Pool

Cultivated rice belongs to the Poaceae family, subfamily Bambusoideae and tribe
Oryzeae. The genus, Oryza, is the only cultivated genera among the 11 genera
belonging to the tribe Oryzeae with an evolutionary history, spanning approximately
15 million years (Stein et al. 2018). It has two cultivated and 25 wild species
representing 11 genomes, namely AA, BB, CC, BBCC, CCDD, EE, FF, GG,
HHJJ, KKLL and genome size variation of upto 3.6 times (Vaughan 1994; Ge
et al. 1999; Jacquemin et al. 2013; Table 3.3). Oryza originated ~130 million
years ago and spread like wild grass in the erstwhile Gondwanaland and spread
3 Rice Breeding 117

Table 3.3 The different species of genus Oryza with their genomes, chromosome number and
distribution
Somatic
chromosome
Species Genome number (2n) Distribution
Oryza sativa L. AA 24 Worldwide
O. glaberrima Steud. AgAg 24 West Africa
O. nivara Sharma et Shastry AA 24 Tropical and subtropical
Asia
O. rufipogon Griff. AA 24 Tropical and subtropical
Asia, tropical Australia
O. breviligulata A. Chev. Et AgAg 24 Africa
Roehr. (O. barthii)
O. longistaminata A. Chev. AlAl 24 Africa
et Roehr.
O. meriodionalis Ng AmAm 24 Tropical Australia
O. glumaepatula Steud. AgpAgp 24 South and Central America
O. punctata Kotschy ex BB 24 Africa
Steud.
O. minuta J.S. Presl. Ex BBCC 48 The Philippines and Papua
C.B. Presl. New Guinea
O. schweinfurthiana BBCC 48 Africa
Prodoehl
O. officinalis Wall ex Watt CC 24 Tropical Australia
O. rhizomatis Vaughan CC 24 Sri Lanka
O. eichingeri A. Peter CC 24 South Asia and East Africa
O. alta Swallen CCDD 48 South and Central America
O. grandiglumis CCDD 48 South and Central America
(Doell) Prod.
O. latifolia Desv. CCDD 48 South and Central America
O. australiensis Domin. EE 24 Tropical Australia
O. brachyantha A. Chev. et FF 24 Africa
Roehr.
O. granulate Nees et GG 24 South and Southeast Asia
Am. Ex Watt
O. meyeriana (Zoll. Et (Mor. GG 24 Southeast Asia
Ex Steud.) Baill.
O. longiglumis Jansen HHJJ 48 Indonesia and Papua New
Guinea
O. ridleyi Hook. F. HHJJ 48 South Asia
O. schlechteri Pilger HHKK 48 Papua New Guinea
O. coarctata Roxb. KKLL 48 South Asia

across different continents, namely Asia, Africa, Australia and America, after the
continental drift separated these continents.
The genus Oryza has been classified into four species complexes, namely:
118 S. Gopala Krishnan et al.

(a) Sativa complex consisting of eight diploid species (2n ¼ 24) belonging to the
AA genome. It includes two cultivated species, namely O. sativa and
O. glaberrima; and six wild species, namely O. nivara, O. rufipogon,
O. breviligulata (O. barthii), O. longistaminata, O. meridionalis and
O. glumaepatula. All of them belong to the primary gene pool and are easily
crossable with cultivated rice.
(b) Officinalis complex consisting of six diploid species, namely O. punctata,
O. officinalis, O. rhizomatis, O. eichengiri, O. australiensis and
O. brachyantha, and six allotetraploid species, namely O. schweinfurthiana,
O. minuta, O. malampuzhaensis, O. latifolia, O. alta and O. grandiglumis. The
species in the officinalis complex belong to a secondary gene pool as crosses can
be achieved through embryo rescue.
(c) Meyeriana complex consisting of three G genome diploid species, namely
O. meyeriana, O. granulata and O. neocaledonica.
(d) Ridleyi complex consisting of two tetraploid species, namely O. longiglumis and
O. ridleyi. Besides these, there are two other tetraploid species, namely
O. schlechteri and O. coarctata, which are under unclassified groups. The
species belonging to meyeriana, ridleyi complexes and the unclassified group
constitute the tertiary gene pool (Chang, 1964; Fig. 3.2).

Several of the wild species are naturally distributed in South and Southeast Asia
especially in eastern and central India. Among these O. rufipogon is widely
distributed (Fig. 3.3), followed by O. nivara and weedy rice.

3.3 Origin and Evolution of Rice

The genus Oryza originated about 130 million years ago in the erstwhile superconti-
nent Gondwanaland, and different species got distributed into different continents as
the supercontinent broke up and drifted apart. Rice was domesticated around 10,000
years ago. The two cultivated species of the Oryza, namely O. sativa, and
O. glaberrima, originated from a common A genome ancestor, O. perennis, which
is possibly extinct (Khush 1997). O. sativa is commonly cultivated across Asia and
in general referred to as Asian cultivated rice, while O. glaberrima is mainly
cultivated in western Africa and is known as African rice (Fig. 3.4). The domestica-
tion of rice has been a subject of debate with contradictory findings on single or
multiple independent domestication events. Kato et al. (1928) proposed independent
origin of the indica and japonica subspecies of O. sativa, which have been
substantiated by interspersion pattern of short interspersed elements (SINEs)
(Cheng et al. 2003); cytoplasmic diversity (Kawakami et al. 2007); estimates of
genomic divergence between indica and japonica (0.4–0.2 Mya), preceding domes-
tication (Vitte et al. 2004; Zhu and Ge 2005) and phylogeographic haplotype
association (Londo et al. 2006). On the other hand, identical mutation for
non-shattering grains (Sh4) (Li et al. 2006), red pericarp (Rc) (Sweeney et al.
2006) and severe domestication bottleneck (Zhu et al. 2007) supports single
3 Rice Breeding 119

Fig. 3.2 The gene pool of the genus Oryza

domestication event (Chang 1976; Vaughan et al. 2008). The domestication of rice
in Africa occurred later than the Asian rice. Carbon dating of the archaeobotanical
data from the site of Dia, in the middle Niger Delta, and Mali suggests O. glaberrima
has domesticated 3500 years ago (Murray 2004).
The two key domestication traits in cultivated rice are loss of shattering and
secondary dormancy. Japonica varieties do not possess an abscission layer at the
base of the spikelet making them non-shattering and hard to thresh. The indica
varieties have a partial abscission layer making them free threshing, while the wild
and weedy rice possesses a complete abscission layer rendering them prone to
shattering (Vaughan et al. 2008). One of the most universal changes during the
domestication of cereal crops is the loss of grain shattering, which enabled efficient
harvesting of the crop. The gene governing shattering, Sh4 is a transcription factor
involved in the formation of the abscission layer through the cell wall. A large-effect
Quantitative Trait Locus (QTL) on chromosome 12 explaining about 50% of the
120 S. Gopala Krishnan et al.

Fig. 3.3 Oryza rufipogon grows in natural swamps near Goria Karma (Jharkhand state) during the
rainy season

phenotypic variance was mapped in a Thai accession (Gu et al. 2005). QTLs/genes
associated with other major domestication syndrome traits such as grain shattering,
growth habit, panicle and ligule development, grain number, pericarp colour, hull
colour, awn length, grain width and grain filling are listed in Table 3.4.
After domestication, indica rice spread to Madagascar, East and West Africa,
while it also spread eastwards to Southeast Asia and north to China. The japonica
rice moved north of China to become a temperate japonica, which was then
introduced into Korea and Japan at the beginning of the first century. In the hilly
areas of Southeast Asia, japonica rice was cultivated in uplands as well as lowlands.
Both indica and japonica rice were introduced later to Malaysia, Philippines and
Indonesia, and from Philippines to Taiwan (Khush 1997).

3.4 Rice Ecosystems

Rice is grown across the world from 39 S in Australia to 50 N latitude in China.
Broadly, rice is produced from four different ecosystems, namely irrigated, rainfed
lowland, upland and flood-prone ecosystems. Under irrigated ecosystem, rice is
grown maintaining flooding of water with adequate water control measures in
place. Irrigation is provided from various sources such as canals, reservoirs and
wells. The rainfed lowland production ecologies rely on the rainfall for the source of
3 Rice Breeding 121

Fig. 3.4 Evolution of two cultivated A genome rice species and their subspecies from a common
ancestor

Table 3.4 QTLs/genes associated with other major domestication syndrome traits
Genes Gene ID Chromosome Trait Reference
Gn1a Os01g0197700 1 Grain number Ashikari et al.
(2005)
Rd Os01g0633500 1 Pericarp colour Furukawa et al.
(2006)
qSH1 Os01g0848400 1 Grain Shattering Konishi et al.
(2006)
Bh4 Os04g0460000 4 Hull colour Zhu et al. (2011)
sh4 Os04g0670900 4 Grain shattering Li et al. (2006)
LABAI1 Os04g0518800 4 Awn length Gu et al. (2015)
GIF1 Os04g0413500 4 Grain filling Wang et al.
(2008)
OsLG1 Os04g0656500 4 Panicle shape and ligule Ishii et al. (2013)
development
qSW5 Os05g0187500 5 Grain width Song et al.
(2007)
PROG1 Os07g0153600 7 Growth habit Tan et al. (2008)
Rc Os07g0211500 7 Pericarp colour Sweeney et al.
(2006)
122 S. Gopala Krishnan et al.

water, and the fields are bunded to retain the water from the rainfall. The rainfed
lowlands are further sub-classified into:

(a) Rainfed shallow favourable ecosystem with adequate rainfall throughout the
crop season so that the crop is free from any moisture stress/even if stress is
experienced, its occurrence is limited to shorter periods.
(b) Rainfed shallow drought-prone ecosystem, which experience short rainy period
from 90 to 100 days. As they are completely dependent on rainfall, this
ecosystem is bound to suffer from mild to severe stress during the crop growth
period.
(c) Rainfed shallow submergence-prone ecosystems which experience very heavy
rainfall for upto 10 days and rains for longer periods over the growing season.
(d) Rainfed medium-deep ecosystems, where the field are low lying and gets
flooded with water stagnating for 2–5 months due to poor drainage. In the
rainfed upland ecosystems, rice is solely grown with rainwater without any
supplementation with surface water. The flood-prone ecosystems, which are
prone to submergence due to inundation from excess rains/overflow of rivers/
streams, to a depth exceeding 100 cm for a period ranging from 10 days to
5 months, as there are no structured water control options available in this
ecosystem.

In India, rice is grown under diverse conditions from 79 to 90 E longitude and
16 to 28 N latitude under varying agro-ecological zones. Rice is grown in a wide
range of environments, varying in water availability (from exclusively rainfed crop
completely dependent on monsoon rains to deep waters, where the water level
reaches 5 meters or more); regions varying in altitudes, right from below sea level
in Kerala to 2000 MSL (6600 ft) in Jammu and Kashmir; at different temperature
regimes from 4 C to 45 C and varying rainfall from 25 cm in Rajasthan to 1250 mm
in Assam. A wide range of rainfall distribution patterns (drought, submergence and
deep water) and distinct differences in soils (coastal and inland salinity, alkalinity
and acidity), agro-climatic situations (high humidity, dry) and seasons exist in the
country, necessitating the cultivation of a large number of diverse rice varieties.
Depending on the patterns of rainfall distribution, it is cultivated as a completely
rainfed upland crop in Jharkhand, Chhattisgarh, Western Orissa (Jeypore), parts of
Rajasthan, Uttarakhand and West Bengal (Purulia and Bankura regions). On the
contrary, it is also grown in shallow (upto 30 cm), semi-deep (30–100 cm) and deep
water (>100 cm) ecosystems in eastern Uttar Pradesh, Bihar, West Bengal, Assam
and Orissa. The area under various rice ecologies, production and productivity is
presented in Table 3.5.
Improved rice varieties with high productivity are preferred in irrigated as rainfed
shallow favourable ecosystems, and they are comparatively high in productivity.
Drought-tolerant, photoperiod-insensitive short duration varieties are preferred for
rainfed shallow drought-prone ecosystems as well as rainfed uplands; while
photoperiod-sensitive long duration varieties with high productivity are preferred
in rainfed shallow submergence-prone ecosystems; and varieties tolerant to stagnant
3 Rice Breeding 123

Table 3.5 Area, production and productivity of rice in India and world in different ecologies
Flood prone/
Irrigated Rainfed lowland Rainfed upland deep water
Parameter World India World India World India World India
Area (mha) 79.2 17.8 40.6 15.0 17.2 7.0 11.5 2.4
(55.0) (42.0) (25.0) (35.5) (12.0) (16.8) (8.0) (5.7)
Production 484.0 52.0 108.8 22.0 27.6 4.7 24.6 3.3
(mt)a (75.0) (63.5) (16.9) (26.8) (4.3) (5.7) (3.8) (4.0)
Productivity 5.00 2.97 2.00 1.47 1.20 0.67 1.60 1.37
(t/ha)a
Figures within parenthesis represent percentage area/production. mha million hectares, my million
tons
a
Milled rice in mt

flooding are preferred in rainfed medium deep ecosystems. Deepwater long duration
photosensitive varieties with an inherent ability to elongate in tune with the flood
water levels with excellent kneeing ability to avoid complete lodging due to an
increase in plant height during the vegetative stage.

3.5 Rice Genetic Resources

Genetic resources form the foundation for crop improvement. The collection of
indigenous land races started with the establishment of rice research facilities at
Dacca (part of erstwhile India) in 1911 and the Paddy Breeding station at
Coimbatore in the following year (1912). The Central Rice Research Institute
(presently ICAR-National Rice Research Institute, Cuttack) was established in
1946. Concurrent efforts were made for the collection of the rice germplasm at
different research stations across India and better performing accessions among the
collections were released as varieties through pureline selection. Systematic
explorations were made in the Jeypore tract of Odisha and erstwhile Madhya
Pradesh from 1955 resulting in 1745 collections. During 1965 to 1967, 900 tradi-
tional cultivars from Manipur were collected. A large number of collections were
also made from Assam famously known as Assam Rice Collection (ARC) between
1968 and 1973 (Sharma 1982). Another noteworthy collection of 19,116 local rice
cultivars from Madhya Pradesh was made by Dr. R.H. Richharia from 1971 to 1976.
The National Bureau of Plant Genetic Resources, New Delhi, was established in
1976 with a mandate of undertaking systematic exploration, collection,
characterisation, evaluation, conservation and documentation for germplasms of
crops including rice. Since then, a large number of rice germplasm collections
have been made from different parts of the country.
In rice, ~5,00,000 accessions are conserved in the gene banks across the world,
which also includes duplicates in different gene banks. Around 70.0% of the
germplasm accessions of rice are conserved in six gene banks located in Asia,
with half of the collections maintained in the gene banks at International Rice
124 S. Gopala Krishnan et al.

Table 3.6 Rice germplasm accessions conserved in the gene banks across the world
No. of germplasm accessions
No. Institute/Country conserved
1. International Rice Research Institute, Philippines 1,32,123
2. ICAR-National Bureau of Plant Genetic 1,05,019
Resources, India
3. China National Rice Research Institute, China 74,184
4. USDA, United States of America 52,660
5. NIAS, Japan 28,000
6. Brazil 36,018
7. RDA, South Korea 24,673
8. Africa Rice, Cote d’ Ivoire 21,815
9. Myanmar 7484
10. Russia 4228
11. Indonesia 3891
12. Australia 1732
13. Kenya 1303
14. Portugal 1138
15. Bulgaria 888
16. Italy 719
17. Ukraine 700
18. Romania 669
19. Malaysia 632
20. North Macedonia 276
21. Zambia 258
22. Hungary 253
23. Albania 102
24. Spain 67
25. United Arab Emirates 55
26. United Kingdom 22
27. Ethiopia 17
28. Israel 11
29. Azerbaijan 3
30. Costa Rica 3
Total accessions 4,98,943

Research Institute (IRRI), Philippines and ICAR-National Bureau of Plant Genetic

Resources (NBPGR), India. These gene banks along with those from China, USA,
Japan, Brazil, South Korea, Côte d’Ivoire, Russia and Australia house long-term
seed storage facilities capable of conserving rice collections for future prosperity.
The remaining germplasm of the global holdings is distributed across a large number
of national collections widely distributed throughout rice-growing countries of the
world (Table 3.6). Among these, the wild rice accessions, which are difficult to
conserve as seeds are also conserved ex situ in some field gene banks at IRRI,
Philippines and at Chinese Academy of Agricultural Sciences, China. In India, ex
3 Rice Breeding 125

Table 3.7 Safety duplicates of different species of rice conserved at the Svalbard Global Seed
Vault
Species Accessions Depositors Country of collection
Oryza sativa 1,60,619 18 136
Oryza glaberrima 5473 3 39
Oryza nivara 1567 2 13
Oryza rufipogon 1075 3 19
Oryza hybrid 454 4 19
Oryza spp. 332 3 27
Oryza officinalis 307 2 14
Oryza spontanea 262 2 11
Oryza barthii 261 2 17
Oryza longistaminata 213 3 23
Oryza latifolia 99 3 15
Oryza punctata 83 1 16
Oryza meridionalis 68 2 2
Oryza minuta 64 1 3
Oryza australiensis 63 2 2
Oryza glumaepatula 59 2 8
Oryza granulata 24 1 11
Oryza eichingeri 22 1 3
Oryza rhizomatis 21 1 1
Oryza brachyantha 17 1 6
Oryza grandiglumis 15 2 2
Oryza alta 12 1 7
Oryza ridleyi 12 1 4
Oryza meyeriana 8 1 2
Oryza longiglumis 6 1 2
Total 1,71,136 63 402

situ field gene banks for conserving wild species of Oryza are located in ICAR-
National Rice Research Institute, Cuttack, and Paddy Breeding Station, Tamil Nadu
Agricultural University, Coimbatore.
A duplicate set of rice germplasm conserved at many of these gene banks is also
stored at the Svalbard Global Seed Vault in Norway as a safety duplicate under
permafrost conditions. The seeds of diverse species originating from diffferent
countries are stored in the Norwegian Archipelago of Svalbard under black box
conditions, as safety duplicate to tide over any eventuality following international
laws including the International Treaty for Plant Genetic Resources for Food and
Agriculture (Table 3.7). As many as 63 organisations have contributed to the safety
duplicate include IRRI, Africa rice, the National Plant Germplasm System from the
USA, Taiwan, Brazil, Korea, India, etc.
126 S. Gopala Krishnan et al.

3.6 Floral Biology

The rice inflorescence is a raceme, commonly known as panicles, because of its

conical shape (Itoh et al. 2005). The inflorescence of the rice plant is a modified
shoot. The shoot apical meristem under favourable conditions gets converted into an
inflorescence meristem. The panicle is borne on the uppermost internode of the
culm. The uppermost leaf in the culm is known as flag leaf. The extent to which the
panicle and a portion of the uppermost internode extend beyond the flag leaf sheath
determines the exsertion of the panicle (Chang and Bardenas 1965). The panicle has
two types of meristems, namely rachis meristem and branch meristem. The rachis
meristem forms bracts and branches as lateral organs, and finally aborts and remains
as a vestige near the uppermost branch. The branch meristem differentiates into
spikelets and branches and is ultimately converted into a terminal spikelet. The main
axis of the panicle is called the rachis, which bears 10 or more primary rachis
branches and the flowers on these branches known as spikelets. The primary
branches are arranged in spiral phyllotaxy, which is completely different from that
of 1/2 alternate phyllotaxy observed in the vegetative phase. The spikelets on the
primary branches are arranged in a biased distichous phyllotaxy. The length of the
fourth or fifth primary branch is the largest from where it gradually decreases
towards the apex. The primary branches bear secondary branches and spikelets.
The number of secondary branches is correlated with the length of the primary
branch length. The length of the inflorescence/rachis and the number of primary
branches vary widely among cultivars (Ikeda et al. 2004).
The rice spikelet is borne on the pedicel (spikelet axis), which is morphologically
a peduncle (Fig. 3.5). The spikelet of Oryza comprises of three flowers, two of which
were reduced in development resulting in an enlarged, cup-like apex consisting of
two very small sterile glumes called the rudimentary glumes. Above the inner

Fig. 3.5 Spikelet of rice

3 Rice Breeding 127

rudimentary glume, there are two more small lower bracts which are always sterile
and are comparatively larger than the rudimentary glumes called the sterile lemmas.
The upper bracts consist of two interlocking large glumes, the lemma (fertile lemma)
and palea. The lemma, palea, and the included flower form the floret. The sterile
lemmas are generally shorter than the lemma and palea, never exceed one-third
length of the latter. The lemma is larger and partly envelops the palea. It is indurate
(hardened) with five vascular bundles/nerves, whereas the palea has three vascular
bundles/nerves. The six glumes are arranged in 1/2 alternate phyllotaxy. The rice
flowers are devoid of sepals. Inside the palea, two lodicules (corresponding to petals)
biased to the lemma side are present in the whorl. Lodicules are small and whitish in
structure, which plays a vital role in the opening of the floret. The rice spikelet
consists of six stamens positioned inside the lodicules and one pistil at the centre of
the whorl. The pistil consists of a single carpel with a bifid hairy stigma at the apex.
The extended tips of the lemma and the palea are the apiculi. Some rice genotypes
may possess awn in the spikelet, which is a filiform extension of the keel of the
lemma (Chang and Bardenas 1965).
Panicle initiation in rice starts almost 30 days before the emergence of the panicle.
The flag leaf usually emerges about 18 days before anthesis. The flag leaf sheath
thickens 6 days before anthesis due to panicle growth which is referred to as the
booting stage. The panicle emergence from the flag leaf sheath is completed within a
day. Days to complete flowering from the panicle emergence usually vary from 5–15
days in rice depending on the variety (Yoshida 1981). Anthesis in rice commences
immediately after the emergence of the panicle. The spikelet opening begins with the
opening of the tip portions of the lemma and palea, following which the filaments
elongate leading to exsertion of anthers as well as the tip of the stigma. Each spikelet
remains open for about 30 min. Anther dehiscence occurs just before or at the
opening of lemma and palea due to which many pollen grains fall into the stigma
of the same spikelet leading to self-pollination. Anthesis starts in the spikelets of
primary branches at the tip of the panicle and proceeds basipetally towards the
bottom of the panicle. It takes 7–10 days to complete the anthesis of all the spikelets
within a panicle. The time of anthesis during a given day varies with weather
conditions. If there is a time lag between opening of spikelet and the anther
dehiscence, it may lead to cross pollination in rice. Under normal weather in the
tropical region, anthesis begins at 8:00 AM and continues upto 01:00 PM, attaining
the maximum anthesis between 10:00 AM to 11:00 AM. An individual spikelet
remains open only for a short period, ranging from 30 to 90 min on a given day
(Hector 1913). However, the opening of spikelets and anthesis is dependent on
temperature, relative humidity (RH) and light. Temperature ranging from 28 C to
31 C, RH of 70–80% and orange light are the ideal parameters to accelerate spikelet
opening and anthesis in rice (Nguchi 1929). Pollen grains are viable only for 5 min,
while the stigma remains receptive for 3–7 days. Normally, the pollen grains
germinate on the stigma in 3 min after pollination. Fertilisation normally takes
place within 5–6 h after anthesis. The fertilised ovary develops into caryopsis
about 30 days after fertilisation.
128 S. Gopala Krishnan et al.

3.6.1 Emasculation and Pollination

Emasculation is done for attempting hybridisation between selected genotypes

through controlled pollination. Emasculation is done one day earlier before the
beginning of anthesis in the evening hours. Even though it is possible to emasculate
early in the morning well ahead of anthesis before 8:00 AM, emasculation in the
morning is avoided in general, to avoid inadvertent self-pollination. Since the
maximum number of spikelets open on the third or fourth day of anthesis, panicles
of that stage are selected for emasculation. As many as seven different methods of
emasculation have been described for effecting hybridisation in rice. The methods
widely used for hybridisation in rice include:

(a) Clipping method, which involves clipping one-third portions of both the top and
bottom portions of the panicle of the desired female parent in the previous day
evening using scissors leaving the middle spikelets (Torrens 1930). In the
middle spikelets, the top one third in each spikelet is clipped-off in a slanting
position. Emasculation is done by removing six anthers in each spikelet with the
help of the forceps/needles (Emasculation) with appropriate care to not damage
the gynoecium. The emasculated spikelets are then covered with a butter/
parchment paper bag to avoid contamination with the undesired pollen. The
bloomed panicle from the desired male parent is collected the next day morning
(at about 9:00 AM) for effecting pollination. The top portion of the butter/
parchment paper bag covering the emasculated panicle in the female parent is
cut to expose the panicle. The male parent panicle is inserted in an inverted
position into the butter paper bag and turned in both ways to disperse the pollen.
After ensuring the abundant disbursement of pollen, the opened butter paper bag
is closed using a pin. Tagging is done with labels in the pollinated panicles
indicating the date of pollination and parentage.
(b) Hot water method, which utilises the differential response of pollen grains and
ovary to high temperature using hot water treatment (Jordon 1938). The pollens
are highly sensitive to high temperatures and lose their viability with hot water at
43 C for 7 h while stigma receptivity is not affected. The desirable panicles are
selected from the female parents and an hour or so before anthesis (~ at 7:
00 AM), the underdeveloped and opened spikelets are removed. Then, the tiller
is bent over carefully (to avoid breaking), and the selected panicle is immersed
in hot water at 40–44 C contained in an insulated bottle for 5 to 10 min. This
treatment causes the florets to open in a normal manner and avoids injury. Then,
emasculation is done by removing the six dead stamens by fine forceps or
needles and then pollination is done.
(c) Dr. Ramiah’s method, wherein the selected panicle is covered with a wet cloth
after removing the top and lower spikelets, and the air is blown from the mouth.
This increases humidity and facilitates the opening of spikelets. After 2–3 min,
the wet cloth is removed and the anthers are removed from the open spikelets.
(d) Vacuum emasculation method, which works on the principle of suction pressure
(Mulimbayan 1936). The spikelets of the desirable panicles are clipped off
3 Rice Breeding 129

before exposure to vacuum suction. Minute pipettes are pointed towards the
anthers in the clipped spikelets, and the anthers are sucked in due to vacuum
pressure. Upto six panicles can be emasculated at a time, using a Vacuum
emasculator with six nozzles. Vacuum emasculation is a high throughput
method, through which six persons can emasculate 3000 to 3600 florets/hour
simultaneously as compared to hand emasculation where a person can emascu-
late a maximum of 100 florets only.
(e) Cuttack method, which was developed at erstwhile Central Rice Research
Institute (now ICAR-National Rice Research Institute), Cuttack. The panicle
to be emasculated is inserted into a hollow piece of bamboo closed at one end
and plugged with cotton wool and split cork at the other end. These spikelets in
the enclosed panicles will open within 5–10 min after which the anthers are
removed.
(f) Brown paper method, wherein the panicles are covered in a brown paper cover
couple of hours before blooming. The anthers extrude within 15–30 min due to
heat inside the brown paper bag but do not dehisce, which makes it easier to
remove the anthers (Ramiah 1927). The stigmatic surface is then dusted with
pollen grains collected from the desired male parent.
(g) Rhind’s method, which uses the warmth and humidity in the flask which is filled
with hot water and decanted. The panicle to be emasculated is inserted into the
flask and leftover for some time. Due to high temperature and humidity, the
spikelets open and the anthers protrude out, which makes it easy to remove them
with the help of forceps.

3.7 Cytology and Molecular Cytogenetics

Kuwada (1910) carried out the first study of microsporogenesis, megasporogenesis

and mitosis in Oryza sativa and determined its somatic chromosome number as
2n ¼ 24. Nandi (1936) reported that the variation in the length of somatic
chromosomes ranged from 0.7 μ to 2.8 μ. Nandi (1936) described the morphology
of metaphase chromosomes, based on which they were classified into largest pair of
chromosomes with medium constrictions, medium sized chromosomes with medial
insertion region and small chromosomes. The largest chromosome measured 2.1 μ,
while the smallest one was 1.4 μ (Sethi 1937). At meiosis, the chromosomes in both
O. sativa and O. glaberrima form 12 bivalents in pollen mother cells (PMCs). The
chromosomes of O. officinalis were reported to be slightly larger than that of
O. sativa (Ramanujam 1938). Sen (1963) reported the only description of a gameto-
phytic karyotype in the first microspore division. Shastry et al. (1960) reported the
morphology of the pachytene chromosome complement in rice for the first time. The
occurrence of triploids and tetraploids in rice was first reported by Nakamori (1932).
Morinaga and Fukushima (1931) along with Ramiah et al. (1933) reported the first
occurrence of haploids.
However, rice chromosomes are very small and morphologically similar making
it difficult to peruse them using any cytogenetic tools/banding technique before
130 S. Gopala Krishnan et al.

1960. Hu (1961) first reported the differences in chromosome size among different
wild species, namely B, C, D, E, F and G genomes. Dr. Nori Kurata from Kyushu
University invented a technique that revealed rice somatic prometaphase
chromosomes with clear-cut centromere position and variations in chromosome
length. Even though the sizes of chromosomes and genome varied among different
wild rice genomes (Kurata and Fukui 2003), the genomes exhibited very little
morphological variations (Kurata 1985). Primary trisomics were utilised by Iwata
and Omura (1975) for establishing the association between eight primary trisomics
with linkage groups. Khush et al. (1984) established the association between the
12 linkage groups with cytologically identifiable chromosomes at the pachytene
stage of meiosis for the first time, using the complete set of 12 primary trisomics in
rice. However, due to the lack of an objective method, there were several
discrepancies in the cytological characterisation and identification of the rice
chromosomes (Oka and Wu 1988).
Molecular cytogenetics combining molecular techniques and cytogenetics have
contributed to our understanding of chromosome and genome structure, phylogeny
and genome evolution in the Oryza species. Genome analysis of the Oryza genus
including 2 cultivated species and 24 wild species has identified 11 genomes.
Assessing genome size helps assess its complexity and difficulty in mapping and
map-based cloning of genes (Martinez et al. 1994). The nuclear DNA content of
different Oryza species has been estimated microspectrophotometrically through
fuelgen staining of prophase nuclei (Iyengar and Sen 1978) and by flow cytometry
(Martinez et al. 1994) and employing flow cytometry and chromosome analysis
(Miyabayashi et al. 2007). Even though the genome size of Oryza species exhibits
good correspondence to the enlargement of chromosomes with more than twofold
difference in genome sizes, the chromosome complements of all species show very
similar morphology (Kurata 2008). To identify combinations of alleles and regions
of the genome responsible for heterosis and transgressive variation and learn how to
predict which introgressions from diverse wild or exotic donors are likely to enhance
performance in elite genetic backgrounds of interest, several groups have
constructed libraries of chromosome segment substitution lines (CSSLs), which
greatly facilitate the identification of agronomically valuable genes introduced
from wild or unadapted donors (Tian et al. 2006; Ali et al. 2010).
Technological advances in cytology have enabled visualisation of nucleotide
sequences localised onto chromosomes, nuclei and tissues. Fukui et al. (1987)
produced the first reliable in situ hybridisation to locate the 18S-5.8S-25S ribosomal
RNA gene (45S rDNA) onto pair of rice chromosomes using 125iodine labeled
ribosomal RNA. Imaging techniques in combination with staining (Fukui and Iijima
1991) and non-radioactive labelling using haptenes such as biotin (Iijima et al. 1991)
enabled quantitative estimation of the condensation pattern at the prometaphase
stage, thereby helping in the development of the somatic map of rice chromosomes.
Although the detection technique was stable and safe, they suffered from low spatial
resolution, limitations in probe size and number. Based on further technological
advances in enzymatic and fluorescence techniques in conjecture with new imaging
methods such as cooled CCD camera to capture even the faint fluorescence signals, a
3 Rice Breeding 131

reproducible and convenient fluorescence in situ hybridisation (FISH) technique was

developed in rice (Fukui et al. 1994; Ohmido et al. 1998). With the manifold
advantages offered by FISH including good sensitivity and high spatial resolution,
the ability to simultaneously detect several probes using different fluorochromes and
the versatility of three-dimensional analyses, FISH made it possible for dramatic
advances in molecular cytological studies in rice (Ohmido et al. 2010).
The pachytene chromosomes of rice are ideal for FISH mapping. FISH has been
very useful in identifying the genome-wide distribution of different types of repeti-
tive sequences. TrsA repeats of 355 bp length were one of the first tandem repeat
sequences identified in rice (Ohtsubo et al. 1991). It is detected in the subtelomeric
regions of both cultivated and wild species of rice (Ohmido and Fukui 1997). TrsA
also contributes to the rice terminal structures and genome sizes of various rice
species (Ohmido and Fukui 2004). Fibre DNA technology provided a breakthrough
for estimating the distance between TrsA and telomere sequences at a chromosomal
end. Extended DNA fibres (EDFs) isolated from rice nuclei, in tandem with FISH
provides higher spatial resolution, thereby allowing accurate estimation of the
number of copies of the repetitive sequence and the physical length of target
nucleotide sequences (Ohmido et al. 2000). Multicolour FISH (McFISH) using
telomere- and TrsA-specific probes on rice somatic cells, pachytene chromosomes
and EDFs enables determination of the size of telomeres in rice. The improved
sensitivity of FISH is also used in detecting DNA-protein interactions with the use of
Chromatin immunoprecipitation (ChIP) and immunostaining.
Genomic in situ hybridisation (GISH) which uses total genomic DNA as the
probe is a versatile tool for cytology and molecular cytogenetics in plants (Heslop-
Harrison et al. 1990). GISH enables the characterisation of polyploids, F1s, and
Recombinant lines through the comparison of chromosomes and genomes of differ-
ent species. Fukui et al. (1997) demonstrated that GISH is effective in discriminating
the B, C and D genomes of rice with very small chromosomes. Multicolour GISH
(McGISH) with two genomic probes one for A and another for C genome, and DAPI
staining has been used to characterise the introgression of chromosomal fragments
among different genomes of rice species in somatic hybrids between O. sativa
(AA) and O. punctata (BBCC). Chromosome painting is a powerful method for
the detection of specific chromosome regions or entire chromosomes based on
chromosome specific probes. It is a powerful tool to study genome duplication,
chromosomal rearrangement and the evolution of species (Lysak et al. 2001). Uozu
et al. (1997) utilised chromosomal painting to determine the distribution pattern of
genome specific repetitive DNA sequences in twelve diploid species of rice with A,
B, C, E and F genomes to show that the amplification of the repetitive DNA
sequences causes the variation in the chromosome morphology and genome size
of rice.
132 S. Gopala Krishnan et al.

3.8 Genetics of Qualitative and Quantitative Traits

A basic understanding of the extent of genetic variability for traits as well as the
nature of inheritance is very important for its use in crop improvement. Elucidating
the mode of inheritance of traits is of utmost importance as it will help in planning an
appropriate selection strategy for the improvement of the trait in rice breeding. Rice
genetics is rich with valuable information on the genetics of a large number of traits
as well as the linkage relationships, which have been documented systematically in
the rice genetics newsletter since 1989. The sequencing of the rice genome through
the international consortium initiative of the International Rice Genome Sequencing
Project in 2002 has enabled map-based cloning as well as the identification of a large
number of QTLs governing complex traits. A large number of genes and QTLs
governing various agro-morphological traits, resistance to various stresses, and
physiological traits have been identified and cloned in rice, which have been
documented in QTL Annotation Rice Online (Q-TARO) database (http://qtaro.abr.
affrc.go.jp). A snapshot of the functionally characterised genes and QTLs mapped is
presented in Table 3.8.

3.9 Rice Research in India

The first experimental research for rice was initiated at Dacca (now in Bangladesh) in
the year 1911. The first botanist in India to work on rice was Dr. Hector. However,
Mr. Parnell was the first crop specialist (later designated as paddy specialist) fully
devoted to rice research appointed at the Paddy breeding station (PBS), Coimbatore
in Tamil Nadu, established in 1912. Dr. Ramiah succeeded him as paddy specialist at
PBS (now a part of Tamil Nadu Agricultural University, Coimbatore). The estab-
lishment of the Central Rice Research Institute (presently ICAR-National Rice
Research Institute), Cuttack, in 1946 is a landmark event in rice research in India.
A large number of research stations/institutes were established across the country to
cater to the needs of rice farmers from different regions and ecologies (Table 3.9).
The All India Coordinated Rice Improvement Project (AICRIP) was established in
1965, which was upgraded as Directorate of Rice Research (presently ICAR-Indian
Rice Research Institute), Hyderabad, with the mandate of development of an
integrated national network of cooperative experimentation on various aspects of
rice production with rice varietal improvement as a core activity.

3.10 Breeding Objectives

3.10.1 Yield

Rice yield is a complex trait that is a function of several traits including the number
of panicles per plant, number of grains per panicle and thousand grain weight (Xing
and Zhang 2010). Traditional rice varieties were in general tall, photosensitive, less
3 Rice Breeding 133

Table 3.8 Summary of functionally characterised genes and QTLs mapped in rice
Genes QTLs
Traits identified Important genes mapped Important QTLs
Morphological traits
Culm leaf 204 nal7, lax, Osgl1–2, ygl7 66 qFL1–1, qPN1
Plant height 214 sd1, gid2, bu1 47 Eui, eui2, qPHT2
Panicle flower 126 sh4, Gn1a, WFP, IPA1, 111 qSH1, yld1.1
DEP1
Root 106 SOR1, SLL1, OsRAA1 60 qRTH2, qSTA2
Seed 80 GS3, GW2, GW5, TGW6 93 qGL3a, qDTH6
Seedling 51 ysa, ylc1 31 qCER4–1, qRA6–1
Others 5 TDR, OsEXPA3 – –
Resistance or tolerance to stresses
Bacterial blight 81 xa5, Xa7, xa13, Xa21, 1 qSB3
resistance Xa38
Blast resistance 108 Pi1, Pi2, Pi5, Pib, Pi9, 45 qNBL5, qLN1–1
Pi40, Pi54, Pita
Sheath blight 4 OsGLP8, Osoxo4 6 qSB9, qSBR3
resistance
Other diseases 6 rim1 7 qstv1
Insect resistance 11 Bph14, Bph 19, Bph20 28 qbph6, qbph10,
qOVA4
Drought 109 Dro1, DST 111 qDTY1.1, qDTY3.1,
tolerance qDTY12.1
Cold tolerance 48 qLTG3.1 25 qCT1, qLTG7
Salinity 102 SKC1, DST 5 Saltol, qSNC7
tolerance
Submergence 8 Sub1A, SK1, SK2 19 qTIL12, qNEI12
tolerance
Lodging 19 SCM2 2
resistance
Soil stress 80 PSTOl1, NRAT1 72 qDSR8, qDLTR11
tolerance
Other stresses 79 ALS, OsBADH1 9 qTRA7, qUVR10
Physiological traits
Culm leaf 11 OsGUN4, EPSPS – –
Eating quality 65 wx, BADH2, lpa1, flo2, 83 qER2, qGT6,
LOX3, gpa2 qPGWC8
Flowering 76 RFT1, Ehd2, Hd3a, Ghd7 49 qDTH8, QHd7,
qEHd1
Germination, 36 ARAG1, Osdsg1, Sdr4 17 qGRV8, qSD12
Dormancy
Panicle flower 19 cl7(t), rip3, OsUDT1 – –
Root 14 OSPT9, OsAMT3:1 – –
Seed and 21 MET1a, OsWR2, OsJAR1 – –
Seedling
Source activity 96 FLO6, SS1, ADH1 64 qLCC7, qFRP4–1
(continued)
134 S. Gopala Krishnan et al.

Table 3.8 (continued)

Genes QTLs
Traits identified Important genes mapped Important QTLs
Sterility 115 TMS9–1, tms5, PAIR2, 45 qSS7a, qLTSPS2
Rf3, sRf4
Others 74 OsMet1, OsDDM1a 42 Gy3a, qHUS1–2

responsive to increased fertiliser application, poor yielding as well as highly suscep-

tible to lodging at maturity. As a result of which, the average productivity of rice in
India during 1950 was only a meagre 771 kg/ha. Therefore, ever since rice breeding
started, one of the prime objectives has been the improvement of yield, to feed the
large majority of rice eating populations of Asia, where more than 90% of the
population is dependent on this crop. Genetic improvement for rice yield has been
the focal point of rice breeding, employing five different concepts, viz.

(a) Indica/japonica hybridisation (including Tongil rice development through

japonica/indica hybridisation)
(b) Development of semi-dwarf varieties.
(c) Breeding for new plant type.
(d) Super rice breeding.
(e) Heterosis breeding.

However, in the past century of rice breeding efforts, only two of the above major
genetic improvement strategies have helped in realising quantum jump in rice yields,
namely (1) semi-dwarf varieties through the incorporation of sd1, which helped in
improving the plant architecture as well as the harvest index, and (2) production of
hybrids that exploit heterosis.

3.10.2 Indica/Japonica Hybridisation

The first attempt of indica/japonica hybridisation was made in 1928 in Burma (Kirk
and Silow 1951), involving D17-88/Shinriki, but discontinued due to sterility.
Immediately after World War II, the shortage of food supplies and the immediate
threat of population increase directed world attention towards finding ways to
increase the production of rice. The International Rice Commission (IRC) was
established on 4th January in 1949 within the framework of FAO with the objective
of promoting national and international action in respect of production, conserva-
tion, distribution and consumption of rice. It was a milestone in the advance of
cooperative rice research. Based on the recommendations of the first meeting of the
working party of IRC held at Yangoon in 1950 (IRC, 1950), the Food and Agricul-
tural Organisation (FAO) of the United Nations initiated one of the first major
international efforts towards yield improvement for improving rice production. A
collaborative project on indica/japonica hybridisation began in Southeast Asian
3 Rice Breeding 135

Table 3.9 Establishment of major rice research institutes/stations in India

Year Institute Location
1912 Paddy Breeding Station (Presently Department of Coimbatore, Tamil Nadu
Rice)
1913 Rice Research Station Karimganj, Assam
1919 Regional Agricultural Research Station Karjat, Maharashtra
1922 Rice Research Station (Presently Zonal Research Nagina, Uttar Pradesh
Station)
1922 Agricultural Research Station (Presently Tamil Nadu Aduthurai, Tamil Nadu
Rice Research Institute)
1923 Agricultural Research Station Dharwad, Karnataka
1923 Rice Research Station Titabar, Assam
1923 Rice Research Station Ratnagiri, Maharashtra
1924 Rice Research Station Kanpur, Uttar Pradesh
1927 Rice Research Station Pattambi, Kerala
1928 Rice Section (Agricultural Research Institute) Rajendranagar, Telangana
1935 Indian Agricultural Research Institute New Delhi, Delhi
1936 Regional Research and Technology Transfer Sub Jeypore, Odisha
Station
1940 Rice Research Station Kuttanadu, Kerala
1946 Central Rice Research Institute (Presently ICAR- Cuttack, Odisha
National Rice Research Institute)
1950 Mountain Research Centre for Field Crops Khuwani, Jammu & Kashmir
1951 The Crop Research Farm Masodha, Uttar Pradesh
1951 Agricultural Research Station Ponnampet, Karnataka
1959 Rice gall fly (Regional Agricultural Rsearch Station) Warangal, Telangana
1956 Agricultural Research Station Gangavati, Karnataka
1960 Main Rice Research Station Nawagam, Gujarat
1962 Regional Rice Research Station Kapurthala, Punjab
1963 Regional Agricultural Research Station Pattambi, Kerala
1963 Rice Research Station Wangbal, Manipur
1965 Establishment of All India Coordinated Rice CRRI, Cuttack (Presently at
Improvement Project (AICRIP) IIRR, Hyderabad)
1965 Andhra Pradesh Rice Research Institute Maruteru, Andhra Pradesh
1965 Rice Research Station, Directorate of Agriculture Chinsurah, West Bengal
1966 Department of Genetics and Plant Breeding Pantnagar, Uttarakhand
1968 Rice Research Station Raipur, Chhattisgarh
1969 Agricultural Research Station, VC Farm Mandya, Karnataka
1969 Regional Agricultural Research Station Titabar, Assam
1970 Rice and Wheat research Centre (Kangra) Malan, Himachal Pradesh`
1974 The Rice Research Station Moncompu, Kerala
1975 Agricultural Rsearch Station Kota, Rajasthan
1983 Directorate of Rice Researcha (presently ICAR-Indian Hyderabad, Telangana
Institute of Rice Research)
a
Instituted as AICRP and later given independent research status
136 S. Gopala Krishnan et al.

Fig. 3.6 Pusa 2090—a high yielding genotype derived through indica/japonica hybridisation with
typical short flag leaves and panicles at the top

countries in 1952 to combine the desirable attributes of japonica subspecies such as

strong culm, dark-green erect leaves, high photosynthetic efficiency with high
tillering and response to fertiliser with resistance to specific diseases and insects,
and better grain quality of indica rice. A parallel scheme with similar objectives was
adopted by the ICAR. These two projects used 192 improved indica varieties
selected by the participating Asian countries and Indian states and produced a total
of 710 japonica/indica hybrids (Parthasarathy 1972).
The F1 seeds were distributed to the participating countries or states for growing
the F2 and subsequent generations and to breed varieties suited to local conditions.
However, it could not result in a breakthrough owing to several reasons including
(1) sterility induced due to cryptic structural hybridity (Oka 1957; Shastry 1964),
(2) inability to screen the segregating populations under high fertility, (3) quantitative
nature of the traits, (4) low population size in segregating generations leading to less
selection efficiency, (5) inherent differences in the photo- and thermo-sensitive
response of indica and japonica cultivars leading to the inefficient selection,
(6) the incorrect belief at that time, that increased yield is associated with an increase
in height and duration, (7) environmental influence on plant height and duration,
(8) inherent differences in grain and cooking quality of the two subspecies, and
(9) emphasis on yield improvement alone (Seetharaman 1981). Only a few rice
varieties were developed and released including Malinja and Mahsuri in Malaysia,
ADT 27 in India and Circna in Australia (Parthasarathy 1965). This could have been
averted if tropical japonica genotypes adapted to Indian tropical environment such
3 Rice Breeding 137

as Taichung 65, Tainan 3, Herunchu, etc. were used in the hybridisation programme
instead of the typical temperate japonica varieties such as Norin 6, Norin 8, Rikue
12, etc. (Rao and Nagaraju 1974) and possibly by attempting one backcross with the
indica cultivars to reduce the spikelet sterility as well as improve the grain and
cooking quality. With the discovery of wide compatibility (S5) locus, the interest in
indica/japonica hybridisation has been reinvigorated and efforts are underway to
develop improved varieties (Fig. 3.6).
Parallelly, efforts were also made to introduce japonicas in India, but it was met
with no success, except in the hills and some cool areas. Japonicas were both
photoperiod and temperature sensitive, which flowered in 35–40 days leaving
insufficient time for proper tillering and vegetative growth. Therefore, they were
not as productive as indicated under Indian conditions. Another scheme was also
launched by the Central Rice Research Institute (CRRI) in 1960 to breed high
yielding fertiliser responsive hybrid varieties with japonicas in 11 states, which
did not prove much successful either. At CRRI, Cuttack, a late-maturing tall and
non-lodging rice variety, CR 1014, with medium slender grains and good cooking
quality was developed from the indica/bulu ( javanica or tropical japonica), cross
between T 90 and Urang Urangan (Seetharaman 1981). However, the development
and the introduction of semi-dwarf varieties into India brought an abrupt end to this
scheme in 1966.

3.10.3 Japonica/Indica Hybridisation

On the other hand, the hybridisation involving japonica and indica varieties of
O. sativa has been very successful in Korea in the development of the ‘Tongil’
cultivar, where the hybrid sterility in indica-japonica hybrids was overcome three-
way crosses (Chung and Heu 1980). The japonica variety was crossed with semi-
dwarf indica variety (possessing sd1 gene, a breakthrough in rice improvement
across the world, described in the following portion), which was further backcrossed
or top crossed with semi-dwarf indica variety. This strategy of three-way crosses
provided twofold advantage, namely (1) overcoming the grain sterility in japonica-
indica hybrid populations and (2) improvement of the selection efficiency (Heu and
Park 1973). The top cross, IR667 (IR8//Yukara/TN), showed good adaptability, and
the line, Suweon 213, was released as ‘Tongil’ (literally meaning ‘together one’ in
Korean) in 1971.
The development of Tongil rice resulted in a significant yield increase from 4 to
5 t/ha, corresponding to a 30% yield increase relative to the leading japonica
varieties grown in Korea (Choi et al. 1974). Tongil rice is characterised by
medium-long and erect leaves, thick leaf sheaths and strong culms, short plant
height but relatively long panicles, open plant shape, lodging resistance and easily
shattered grain (Chung and Heu 1991). However, the Tongil rice cultivars also
possessed some undesirable characters, such as grain quality and susceptibility to
low temperature. Through concerted efforts, these problems have been overcome
and as many as 25 Tongil cultivars, including the popular Tongil varieties such as
138 S. Gopala Krishnan et al.

Tongil, Milyang 23, Samgangbyeo, Jungwepnbyeo, Yongmoonbyeo, Dasnbyeo,

Arumbyeo and Hanarumbyeo have been released till 2002 with yield improvement
from 5.0 t/ha in Suweon 213 to 7.53 t/ha in Hanarumbyeo.

3.10.4 Development of Semi-Dwarf High Yielding Rice Varieties

A landmark event in rice yield improvement was the identification of a short statured
genotype, Dee-geo-Woo-gen (meaning ‘short legged, brown tipped’) from a
Taiwanese cultivar, ‘Woo-gen’ (Huang 1957). The first semi-dwarf rice variety,
‘Taichung Native 1’, was developed from the cross, Dee-geo-woo-gen/Tsai Yuan
Chung made in 1949, aimed at combining the semi-dwarf statue and profuse tillering
of Dee-geo-woo-gen with disease resistance of the tall cultivar, Tsai-Yuan Chung
(Huang et al. 1972). It is semi-dwarf (83–85 cm), matures in 127–130 days
possessing an average of 19 panicles/hill, with a panicle length of 20–22 cm and
long (7.5 mm), medium grains. Taichung Native 1 along with two other semi-dwarf
genotypes, Dee-geo-Woo-gen and I-Geo-tze were utilised in hybridisation at Inter-
national Rice Research Institute, Manila, the Philippines, in 1960. IR 8-288-3, a
semi-dwarf high yielding genotype derived from the cross, Peta/Dee-geo-Woo-gen,
was released as IR 8 in 1965.
The release of IR 8 with a yield potential of upto 7.0 t/ha marked the beginning of
an era where the semi-dwarf short statured varieties provided a breakthrough
achievement in improving rice yields, which had long lasting impact across the
world (Huang et al. 1972). Both IR 8 and Taichung Native 1 were introduced in
India in 1966. These two varieties were utilised in the national programme leading to
the development and release of 14 semi-dwarf high yielding rice varieties (including
three introductions) in India between 1966 and 1970 (Freeman and Shastry 1972).
Jaya and Padma developed from the cross, TN1/T 141 and the reciprocal cross, T
141/TN1, respectively were the first semi-dwarf rice varieties released in India in the
year 1968 (Seetharaman 1981). The introduction of semi-dwarf varieties in the
mid-1960s and their utilisation in the national programme for the development of
new semi-dwarf high yielding rice varieties marked a new era of ‘Green Revolution’
(Coined by Dr. William Gaud of the US Department of Agriculture in 1968) helping
to achieve self-sufficiency in food production in India.
Although mutants with short plant height, better tillering than the cultivar GEB24
and adapted to fertile soils were identified earlier in India, they were popular among
the farmers because the critical tests of fertiliser response were not conducted then
and the farmers preferred longer straw to feed the animals (Ramiah and Rao 1953).
Therefore, the yield improvement was possible due to convergence of improved
plant type along with appropriate management practices and production
environments to enable them to realise their yield potential. During the decade,
starting 1965, as many as 72 high yielding varieties suited for different ecosystems
were released of which the majority of them were semi-dwarf rice cultivars. The
adoption of these high yielding semi-dwarf rice varieties increased the average
annual productivity from 0.67 t/ha in 1950–1951 to 1.12 t/ha in 1970–1971, thereby
 3
Rice Breeding

Fig. 3.7 A snapshot of the rice varieties released for diverse ecologies in India
139
140 S. Gopala Krishnan et al.

doubling the rice production in India. In highly productive irrigated ecosystems of

Punjab, the average yields improved to as high as 2.24 t/ha in 1970–1971. Till date,
as many as 1439 rice varieties have been released for diverse ecologies across the
country (Fig. 3.7).

3.10.5 New Plant Type Concept

Donald (1968) proposed the ideotype approach to plant breeding, wherein an

‘ideotype’ is an idealised plant type with a specific combination of characteristics
for photosynthesis, growth and grain production based on the knowledge of the
crop’s physiology and morphology. In rice, it was observed that varieties with high
yield potential and better fertiliser responsiveness had the short sturdy stem, and
short, erect, narrow, thick and dark green leaves (Tsunoda 1962) based on which
‘Plant type concept’ was proposed (Yoshida 1972). Predictions using simulation
modelling indicated that the yield potential can be increased by 25% through
modification of certain physiological and morphological characters, such as
(1) enhancing leaf growth with reduced tillering during early vegetative growth,
(2) reducing leaf growth and increasing foliar N concentration during late vegetative
and reproductive growth, (3) making the vertical N concentration gradient in the leaf
canopy slope steeper with a greater proportion of total leaf N in the upper leaves,
(4) increasing the carbohydrate storage capacity in stems and (5) creating better
reproductive sink capacity as well as extending the grain-filling period (Dingkuhn
et al. 1991). The key morphological traits of the basic ideotype was conceptualized
by Janoria (1989). The characteristic features of ideotype includes tall stature,
lodging resistance, upright growth habit, fewer but all effective tillers, fewer, well-
spaced, thick, not-too-short, stiff leaves, heavy panicles, limited intraplant variation
in panicle yield, and deep, extensively branched roots. These ideotypes were
conceptualized for growing at closer spacing. He also developed the first prototype,
Rewa 353 (PAU125-1-2/Lalco 14). It was 130 cm tall, with an average of six very
upright, stiff tillers (all effective)/ plant. Highly synchronous panicles yield an
average 4 g of long, slender grains with < 10% sterility and a harvest index of
0.50. It produced 4.3 t/ ha in 85 days over 19 locations, compared with 3.85 t/ ha
produced by semidwarf check variety of same duration, Rasi.
The ‘New Plant Type’ (NPT) was conceptualised to improve yield potential by
15–20% in 1988 (Khush 2007). The proposed plant type included modifications in
key traits such as plant height of 90–100 cm, low tillering (3–4 tillers under direct
seeding), no/low unproductive tillers, 200–250 grains per panicle, thick sturdy
stems, dark-green, thick and erect leaves, vigorous and deep root system, 100–130
days growth duration and increased harvest index (Peng et al. 1994). Breeding for
the first-generation NPT lines began in 1989, with the identification of donors for
these traits in ‘bulu’/javanica (tropical japonica) germplasm from Indonesia and as
many as 500 NPT lines were developed within 5 years (Khush 1995). Although the
NPT genotypes were resistant to lodging with large panicles and few unproductive
tillers, they were not released due to their poor yield. Low yield realisation was due
3 Rice Breeding 141

to low biomass production and poor grain filling, probably due to a lack of apical
dominance within a panicle (Yamagishi et al. 1996), compact arrangement of
spikelets on the panicle (Khush and Peng 1996), less number of large vascular
bundles for assimilate transport and source limitation due to early leaf senescence
(Ladha et al. 1998). Further they were also susceptible to diseases and insects and
poor grain quality.
Consequently, in 1995, the development of second-generation NPT lines began
by crossing first-generation tropical japonica NPT lines with new modern high-
yielding indica varieties/elite lines. Genes from indica parents helped to reduce the
panicle size, increase the tillering capacity, improving the grain quality, disease and
insect resistance. From these efforts, an NPT line, IR77186–122–2-2-3, was released
as NSIC Rc158 in the Philippines in 2007 (Peng et al. 2008). However, due to
concomitant improvement in indica rice breeding, there was no significant differ-
ence in grain yield between the second-generation NPT lines and elite indica check
varieties (Peng et al. 2004; Yang et al. 2007).

3.10.6 Super Rice Breeding

China established a nationwide mega project on the development of ‘super’ rice in

1996 (Cheng et al. 1998), with the objectives (i) to develop ‘super’ rice varieties with
a yield of 9–10.5 t/ha by 2000, 12 t/ha by 2005 and 13.5 t/ha by 2015 from a large
area of at least 6.7 ha. (ii) to develop ‘super’ rice varieties with yield potential of 12 t/
ha by 2000, 13.5 t/ha by 2005 and 15 t/ha by 2015 from experimental and demon-
stration plots, and (iii) to raise the national average rice yield to 6.9 t/ha by 2010 and
7.5 t/ha by 2030. Additionally, the ‘super’ rice variety should outyield widely grown
local check varieties by 10% with acceptable grain quality and pest resistance.
Another goal of ‘super’ rice is to produce 100 kg grain/ha/day. Parallelly, a
‘super’ hybrid rice breeding programme was started in 1998 by Longping Yuan,
by combining the ideotype approach with the use of intersubspecific heterosis (Yuan
2001).
The proposed ‘super rice’ ideotype aimed to combine several morphological
traits, namely (1) moderate tillering capacity (270–300 panicles/m2); (2) heavy
(5 g per panicle) and drooping panicles at maturity; (3) plant height of at least
100 cm (from the soil surface to unbent plant tip) and panicle height of 60 cm (from
the soil surface to the top of panicles with panicles in natural position) at maturity;
(4) top three leaves featuring a flag-leaf length of 50 and 55 cm for the second and
third leaves, which are positioned above the panicle height; (5) leaves remain erect
until maturity with leaf angles around 58, 108 and 208 for the flag, second, and third
leaves, respectively; (6) narrow and V-shape leaves (2 cm leaf width when flat-
tened); (7) thick leaves (specific leaf weight of top three leaves ¼ 55 g/m2); (8) leaf
area index (LAI) of top three leaves is about 6.0; and (9) harvest index of about 0.55
(Peng et al. 2008).
By 2001, seven ‘super rice’ varieties and 44 hybrids were released (Min et al.
2002). During 1998–2005, 34 ‘super’ hybrid rice varieties were commercially
142 S. Gopala Krishnan et al.

Table 3.10 Key morphological traits of the popular super rice hybrids, Xieyou9308 and
Liangyoupeijiu
S. No. Traits Xieyou9308 Liangyoupeijiu
1. Total duration (days) 150 135
2. Plant height (cm) 120–135 115–125
3. Flag leaf length (cm) 45 35–45
4. Flag leaf angle <10 <10
5. Panicle length (cm) 26–28 24–26
6. Panicles/m2 250 200–250
7. Spikelets per panicle 170–190 190–210
8. Grain filling (%) 90 85
9. 1000-grain weight (g) 28.0 26.0–27.0

released, occupying an area of 13.5 mha and producing an additional 6.7 mt of rough
rice in China (Cheng et al. 2007). Among these, two super rice hybrids, namely
Xieyou9308 and Liangyoupeijiu, have gained popularity due to high yield and good
grain quality. Xieyou9308 is a three-line intersubspecific super rice hybrid with
Xieqingzao-A as female and Zhonghui9308 as the male parent, with a yield potential
of 12.23 t/ha released in 1999 (Mao et al. 2003). Zhonghui9308 is an intermediate
type with canopy morphology close to a japonica type and panicle morphology close
to an indica type. Liangyoupeijiu is a two-line intersubspecific super rice hybrid with
Pei’ai64S as the female and 9311 as the male parent, with a yield potential of 12.11 t/
ha released in 1999 (Yuan 2001). The key morphological traits of the popular super
rice hybrids, Xieyou9308 and Liangyoupeijiu are presented in Table 3.10.
The success of China’s ‘super hybrid rice’ suggests that the ideotype approach in
combination with intersubspecific heterosis is effective for breaking the yield ceiling
of the irrigated rice. Unlike the NPT concept of IRRI, the emphasis was more on the
top three leaves and panicle position within the canopy. Source–sink relationship
was also well balanced in China’s ‘super’ hybrid rice breeding project by improving
photosynthesis, increasing the distance between panicle height and plant height
(essentially by increasing plant height), and delaying leaf senescence of the top
three leaves during the ripening phase.

3.11 Harnessing Heterosis and Hybrid Breeding

Jones (1926) reported heterosis in rice for culm number and yield. Even though
heterosis to an extent of 20% or more was realised in rice through manual crosses,
there was no interest in commercial exploitation in rice. The role of cytoplasm in
causing male sterility in rice and its possible utility in breeding hybrid rice was first
reported by Sampath and Mohanty (1954). Richharia (1962) also suggested clonal
propagation as a practical means of exploiting hybrid vigour in rice. Even though the
idea of commercial exploitation of heterosis in rice re-emerged in 1960, except in
China, heterosis breeding in rice was not intensively pursued owing to the self-
3 Rice Breeding 143

Fig. 3.8 Scheme for maintenance of cytoplasmic male sterility and production of hybrid seeds
using three-line system

pollinated nature of the rice crop, there was difficulty in producing large quantities of
hybrid seeds. Initially, hybrid rice seeds were produced using chemical hybridising
agents (gametocides), such as ethrel, ethryl 40 fluoro oxanilate, sodium methyl
arsenate, zinc methyl arsenate, etc. in the 1970s; however, it was discontinued
after the discovery of cytoplasmic male sterile systems. The basis of hybrid rice
technology revolves around three basic genetic elements, necessary for commercial
production of hybrid seed of crops, namely (1) a complete and stable cytoplasmic
male sterility without any substantial negative effect on CMS lines and hybrids, (2) a
genetic system that maintains the male sterility through a maintainer line or a
particular environmental condition and (3) a genetic system that completely restores
male fertility in hybrids. The male sterility in the CMS lines is due to aberrant
mitochondrial genes encoding cytotoxic proteins.
The first cytoplasmic male sterile (CMS) line for producing commercial F1 rice
hybrids was developed from a naturally occurring male sterile plant in a population
of wild rice (Oryza sativa f. spontanea) on Hainan island in 1970 in China (Yuan
1977). Designated as Wild Abortive or WA type, this was a landmark event in the
history of hybrid rice breeding. This formed the basis of the first generation of hybrid
rice technology involving a ‘three-line system’ consisting of a CMS line (A line), the
maintainer line (B line) and a restorer line (R line). The CMS line (A line) is
maintained by the isonuclear maintainer line (B line) while crossing the CMS line
(A line) with the restorer line (R line) produces the hybrid seeds (Fig. 3.8). China
released the first commercial rice hybrid, Nanyou 2 in 1973 (Yuan 1977). A large
144 S. Gopala Krishnan et al.

number of WA-CMS-based hybrid varieties have been deployed for commercial rice
production in China due to their yield advantage over the inbred varieties. Since the
identification and commercial utilisation of the WA-CMS system, several CMS lines
have been developed with various sources of CMS (Lin and Yuan 1980); however,
only a few are in commercial production mainly due to the drawbacks, such as
abnormal flowering behaviour of CMS lines/instability of male sterility expression
over environments/non-availability of effective restorers (Table 3.11).
WA-CMS is the most widely used CMS system in hybrid rice production across
the world. It encodes a mitochondrial protein, WA352, that inhibits the nuclear
encoded mitochondrial transmembrane protein, OsOCX11, to induce pollen abor-
tion through premature programmed cell death of tapetal cells at the uninucleate
stage of microspore development (Luo et al. 2013). The pollen abortion in WA-CMS
is determined by the genotype of the sporophytic tissues. The restorer lines possess
specific fertility restorer (Rf) genes that repress the functioning of the CMS genes,
either post-transcriptionally or post-translationally (Luo et al. 2013). A large number
of Rf genes have been identified, mapped and cloned in rice (Table 3.12).
Hybrid rice research at the International Rice Research Institute (IRRI), Manila,
the Philippines, was initiated in 1970; however, it did not receive much attention
until 1979, when heterosis breeding gained significance as a means to improve
productivity in rice after China’s success with hybrid rice. But the Chinese source
germplasm for hybrid rice development was neither adapted nor easily available to
other tropical rice growing countries. Subsequently, several national rice research
programmes in the tropical countries including India, Indonesia, South Korea,
Malaysia, the Philippines, Thailand and Vietnam also joined the network with
IRRI intending to harness heterosis in rice. A major collaborative effort between
the Food and Agriculture Organization (FAO) with IRRI, China, Japan and selected
national agricultural research centres from Indonesia, India, Brazil, Colombia,
Vietnam, People’s Republic of Korea and France promoted hybrid rice research
and development, with emphasis on the rapid transfer of any major innovation in rice
hybrid technologies.
Buoyed by the success story of hybrid rice in China, India launched a goal-
oriented, systematic research on hybrid rice technology, which was initiated in
December 1989 under the aegis of the Indian Council of Agricultural Research
(ICAR), focusing on hybrids for irrigated cultivation (Janaiah 2002). This project
was implemented through a well-organised national network system, comprising of
12 centres located across the country. Subsequently, various research programmes
funded by the United Nations Industrial Development Organization (UNIDO) and
Food and Agriculture Organization (FAO) during 1991–1996 and 1999–2001; the
Mahyco Research Foundation (renamed the Barwale Foundation since 2005) during
1997–2000; the Asian Development Bank (ADB) and IRRI during 1999–2000; and
the National Agricultural Technology Project and India’s Ministry of Agriculture
during 2003–2008 and 2015–2017 were taken in India to improve rice productivity
through hybrid rice technology (Spielman et al. 2013). The first hybrid APHR 1 was
developed and released for commercial cultivation in India in 1994, followed by
MGR 1, KRH 1 and APHR 2 in the same year. Despite investments to the tune of
3 Rice Breeding 145

Table 3.11 Cytoplasmic male sterile (CMS) types, their origin and nature used in three line hybrid
rice breeding
Source of the cytoplasm Popular
Type Species Strain/variety CMS lines Subspecies Nature
WA- and WA-like CMS
Wild O. sativa Male sterile Zhenshan indica Sporophytic
Abortive f. spontanea wild rice 97A, V20 A
(WA-CMS)
Kalinga I O. sativa L. Kalinga I CRMS32A indica Sporophytic
(Kalinga
I-CMS)
Dissi O. sativa L. Dissi D-Shan A, indica Sporophytic
(D-CMS) D62A
Dwarf O. rufipogon Dwarf wild rice XieQingZao indica Sporophytic
Abortive A
(DA-CMS)
Gambiaca O. sativa L. Gambiaca Chaoyang indica Sporophytic
(GA-CMS) 1A,
Gang46A
Indonesia O. sativa L. Indonesian II 32A, You indica Sporophytic
(ID-CMS) paddy 1A
Luihui O. sativa L. Luihui rice Yue 4A indica Sporophytic
(LX-CMS)
Maxie O. sativa L. Maweizhan Maxie A indica Sporophytic
(Maxie-
CMS)
NX-CMS O. sativa L. Male sterile F2 Neixiang indica Sporophytic
segregant from 2A,
Wanhi88/ Neixiang 5A
Neihui92–4
Yegong O. sativa L. Yegong Y Huanong indica Sporophytic
(Y-CMS) A
K-CMS O. sativa L. K52 K-17A japonica Sporophytic
Baotai (BT) and BT-like CMS
Boro T O. sativa L. Chinsurah Boro Li-Ming A, japonica gametophytic
(BT-CMS) II Xu 9201A
Lead Rice O. sativa L. Lead rice Fujisaka5A indica gametophytic
(LD-CMS)
Dian1 O. sativa L. Yunnan high Yongjing indica gametophytic
(Dian1- altitude rice 2A, Ning
CMS) 67A
HI O. sativa Common wild QingSi-Ai A indica gametophytic
f. spontanea rice
TI O. sativa L. E-Shan-Ta-Bai Liu-Qian- japonica gametophytic
Xin A
Others
Honglian O. rufipogon Red awned wild Yuetai A, indica gametophytic
(HL-CMS) rice Luohong 3A
 146

Table 3.12 Details of fertility restorer gene(s) identified for restoring fertility in different cytoplasmic male sterile (CMS) systems in rice
Rf CMS Encoded Gene based/gene
genes restored Restorers Chromosome Causative gene(s) product linked marker Reference
Rf1a, CMS-BT IR24, BTR, MTC10R, 10 PPR8–1, PPR791, PPR InDel-Rf1a Tao et al. (2013)
Rf1b C9083 Rf1A, Rf1B
Rf2 CMS-LD Kasalath, Minghui 63 2 LOC_Os02g0274000 Gly. Rich CAPS42–1 Itabashi et al.
protein (2011)
Rf3 CMS- Swarna, PRR78 2 – PPR DRRM-Rf3–10 Katara et al.
WA (2017)
Rf4 CMS- IR 24, PRR 78 10 PPR782a PPR RM6100 Katara et al.
WA (2017)
Rf5(t) CMS-HL Milyang 23 10 PPR791 PPR RM3150 Liu et al. (2004)
Rf6 CMS-HL – 10 & 8 – – RM5373 Liu et al. (2004)
Rf17 CMS-CW CWR 4 PPR2 RNA AT10.5–1, SNP 7–16 Fujii and
interference Toriyama (2005)
Rf98 CMS- RT98C 10 PPR762 PPR UK Igarashi et al.
RT98A (2016)
Rf102 CMS- RT102C, K102-Oryza 12 UK UK UN Okazaki et al.
RT102A rufipogon. T (2013)
S. Gopala Krishnan et al.
3 Rice Breeding 147

over eight million US $, the hybrid rice development and delivery in India faces
several challenges that have resulted in a delay of the Indian government’s goal of
spreading hybrid rice to about 25% of the cultivated rice area by 2015. Presently, the
area under hybrid rice is estimated to be only 3.0 mha, which is only 7.0% of the total
44 million hectares under rice cultivation in India.
Presently, the national network on hybrid rice including a network of 20 voluntary
centres represented by public, private and NGO sectors is coordinated by the
ICAR-Indian Institute of Rice Research (IIRR), Hyderabad. Besides this, effective
linkages have been established with various national and international agencies for
the development and promotion of hybrid rice. As a result of concerted efforts for the
past three decades, so far more than 127 rice hybrids have been released for
commercial cultivation in India. The landmark hybrids developed and
commercialised in India are presented in Table 3.13.
During the first decade of their release for commercial cultivation, the spread of
rice hybrids was not as rapid as expected due to their poor grain quality, high seed
cost, non-availability of quality seeds, low market price, susceptibility to pests and
diseases, low head-rice recovery, and chaffy or sterile grains (Ou 1985; Spielman
et al. 2013). In India, the adoption of hybrid rice has been slow; however, hybrid rice
is gaining popularity among the rice farmers of northern Indian states, such as Uttar
Pradesh, Bihar, Jharkhand, Punjab, Haryana and also in southern states like
Maharashtra, Karnataka, Madhya Pradesh and Chhattisgarh, mainly due to it less
fertiliser and water requirement as compared to the high yielding varieties (HYVs)
(Hariprasad et al. 2011).
Three factors crucial for the commercial success of hybrid rice technology
include high standard heterosis, stable male sterile source and efficient package for
producing higher seed yields. However, CMS systems suffer from several intrinsic
problems such as (1) a limited number of restorer lines in the germplasm (only 2–5%
of rice germplasms possess Rf genes) and it is tedious to develop restorer lines as
there is a need to assess combining ability of the restorers in each backcross leading
to enormous workload. (2) It is difficult to breed new CMS lines, and (3) some of the
CMS genes are unstable in different nuclear backgrounds, which makes it difficult to
utilise in hybrid rice breeding.
In rice, a ‘two-line system’ has been successfully identified and utilised for hybrid
seed production. The two-line system or the environment-sensitive genic male
sterility (EGMS) is mainly dependent on environmental factors such as temperature
and/or photoperiod, duration, or concentration at a sensitive stage such as panicle
initiation during plant development (Nas et al. 2005). The EGMS makes use of
photoperiod and/or temperature to control the sterility/fertility behaviour of the
female parent. The EGMS was first identified from tomatoes (Rick 1948). Under
permissive conditions (usually short photoperiod and/or low temperature), the
EGMS line is male-fertile, enabling their multiplication by selfing without the
need of a maintainer line as compared to the CGMS system. Whereas under
restrictive conditions that inhibit male fertility, photoperiod- and thermo-sensitive
genic male sterile (PTGMS) lines outcross with paternal lines to produce hybrid
seeds (Fig. 3.9).
148 S. Gopala Krishnan et al.

Table 3.13 Popular rice hybrids released in India

Year
of Duration Yield Recommended
S. No. Rice hybrids release (days) (t/ha) Developed by for (specialty)
1. APHR 1 1994 130–135 7.14 APRRI, AP
Maruteru
2. APHR 2 1994 120–125 7.52 APRRI, AP
Maruteru
3. MGR 1 1994 110–115 6.08 TNAU, TN
Coimbatore
4. KRH 1 1994 120–125 6.02 VC Farm, KA
Mandya,
UAS,
Bangalore
5. CNRH 3 1995 125–130 7.49 RRS, WB
Chinsurah
6. DRRH 1 1996 125–130 7.30 DRR, AP
Hyderabad
7. KRH 2 1996 130–135 7.40 VC Farm, BH, KA, TN,
Mandya, TR, MH, HR,
UAS, UK, OR, WB,
Bangalore PY, RJ
8. Pant Sankar 1997 115–120 6.80 GBPUAT&T, UP
Dhan 1 Pantnagar
9. PHB 71 1997 130–135 7.86 Pioneer HR, UP, TN, AP,
Overseas KA
Corporation,
Hyderabad
10. PA 6201 2000 125–130 6.20 Bayer AP, KA, BH,
Bio-Science, OR, MP, UP,
Hyderabad WB, TN, TR
11. PA 6444 2001 135–140 6.11 Bayer UP, TR, OR, AP,
Bio-Science, KA, MH, UK
Hyderabad (popular long
duration hybrid)
12. Pusa RH 10 2001 120–125 4.35 IARI, New HR, DL, WUP,
Delhi UK (long slender
aromatic hybrid)
13. Rajlakshmi 2005 130–135 5.84 CRRI, Cuttack AS (Boro areas),
(CRHR 5) OR (long
duration hybrid)
14. Ajay (CRHR 2005 130–135 6.07 CRRI, Cuttack OR (irrigated
7) areas)
15. JRH4 2007 110–115 7.50 JNKVV, MP
Jabalpur
16. PA 6129 2007 115–120 6.58 Bayer PB, TN, PY
Bio-Science,
Hyderabad
17. Sahyadri 4 2008 115–120 6.80 RARS, Karjat HR, WB, UP,
(BSKKV) MH, PB
(continued)
3 Rice Breeding 149

Table 3.13 (continued)

Year
of Duration Yield Recommended
S. No. Rice hybrids release (days) (t/ha) Developed by for (specialty)
18. DRRH 2010 131 6.07 DRR, AP, GJ, MP, OR,
3 (IET19543) Hyderabad UP, CI (medium
slender grain
hybrid)
19. US - 312 2010 125–130 5.76 Seed Works AP, BH, KA,
International, TN, UP, WB
Hyderabad
20. 27P61 2012 132 6.70 PHI Seeds Pvt. CH, GJ
(IET21447) Ltd.
Hyderabad
Two line hybrid (TGMS system)
21. SAVA 127 2015 115–120 7.5 Savannah seed UP (first two line
Pvt. Ltd. hybrid released
in India)
AS Assam, AP Andhra Pradesh, KA Karnataka, TN Tamil Nadu, BH Bihar, TR Tripura, MH
Maharashtra, HR Haryana, UK Uttarakhand, OR Odisha, PY Pondicherry, RJ Rajasthan, UP
Uttar Pradesh, MP Madhya Pradesh, DL Delhi, WUP Western UP, PB Punjab, GJ Gujarat, CI
Central India, CH Chhattisgarh

Shi discovered the source material for the two-line system male sterile line,
Nongken58S in rice in Hubei, China, in 1973 and studied in detail the influence of
photoperiod and temperature on male sterility of this genotype (Shi 1981). EGMS is
further classified as thermo-sensitive genic male-sterility (TGMS) and photosensi-
tive genic male-sterility (PGMS). In the PGMS system, the plant behaves as sterile at
longer photoperiod (>14 h) and fertile at shorter photoperiod (<13.75 h) as
observed in Nongken58S (Shi and Deng 1986), a japonica type of PGMS source.
In the case of the TGMS system, the plant behaves as sterile at a high temperature
regime (>28 C) and fertile at a low temperature regime (<23 C) in AnnongIS (Tan
et al. 1990), an indica type of TGMS source. The TGMS system is more preferable
to take advantage of the wide temperature range through TGMS sources. Unlike the
PGMS, wherein the phenomenon of fertility–sterility transformation is greatly
influenced by temperature, TGMS is less affected by day length. Hence, the
TGMS system is advantageous over the PGMS system (Huang et al. 2014).
The plant behaves male sterile in one set of temperature conditions (restrictive
condition) while reverting to male fertility in another set of temperature conditions
(permissive condition), which forms the basis for the use of the TGMS system as a
two-line system for hybrid seed production. The plant behaves as male sterile at high
temperature regime and fertile at low temperature regime in Annong1S (Tan et al.
1990), an indica type TGMS source. It is the first report of TGMS in rice due to a
spontaneous mutant isolated from the Hunan Province, China. The mutant and its
derivatives (5460S, R59TS, etc.) behave sterile at relatively higher temperatures
(33–28  C) and revert to male fertility under relatively low temperature conditions
(27–22  C) (Sun et al. 1989; Yang and Wang 1990). After the discovery of
150 S. Gopala Krishnan et al.

Fig. 3.9 Scheme for maintenance of TGMS line and production of hybrid seeds using two-line
system

Annong1S, a gamma ray induced TGMS mutant ‘NorinPL12’ from Reimei, which is
male sterile between 31 and 24  C, partially fertile at 28–21  C and completely fertile
between 26 and 18  C, was developed in Japan (Maruyama et al. 1990). To date,
there have been more than 20 TGMS lines discovered/developed through spontane-
ous mutations, induced mutations as well as introgression breeding (Table 3.14).
Based on the critical temperatures for fertility transformation, the TGMS system
can be classified into four types, namely (1) high CSP (critical sterility point)-high
CFP (critical fertility point), (2) high CSP-low CFP, (3) low CSP-low CFP and
(4) low CSP-high CFP based on the CSP, CFP and PRTA (photoperiod range for
temperature activity). The line possessing a high sterility point, low fertility point
and wide range of PRTA is considered as the best line for seed production and
multiplication. A new source called JP38, which behaves sterile at low temperature
and fertile at a high temperature known as reverse TGMS has also been reported in
rice (Jiang 1988). However, it has not been used in commercial hybrid seed
production. Precise information on the determination of critical temperature and
stage of development sensitive to temperature and minimum duration of effective
temperature treatment required for the reversion to fertile phase is not completely
available in rice.
To date, around 14 genes governing thermo-sensitive genic male sterility have
been mapped in rice (Table 3.15), which provides valuable tools for marker-assisted
transfer of these genes for the development of new TGMS lines. Among these genes,
tms5 is the major gene involved in two-line breeding in China accounting for more
3 Rice Breeding 151

Table 3.14 TGMS sources in rice, their origin, and critical temperatures for sterility-fertility
transformation
Sub- CSP/CFP
Source species Origin ( C) Reference
5460 S indica Induced (R), China 28.0–26.0 Yang et al. (1990)
IR32364 indica Induced (R), IRRI 32.0–24.0 Virmani and Voc
(1991)
IR68945 indica Introgression from Norin PL 30.0–24.0 Virmani (1992)
12, Japan
IR68949 indica Introgression from Norin PL 30.0–24.0 Virmani (1992)
12, Japan
H 89–1 japonica Induced (R), Japan 31.0–28.0 Maruyama et al.
(1990)
Annong indica Spontaneous mutation, China 30.2–27.0 Tan et al. (1990)
1S
R 59TS indica Induced (R), China – Yang and Wang
(1990)
Xianquang indica Breeding population, China 30.0–24.0 Cheng et al. (1995)
26 Zhi indica Induced (R), China 23.0–25.0 Shen et al. (1993)
ZaoS
N5088 S indica Introgression from Nongken 30.0–22.0 Zhang et al. (1994)
58 S
SM 5 indica Spontaneous, India 32.3–22.0 Ali et al. (1995)
SM 3 indica Spontaneous, India 32.0–22.0 Ali et al. (1995)
JP 2 indica Spontaneous, India 33.9–23.0 Ali et al. (1995)
SA 2 indica Induced mutation (C) India 31.7–20.0 Ali et al. (1995)
F 61 indica Induced mutation (C) 30.9–22.0 Ali et al. (1995)
JP indica Breeding population, India 30.9–20.0 Ali et al. (1995)
8-1A-12
JP 24A indica CMS, India 33.8–23.0 Ali (1993)
JP38 indica Spontaneous mutation, India 24.0–30.5 Ali (1993)
Dianxin/A japonica CMS, China 23.0–20.0 Lu et al. (1994)
Hennong indica Crossbreeding, China 30.0–29.0 Lu et al. (1994)
S
IV A indica Crossbreeding, China 24.0–28.0 Zhang et al. (1991)
J207S indica Spontaneous mutation, China 31.0 to Jia et al. (2001)
>31.0
B06S indica Spontaneous mutation, China 24.0 to He et al. (2005)
>24.0
CSP critical sterility point, CFP critical fertility point, R irradiation, C chemical mutagen
Source: Virmani et al. (2003)

than 71% of all two-line hybrid rice cultivars (~2.9 million hectares) grown two-line
hybrid rice in China during 2011 (Zhou et al. 2014a). tms5 is used in the develop-
ment of a large number of TGMS lines, and they are used in as many as 71 commer-
cial two-line hybrid rice cultivars in China. In India, development of TGMS lines
and two-line hybrids is being actively pursued only at ICAR-IARI, New Delhi;
152 S. Gopala Krishnan et al.

Table 3.15 Different sources of EGMS genes in rice, their chromosomal location and their linked
markers
Gene Source Chr. LD (cM) Markers References
PGMS genes
pms1 32001S 7 3.5–15.0 RG477- Zhang et al. (1994)
RG511,
RZ272
pms
1(t) Pei’ai64S 7 0.2, 0.2 RM21242, Zhou et al. (2011)
YF11
pms2 32001S 3 10.6, 7.0 RG348, Zhang et al. (1994)
RG191
0.1, 6.0 RG477/ Liu et al. (2001)
R277,
R1807
pms3 Nongken 58S 12 5.5, 9.0 RZ261/ Mei et al. (1999)
C751,
R2708
Nongken 58S 12 0.0 LJ47, Lu et al. (2005) and
LJ265 Ding et al. (2012)
pms4 Mian 9S 4 3.0, 3.5 RM6659, Huang et al. (2008)
RM1305
p/ Pei’ai64S 12 – PA301, Zhou et al. (2012)
tms12–1 PAIDL2
rpms1 YiD1S 8 0.9, 1.8 RM22980, Peng et al. (2008)
RM23017
rpms2 YiD1S 9 0.9, 0.9 RM23898, Peng et al. (2008)
YDS926
rpms3 D52S 10 6.6, 4.6 RM5271, Joseph et al. (2011)
(t) RM244
TGMS genes
1. tms1 5460S 8 6.7 TGMS 1.2 Wang et al. (1995)
2. tms2 Norin PL12 7 5.0 R643A, Yamaguchi et al. (1997)
R1440; and Lopez and Virmani
RM11 (2000)
3. tms3 IR32364 6 7.7 F18FM/ Lang et al. (1999)
RM
4. tms4 TGMS-VN1 2 22.3 RM27 Dong et al. (2000)
5. tms5 AnnongS-1 2 5.2 RM492 Wang et al. (2003)
6. tms5 DQ200047–12 2 0.0 RM174 Jia et al. (2000)
7. tms6 Sokcho-MS 5 5.8, 0.1 RM440, Lee et al. (2005)
RM3351
8. tms6(t) G20S 10 3.0, 1.1 RM3152, Liu et al. (2010)
RM4455
9. tmsx XianS 2 1.0, 2.0 RMAN81, Peng et al. (2010)
RM7575
10. rtms1 J207S 10 3.6, 4.2 RM239, Jia et al. (2001)
PRev1
11. TGMS SA-2 9 6.2 RM257 Reddy et al. (2000)
(continued)
3 Rice Breeding 153

Table 3.15 (continued)

Gene Source Chr. LD (cM) Markers References
12. ms-h ms-h(t) 9 RG451 Koh et al. (1999)
13. tms 9 Zhu 1S 2 30.2 kB Indel Sheng et al. (2015)
91, 101
14. p/ PA64S 12 5.8 kB PA301, Zhou et al. (2012)
tms12–1 PAIDL2
LD linkage distance, Chr chromosomal location

TNAU, Coimbatore; and GB Pant University for Agriculture and Technology,

Pantnagar.
Two-line hybrids offer several advantages over three-line hybrids, which includes
(1) the simplification in multiplication, as they do not need a maintainer line for
propagation of the male sterile lines; (2) male sterility in PTGMS lines is mainly
controlled by recessive nuclear genes, and when crossed with any plants carrying the
wild type fertility gene, the fertility in hybrids is restored. Therefore, this system
increases the frequency of heterotic hybrids, as there is no need for fertility restorer
genes as in the case of the CGMS system and therefore, any fertile line can be used as
a male parent; (3) it is free from cytoplasmic negative effects, if any, associated with
the abnormal mitochondrial genes in the sterility-inducing cytoplasm are also
eliminated (Yuan 1990; Siddiq and Ali 1999). Hence the EGMS system is the
most promising and developing method of male sterility in many crops. Because
of these advantages, it was quickly adopted for hybrid rice production, since the
initial application in the 1990s, and hundreds of environment-sensitive genic male
sterile lines and two-line hybrids have been released for commercial production.
Even though PTGMS systems are advantageous over CGMS systems, there are
also some disadvantages associated with this system. Most of the commercial TGMS
lines behave sterile under restrictive conditions of a long day and high temperature
(critical sterility temperature >25  C) and revert to fertile phase under permissive
conditions of short day and low temperature (<24  C) during the booting stage
(Li et al. 2007). Stringent environmental conditions should be met for the multipli-
cation of the PTGMS lines and production of hybrid seeds, as there is a very small
window of the critical temperatures for fertility transformation (CTFT). Even a
minor change in temperature at the booting stage can affect the production of
PTGMS lines and hybrid seeds under unpredictable weather conditions (Liao et al.
2021). For example, during multiplication under locations with permissive weather
conditions, a sudden increase in temperature can reduce fertility, thereby decreasing
the yield of PTGMS seeds.
Alternatively, during hybrid seed production under locations with restrictive
weather conditions, a sudden dip in temperature will enable the PTGMS line to
revert to fertility, enabling self-pollination thereby causing genetic impurity of the
hybrid seeds. Both these unforeseen weather conditions can cause failure in hybrid
seeds production, which leads to huge losses. Further, the CTFT in PTGMS lines
often shifts up after a few generations of propagation, and the increase in fertile
154 S. Gopala Krishnan et al.

temperature brings a higher risk to hybrid seeds production. Therefore, there is a

constant need for purifying PTGMS individuals of suitable CTFT repeatedly during
production. Additionally, the CTFT trait is also influenced by minor QTLs, which
imposes difficulty and uncertainty in breeding new PTGMS lines through marker-
assisted transfer of these genes into different genetic backgrounds.

3.11.1 Fixation of Heterosis

In rice, the feasibility of asexual reproduction and maintenance of hybrids clonally

through seed propagation has been demonstrated by combining genome-editing to
substitute mitosis for meiosis (MiMe) with the expression of BABY BOOM1 (BBM1)
in the egg cell. The clonal progenies of rice retained genome-wide parental hetero-
zygosity and the asexual propagation trait is heritable through multiple generations
of clones (Khanday et al. 2019). Through simultaneous editing of four genes, namely
REC8, PAIR, OSD1 and MTL using CRISPR-Cas9 the rice seeds from F1 hybrids,
were able to proliferate clonally through seeds (Wang et al. 2019).

3.12 Genes Associated with Yield and Yield Component Traits

A large number of genes governing yield and yield component traits have been
mapped and cloned in rice (Table 3.16). Most of them including DEP1, Gn1A, GS3
and, GW5 negatively regulate yield. Spontaneous mutant alleles with desirable
mutations have been selected by farmers and breeders to improve yield. Although
these mutations have improved riceyields, there exists a possibility that more elite
alleles of these cloned genes could be created through modern approaches like
genome-editing and combined to further boost the yields in rice.

3.12.1 Rice Grain Quality

With major gains achieved in improving grain yield spurred by the green revolution,
many rice eating countries across the world achieved self-sufficiency in food pro-
duction. With food security and the subsequent improvement in affordability of the
population, there has been an emphasis on the improvement of grain quality in rice.
Rice grain quality is one of the major factors dictating the market value and plays a
key role in the adoption and popularity of rice varieties. Grain quality in rice includes
processing quality, physical appearance, biochemical, cooking and sensory quality
as well as nutritional quality (Fitzgerald et al. 2009). Grain quality is a complex trait
determined by numerous interrelated factors making rice quality improvement a
challenge. Further, the perception of quality changes with the stakeholders. For
producers, grain quality means the gross physical appearance which determines
the price and profitability, whereas for rice millers priorities are on overall milling
yield, head rice recovery and storage quality, while for the consumers, the processed
 3

Table 3.16 List of yield-associated genes cloned and their mode of increasing grain yield in rice
Gene Gene symbol Locus ID Trait Mode of function Reference
Tillering
Tillering and dwarf 1 TAD1/TE LOC_Os03g0123300 Shoot branching G-A substitution, Xu et al.
LoF (2012)
Rice Breeding

Teosinte branched 1 TB1/FC1 LOC_Os03g0706500 Lateral branching LoF Takeda et al.

(2003)
Dwarf high Tillering ability 34 DHTA34 LOC_Os03g0203200 High tillering, Dwarf G-A substitution, Liang et al.
LoF (2019)
High Tillering and dwarf 1 HTD1 LOC_Os04g0550600 High tillering, Dwarf C-T substitution, Zou et al.
LoF AM growth (2005)
Monoculm 1 MOC1 LOC_Os06g0610350 AM formation, Tillering GoF Li et al.
(2003)
Tiller enhancer TE LOC_Os03g0123300 Tillering, Dwarf, Twisted leaf angle Deletion and Lin et al.
substitution, LoF (2012)
Grain number/panicle size
Grain number 1a Gn1a LOC_Os01g0197700 Grain number, cytokinin catabolism Deletion, LoF Ashikari
et al. (2005)
Aberrant panicle organisation APO1 LOC_Os06g0665400 Grain number GoF Ikeda et al.
1 (2005)
Grain number, plant height Ghd7 LOC_Os07g0261200 Flowering time under long day GoF Yan et al.
and heading date 7 (2013)
Wealthy farmer’s panicle IPA1/WFP LOC_Os08g0509600 Panicle branching, Grain yield GoF Miura et al.
(OsSPL14) (2010)
Grain number, plant height Ghd8 LOC_Os08g0074500 Flowering under short day; delayed GoF Yan et al.
and heading date 8 flowering under long day (2011
Dense and erect panicles 1 DEP1 LOC_Os09g0441900 Dense and erect panicle, wider, shorter Deletion, LoF Huang et al.
leaves, tiller number (2009)
Long panicle 1 LP1 LOC_Os09g0456100 Panicle length GoF Liu et al.
(2016)
155

(continued)
Table 3.16 (continued)
156

Gene Gene symbol Locus ID Trait Mode of function Reference

Grain size
Grain size 3 GS3 LOC_Os03g0407400 Grain size, stigma exertion Substitution, LoF Fan et al.
(2006)
Grain length 3.1 qGL3/GL3.1 LOC_Os03g0646900 Grain length GoF Qi et al.
(2012)
Grain weight 2 GW2 LOC_Os02g0244100 Grain width and weight Deletion, LoF Song et al.
(2007)
Grain size 5 GS5 LOC_Os05g0158500 Grain size GoF Li et al.
(2011)
Grain weight 5 GW5 DQ991205 Grain size Deletion, LoF Weng et al.
(2008)
Grain weight 6a GW6a LOC_Os06g0650300 Grain size GoF Song et al.
(2015)
Oryza sativa squamosa OsSPL13 LOC_Os07g0505200 Grain size GoF Si et al.
promoter binding-like 13 (2016)
Grain weight 8 GW8 LOC_Os08g0531600 Grain size, grain shape GoF Wang et al.
(OsSPL16) (2012)
Glutamine synthase 2 GS2/ LOC_Os04g0659100 Salinity tolerance photorespiration GoF Hu et al.
OsGRF4 (2015)
Grain weight and filling
Thousand grain weight 6 TGW6 LOC_Os06g0623700 Grain size, grain yield Deletion, Lof Ishimaru
et al. (2013)
Oryza sativa squamosa OsSPL18 LOC_Os09g0507100 Grain weight and number GoF Yuan et al.
promoter binding-like 18 (2019)
Grain incomplete filling 1 GIF1 LOC_Os04g0413500 Grain filling, grain size GoF Wang et al.
(2008)
LoF loss of function, GoF gain of function, AM apical meristem
S. Gopala Krishnan et al.
3 Rice Breeding 157

Table 3.17 QTLs/genes affecting milling quality parameters in rice

QTL/
Gene Locus ID Trait Reference
qBRR10 LOC_Os10g0459800 Brown rice recovery rate; reduced glume Ren et al.
thickness (2016)
Chalk5 LOC_Os05g0156900 Increased chalkiness of grains Li et al.
(2014)
FLO5/ LOC_Os08g0191433 White core floury endosperm Ryoo et al.
SSIIIa (2007)

rice appearance, cooking and eating qualities are important. More recently, the
nutritional value of the rice grain includes the glycemic index, Zn, protein content
and other nutraceutical properties.
The majority of the rice produced across the world is consumed after polishing as
milled rice/white rice. Rice grains need to be processed by removal of husks and the
bran portion by dehusking and milling in order to produce milled rice/white rice.
Rice processing quality is a very important factor in determining the processing
ability of a variety as it affects the milled rice yield. Even though there are
differences in the consumer preference for grain quality, the processability of a
rice variety into unbroken whole milled rice kernels is an important parameter for
any rice variety. The grains harvested from the rice plant are known as paddy or
rough rice. Rice hulls (lemma and palea) are easily removed from the grain using a
deshusker. These dehusked rice grains are known as brown rice and the proportion
of brown rice after dehusking is Hulling percentage (%). The brown rice is polished
in a rice miller to remove the bran from the endosperm, which produces the milled
rice and the proportion of milled rice after dehusking is milling percentage (%).
The process of removing husk as well as the bran from the rice grains to produce
milled rice kernels is called milling. The proportion of unbroken white rice kernels
(also known as head rice) from a given quantity of milled rice kernels is head rice
recovery percentage (HRR %), which is a very important processing parameter in
rice. The HRR (%) is an important factor in the trade as the majority of the
consumers prefer unbroken milled rice. Poor milling quality can cause economic
losses due to a reduction in the quantity of milled rice realised from the paddy
harvested. As much as 30% loss in rice grain can happen due to breakage during the
milling process (Hodges et al. 2011). All these parameters, namely hulling (%),
milling (%) and HRR (%) are complex, showing quantitative inheritance, as a result
of which show high environmental interaction. Advances in rice genomics, have
enabled the mapping of QTLs governing these processing traits. As many as 26, 41
and 35 QTLs governing brown rice recovery rate (hulling %), Milling % and HRR,
respectively have been mapped in rice (Zhou et al. 2019). Among them, the major
genes affecting milling parameters in rice are listed in Table 3.17. Chalk5 and GS3
negatively affect the HRR in rice. Three QTLs for crack resistance, namely qFIS1–1,
qFIS1–2 and qFIS1–8, have been mapped by Pinson et al. (2013). Grain shape,
uniformity and translucence are important parameters for consumers, millers, and
traders, which are quantitative. More than 400 QTLs governing physical appearance
158 S. Gopala Krishnan et al.

Table 3.18 Major genes governing physical appearance of grains that have been cloned in rice
Gene Locus ID Protein Encoded Reference
Grain length
GS3 LOC_Os03g0407400 Member protein with multiple Fan et al. (2006)
domains
qLGY3/ LOC_Os03g0215400 MADS-domain transcription factor Liu et al. (2018)
OsLG3b OsMADS1 and Yu et al.
(2018)
GL3 LOC_Os03g0646900 Protein phosphatase with Kelch- Zhang et al.
like repeat domain (OsPPKL1) (2012) and Qi
et al. (2012)
GW6a LOC_Os06g0650300 A novel Histone acetyltransferase Song et al. (2015)
TGW3/ LOC_Os03g0841800 A GSK3/SHAGGY-like kinase Ying et al. (2018)
qTGW3/
GL3.3
GLW7/ LOC_Os07g0505200 Plant-specific transcription factor Si et al. (2016)
OsSPL13 OsSPL13
GL7/GW7 LOC_Os07g0603300 Protein homologous to Arabidopsis Wang et al.
thaliana LONGIFOLIA proteins (2015a, 2015b)
Grain width
GW2 LOC_Os02g0244100 Ring-type E3 ubiquitin ligase Song et al. (2007)
GS2/GL2 LOC_Os02g0701300 Plant-specific transcription factor Che et al. (2016)
OsGRF4
GW5/ DQ991205 Arginine-rich protein of 144 amino Weng et al. (2008)
qGW5 acids and Shomura et al.
(2008)
GS5 LOC_Os05g0158500 Serine carboxypeptidase Li et al. (2011)
GS6 LOC_Os06g0127800 GRAS-domain protein Sun et al. (2013)
GW8/ LOC_Os08g0531600 SQUAMOSA promoter-binding Wang et al. (2012)
SPL16 protein-like 16
Grain chalkiness
ms-h/ LOC_Os09g0553200 UDP-glucose pyrophosphorylase 1 Woo et al. (2008)
UGPase1
GIF1 LOC_Os04g0413500 Cell wall invertase Wang et al. (2008)
Chalk5 LOC_Os05g0156900 Increased chalkiness of grains
FLO5/ LOC_Os08g0191433 Starch Synthase IIIa Ryoo et al. (2007)
SSIIIa

of the grains, including grain length, grain width and grain chalkiness, have been
mapped and 17 of them have been cloned (Table 3.18), which includes as many as
10 genes affecting starch quality in the rice endosperm.
A large cache of biochemical traits influences the cooking, eating and nutritional
quality of rice grain and several genes determine these quality traits that have been
cloned in rice (Table 3.19). The differences in cooking and eating properties of rice
are due to inherent differences in the composition and structure of starch granules in
the endosperm. Amylose content is an important biochemical trait that determines
the relative stickiness or fluffiness of the cooked rice kernels. The major gene
3 Rice Breeding 159

Table 3.19 Major genes governing grain, cooking, eating and nutritional quality in rice
Gene Locus ID Trait Protein encoded Reference
Wx/GBSS I LOC_Os06g0133000 Amylose content Granule bound Hirano and
starch synthase I Sano (1991)
ALK/SSIIa LOC_Os06g0229800 Gelatinisation Soluble starch Gao et al.
temperature synthase IIa (2003)
BADH2 LOC_Os08g0424500 Aroma (popcorn Betaine aldehyde Bradbury
like) dehydrogenase 2 et al. (2005)
BADH1 LOC_Os04g0464200 Aroma (popcorn Betaine aldehyde Bradbury
like) dehydrogenase 1 et al. (2008)
OsGAPDHB Creamy popcorn- Glyceraldehyde- Lin et al.
like aroma 3-phosphate (2014)
dehydrogenase B
qPC1/ LOC_Os01g0878700 Grain protein A putative amino Peng et al.
OsAAP6 content acid permease, (2014)
OsAAP6
OsZIP4 LOC_Os08g0207500 Zinc content Zinc transporter Ishimaru
et al. 2005
OsZIP8 LOC_Os07g0232800 Zinc content Plasma- Lee et al.
membrane (2010)
localised zinc
transporter
RPBF/ LOC_Os02g0252400 Lysine content bZIP Kawakatsu
OsDof3 transcription and
factor, DOF Takaiwa
transcription (2010)
factor
Kala4/OsB2 LOC_Os04g0557500 Anthocyanin bHLH Oikawa
content transcription et al. (2015)
factor
Kala3 – Anthocyanin R2R3-Myb Maeda et al.
content transcription (2014)
factor
Kala1/Rd Os01g0633500 Proanthocyanidin Dihydroflavonol- Furukawa
biosynthesis 4-reductase et al. (2006)
LPA1 LOC_Os03g0237250 Low phytic acid Myo-inositol Kim et al.
kinase (2008)
LOX3 LOC_Os03g0699700 Grain storability Lipoxygenase Suzuki et al.
(reduced lipid (1993)
peroxidation)

governing amylose content in rice is Waxy/GBSSI, and as many as seven functional

variants accounting for the range of 0–30% amylose content in diverse rice cultivars
have been identified (Zhou et al. 2021). Gelatinisation temperature is another
160 S. Gopala Krishnan et al.

important parameter affecting the resistance of milled rice to cooking. ALK regulates
the gelatinisation temperature of milled rice kernels (Nakamura et al. 2005).
Aromatic rice varieties are premium quality rice fetching higher prices in the
international markets. Although more than 300 volatile compounds have been
identified from different aromatic rice cultivars, 2-acetyl-1-pyrrolidone (2-AP), is
the key compound determining a popcorn-like fragrance in the cooked rice. Two
genes, namely BADH2 and BADH1, govern fragrance in rice (Bradbury et al. 2005,
2008). Anthocyanins are water-soluble pigments with high anti-oxidant activity. In
black rice varieties, the pericarp is black due to the accumulation of anthocyanins.
Although rice grains possess diverse nutrients, they are generally low in propor-
tion. Peng et al. (2014) cloned OsAAP6, regulating the content of storage proteins in
rice. Homology based predictions have helped in identifying as many as 15 genes for
glutelin (Kawakatsu et al. 2008), 34 prolamin genes (Xu and Messing 2009),
3 globulin genes (Sun et al. 1996) and 7 albumin genes (Alvarez et al. 1995) in
rice. Kawakatsu and Takaiwa (2010) showed that free lysine content in rice grains
can be increased by downregulation of the transcription factor, RPBF/OSDof3. Two
micronutrients, Fe and Zn, play a very important role for human health. The major
genes associated with iron content in rice grains are OsFER1, OsNRAMP4,
OsNRAMP5, OsNRAMP6, OsYSL6, OsYSL12, OsYSL4, OsZIP8 and OsZIP10. As
many as eight ZIP proteins, namely OsIRT1, OsIRT2, OsZIP1, OsZIP3, OsZIP4,
OsZIP5, OsZIP7 and OsZIP8, associated with zinc concentration in rice have been
identified, among which OsZIP4 and OsZIP8 are particularly important for Zn
transport to seeds. As many as nine rice varieties biofortified with zinc content
ranging from 22.6 ppm to 27.4 ppm, one variety with 10.3% protein and two
varieties biofortified with both protein and zinc have been developed through
conventional breeding and released for commercial cultivation in India (Table 3.20).

Table 3.20 Biofortified S. No. Rice varieties Content in milled rice

rice varieties enriched with
Zinc biofortified varieties
zinc and/or protein released
in India 1. DRR Dhan 45 22.6 ppm
2. DRR Dhan 48 24.0 ppm
3. DRR Dhan 49 25.2 ppm
4. Zinco Rice MS 27.4 ppm
5. Surabhi 22.8 ppm
6. CGZR 1 22.0 ppm
7. CGZR 2 25.0 ppm
8. HPR 2720 20.9 ppm
9. CR Dhan 315 24.9 ppm
Protein biofortified varieties
10. CRR Dhan 310 10.3%
Both zinc and protein biofortified varieties
11. Protazin 20.9 ppm + 9.4%
12. CRR Dhan 311 20.1 ppm + 10.3%
3 Rice Breeding 161

3.13 Basmati Rice Improvement

Basmati rice is a nature’s gift to the Indian subcontinent, known for its exquisite
quality with a harmonious combination of uniform kernels free from chalkiness,
cooked kernels are sweet without bursting exhibiting kernel elongation ratio of
nearly twice and neither too hard nor too soft eating quality (Ramaiah and Rao
1953; Singh 1994). The traditional Basmati rice varieties are low yielding, photo-
sensitive, long duration and prone to lodging. Basmati 370 and Type 3 developed
through pureline selection were the most popular Basmati rice cultivars with farmers
till mid-1970s. Since 1965, systematic crop improvement with basic studies on grain
and cooking quality traits at ICAR-Indian Agricultural Research Institute, New
Delhi helped in understanding the basis of grain and cooking quality in Basmati
rice (Sood and Siddiq 1978; Sood et al. 1979). Through a stepwise convergent
breeding approach, the first high yielding semi-dwarf, weakly thermo and photosen-
sitive Basmati rice variety, Pusa Basmati 1 was developed and released in 1989.
Pusa Basmati 1121 is another popular Basmati rice variety with a milled rice kernel
length of 8.40 mm and exceptional cooked rice length of 20.00 mm, which was
developed and released for commercial cultivation in 2003 (Singh et al. 2018). Pusa
Basmati 6 is a popular Basmati rice variety known for its unique cooking quality
especially for its exceptional taste.
Two short duration Basmati rice varieties, namely Pusa Basmati 1509 (2013) and
Pusa Basmati 1692 (2020) (Fig. 3.10), with excellent Basmati quality grains and
cooking have also been developed and released by ICAR-IARI, New Delhi. As
many as 37 Basmati rice varieties including 15 varieties through SVRC have been

Fig. 3.10 Pusa Basmati 1692—a short duration high yielding semi-dwarf Basmati rice variety
162 S. Gopala Krishnan et al.

Table 3.21 Improvement in grain and cooking quality characteristics of the Basmati rice varieties
compared to traditional Basmati rice variety Basmati 370
Year of Milling HRR KLBC KBBC KLAC
Variety release (%) (%) (mm) (mm) (mm) ER
Basmati 370 1976 72.50 53.00 6.89 1.85 13.40 1.97
Pusa Basmati 1989 68.90 58.50 7.38 1.80 14.30 1.93
1
Pusa Basmati 2003 64.40 53.80 8.44 1.94 17.37 2.06
1121
Pusa Basmati 2013 68.10 49.50 8.19 1.86 18.20 2.22
1509

released in India. The popularity of Pusa Basmati 1, Pusa Basmati 1121, Pusa
Basmati 6 and Pusa Basmati 1509 have helped in significant improvement in the
Basmati rice exports from India from a mere Rs. 317 crores during 1987–1988 to
Rs. 29,840 crores during 2020–2021, revolutionising Basmati rice cultivation in
India. The improvement in grain and cooking quality traits of Basmati rice varieties
over the years are presented in Table 3.21.

3.14 Breeding for Resistance to Biotic Stresses

Rice is affected by more than 100 pathogens and pests, of which about 20 of them
can cause yield losses to the tune of 30–40%. Bacterial, fungal and viral pathogens
affect rice crop. Major disease of rice includes bacterial blight caused by
Xanthomonas oryzae pv. oryzae, blast by Magnaporthe oryzae, sheath blight by
Rhizoctonia solani, false smut by Ustilaginoidea virens, brown spot by
Helminthosporium oryzae, sheath rot by Sarocladium oryzae, stem rot by Sclerotium
oryzae and rice tungro virus. However, the spectrum and intensity of diseases are
changing continuously. A severe outbreak of brown spot disease in the winter rice
crop of Bengal was responsible for the outbreak of the infamous Bengal famine in
1943. Till 1960, blast and brown spot was the major diseases reported in rice. With
the introduction, development and adoption of high yielding fertiliser responsive
semi-dwarf rice varieties during the green revolution, bacterial blight, followed by
rice tungro, sheath blight attained the status of major diseases by 1990 in addition to
blast and brown spot. By 2005, two more diseases, namely false smut and sheath rot,
were causing major losses in rice. Of late, intensive rice cultivation with the adoption
of high yielding rice varieties, and climate change have led to the emergence of
several diseases, such as bakanae caused by Fusarium fujikoroi, glume discoloration
caused by Burkholderia glumae and stem rot, have attained major proportions
causing economic losses in yields in rice. The screening of a large number of rice
germplasm in the disease nurseries over the years has helped in identifying rice
3 Rice Breeding 163

Table 3.22 Rice varieties with resistance to different diseases

Diseases Resistant rice varieties/donors identified
Bacterial Improved Pusa Basmati 1, Pusa Basmati 1718, Pusa Basmati 1728, Pusa
blight Basmati 1847, Pusa Basmati 1885, Pusa Basmati 1886, Pusa 1927, Pusa 1592,
Improved Samba Mahsuri, Ajaya, ADT 39, CR 837, HKR 95-128, HKR
95-131, IRBB 58, IRBB 59, IRBB 60, IR 64, OR 2329-22, PAU1061-19-22,
PR 110, PR 111, PR 114, PR 118, PR 120, Pant Dhan 10, Pant Dhan 11, Saket
4, Sita, PR 4141, Bhudeb, Khitish, Sabita, ADT 39, ADT 36 and Co 43
Blast Pusa Basmati 1637, Pusa Basmati 1847, Pusa Basmati 1885, Pusa Basmati
1886, Pusa 1884, Pusa Samba 1850, Rasi, IR 36, IR 64, Sasyasree, Srinivas,
Tikkana, Simhapuri, Parijatha, Salivahana, Gauthami, Haryana Mahak
11, Tadukan, Tetep and Zenith
Sheath blight Swarnadhan, Vikramarya, Radha, Pankaj, Manasarovar, IR 40, IR
64683–-87-2-2-3-3, RP Bio Path 3, RPHR 25-104-1-2 and Tetep
Sheath rot Bala, Cauvery, Kakatiya, Janaki, Tella Hamsa, Sabarmati. Swarnadhan, Vikas,
Rajavadlu, Phalguna, Vikramarya
False smut Bala, Cauvery, Sabarmati, Prakash, Pankaj, HKR 47, HKR 127, HKR 98-418,
IR 48725-B-B-86-2-2, IR 65907-191-1-B
Brown spot Rasi, Jagannath, IR 36
Stem rot Jagannath, Sabarmati, Pankaj, Govind, Jalmagna, Cherno Fingo, CSR
30, IRBB 60, and RP Bio Path 3
Rice Tungro Vikramarya, Manasarovar, Nidhi, Bharani, Nagarjuna, Srinivas, Janaki, Radha,
virus Annapurna, Badami, Ghanteswari, Kshira, Lalat, Nilagiri, Parijat, Prachi,
Rajeswari, Vanaprabha, Barathidasan, ADT 38, ADT 44, ASD 16, ASD17,
Dinesh, Ambemohar 102, Kataribhog, Latisail and Pankhari 203

Table 3.23 Genes/QTLs governing resistance to different diseases mapped in rice

No. of No. of Genes
Diseases QTLs genes cloned Effective genes/QTLs
Blast ~350 118 25 Pi9, Pi2, Pi54, Pita, Pita2, PigmR/S,
Pi40, Pi21
Bacterial – 42 9 xa5, xa13, Xa21, Xa38, Xa7, Xa4,
blight Xa33
Sheath blight 45 – – qSBR11–1
Bakanae 12 – – qBK1.1, qBK1.2
False smut 2 – – –
Brown spot 19 – – qBS9, qBS11
Bacterial 13 – – –
grain rot
Rice tungro 2 – – –
virus

varieties with resistance to different diseases (Table 3.22). Further, a number of

genes and QTLs, governing resistance to different diseases, have been mapped in
rice, which offers possibilities for molecular breeding for the development of
cultivars (Table 3.23).
164 S. Gopala Krishnan et al.

3.14.1 Pests

Insect pests affecting rice crop have been continuously evolving with the evolution
and use of high yielding varieties. By early 1965, there were only three pests of
major concern, namely gall midge, stem borer and green leafhopper. However,
intensification of rice cultivation through the adoption of high yielding semi-dwarf
rice varieties and cultivation practices have resulted in as many as 19 pests, including
brown plant hopper (BPH), yellow stem borer, pink stem borer, gall midge, white
backed plant hopper (WBPH), green leaf hopper, mites, case worm, gundhi bug,
hispa, thrips, mealy bug, root weevil, black bug, blue beetle, army worm, leaf miner
and chaffer beetle, attaining epidemic proportions and some of them have achieved
major pest status in recent years. Several multiple pest resistant donors, such as
Velluthacheera, Banglei, Aganni, Chennellu with resistance to gall midge, BPH and
WBPH, have been identified in rice. The earliest reference to breeding for resistance
to insect pests is from India. In Uttar Pradesh, the rice bug (Leptocorisa varicornis)
was causing extensive damage to rice at ripening stages. A cleistogamous variety,
‘Saathi’, whose ripening grain was protected by a leaf sheath enclosing the panicle
without emergence was identified as tolerant and used in breeding for resistance to
rice bug (Sethi et al. 1937). Utilising the multiple pest resistant genotypes as donors,
many multiple stress-resistant high yielding rice varieties like Suraksha,
Vikramarya, Rasmi and Daya have been developed. The screening of a large number
of rice germplasm in the pest screening nurseries over the years has helped in
identifying rice varieties with resistance to different pests. A number of genes and
QTLs governing resistance to different pests have been mapped in rice, which offers
possibilities for molecular breeding for the development of cultivars (Table 3.24).

3.14.2 Weed Stress

Weeds cause significant yield losses especially in upland and direct seeded
conditions. Although direct seeded rice helps in saving water and labour needed
for puddling and transplanting, respectively. Weeds compete with the crop for water,
nutrients, light and other resources leading to stress on the crops thereby affecting its
yield significantly. If the rice variety is not competitive, it can result in significant
crop loss. Moreover, majority of the notorious weeds in rice fields are C4, and rice is
a C3 plant. Under elevated CO2, the C4 weeds produce higher biomass and broader
leaves, stifling the rice crop (Korres et al. 2016). Weeds can be managed through
weedicides, but it will increase the cost of production. Weed control may account for
upto 30% of the cost of cultivation for rice in India (Rao and Chauhan 2015; Rao and
Matsumoto 2017).
To stay competitive, a rice cultivar needs to germinate fast, develop roots faster
and deeper, possess slightly broader leaves and be vigorous so as to enable early
above ground cover, with rapid leaf area and establish the canopy faster. Majority of
these traits are quantitative in nature. Early seedling germination and early seedling
vigour are the key traits for the weed competitive ability of rice. As many 29 QTLs
3 Rice Breeding 165

Table 3.24 Genes/QTLs governing resistance to different pests mapped in rice and resistance
donors
No. No.
of of Genes
Pests QTLs genes cloned Effective genes/QTLs Resistant varieties
Brown 111 38 8 Bph31, Bph33, Bph34, Mudgo, PTB33,
plant Bph17, bph19, Bph20, Rathuheenati, ASD7,
hopper Bph21, Bph26, Bph27, Babawee, ARC10550,
Bph3, Bph4, Bph14, Swarnalata, T12, Chin
bph29 Saba, Balamawae, Sinna
Sivappu, 1R9-60,
IR747B2-6-3, and IR
1154-243, Chaitanya,
Krishnaveni, Vajram,
Pratibha, Makom,
Pavizham, Manasarovar,
Co42, Chandana,
Nagarjuna, Sonasali,
Rasmi, Jyothi, Bhadra,
Neela Annanga, Daya,
Aruna, Kanaka, Remya,
Bharatidasan, Karthika,
Vijeta, Cotton Dora
Sannalu, ADT37
White 88 14 – Wbph1, Wbph2, Wbph3, Laatha, Narendra 2002,
backed Wbph4, Wbph5, Wbph6, Jitendra, Satyaranjan
plant Wbph7, Wbph8,
hopper wbphM1, wbphM2,
wbphAR, wbphN,
wbphO, Ovc
Small 34 – – –
brown
plant
hopper
Green 11 – – – DM-27. DS-I, DK-I, and
leafhopper DNJ-27
Gall 11 7 – Gm4, Gm8, Gm1, Gm2, ARC5984, ARC5833,
midge Gm5, Gm6 W1263, Phalguna,
RP2068-18-3-5,
Abhaya, Jhitpiti, Sneha,
Pothana, Kakatiya
Erramallelu, Kavya,
Rajendradhan
202, Karna, Ruchi,
Samridhi, Usha, Asha,
MDU 3, Bhuban,
Samalei, Orugallu,
Abhaya, Shakti,
Suraksha, Daya, Pratap,
Udaya, IR36,
Shaktiman, Tara, Kshira,
Sarasa, Neela, Lalat,
(continued)
166 S. Gopala Krishnan et al.

Table 3.24 (continued)

No. No.
of of Genes
Pests QTLs genes cloned Effective genes/QTLs Resistant varieties
Phalguna, Mahaveer,
Vibhava, Divya, Dhanya
Lakshmi, Surekha,
Vikram, Kunti, Triguna,
Sita, Samleswari, Karma
Mahsuri, Dhanarasi,
Mahamaya, Jyothi
Stem 12 – – – TKM6, PSBRc68, IR46,
borer CO14
Root knot 32 – – qYR5.1, qYR11.1, Phule Radha,
nematode qMGR4.1, qMGR7.1, IR78877–208-B-1-2,
qMGR9.1 LD24, Khao Pahk Maw,
NKSWR30,
NKSWR259

associated with early seed germination traits and 15 QTLs with early seedling vigour
including two QTL hotspots, one in chromosome 11 and another in chromosome
2 have been identified in rice (Dimaano et al. 2020). QTLs governing early uniform
emergence (qEMM11.1) and early vigour (qEVV9.1) have been mapped in rice
(Dixit et al. 2015; Sandhu et al. 2015).
Alternatively, weeds can be controlled by using herbicides. Selective herbicides
such as Pendemthalin and Bispyribac Sodium have been used in rice crop for
managing weeds. Broad spectrum non-selective herbicides offer better weed control
at lower doses, flexibility in timing of application, are cost effective and eliminate the
possibility of any injury to the crop. However, to use non-selective herbicides,
phytotoxicity to the rice crop needs to be avoided through the use of herbicide
tolerant mutants. Fortunately, in rice, herbicide tolerance genes with different modes
of action have been identified (Table 3.25), which can be incorporated into popular
rice varieties through marker-assisted backcross breeding to develop an herbicide
tolerant rice variety (Grover et al. 2020). Imidazolinone group of herbicides
(imazapyr, imazapic, imazethapyr, imazamox, imazamethabenz and imazaquin,
etc.) kills weeds by inhibiting acetohydroxyacid synthase (AHAS) enzyme, also
called acetolactate synthase (ALS). It is a critical enzyme involved in the biosynthe-
sis of branched-chain amino acids such as leucine, isoleucine and valine in plants.
Imidazolinone group is most widely used for weed control in crops like soybean,
groundnut, etc., which possess natural tolerance to these herbicides. However, rice is
highly sensitive to imidazolinones. Allelic variants of AHAS conferring tolerance to
imidazolinone herbicides have been created through mutagenesis and
commercialised as Clearfield® rice. Imidazolinone herbicides offer broad spectrum
control of grass and broadleaf weeds in imidazolinone-tolerant crops (Tan et al.
2005). Besides, AHAS/ALS, mutations in two more genes have been found to
provide herbicide tolerance in rice (Table 3.25).
 3
Rice Breeding

Table 3.25 Mutations in major genes governing herbicide tolerance in rice

Amino acid
Gene Locus ID Mutant/genotype Mutation substitution Target herbicide group Reference
AHAS/ LOC_Os02g0510200 93-AS3510 G-A G654E Imidazolinones Croughan (1998)
ALS
AHAS/ LOC_Os02g0510200 IMINTA1, G-A A122T Imidazolinones Tan et al. (2006)
ALS IMINTA4
AHAS/ LOC_Os02g0510200 Robin G-A S627N Imidazolinines Shoba et al.
ALS (2017)
AHAS/ LOC_Os02g0510200 JD164 G-A S627N Imidazolinines Piao et al. (2018)
ALS
ACCase LOC_Os05g0295300 Sabbore R line G-T W2027T fops, dims, phenylpyrazolin (ACCase Andrade et al.
Inhibitors) (2018)
HIS1 LOC_Os02g0280700 Koshihikari 28-bp Nonsense mutation β-triketones (4-HPPD inhibitor) Maeda et al.
deletion (2019)
167
168 S. Gopala Krishnan et al.

3.15 Breeding for Abiotic Stress Tolerance

Rice is affected by various abiotic stresses tolerance such as drought, submergence,

salinity, extremes of temperature (cold/heat stress), low nutrients and high radiation.
Drought is one of the most important abiotic stress limiting rice yields especially
under upland rainfed ecologies (Vinod et al. 2019). Rice in general has a small
fibrous root system, thin cuticle and swift stomata closure, which makes it highly
susceptible to drought stress. Therefore, breeding for tolerance to drought is one of
the major breeding objectives for rainfed ecologies. Rice is highly sensitive to salt
stress both at seedling and reproductive stages, which necessitates the introgression
of tolerance at both seedlings as well as reproductive stages (Vinod et al. 2013). Rice
is semi-aquatic, but most of the genotypes are susceptible to complete submergence
for even a short period. Flash floods cause more mechanical damage than inundation.
However, waterlogging for a longer period can result in substantial yield loss. More
than 16 million ha of rice in South and Southeast Asia is prone to floods (Dwiyanti
and Yamada 2013).
In India, the eastern part of the country including eastern Uttar Pradesh, Bihar,
West Bengal and Assam constitute the submergence prone ecologies under rice.
Rice is highly sensitive to high temperature stress, particularly during the reproduc-
tive stage (Cao et al. 2008), resulting in poor panicle exsertion and spikelet sterility
causing major yield loss. Reproductive stage heat stress not only results in yield loss
but also there is a serious deterioration of grain quality, such as increased chalkiness,
shrivelling of grains, as well as reduced storage proteins. Rice in general is adapted
to the tropics and therefore is sensitive to low temperature. Low temperature
tolerance is a key trait in hilly ecologies, where a sudden drop in temperature can
result in productivity losses. Rice utilises significant quantities of nutrients from the
soil for grain production (60% for N, 67% for P and 15% for K), and the balance is
retained in the straw (Dobermann and Fairhurst 2000) followed by P, Ca, Mg and
S. Genetic improvement of rice to improve nutrient use parameters under low
fertility conditions by enhancing nutrient foraging, faster uptake, solubilising ability,
microbial symbiosis, and terminal mobilisation of nutrients to grains thereby increas-
ing yield conversion efficiency. Rice is endowed with a wealth of germplasm
possessing tolerance to these major stresses (Table 3.26). Tolerance to a majority
of these stresses show polygenic inheritance. Advances in genetics and genomics
have enabled mapping a large number of genes/QTLs for tolerance to each of these
stress factors in rice. Several drought tolerant rice varieties have been developed
through conventional breeding and released for commercial cultivation in India
(Table 3.27).

3.16 Breeding Approaches for Rice Improvement

Genetic variability is the foundation for any crop improvement. Rice is endowed
with enormous variability. The selection and release of GEB24, a spontaneous
mutant from a landrace ‘Konamani’ marked the beginning of rice breeding. Since
3 Rice Breeding 169

Table 3.26 Genes/QTLs mapped and tolerance sources for various abiotic stresses in rice
No. No.
of of Genes Effective QTLs/ Tolerant varieties/
Abiotic stress QTLs genes cloned genes genotypes
Drought 874 2 2 qDTY1.1, Nagina 22, Vandana,
qDTY12.1, IR94225-B-82-B, Annada,
qDTY2.1, Varanideep, Azucena,
qDTY3.1, PTB42, PTB43, PTB55
qDTY2.2, Dro1,
OsDREB1a
Salt 876 1 2 Saltol, SKC1, SalT Pokkali, FL478,
Nonabokra, CSR11,
KR1–24, PTB44
Submergence 23 1 4 Sub1A, OsTPP7 FR13A, Dhalputtia,
Nimbuiya, Beller,
Amghaud, Malhi qud,
Ramkajari
Heat 208 – – TT1, qHTSF1.1, Nagina 22, NL44, NH
qHTSF4.1 219, Dular, Nipponbare,
WAB56–12
Cold 491 42 – qPSST3, qPSST7, K-39, K-78, K348,
qPSST9, qCTS4a, Geumobyeo, W1943,
qCTS4b M202, Leimaphou
Aluminium 5 1 1 NRAT1 Ca 902/B/21, Goria,
toxicity Karkati 87, DM59, and P
737
Low 4 – – PSTOL1, qPU5.2 Kasalath, Rasi
Phosphorus
Deep water – 2 2 Snorkel1, Snorkel2 Jalmagna, TCA
269, TCA4, Jalnidhi,
PTB47, PTB48
Oxidative 353 31 – – –
stress
Nitrogen 113 – – NRT1.1B, OSNR2, 9311
deficiency OsTCP19, NGR5,
SMOS1, GRF4,
qNU5.1

then, various strategies have been adopted by the rice breeders, to create variability
as well as to recombine the available variability in the rice germplasm to develop rice
varieties with improved productivity. Although yield improvement remains a major
focus, the priorities in rice breeding have been changing from time to time. Rice
improvement has also seen the adoption of various breeding approaches at different
periods based on the priorities. The major breeding approaches in rice include
(a) introduction, (b) pureline selection, (c) pedigree breeding, (d) mutation breeding,
(e) marker-assisted breeding, (f) population improvement and (g) genomic selection,
and more recently (g) genome-editing. The breeding approach for rice improvement
has changed with the new scientific discoveries and molecular tools not only
170 S. Gopala Krishnan et al.

Table 3.27 Major abiotic stress tolerant varieties released for commercial cultivation in India
Variety Year Genotype Parentage Ecosys
Drought
Nagina 22 1978 – A selection from Rajbhog UL
BR34 1985 – Pureline selection from Dolangi RL
TKM10 1993 IET12270 CO31/C-22 UL
Birsa Dhan 106 1996 IET12052 Bala. Black Gora. OS-36/ UL
CH1039
MDU5 1997 – O. glaberrima/Pollali UL
Vandana 2002 RR 167-982 C-22/Kalakeri UL
Anjali 2002 IET164030 PR-19-2/RR-149-1129 UL
Jaldi Dhan 13 2006 PNR 591-18 – –
Sahbhagi Dhan 2010 IR74371-70-1-1 IR55419-04*2/Way Rarem RL,
UL
DRR Dhan 43 2014 IR83876-B-F3 IR03L03/IRRI148 RL
DRR Dhan 44 2014 IR93376-B-B-130 IR71700-247-1-1-2/IR03L120 UL
CR Dhan 201 2014 IR83380-B-B-124-1 IR72022-46-2-3-3-2/PSB RC UL
18
CR Dhan 202 2014 IR84899-B-154 IR78877-208-B-1-1/IR55423- UL
01
CR Dhan 203 2014 IR84899-B-185 IR78877-208-B-1-1/IR55423- UL
01
CR Dhan 204 2014 IR83927-B-B-279 IR78888-208-B-1-2/CT6510- UL
24-1-2
CR Dhan 205 2014 IR86931-B-578 Nagina22/Swarna UL
Tripura 2014 IR83928-B-B-56-4 – UL
Hakuchuk 1
Tripura 2014 IR82589-B-B-138-2 IR55423-01/IRRI148 UL
Hakuchuk 2
Swarna Shreya 2016 IR84899-B-179-16- IR78877-208-B-1-1/IR55423- RL
1-1-1-1 01
Submergence (Flash flood)
Tulashi 1989 IET 8548 CR-151-79/CR-1014 RL
Swarna Sub1 1999 CR AC 2539-1 Swarna/FR13A//Swarna*3 RL
Samba Sub1 2011 BPT5204/FR13A/? RL
BPT5204*3--
Ranjtih Sub1 2016 Ranjith/Swarna Sub1// RL
Ranjtih*3
Bahadur Sub1 2016 Bahadur/Swarna Sub1// RL
Bahadur*3
CR1009 Sub1 2015 IET 22187 CR1009/FR13A//CR1009*3 RL
CO43 Sub1 2018 Co43/FR13A//Co43*3 RL
Deep water rice with tolerance to prolonged flooding
Jaladhi 2 1982 – Pureline selection from Baku DW
Jalnidhi 1994 – Local selection from Goantis DW
Jalpriya 1994 – IET5060/Jalmagna DW
Jalprabha 1997 IET11870 Selection from composite DW
(continued)
3 Rice Breeding 171

Table 3.27 (continued)

Variety Year Genotype Parentage Ecosys
Salinity/Sodicity
CSR13 1998 IET10348 CSR1/Basmati370??CSR5 SD
CSR23 2004 IET13769 IR64//IR4630-22-2-5-1-3/ SD
IR964-45-2-2
CSR27 1998 IET13765 Nona Bokra/IR565-33-2 SD
CSR30 2001 IET14720 BR4-10/Pak. Basmati SD
CSR36 2005 IET17340 CSR13/Panvel//IR36 SD
Cold
Leimaphou 1990 KD 2-6-3 Moirangphou/Lawagin HE
Sanaphou 1999 KS 2-7-6-2 Moirangphou/Lawagin HE
RL rainfed lowland, UL upland, SD sodic, DW deep water, HE hill ecology

enabling precise selection of genotypes but also the precise creation of superior
alleles at various clones genes aided by the advances in rice functional genomics and
molecular biology in rice. However, the utility of these breeding approaches is still
relevant even today in order to meet the challenges imposed for improving as well as
sustaining rice productivity.

3.16.1 Introduction

The introduction is one of the simplest methods in breeding, wherein the high
yielding varieties released from other countries/states within India are directly
introduced and released as varieties. It helps address two important objectives of
breeding, namely improving productivity as well as enriching the variability of the
elite germplasm available for further crop improvement. In the early 1950s, a large
number of temperate japonica rice varieties were introduced from China and Japan
for the hill ecologies of Himachal Pradesh, Kashmir and Uttarakhand, some of which
became very popular. The noteworthy introductions from China include Shinei,
China 45, China 988 and China 1039, and Japanese varieties include Koshihikari
and Narahikari. During the green revolution era, several semi-dwarf high yielding
rice varieties were introduced, which were used as the source germplasm for semi-
dwarfing genes in India. Some of the landmark varieties were Taichung Native
1, Taichung 65, Tainan 3, Dee-Gee-woogen and IR8 from IRRI, Philippines. One
the indica/japonica derived ‘Mahsuri’ was also introduced in India and has been
utilised in breeding mega varieties, such as Swarna and BPT5204. IR20, IR36, IR50
and IR64 are some more varieties introduced and released as varieties in India, out of
which IR36 and IR64 are still popular among the farmers. Many of the varieties such
as Jaya, Rasi, Padma and Swarna from India were also introduced in several
countries across the world (Table 3.28).
Although introductions were easy during earlier years, with the Intellectual
Property Rights gaining importance in the agriculture sector, the exchange of
172 S. Gopala Krishnan et al.

Table 3.28 Varieties from India introduced and adopted in countries across the world
Countries and varieties introduced Year of release Released as (variety name)
Afghanistan
a
CR 44-11, Cauvery, Padma 1975
a
Cambodia
OR 142-99 – a

PR China
M114 1981 8085
Myanmar
Mahsuri mutant 1977 Ma Naw Thu Kha
RP 1057039301 1995 Yezin
RP 1674-690-39-14 2005 Shwe Myanmar
Nepal
CR 123-23 1978 Durga
Rasi 1981 Bindeswari
K-39-96-1-1-1-2 – Khumal 3
Pakistan
Khitish 1984 DR82
Vietnam
Jaya – a

Iran
Sona 1982 Amol 3
a
Released in the same name

germplasm between countries across the world during recent years has come down
drastically. The International Network for Genetic Enhancement of Rice (popularly
known by the acronym INGER), an open access initiative by IRRI established in
1975 has been a valuable source of advanced pre-variety breeding lines as well as
varieties developed by IRRI and other NARES partners involved in rice improve-
ment. INGER has provided more than 70,000 breeding lines to 600 research stations
in about 85 countries, which has facilitated more than 1300 varieties in different rice
producing countries. The INGER nurseries are shared through a standard material
transfer agreement under FAO International Treaty on Plant Genetic Resources for
Food and Agriculture (PGRFA).
Introductions of varieties released by SVRC for one state to another state within
India have also been highly successful including Swarna from Andhra Pradesh to
Odisha, Madhya Pradesh, Uttar Pradesh, Bihar and West Bengal; BPT5204 released
in Andhra Pradesh has been successfully adopted in Karnataka, Tamil Nadu, Uttar
Pradesh, Bihar, Odisha and West Bengal. Both these varieties are very popular
attaining the status of mega varieties in India. During recent years, the varieties
released by SVRC, such as MTU1010, CO51 and PR114, have gone on to become
popular in other states.
3 Rice Breeding 173

3.16.2 Pureline Selection

Pureline selection advocated by Johannsen (1903) was one of the most widely
adopted and successful breeding approaches for rice improvement during the early
quarter of the nineteenth century. This approach helped in bringing out the cream
from the traditional rice varieties, with wide adaptation, high yielding under low
inputs and resistant to local insect pests and diseases. However, they were all tall and
lodged under heavy manuring. One of the first rice varieties to be released by
pureline selection was CO1 by Paddy Breeding Station, Coimbatore, in 1923,
following which as many as 14 rice varieties from this station were released till
1940 through pureline selection. A drought tolerant variety CO2 and a blast resistant
rice variety CO4 were released through pureline selection (Parthasarathy 1972).
Owing to the selection from the germplasm adopted to specific ecologies, most of
the pureline selections were released for that particular state only. More than
50 varieties were developed and released through pureline selection from 1923 to
2002. Some of the popular rice varieties developed through the pureline selection
approach are presented in Table 3.29. Most of the varieties developed through
pureline selection before the green revolution were all tall and highly susceptible
to lodging.

3.16.3 Pedigree Breeding

Pedigree breeding involves hybridisation and selection through controlled crossing

of selected rice genotypes followed by selection in the segregating generations or
fixed generations for traits based on the breeding objective. Hybridisation is
formulated to ensure the recombination of desirable characteristics in the segregating
generations providing scope for selecting superior genotypes with desirable charac-
teristic features. The hybridisation can be effected through two-way crosses, which
involve 2 purelines; three-way crosses, which involve crosses between purelines and
an F1 (also known as a top cross); double crosses, where two F1s from two different
crosses are intercrossed to generate segregating populations. Top crosses and double
crosses are attempted to combine desirable traits from multiple parents. More
recently multiparent crosses involving 8 parents, 16 parents called MAGIC
(Multiparent Advanced Generation Intercrosses) have also been proposed to recom-
bine superior alleles from as many parents as possible.
The F1s generated by crossing selected parents are advanced by selfing, and
phenotypic selection for highly heritable traits are carried out from the segregating
generations till F5 to F7 generations, after which the selected lines are evaluated in
preliminary yield trials (PYT), followed by station trials for 2 years (ST1, ST2), after
which the genotypes are nominated for testing in the trials conducted by the All India
Coordinated Rice Improvement Programme (AICRIP, described in detail later in this
chapter). The various steps adopted in pedigree breeding are outlined in Fig. 3.11.
During the initial years of rice breeding, only one crop was raised per year
especially under north Indian conditions during Kharif season only. If only one
174 S. Gopala Krishnan et al.

Table 3.29 Some of the popular rice varieties developed through pureline selection approach
Pureline Year
selection of
S. No. Variety from release Eco-system Salient features
1. CO4 Anaikomban 1923 Irrigated Resistant to blast disease
transplanted
2. Madhukar Gonda 1969 Semi-deep Tolerant to stagnant flood
water
3. T-23 Kala sukhdas 1975 Upland Tall, long slender grains
irrigated
4. Giza-14 Giza-4 1978 Hill rice Semi dwarf, short bold
irrigated grains, good cooking quality
5. Jalmagan Barho 1978 Flood prone Very tall (upto 4 m), short
bold grains
6. Nagina 22 Rajbhog 1978 Upland Resistant to drought, tall,
short bold grains
7. Type 3 Dehraduni 1978 Irrigated Basmati rice, tall, long
basmati transplanted slender grains
8. Type 100 Bhanslot 1978 Saline Tall, short bold grains
9. Vytilla 2 Cheruvirippu 1982 Saline Tall (154 cm), medium bold
grains, red pericarp
10. Jaladhi 1 Kalakhersail 1982 Water Very tall (upto 4 m), bold
logged grains
11. BR-34 Dolangi rice 1985 Rainfed Tall, medium slender grains,
moderately resistant to BB
and SB, tolerant to drought
12. SR26B Kalambanka 1988 Rainfed Salinity tolerant
shallow
lowland
13. Improved White ponni 1989 Irrigated Medium slender grains, tall,
white transplanted resistant to RTV, moderately
ponni resistant to brown spot and
blast
14. Birsa Gora rice 1993 Uplands Tall, medium bold grains
Gora102
15. Taraori Karnal local 1996 Irrigated Basmati rice, tall
basmati transplanted
16. Ranbir Basmati370 1996 Irrigated Early maturing basmati rice
basmati transplanted
17. Sravani IR 50 2000 Irrigated Dwarf (80–85 cm), long
transplanted slender grains, resistant to
blast, brownspot, BB
18. Maruteru Oodasannalu 2000 Irrigated Dwarf (90–95 cm), medium
sannalu transplanted slender grains
19. Mangala Mahsuri 2002 Irrigated Tall (123 cm), Short bold
mahsuri transplanted grains, moderately resistant to
SB and blue beetle
3 Rice Breeding 175

Fig. 3.11 A schematic

overview of the pedigree
breeding approach followed
by testing for release of the
variety. (a) indicates a
situation, where only one crop
is taken up per year and (b)
indicates where two crops are
raised in a single year

crop is raised per year, it takes 8 years from attempting crosses to develop elite
breeding lines and including the testing in AICRIP trials, it takes 15 years to release a
rice variety through pedigree breeding. However, extending the concept of shuttle
breeding in rice, institutes like ICAR-IARI, New Delhi, has established an offseason
nursery, Rice Breeding and Genetics Research Centre, IARI at Aduthurai, in the
campus of Tamil Nadu Rice Research Institute, Aduthurai which has enabled taking
up of two crops per season is being taken up since 1968. Shuttle breeding using the
offseason nursery at RBGRC-IARI, Aduthurai has halved the number of years for
the development of elite genotypes to 4 years and reduced the time taken for
development and release of improved rice varieties significantly.
176 S. Gopala Krishnan et al.

Further, shuttle breeding also offers the additional advantage of exposing the
segregating populations to two different environments varying for soil, weather and
disease pressure providing an opportunity for selection of better performing
genotypes with better stability and adaptability. Several other methods have been
utilised for rapid fixation of genotypes in rice, including doubled haploids (DH),
single seed descent (SSD) (Goulden 1939) in combination with rapid generation
advancement (RGA) and speed breeding. Among these DH enables rapid fixation of
genotypes in a single step (Collard et al. 2017). However, it provides opportunity for
only one cycle of recombination, whereas in other methods multiple cycles of
recombination happens during the fixation process, thereby providing better chances
of recombination of favourable alleles during the breeding process.
RGA under greenhouse conditions have been utilised in Japan and Korea (Heu
et al. 1982; Ikehashi 1977). As many as 24 leading Japanese varieties including the
popular japonica rice variety, Nipponbare (Used for generating reference genome of
rice) were bred using RGA (Ikehashi and Fujimaki 1980). It could shorten breeding
cycle thereby saving time while enabling breeding for cold tolerance as well (Heu
et al. 1982). Recently, Field RGA enabling advancing multiple generations under
field conditions have been utilised in IRRI and Bangladesh, thereby reducing the
fixation time from 4 years to 2 years (Collard et al. 2017). RGA has several
advantages, namely (1) technical simplicity, requirement of less resources including
field and labour thereby saving time and money (Stoskopf et al. 1993); (2) no need
for strict record keeping as in pedigree breeding; (3) only one step seed increase
needed to produce sufficient seeds for evaluation. However, it has its own inherent
disadvantages such as (1) retention of poor performing genotypes during generation
advancement as there is no selection during line fixation; (2) a general perception
that it does not capture adequate genetic variation; (3) lines through RGA are
considered inferior compared to lines generated through early-generation visual
selection (Jensen 1988).
Pedigree breeding is one of the most popular methods of breeding in rice
improvement (Khush and Virk 2005). Large population size in the F2 generation
(around 2000 plants in 2-way crosses, 3000–5000 in 3-way crosses) must be raised
to ensure desirable recombinants especially when the parents are contrasting for
many traits of interest. However, in practice it is widely used due to several reasons,
the availability of resources being one of the major constraints. During the initial
years of the green revolution, consciously large populations of F2 upto 13,200 plants
were grown from the biparental crosses involving tall indica varieties, namely T90,
GEB24, T141, SK20, SLO16, Basmati 370 and the semi-dwarf varieties, Taichung
native 1, Dee-geo-woo-gen, IR8 (Freeman and Shastry 1972), so that a large number
of semi-dwarf genotypes from the F2 population could be selected for further
selection in the following generations. However, the actual population size depends
largely on the resources available to the breeders and the extent of segregation. In
recent years, where the crosses between largely elite genotypes (elite/elite) fixed for
favourable alleles at a given locus are attempted, reasonable population sizes of
500 are adequate to capture the desirable recombinants.
3 Rice Breeding 177

The crosses during the initial years of breeding at paddy breeding station,
Coimbatore, were mainly aimed at the development of (1) blast resistant rice
varieties and (2) non-lodging rice varieties suited for partly submersible ecosystems.
These efforts resulted in the development and release of the rice varieties, namely
CO14, CO15 and CO16 in 1940. CO14 from the cross, CO3/T275, was the first
variety developed through pedigree breeding approach released for commercial
cultivation in India in 1940. CO15 (Jada Molakolukulu) was the first blast resistant
variety developed from the cross GEB24/ADT10 (also known as Korangu Samba) in
1940 (Parthasarathy 1972). ADT27 from the cross Norin 10/GEB24 is a landmark
variety developed and released through pedigree breeding under the indica/japonica
hybridisation programme funded by FAO. CR 1014, a late maturing tall and
non-lodging rice variety with medium slender grains and good cooking quality
was developed from the indica/bulu ( javanica or tropical japonica) cross, T
90/Urang Urangan in the mid-1960s. Following the introduction of semi-dwarf
rice varieties such as Taichung Native 1 (TN1), IR8 and Dee-Geo-Woo-Gen in
1965, a large number of crosses were attempted between the tall indica varieties and
the three semi-dwarf rice varieties leading to the development of several popular
semi-dwarf high yielding rice varieties (Table 3.30).

3.16.4 Mutation Breeding

Mutations either spontaneous or induced play a key role in creating variability which
is vital for plant breeding. Mutation breeding has been utilised for creating useful
mutants for rice improvement. Spontaneous mutations have also been utilised in rice
varietal improvement. GEB24 was the first landmark variety identified and released
in rice, which was a spontaneous mutant selected from a rice variety, ‘Konamani’
from Godavari delta with exceptional grain and cooking quality by Parnell and his
associates at Paddy Breeding Station, Coimbatore in 1921. It is popularly known as
‘Kitchili Samba’ and has been widely used as a donor for grain quality in rice
breeding programmes across the world. GEB24 is ranked fifth for use as a parent in
the genealogy of released rice varieties till 1991. It is in the development of 554 rice
varieties released across the world. It is also one of the parents of popular medium
slender grain rice variety, ‘BPT5204’. Another noteworthy variety developed
through the selection of a spontaneous mutant from Basmati 370 is ‘Ranbir
Basmati’, which is short duration Basmati rice variety released for Jammu regions
of Jammu and Kashmir in 1996.
Ramaiah and Parthasarathy (1938) first used X-rays for producing mutations in
rice. Thirty-six mutations affecting different characters, namely plant habit, height,
panicle length, arrangement of spikelets in the panicle, spikelet fertility and 16 chlo-
rophyll deficient types were generated. Induced mutagenesis gained importance in
the late 1960s and 1970s with the funding and support from the International Atomic
Energy Agency (IAEA) for generating basic knowledge and translating the potential
of mutation in rice improvement.
178 S. Gopala Krishnan et al.

Table 3.30 Some important rice varieties developed and released in India using the semi-dwarf
rice varieties introduced from IRRI
Name of
variety Parentage Year Eco-system Salient features
Jaya TN1/T141 1968 Irrigated Dwarf, long bold grains, resistant to
(IET723) blast
Padma T141/TN1 1968 Irrigated Semi-dwarf, coarse grain, moderately
resistant to BS
Bala TN1/N22 1970 Rainfed Semi-dwarf, tolerant to drought
upland
Cauvery TN1/ 1974 Rainfed Dwarf, short bold grains, resistant to
TKM6 upland or BLS, moderately resistant to SB
irrigated
Karishma GEB24/ 1974 Rainfed (late MS grains, very high head recovery,
TN1 showing) resistant to blast, leaf spot and SB
Ratna TKM6  1975 Upland and Dwarf, LS grains, moderately resistant
IR8 direct seeded to blast, LH and tolerant to SB
Saket4 TKM6/ 1975 Upland Dwarf, LS grains, lodging resistant,
IR8 irrigated or moderately resistant to BLB, GLH and
rainfed SB
Tella Hamsa HR-12/ 1975 Irrigated LS grains, cold tolerant, resistant to SB
TN1 areas
ORS11 T141/IR- 1975 Rainfed Dwarf, long bold grains, moderately
8-246 coastal resistant to BLB, blast and GLH
saline
Karuna IR8/ 1976 Irrigated Dwarf, short stature, short bold grains
ADT27 early
Jyothi PTB10/ 1977 Wetland Dwarf, long bold grains, red pericarp,
IR8 areas resistant to blast
Rasi TN1/ 1978 Rain fed Semi dwarf, MB grains, resistant to
CO29 upland areas blast, moderately resistant to RTV
Bharthi PTB10/ 1978 Irrigated Semi dwarf, long bold grains, red
IR8 early pericarp
Bhavani Peta/BPI- 1978 Irrigated Semi tall, long bold grains, moderately
76 medium resistant to blast, BLB
Gautami IR8/SLO 1978 Coastal areas Dwarf, short bold grains, resistant to
13 blast
Pankaj Peta/ 1978 Low-land Semi dwarf, long bold grains,
Tongkai areas moderately resistant to blast and RTV
Rotan
Phalguna IR8/Siam- 1978 Coastal areas Dwarf, LS grains, resistant to GM
29
Vasista IR8/ 1978 Rainfed Grains: short bold, resistant to blast,
SLO13 shallow moderately susceptible to BLB and SB.
PR 103 IR8/IR27 1982 Irrigated Semi dwarf, LS grains, resistant to blast
medium and Helminthosporium
Sarjoo 52 TN1/ 1982 Irrigated Semi dwarf, erect, long bold grains
Kashi
(continued)
3 Rice Breeding 179

Table 3.30 (continued)

Name of
variety Parentage Year Eco-system Salient features
TKM9 TKM7/ 1982 Irrigated Semi dwarf, short bold grains, red
IR8 early pericarp
ADT36 Triveni/ 1982 Irrigated Semi dwarf, MS grains
IR20 early
Himalaya 2 Sabarmati/ 1983 Low and mid Semi dwarf, long bold grains, aromatic,
Ratna hills resistant to blast, SB and RH
KMP1 CR-1014/ 1984 Irrigated Semi dwarf, super fine grains, tolerant to
(Mandyavan) IR8 medium blast and BPH
Parijat TKM6/ 1985 High and Dwarf, Medium slender grains
TN1 medium
lands
Dhan Bella 1983 Irrigated or Dwarf, short bold grains, multiple stress
Narendra-1 Patna/IR8 rainfed resistant variety
Panvel 1 IR8/Bhura 1985 Coastal Semi dwarf, short bold grains, resistant
Rata 4–10 saline area to neck blast
SKL6 Nagpur27/ 1985 Irrigated Semi dwarf, LS grains, resistant to blast
IR8 areas and blight

Two most important traits for improvement through induced mutagenesis have
been semi-dwarfism and earliness. Additionally, mutants for other traits such as high
tillering, blast resistance, improved grain quality and photoperiod insensitiveness
have also been derived through mutagenesis. Recently, Ethyl Methane Sulphonate
induced mutant of Nagina 22, ‘Robin’ has been developed for tolerance to
Imazethapyr, an herbicide (Shoba et al. 2017). Robin is currently being used in
developing improved Basmati rice varieties suited for dry direct seeded rice cultiva-
tion. A semi-dwarf mutant, Reimei, derived from the variety, Fujiminori was the first
mutant variety released in Japan in 1966. As many as 434 rice varieties have been
developed through mutation breeding across the world. Many rice varieties have also
been released through mutation breeding in India (Table 3.31), among which
‘Jagannath’ is very popular having been developed from T141 by X-ray mutagene-
sis. Jagannath is a semi-dwarf fertiliser responsive high yielding rice variety with
medium slender grains.

3.16.5 Marker-Assisted Breeding

Rice is endowed with rich genetic and genomic resources, wherein a large number of
genes governing economically important traits such as resistance to diseases, pests,
grain quality, tolerance to drought, salinity, low phosphorus and herbicide have been
mapped and many of them have been cloned. Availability of genes, a gene linked or
gene-based markers and donor germplasm enable the use of marker-assisted breed-
ing in rice. Marker-assisted breeding provides an excellent opportunity to the
180 S. Gopala Krishnan et al.

Table 3.31 Mutant rice varieties released for commercial cultivation in India
Variety Parentage Year Ecosystem Salient features
Spontaneous mutation
GEB24 Mutant of 1921 IR Medium slender grain,
Konamani exceptional grain and cooking
quality
ADT41 Mutant of 1994 IR Semi dwarf, extra LS grains, mild
Basmati 370 aroma
Ranbir Basmati Mutant of 1996 IR Short duration Basmati, long
Basmati370 slender grains and strong aroma
Induced mutation
Jagannath Mutant of 1975 CS Semi Dwarf, MS grains, resistant
T141 to lodging, blast
CNM25 A mutant of 1978 LA Dwarf, long bold grains,
IR8 moderately resistant to blast
CNM31 A mutant of 1978 MLL Semi dwarf, LS golden grains,
IR8 resistant to BS
Lakshmi A mutant of 1982 UL Dwarf, long bold grains
(CNM6) IR8
Biraj (CNM539) Mutant 1984 RL Tall, long bold grains
Prabhavati Mutant of 1985 IU Dwarf, coarse grains, aromatic,
(PBN1) Ambemohar tolerant to Iron chlorosis
Padmini Mutant of 1989 RSL Superfine grains, highly tolerant
CR1014 to BLB
Lunisree Mutant of 1992 CSS, WL Tall, Long Slender grains
Nonasai
Gautam Mutant from 1996 IME Dwarf, long bold grains
Rasi
Malviya Dhan- Mutant of 1997 MLL Medium Slender grains, resistant
36 Mahsuri to major diseases
Radhi (CRM-40) Swarnaprabha 1997 IE Long bold grains, tolerance to
mutant blast and BPH
Revathy (MO17) Mutant of 1998 IR Resistance to BPH
MO1
Remanica Mutant of 1999 IM Short bold grains, resistance to
(MO-15) MO1 BPH and GM
Early Samba Mutant of 2000 IM Dwarf, Medium Slender grains
(RNRM7) BPT5204
Kaum-20-19-4 Mutant of MO 2002 IR Early, Dwarf, medium bold
1 grains, resistant to BPH, ShB and
ShR
CR Boro Dhan 2 Mutant of 2008 IR Boro Medium slender grains, cold
China-45 tolerant (Seedling and tillering
stages)
Anashwara (PTB Mutant of PTB 2006 IR Semi tall, nonlodging, medium
58) 20 bold grains, and excellent cooking
Mutant of 2009 IR Photoinsensitive, high yielding,
MPR 7-2 long grains and aroma
(continued)
3 Rice Breeding 181

Table 3.31 (continued)

Variety Parentage Year Ecosystem Salient features
Malaviya
Sugandh
105 (HUR 105)
Malaviya Mutant of 2009 IR Fine grain and mild aroma
Sugandh 4-3 Lanjhi
(HUR 4-3)
IR irrigated, CS coastal saline, UL upland, RL rainfed lowland, IU irrigated upland, RSL rainfed
shallow lowland, WL water logged, IME irrigated mid-early, MLL medium low land, IE irrigated
early, LA lateritic and alluvial soils

present-day researchers for breeding new crop varieties by designing through the
precise transfer of desirable gene(s) into popular rice varieties. Among the various
breeding approaches, marker-assisted backcross breeding (MABB) helps in
incorporating genes/QTLs governing resistance to disease/pest/improvement in
quality, etc. into an already popular variety within a short span of 3 years.
Molecular markers are deployed in MABB for the foreground, background and
recombinant selection (Singh and Krishnan 2016), where foreground selection is
done for the target gene/QTL using a gene based/gene linked marker, background
selection is exercised for recovery of recurrent parent genome in the plants selected
with desirable alleles of target gene(s)/QTL(s) and recombinant selection is done to
eliminate linkage drag, if any. Additionally, stringent phenotypic selection can also
help in hastening the recovery of desirable phenotype in the improved near isogenic
lines (NILs) derived through marker-assisted backcross breeding (Fig. 3.12).
Molecular marker-assisted breeding through the transfer of gene(s) for resistance
to major diseases such as bacterial blight, blast, tolerance to drought, submergence,
low phosphorus and herbicide has been very successful (Singh et al. 2011). As many
as 39 improved rice cultivars developed through marker-assisted breeding have been
released for commercial cultivation in India. Out of these, 17 varieties have been
improved for bacterial blight resistance with xa5, xa13 and Xa21, while five are
improved with blast resistance, with Pi1, Pi2, Pi9, Pi54 and Pita (Singh et al. 2019)
and three Basmati varieties possessing resistance to both BB and blast diseases
(Table 3.32).
Significant progress has also been made in breeding for resistance to bakanae and
sheath blight, as well as against pests like brown planthopper. Markers have also
been successfully utilised in transferring gene(s)/QTL(s) for tolerance to drought,
submergence, salinity, low phosphorus and herbicide into popular rice varieties
resulting in the release of as many as 14 improved rice varieties with enhanced
tolerance to the above stresses.
182 S. Gopala Krishnan et al.

Fig. 3.12 Schematic

representation of MABB for
rice varietal improvement

3.17 Population Improvement

Breeding methods such as pureline selection, pedigree breeding, mutation breeding

and backcross breeding have helped in making significant improvement in rice but
also for other traits such as resistance to various biotic and abiotic stresses, grain and
nutritional quality. However, these methods suffer from three inherent
disadvantages, namely (1) limited size of the gene pool utilisation, as improvement
is mainly through biparental crosses, (2) low genetic variability and limited recom-
bination due to rapid fixation through inbreeding and (3) lack of crossing among
hybrid progenies (Jensen 1970). This limits any further genetic gain and response to
selection difficult for quantitative traits such as yield (Müller et al. 2017). Diallele
selective mating system involving multiple parents, which helps in creating persis-
tent gene pools, breaking undesirable linkages and accumulating favourable alleles
with simultaneous infusion of variability into breeding population through use of
3 Rice Breeding 183

Table 3.32 MAS derived rice varieties incorporated with gene(s) governing resistance to biotic
stresses released in India
Year of
S. No. Improved rice variety Genes incorporated release Developer
Bacterial blight resistant rice varieties (17)
1 Improved Pusa xa13, Xa21 2007 ICAR-IARI, New
Basmati 1 Delhi
2 Improved Samba xa5, xa13, Xa21 2008 ICAR-IIRR,
Mahsuri Hyderabad
3 Improved Lalat Xa4, xa5, xa13, 2012 ICAR-NRRI,
Xa21 Cuttack
4 Improved Tapaswini Xa4, xa5, xa13, 2012 ICAR-NRRI,
Xa21 Cuttack
5 PR122 Xa4, xa13, Xa21 2013 PAU, Ludhiana
6 PR121 Xa4, xa13, Xa21 2013 PAU, Ludhiana
7 PR123 Xa4, xa13, Xa21 2014 PAU, Ludhiana
8 Pusa 1592 xa13, Xa21 2015 ICAR-IARI, New
Delhi
9 PR124 Xa4, xa13 2015 PAU, Ludhiana
10 Pusa Basmati 1728 xa13, Xa21 2016 ICAR-IARI, New
Delhi
11 Punjab Basmati 3 xa13, Xa21 2016 PAU, Ludhiana
12 CR Dhan 800 xa5, xa13, Xa21 2016 ICAR-NRRI,
Cuttack
13 Pusa Basmati 1718 xa13, Xa21 2017 ICAR-IARI, New
Delhi
14 Punjab Basmati 4 xa13, Xa21 2017 PAU, Ludhiana
15 Punjab Basmati 5 xa13, Xa21 2017 PAU, Ludhiana
16 PR127 Xa45(t) 2018 PAU, Ludhiana
17 DRR Dhan 59 Xa33 2021 ICAR-IIRR,
Hyderabad
Blast resistant rice varieties (5)
18 Pusa 6 (Pusa 1612) Pi2, Pi54 2013 ICAR-IARI, New
Delhi
19 Pusa Basmati 1609 Pi2, Pi54 2015 ICAR-IARI, New
Delhi
20 Pusa Basmati 1637 Pi9 2016 ICAR-IARI, New
Delhi
21 DRR Dhan 51 Pi2 2018 ICAR-IIRR,
Hyderabad
22 Pusa Samba 1850 Pi1, Pi54, Pita 2018 ICAR-IARI, New
Delhi
Both Bacterial blight and blast resistant rice varieties (3)
23 Pusa Basmati 1847 xa13, Xa21, Pi2, 2021 ICAR-IARI, New
Pi54 Delhi
24 Pusa Basmati 1885 xa13, Xa21, Pi2, 2021 ICAR-IARI, New
Pi54 Delhi
25 Pusa Basmati 1886 xa13, Xa21, Pi2, 2021 ICAR-IARI, New
Pi54 Delhi
184 S. Gopala Krishnan et al.

new genotypes (Jensen 1970). Generating synthetic populations and improving them
through recurrent selection (RS) is an efficient alternative breeding strategy. Recur-
rent selection involves cyclical improvement through systematic selection of desir-
able plants from a breeding population followed by intercrossing them to enable
further genetic recombination to form a new population better than the one in
preceding cycle (Fehr 1987). It was originally proposed and extensively utilised in
cross-pollinated crops such as maize (Hull 1945). Although this method has been
utilised in self-pollinated crop like oat (Khadr and Frey 1965), effecting recurrent
crosses between selected progenies to enable further recombination have been a
major bottleneck. Gilmore (1964) suggested the use of male sterility to implement
reciprocal recurrent selection in naturally self-pollinated species for both intra-
population and inter-population improvement such as sorghum.
In rice, recurrent selection facilitated by the use of nuclear recessive male sterility
gene was proposed by Fujimaki (1979). Singh and Ikehashi (1981) developed genic
male sterile mutants in a popular rice variety, ‘IR36’, governed by a single recessive
gene (ms). The use the male sterile mutants can facilitate genetic recombination
naturally, and the naturally outcrossed seeds harvested from male-sterile plants can
be used for recurrent cycles of improvement. Although these strategies were
suggested for implementation of recurrent selection, it was not extensively used in
rice improvement. The first recurrent selection programme mainly for intra-
population improvement of rice was initiated in Brazil and Côte d’Ivoire in 1989,
with the creation of first broad-based CMS indica rice population, CAN-IRAT4
(Taillebois and Neves 1989). This initiative resulted in the release of the world’s first
irrigated rice cultivar, SCSBRS 113 Tio Taka, selected from the genetically
broad-based population CNA-IRAT 4, improved through recurrent selection
(Rangel et al. 2007).
In 1996, rice population improvement through recurrent selection was undertaken
as an alternative means of exploiting rice genetic resources, particularly in Latin
America, with the creation of populations and training of scientists by CIAT,
CIRAD and Embrapa Arroz e Feijão. Three populations were created, namely
(1) PQUI-1 in Chile, combining European (France and Italy) with North American
and Chilean germplasm (Hernaiz et al. 2000); (2) PCT-11, in Colombia, combining
African, European and Brazilian lines of the indica and japonica subspecies (Ospina
et al. 2000) and (3) GPCT-9, by CIAT and CIRAD combining commercial varieties
and lines from several Latin American and Asian countries (Martínez et al. 1997). In
order to maintain the gains, three suggestions have been made which includes,
namely (1) maintenance and assessment of large number of families (250–300
families) of the population; (2) using appropriate evaluation strategy to improve
accuracy of family assessments; and (3) using selection intensity to allow short term
gains without losing genetic variability (Hideo et al. 2002). Even though, genetic
gains for grain yield are reported through recurrent selection, till now only one
cultivar has been released through recurrent selection. A novel dominant gene based
male sterile line ‘Jiabuyu’ was utilised for population improvement of two
populations, subjected to two cycles of recurrent selection through natural
outcrossing. Even though, 45 lines with higher performance as compared to base
3 Rice Breeding 185

population was identified, the improved lines were inferior to the best yield check,
NSIC Rc222 (Pang et al. 2017) (Table 3.33).
In order to improve the population improvement through recurrent selection,
three modifications have been suggested based on the learnings from 15 years of
recurrent selection (Vales 2010). First, adopting a modified method of Back recur-
rent selection (BCRS), a blend of backcross and recurrent selection which involves
the progressive increase of recipient parent plants in the progressive cycles of
population improvement in the ratio of two-third in the first cycle, which is increased
to three-fourth in the next cycle leading to improvement of polygenic traits in the
background of recipient cultivar. Second, is Simple and Efficient Breeding (SERB)
based on the Narrow-Based Population (NBP) consisting of four or five progenitors
with each possessing the very best for each targeted trait. It is simple, inexpensive,
rapidly successful, easy to adjust and feasible. These populations can be readily
adapted suited to breeders’ normal practices, which allows breeders to closely
monitor changes in breeding objectives and complementary tools. The first
narrow-based populations were created in 2000 (Vales et al. 2000). In 2003, the
Fundacion para la Investigacion Agricola (DANAC) of Venezuela extracted from
the narrow-based population PCT-16, which led to the development of three
cultivars, namely ACD 25–28, ACD 25–26 and ACD 25–40, released in Colombia,
Venezuela, Panama, Costa Rica and Equator by Cultivos y Semillas el Aceituno
(Aceituno) of Colombia (Gamboa et al. 2005). Third, is Plant-parasite reciprocal
recurrent selection (2P2RS), which promotes the adaptation of the parasites (patho-
gen such as Magnaporthe oryzae) as a tool for selection of resistant plants during the
breeding to produce genotypes with durable resistance. Alternately, SERB could be
combined with the parallel and interlaced recurrent selection (PAIRS). In PAIRs,
selection is exercised for earliness and grain size in S0 generation, for complete
resistance to leaf blast in S1 plants, partial resistance to leaf and neck blast, earliness,
yield components in S2 lines; gelatinisation temperature and alkali spreading value
in S3 grains (Vales et al. 2009). Morais Junior et al. (2017) estimated a mean genetic
gain of 1.98% for grain yield in CNA12S, a broad-based population of irrigated rice.
Alternately, the efficiency of the recurrent selection method can be improved by
reducing cycle time, increasing selection intensity or through recurrent genomic
selection (Meuwissen et al. 2001).

3.18 Genomic Selection

Even though marker-assisted breeding has helped in shortening the time taken for
rice varietal development, most of the success has been in transferring major genes/
robust QTLs into popular rice varieties. It has found limited use in improving
quantitative traits which are influenced by a large number of genes with small
effects. Genomic Selection (GS) aims to address this limitation with the potential
to improve genetic gain and breeding efficiency in crops. Genome-wide markers and
phenotypic data of the target traits from a training population are used to predict
breeding values (genome estimated breeding values; GEBVs) of the untested
186 S. Gopala Krishnan et al.

Table 3.33 MAS derived rice varieties incorporated with gene(s)/QTL(s) governing with toler-
ance to biotic and abiotic stresses released in India
Improved rice Year of
S. No. varieties QTLs incorporated release Developer
Drought tolerant rice varieties (1)
1 IR64 Drt1 (DRR qDTY2.2, qDTY4.1 2014 ICAR-IIRR,
Dhan 42) Hyderabad
Submergence tolerant rice varieties (6)
2 Swarna Sub1 Sub1 2009 ICAR-NRRI and
IRRI
3 Samba Sub1 Sub1 2011 ICAR-NRRI and
IRRI
4 CR1009 Sub1 Sub1 2013 ICAR-NRRI and
IRRI
5 Ranjit Sub1 Sub1 2016 AAU, Jorhat
6 Bahadur Sub1 Sub1 2016 AAU, Jorhat
7 CO43 Sub1 Sub1 2018 TNAU,
Coimbatore
Both Drought and submergence tolerant rice varieties (3)
8 DRR Dhan 50 qSub1, qDTY2.1, qDTY3.1 2018 ICAR-IIRR,
Hyderabad
9 CR Dhan 801 qSub1, qDTY1.1, qDTY2.1, 2018 ICAR-NRRI,
qDTY3.1 Cuttack
10 CR Dhan qSub1, qDTY1.1, qDTY2.1 2018 ICAR-NRRI,
802 (Subhash) Cuttack
Both Bacterial Blight resistant and salinity tolerant rice varieties (1)
11 DRR Dhan 58 xa5, xa13, Xa21, Saltol 2021 ICAR-IIRR,
Hyderabad
Both Bacterial Blight resistant and low phosphorus tolerant rice varieties (1)
12 DRR Dhan 60 xa5, xa13, Xa21, Pup1 2021 ICAR-IIRR,
Hyderabad
Herbicide tolerance
13 Pusa Basmati 1979 Mutant AHAS allele 2021 ICAR-IARI,
New Delhi
14 Pusa Basmati 1985 Mutant AHAS allele 2021 ICAR-IARI,
New Delhi

populations, which are yet to be phenotyped based on their genotypic data (Crossa
et al. 2017). Unlike MAS, GS does not involve the detection of significant QTLs for
different traits but enables breeding efficiency by enabling selecting elite genotypes
based on GEBVs without the need for phenotyping large populations. GS involves
rapid fixation of the genotypes by employing RGA/DH/Speed breeding from crosses
between ~20 elite lines. A set of around 10,000 fixed lines are generated from
20 crosses, out of which a training population consisting of a subset of ~2000
lines are phenotyped, while all the fixed lines are genotyped. The phenotypic and
genotypic data of the training populations are used for developing prediction models
3 Rice Breeding 187

Fig. 3.13 Schematic representation of genomic selection for rice varietal improvement

based on which the GEBVs of the remaining 8000 lines are predicted. The top
20 lines are taken as parents for the next cycle of improvement, while a set of top
performing lines are taken up for further multi-location evaluation and varietal
improvement. The overall scheme for GS is schematically summarised in Fig. 3.13.
The prediction ability increases with higher marker density and a larger sample
size. Effective GS models can be built using a training population from 2 to 13% of
the total population (Guo et al. 2019). The prediction accuracy improves with the
addition of related genotypes in the training population without compromising on
the genetic variation than increasing the population size. Parametric models such as
genomic best linear unbiased prediction (GBLUP), ridge regressions best linear
unbiased prediction (RRBLUP), partial least square (PLS), least absolute shrinkage
selection operator (LASSO), elastic net, and Bayesian methods including BayesA,
BayesB, BayesC, BayesR, etc. and non-parametric models such as random forest
(RF), support vector machine (SVM), reproducing kernel Hilbert space (RKHS),
deep learning, etc. are used for GS. Comparison of the predictive ability of these
methods has shown varying results. Therefore, it has been suggested to treat the GS
method as a parameter and evaluate the predictive abilities of all methods using cross
validation and select the best method with maximum accuracy for a particular
breeding programme (Xu et al. 2017). In rice, GS has shown moderate to high
predictive ability, with as high as 0.8 for culm length (Onogi et al. 2015) to as low as
0.3 for grain yield (Spindel et al. 2015).
188 S. Gopala Krishnan et al.

GBLUP has been used for predicting a set of top 100 crosses with yield grains of
upto 16% from a set of 21,667 untested hybrids, using a set of 278 hybrids derived
from 210 RILs as training population (Xu et al. 2014). GBLUP has been effectively
used for predicting the performance of 100 hybrids derived from half diallel cross,
involving 21 parents that are different from the parents of hybrids used for develop-
ing models in the training set for six agronomic traits (Cui et al. 2020), which has
demonstrated the use of GS in hybrid rice breeding as well. Genotyping consumes
substantial costs of breeding in GS. SNP arrays of different densities including 44 K,
50 K, Rice 6 K, RiceSNP50, C7AIR and 1 k-RiCA. Optimised experimental
designs, precise high throughput phenotyping platforms, low cost genotyping
technologies and improved models can help in improving rice varieties using GS
(Xu et al. 2021a).

3.19 Genome-Editing

Spontaneous and induced mutagenesis has been used for generating random
mutations of limited density in the genome, out of which only a few of them are
economically useful (Jacob et al. 2018; Shoba et al. 2017). Spontaneous mutations in
the crop genome have been creating a large number of nucleotide substitutions,
which are detected as single nucleotide polymorphisms (SNPs) through genome
sequencing. Among them, a large number of loss of function (LoF) alleles have been
identified from whole genome resequencing data. In rice, 198,609 premature stop
codon inducing single nucleotide variants were found from the 3010 rice genotypes
sequenced (Monroe et al. 2020). LoF alleles from spontaneous mutations have been
greatly helpful in the evolution of modern-day rice crop through loss of shattering
habit, prostrate growth habit, increase in grain size and grain number, better grain
quality (Table 3.34). However, the selection process during domestication and
improvement has created a genetic bottleneck that has reduced the variation avail-
able in the crop for utilisation in further improvement (Shan et al. 2014).
Targeted genome-editing using clustered regularly interspaced short palindromic
repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) such as Cas9 enables
the creation of precise and high-density mutations in the gene of interest (Jinek et al.
2012), which hold enormous potential for the creation of hitherto unknown superior
alleles in economically important genes, so as to enable the development of desired
plants with higher yield, improved grain quality, and resistance to herbicides,
diseases and insect pests (Huang et al. 2018). Gene editing also helps in increasing
the allelic diversity in functional genes of interest, which can help in easy and rapid
improvement of crop like rice, where functional characterisation of a large number of
genes have been accomplished (Hu et al. 2016).
The CRISPR/Cas gene editing creates double strand breaks and two repair
pathways, namely nonhomologous end joining (NHEJ) and Homology directed
repair (HDR) are utilised in creating mutations in the target loci. NHEJ generates
random insertions and deletions at target sites with extreme precision and is a
popular pathway for generating mutants. In contrast, HDR offers generation of
3 Rice Breeding 189

Table 3.34 Some examples of naturally occurring beneficial loss of function (LoF) alleles caused
by spontaneous mutations that have helped in the evolution and improvement of rice
Gene Mutation type Mutation effect Reference
LoF alleles created by single nucleotide substitutions
Bh4 SNP— White hull Zhu et al.
premature stop (2011)
PROG1 SNP— Erect growth Wu et al.
premature stop (2018)
OsWaxy SNP— Glutinous grains Zhou et al.
splicing defect (2016)
SLR1 SNP— Dwarf plant Wu et al.
premature stop (2018)
GS3 SNP— Long grain Lu et al.
premature stop (2013)
LoF alleles created by Insertions and Deletions (InDels)
qSH1 InDel— Non-shattering Konishi et al.
frameshift (2006)
OsGn1A InDels— Increase grain number Ashikari et al.
frameshift (2005)
DEP1 InDels— Reduce length of the inflorescence internode, Huang et al.
frameshift more grains per panicle (2009)
bHLH Indel— White pericarp Sweeney et al.
frameshift (2006)
OsLG3b Indel— Increased grain size Yu et al.
frameshift (2018)
Pi21 InDels— Blast resistance Fukouka et al.
frameshift (2009)
Bad2 Indel— Fragrant grains Chen et al.
frameshift (2008)
Domestication, diversification and improvement

desired mutations precisely at the target site. Additionally, base editors can also
engineer efficient and precise nucleotide substitutions (especially CG to TA, AT to
GC), while prime editing can introduce all types of point mutations and InDels at
target gene without the need for double stranded breaks or donor DNA templates in
rice (Hua et al. 2018; Hua and Tao 2019; Hua et al. 2020a, b; Lin et al. 2020).
Genome-editing approaches involving the CRISPR/Cas9 system and its
modifications including base editing and prime editing have been utilised in rice
for the creation of novel alleles for various agro-morphological traits such as plant
architecture, panicle architecture and grain characters, resistance to biotic stresses
such as blast, bacterial blight and RTSV, tolerance to abiotic stresses such as
drought, salinity and cold stress, improvement of grain, cooking and nutritional
quality and herbicide tolerance (Table 3.35).
190 S. Gopala Krishnan et al.

Table 3.35 Application of genome-editing for improving agro-morphological and stress tolerance
traits in rice
Trait improvement in
S. No. Target trait Target gene(s) mutants References
(1) Genome-editing using CRISPR/Cas9 system
(a) Agro-morphological traits
1. Plant SD1, SCM1, Semi-dwarf plant height Hu et al. (2016) and
Architecture SCM2, SCM3, sturdy stem, No. of tillers Cui et al. (2020)
OsTB1
2. Panicle DEP1, IPA1, Panicle branching, grain Miao et al. (2018)
architecture Gn1a PYL1, number per panicle,
PYL4, PYL6
3. Grain GS3, GW2, Grain size, grain weight, Zeng et al. (2020),
characters GW5, GW6, aroma Xu et al. (2016) and
GW8, Usman et al. (2021)
OsBADH2
(b) Resistance to biotic stresses
4. Blast OsERF922, Resistance to blast disease Wang et al. (2016),
disease OsPi21, Foster et al. (2018)
OSALB1, and Li et al. (2019)
OsRSY1
5. Bacterial OsSWEET11, Resistance to bacterial blight Kim et al. (2019),
blight OsSWEET13, disease Olivia et al. (2019),
disease OsSWEET14 Xu et al. (2019) and
Li et al. (2020)
6. Rice eIF4G Resistance to Rice Tungro Macovei et al.
Tungro Spherical Virus (2018)
Spherical
Virus
(c) Tolerance to abiotic stresses
7. Drought OsPYL9, leaf cuticle wax, stomatal Usman et al. (2020),
DST. conductance, transpiration Liao et al. (2019)
OsSRL1, rate, reduced stomatal and Kumar et al.
OsSRL2 density, enhanced leaf water (2020)
retention, reduced number of
stomata
8. Salinity OsRR22, Salinity tolerance, shoot Kumar et al. (2020),
DST, length, shoot fresh and dry Yue et al. (2020)
OsmiR535 weight osmotic tolerance and Zhang et al.
osmotic tolerance (2019)
9. Cold OsAnn3, Tolerance to cold Shen et al. (2017)
tolerance OsMYB30 and Zeng et al.
(2020)
(d) Improving rice grain quality
10. Physical GS3, GW2, Increasing grain length and Gao et al. (2020),
parameters GW5, TGW6, width Xu et al. (2016) and
OsFWL Zeng et al. (2020)
11. Eating and OsWaxy, Decrease in amylose, high Zhang et al. (2018),
cooking OsBEI, amylose, increase in total Huang et al. (2020),
quality OsBEIIb, Wang et al. (2020),
(continued)
3 Rice Breeding 191

Table 3.35 (continued)

Trait improvement in
S. No. Target trait Target gene(s) mutants References
ISA1, OsAP6, soluble sugar, enhanced Sun et al. (2017)
OsAAP6, aroma and Ashokkumar
BADH2 et al. (2020)
12. Nutritional OsOr, Increased β-carotene content, Endo et al. (2019),
quality OsPLDα1, High linoleic acid; Low Khan et al. (2019),
OsFAD2.1, Cadmium accumulation Abe et al. (2018),
OsNramp5 Tang et al. (2017)
and Chang et al.
(2020)
(2) Genome-editing using base editing approach
13. Grain yield SPL14, Grain weight, size, shape, Hua and TaoX 2019
and its SPL17, number and quality and Hua et al.
components SPL16, 2020a, 2020b)
SPL18,
SPL17, SLR1
14. Nitrogen NRT1.1B High NUE Lu and Zhu (2017)
use
efficiency
15. Grain SBEIIb, Waxy High amylose Li et al. (2017) and
quality Xu et al. 2021a,
2021b
16. Herbicide OsALS1, Tolerance to imidazolinones, Kuang et al. (2020),
tolerance OsACC, Aryloxyphenoxypropionate Liu et al. (2020) and
OsTubA2 and dinitroaniline Liu et al. (2021)
(3) Genome-editing using prime editing approach
17. Panicle OsALS, Dense panicle architecture Tang et al. (2020)
architecture OsKO2,
OsDEP1,
PDS
18. Herbicide OsPDS1, Tolerance to imidazolinones Xu et al. (2020a,
tolerance OsACC1, Aryloxyphenoxypropionate 2020b)
and OsWaxy1 and amylose content
Amylose
19. Herbicide OsALS, Tolerance to imidazolinones, Xu et al. (2020a,
tolerance OsACC, Aryloxyphenoxypropionate, 2020b)
and OsDEP1 high NUE
Nitrogen
Use
efficiency
20. Herbicide OsALS, APO1 Tolerance to imidazolinones Hua et al. 2020a,
tolerance and high grain number 2020b
and panicle
organisation
192 S. Gopala Krishnan et al.

3.20 High Throughput Phenotyping in Rice

Accuracy of phenotyping has been a challenge in rice breeding research from the
beginning. High throughput phenotyping is a contemporary development in crop
research, which involves development of an accurate, non-destructive method for
grain-trait analysis and capability of handling large populations is the key for
improving different traits in rice. With the rapid development of novel sensors,
imaging technology, and analytical methods, a number of platforms have been
developed for phenotyping (Song et al. 2021). Modern integrated sensors (visible
light, near-infrared, far-infrared, fluorescence, multispectral, laser, hyperspectral,
etc.) help in acquisition of plant dynamic growth and development phenotypic
datasets, which contain valuable information about plant genetics and mutations.
These sensors are widely used in the analysis of plant height, chlorophyll content,
LAI, disease susceptibility, drought stress sensitivity, nitrogen content, and yield of
crops. Hyperspectral (such as near-infrared) photos can be combined with multi-
spectral analysis to non-destructively estimate the nutrient components in rice such
as amylose and other carbohydrates. The main application of phenotyping
techniques is integrating a variety of phenotypic technologies to evaluate abiotic
and biotic stress, as well as measure traits associated with yield potential to promote
rice genetic improvement and breeding. Panicle segmentation under field conditions
in rice is challenging due to the complexity of the field environment, involving
illumination differentials and panicle shape deformations. Panicle-SEG-CNN model
based on rice plot images have been developed for robust and accurate results for
rice panicle segmentation in the field (Xiong et al. 2017). A labour-free instrument to
thresh rice panicles, evaluate rice yield traits has been developed, which could
calculate number of filled spikelets, kernel length and width, and 1000-kernel weight
based on an RGB camera and weight sensor, with a throughput of 1440 plants per
day (Duan et al. 2011). Applications have been developed for high throughput
evaluation of tolerance to drought, salinity, disease detection and yield estimation
in rice (Table 3.36).
Deep learning (DL), a subset of Machine Learning, is a versatile tool for
providing reliable predictions of complex and uncertain phenomena by assimilating
large amounts of heterogeneous data. DL have been applied for analysis of
phenotyping data in a wide range of areas from organ counting to crop disease and
pest recognition in rice (Table 3.37). At ICAR-IARI, Nanaji Deshmukh National
Plant Phenomics Facility has been established with different sensors for high
throughput imaging of plants, enabling continuous phenotyping of large number
of plants throughout the developmental stages.

3.21 All India Coordinated Rice Improvement Project System

The All India Coordinated Rice Improvement Project (AICRIP) was established in
1965 at Hyderabad, with the responsibility to organise multi-disciplinary, multi-
location testing for developing suitable varietal and production technologies was one
3 Rice Breeding 193

Table 3.36 Application of high throughput phenotyping techniques in rice

Application Traits Reference
Drought Shoot biomass related traits, leaf stay-green-related Guo et al. (2018)
tolerance traits, morphological traits, histogram texture traits,
and texture traits derived from a gray-level
co-occurrence matrix
Salinity Transpiration rate, plant growth rate, total shoot area, Hairmansis et al.
tolerance senescent shoot area (2014) and
Al-Tamimi et al.
(2016)
Diseases Colour and morphology, transpiration rate, Zhou et al. 2014a,
detection photosynthetic rate, spectral vegetation indices 2014b
Direct yield Panicle traits, spike number, ear density, grain number Xiong et al. (2017)
estimation and size, 3D spike morphological phenotypes and Duan et al. (2011)
Indirect yield Canopy height and structure; leaf area index Zhou et al. (2017)
estimation

Table 3.37 Applications of deep learning (DL) in high throughput phenotyping in rice
Preferred
Broad areas Key issues DL model References
Organ identification Rice detection and counting in the field An Zhou et al.
and counting improved (2019)
R-FCN
model
Flowering panicle detection and heading CNN Desai et al.
date estimation (ResNet-50) (2019)
Leaf and panicle segmentation, and leaf to FPN-mask Yang et al.
panicle ratio (LPR) calculation (2020)
Crop seed variety Identification and differentiation of ten iRSVPred Sharma
classification major varieties of basmati rice based on et al.
seed images (2020)
Crop yield To quantify rice kernels per panicle Faster Wu et al.
prediction RCNN (2019)
(ResNet101)
Weed and crop Rice seedling and weed image FCN Ma et al.
recognition and segmentation at the seedling stage in (SegNet) (2019)
segmentation paddy fields
Crop diseases and To construct video detection system for faster- Li et al.
pest recognition plant diseases and pests RCNN (2020)
CNN convolutional neural networks, FCN fully convolutional network, FPN feature pyramid
networks, iRSVPred a web server for artificial intelligence based prediction of major basmati
paddy seed varieties, RCNN region-based convolutional neural network, ResNet residual network,
R-FCN region-based fully convolutional network

of the milestones in the history of rice research in India. The coordinated testing
programme under AICRIP was envisaged with seven key features (Freeman and
Shastry 1972), which includes:
194 S. Gopala Krishnan et al.

3.21.1 System of Coordinated Testing

The system involves planning by the group conducting the trials and those interested
in testing the performance of their entries in the trials, to organise the trials during
annual workshop sessions, centralised pooling of seed for trials and dispatch by the
coordinating centre, well-defined trial plans from layout to data collection forms,
assembly of data from various centres for compilation and calculation of national
and zonal yields and presentation of data in timely progress reports issued annually.

3.21.2 Intent of State and Central Institutes Towards Achieving

the Common Objective

The development of a working memorandum of understanding between the state

centres and the coordinating centre. Basic to the effectiveness of a written memoran-
dum is the ‘intent’ of the parties involved and the spirit of cooperation that exists
among them. The cooperation had been achieved to a great extent before a memo-
randum of understanding was evolved, since both state and centre agencies usually
have one common objective of rice improvement.

3.21.3 Designing Research for Solving Problems in Rice Production

The research programmes at the coordinating centre and other national and state
centres are designed to solve problems of rice production that will provide early
pay-off in farmers’ yields and national production.

3.21.4 Emphasise the Flexibility of Action

The programme emphasises flexibility of action, with more flexibility than normally
exists in governmental agencies is required for a coordinated programme to function
effectively.

3.21.5 Team Spirit Among Rice Workers

The team spirit among rice workers has developed from the exchange of seed
materials, sharing of ideas in workshops, and information in progress reports.
3 Rice Breeding 195

3.21.6 Multi-disciplinary Approach with Inter- and Intradisciplinary

Exchange of Ideas

A multi-disciplinary approach to the study of the rice crop is used. Some rice
problems such as insects and diseases need to be tackled from several angles, so
efforts of the workers in different disciplines at different locations focus on the same
problem are coordinated. Without the cooperation of breeders on the one hand, and
of pathologists and entomologists on the other, a considerable range of host-plant
resistance could not be developed. Furthermore, it aids intradisciplinary coordina-
tion in studies of the disease organism or of the insect concerned. While more
coordination is required to realise benefits more quickly in both phases, the progress
made in these two aspects of coordination is exemplary. Coordination was pursued
more vigorously to attain rapid progress in solving national problems in rice.

3.21.7 Sharing of Resources for Identifying Productive and Stable

Genotypes

The merit of the multi-location approach helps in testing a large number of entries
across several locations. Limitations in resources of local experiment stations did not
provide a means to quickly evaluate materials or to create populations large enough
to permit the identification of the best strain for a locality. Under the coordinated
system, the crossing done at many locations creates enough progeny for effective
selection, and evaluation at several locations allows potential varieties to be
identified regardless of their origin. More the kinds of environment under which a
variety has been proven, the more stable its performance is likely to be when grown
by farmers in many different environments.
AICRIP was started with 22 centres (19 main and 3 testing centres) with 7 zonal
centres and 12 regional centres. Currently, there are 45 funded centres and 99 volun-
tary centres. AICRIP capitalised upon the available research infrastructure in differ-
ent states of India for multi-location testing and successfully introduced a national
perspective in technology development and testing. AICRIP was later elevated to the
status of Directorate of Rice Research (DRR) from April 1975, with the added
mandate of pursuing research on irrigated rice. The Directorate was upgraded to
ICAR-Indian Institute of Rice Research (ICAR-IIRR) in December 2014.
Realising the complexities in the rice production ecosystem, the prevalence of
insect pests and diseases as well as grain quality requirements of rice consumed,
AICRIP evolved need-based programmes/trials over the years to identify improved
genotypes with better yield potential along with appropriate crop management
practices for release as varieties. Initially, emphasis was on improving yields through
improved plant type and management practices largely for irrigated ecosystems,
which led to the development and release of a large number of short statured high
yielding varieties (HYVs), which heralded the ‘Green Revolution’ in India. Follow-
ing the success in improving yields, priority was given for sustaining the yield and
quality improvement. As a result improved rice varieties with inbuilt resistance to
196 S. Gopala Krishnan et al.

major biotic stresses and desirable grain and cooking quality were developed,
which includes the successful development and release of the first semi-dwarf high
yielding Basmati rice variety (Gopalakrishnan et al. 2008).
The 1990s witnessed efforts in developing hybrid rice technology and multi-
location testing to validate their superiority over varietal checks at least by 10%, and
also non-Basmati grain quality to meet the export markets. At the beginning of the
century, trials to address soil stress problems and aerobic trials were initiated for
developing and testing genotypes for water limited environments and hill trials for
testing genotypes with cold tolerance. With advances in varietal development
through effective use of modern biotechnological tools, guidelines for rapid testing
and release of near isogenic lines (NILs) in the background of popular rice varieties
incorporated with genes governing resistance to biotic and abiotic stresses have
been developed. Separate trials for testing of rice NILs developed through marker-
assisted selection (MAS) have been initiated in 2008 and biofortification trials for
testing genotypes biofortified with micronutrients such as zinc, iron along with
protein started since 2012.

3.22 Varietal Testing in AICRIP Trials

AICRIP led by ICAR-IIRR, Hyderabad, enables testing of promising elite materials

(varieties, hybrids, etc.), thereby helping identify the stable, high-yielding, or supe-
rior genotypes suited for different agro-climatic conditions. A total of 35 varietal
trials and 4 hybrid trials are being conducted in different ecologies, namely Irrigated,
Rainfed Upland (direct seeded), Rainfed Shallow lowland, Semi-deep water, Deep-
water, Hills, Saline alkaline and Boro. The irrigated ecology trial is further classified
into Early transplanted, Mid-early, Medium and Late based on the duration of the
crop season. Additionally, trials are conducted for grain types including Basmati,
Aromatic short grain and medium slender grain. Separate biofortification, low
phosphorus, low nitrogen, new plant type (NPT) and aerobic trials are also
conducted along with NILs trials for Drought, Submergence, Combined stresses,
Bacterial blight and blast diseases. These trials are being conducted at 123 locations
across seven zones in 28 states and 2 union territories across India (Table 3.38).
Among all these trials, Basmati trials are restricted to the regions notified as Basmati
Geographical Indication (GI) vide GI No. 145 of the Geographical Indication
Registry, Government of India through certificate No. 238 dated 15.02.2016, span-
ning seven states, namely Delhi, Haryana, Punjab, Uttarakhand, Himachal Pradesh,
Jammu and Kathua districts of Jammu and Kashmir, and 27 districts from western
Uttar Pradesh.
Thus, the varieties are identified and released, not only for the zones/regions from
where they have been bred but also for other regions if they are found to perform in
different zones across the countries. This also helps in complementing the efforts of
the centres in respective zones, where the breeding programme is either not strong or
still in its infancy and caters to the needs of the specific region. In the process, the
best material gets identified for release in different regions/states.
3 Rice Breeding 197

Table 3.38 Details of zonation and the areas covered under each zone in the AICRIP trials
Zone Name of the
No. zone States
Zone Hilly zone Hilly regions from the states of Himachal Pradesh, Manipur,
I Nagaland, Sikkim, Meghalaya, Hilly regions of Jammu and Kashmir,
Uttarakhand, West Bengal and Karnataka
Zone Northern Northern India including Delhi, Haryana, Punjab, Rajasthan, Plains of
II zone western Uttar Pradesh, plains of Uttarakhand and Jammu and Kashmir
Zone Eastern zone Eastern India comprising of Odisha, Bihar, Jharkhand, West Bengal,
III parts of eastern Uttar Pradesh
Zone North Northeastern India including Assam, Manipur and Tripura
IV Eastern zone
Zone Central zone Central India including Madhya Pradesh, Chhattisgarh, parts of
V Maharashtra
Zone Western zone Western India including Gujarat, Goa and parts of western
VI Maharashtra
Zone Southern Southern India including Andhra Pradesh, Telangana, Karnataka,
VII zone Tamil Nadu, Kerala, Puducherry, Andaman and Nicobar Islands

AICRIP adopts a unique model that facilitates joint planning and implementation
of multi-location testing along with an exchange of breeding and germplasm mate-
rial. The ‘National Evaluation System’ is a three-tier system involving 3 years of
testing in the trials including Initial Varietal Trial (IVT) for 1 year followed by
2 years of advance varietal trials (AVT 1 and AVT 2). Every entry nominated the
first year of trial, either IVT or AVT-1 NILs are assigned an initial evaluation trail
(IET) number. Issuing IET numbers to cultures was first initiated in AICRIP, which
is now adopted by coordinated testing projects in other crops as well. The entries in
the respective trials, which produce consistently superior performance over the best
checks are identified. Under the present system, a given entry needs to exhibit 5%
yield superiority over the best check either on an overall or regional basis for
varieties. For hybrids, there are four Initial Hybrid Rice Trials (IHRT), namely
IHRT-E (Early duration <120 days), IHRT-ME (mid-early duration, 121–130
days), IHRT-M (Medium duration, 131–140 days) and IHRT-MS (Medium Slender
Grains) are constituted based on duration and grain type, respectively. The IHRT
comprises only the experimental hybrids and the corresponding checks, while the
hybrids promoted are tested in AVT 1 and AVT 2 trials under irrigated transplanted
conditions, and the promising hybrids are compared with the promising elite inbred
lines also. The hybrid entries should exhibit 10% yield superiority over the best
varietal check and 5% superiority over the hybrid check. Parallelly, they are also
screened for resistance to major insect pests and diseases at hot spot locations, as
well as controlled conditions with artificial inoculation for 2 years in NSN
1 (National Screening Nurseries 1) and NSN 2 to assess their reaction to evolving
pests and diseases. The entries were also tested for their grain quality and agronomic
performance (Babu et al. 2016).
The promising genotypes identified to perform superior in more than two states
where the performance in the third or final year of testing either overall/regional/
198 S. Gopala Krishnan et al.

states, based on the extensive evaluation for 3 years in AICRIP trials. The concerned
breeder submits the proposal for identification of the said promising variety in the
prescribed proforma along with all the supplementary data and relevant information
for consideration by the Variety Identification Committee (VIC) chaired by either
Deputy Director General (Crop Sciences), which meets annually during the Annual
Rice Group Meeting. Alternately, the genotypes with superior performance in a
specific state either through AICRIP or the State trials are submitted for release by
the State Variety Release Committees (SVRC). The superior test entries identified in
the crop workshop/group meeting or the SVRC are then submitted for release and
notification in the prescribed proforma, along with their DNA fingerprinting data in
comparison with a check variety, Indigenous Collection (IC) number issued by
ICAR-National Bureau of Plant Genetic Resources, New Delhi, by submitting
100 grams of seeds of the candidate variety and good quality photographs for
consideration by the central sub-committee on crop standards, notification and
release of varieties (CSCS&NRV). The proposals are thoroughly discussed by the
CSCS&NRV in the meeting, chaired by the Deputy Director General (Crop
Sciences) and the committee recommends the release and notification of the varieties
either as Central or as State releases, which is then notified in the Gazette of India
under the section 5 of the Seeds Act, 1966 (54 of 1966) by the Ministry of
Agriculture and Farmers Welfare (Department of Agriculture, Cooperation and
Farmers Welfare). The process for varietal testing, identification and release is
depicted schematically in Fig. 3.14.
AICRIP is a continuously evolving system by taking into consideration the
technological developments from time to time and the need in devising testing
protocols for new rice varieties in different rice ecologies through multi-location
testing. Considering the fact that near isogenic trials (NILs) are developed in the
background of popular rice varieties, which have already been tested in the AICRIP
trials, NILs trials have been initiated for fast tracking the products developed through
marker-assisted backcross breeding. The NILs are tested only for 2 years by testing
in AVT 1 NILs and AVT 2 NILs, along with the recurrent and the donor parents for
validating the trait, which has been incorporated through MAS.

3.23 Seed Supply Chain in Rice

Seed is the basic and the most critical inputs for sustainable rice production. Seed is
an important input affecting rice production and it contributes 15–20% of the crop
yield. Therefore the quality of seeds plays a very important role in bridging the gap
between potential yield and realised yield. While breeding addresses the varietal
replacement rates by producing improved varieties with better productivity, seed
replacement rate addresses the adoption of these improved varieties with quality
seeds. Seed system encompasses the framework of institutions (either public/pri-
vate)/and farmers groups and their role in seed multiplication, processing, quality
assurance and marketing of seeds. There exist formal, informal and hybrid (formal
and informal) seed systems in rice. The formal seed system is a systematic,
3 Rice Breeding 199

Fig. 3.14 Testing the nominations under the AICRIP system, identification, release and notifica-
tion of a Central Release rice variety

well-organised system involving a series of activities leading to the production and

supply of certified seeds of varieties notified under section 5 of the Seeds Act, 1966
(54 of 1966). It starts with the development and release of varieties/hybrids, and their
systematic maintenance guided by the principles of maintaining varietal identity,
genetic purity, optimal physical, physiological and sanitary quality (Reddy et al.
2007). At present, the formal seed delivery system in rice consists of 2 national
corporations, namely National Seed Corporation and State Farm Corporation of
India, 16 State Seed Corporations, 25 Seed Certification Agencies, 2 Central and
132 State Seed Testing Laboratories in addition to 187 private registered seed
companies.
The Indian Council of Agricultural Research (ICAR) is mandated to produce
nucleus and breeder seed as per the indent received from the Department of
Agriculture, Cooperation and Farmers Welfare, Ministry of Agriculture and Farmers
Welfare (DAC & FW), Government of India. The nucleus seed of the rice varieties is
maintained as per standard procedures by the respective centres/institutes from
where the rice variety/hybrids are released. The breeder seed is produced based on
indent from different agencies. The breeder seed production is demand driven and
the indents received from National Seed Corporation, State Seeds Corporations,
200 S. Gopala Krishnan et al.

State Farm Corporation of India, other public as well as private sector organisations
such as Seed Association of India, National Seed Association of India, etc. are
consolidated by the seeds division of DAC, which is forwarded to ICAR. In the
ICAR, the Crop Science Division coordinates the breeder seed production of rice in
India, with the cooperation of various State Agricultural Universities (SAUs) and
public sector crop-based institutes (NAAS 2018). The breeder seed indents of rice
varieties received from ICAR are allocated for production to the respective institutes/
SAUs and/or their centres after thorough discussion at the Annual Rice Group
Meeting held every year in April/May. Based on the allocation of breeder seeds to
be produced for different rice varieties, the Breeder Seed Proforma I (BSP-I) is
prepared and sent to the respective centres by the Crop Coordinator of rice, ICAR-
IIRR, Hyderabad, with the details of the quantity of breeder seed allotted for
production for each variety/hybrid by the institute/SAU, which is also uploaded in
the seed net portal (https://seednet.gov.in). Upon receiving the BSP-I proforma, the
seed production is planned at the respective centres and the scientist responsible for
the production of breeder seed plans and takes up the planting of the rice varieties
based on the indent and prepares the BSP II proforma, indicating the name of the rice
variety and the area planted, date of planting, under each variety for breeder seed
production based on the indent.
When the rice crop is at flowering, monitoring of the crop is undertaken with a
monitoring team comprising of originating breeder/sponsoring breeder along with
one representative each from the National Seed Corporation and the respective State
Seed Certification Agency for inspecting the breeder seed production plots. Based on
the inspection by the monitoring team, the inspection report is prepared in the
BSP-III proforma indicating the name of the varieties, area sown, location of the
field, authority under the date of BSP-I, date of proforma BSP-III report of the
monitoring team which is signed by every member of the monitoring team is
distributed to ADG(Seeds), ICAR; Deputy Commissioner (Seeds), DAC; Director,
ICAR-IIRR, Hyderabad; Director, ICAR-IISR, Mau; the competent authority of the
institute/SAU, Nodal officer (Seeds), Chief Seed Certification Officer of the state and
the area manager of National Seed Corporation. After the harvesting, threshing,
processing (in case processing is not complete, estimated likely quantity of
processed seed is indicated in BSP IV) and cleaning of the seeds of different rice
varieties, the scientist responsible for the production of breeder seed production
prepares the BSP IV indicating the quantity of breeder seed produced for each rice
variety against the quantity allocated and distributes to all the concerned as in BSP
III. Based on the allocation, the respective agencies lift the breeder seed produced for
a given rice variety and finally, the BSP-V is filed indicating primarily lifting and
non-lifting position of breeder seed by various agencies. The breeder seed is used to
produce foundation seeds (either one or two stages as FS-I and FS-II), which are then
utilised for the production of certified seeds, which are distributed to the farmers.
Besides certified seeds, significant quantities of truthfully labelled seeds of different
rice varieties are also produced under the supervision of the breeders/seed scientists
which are distributed to the farmers. A schematic diagram presenting the
3 Rice Breeding 201

Fig. 3.15 The seed supply chain for rice varieties

interlinkage between different organisations involved in the production of quality

seeds is presented in Fig. 3.15.
Of the 1436 rice varieties released in the country as many as 320 rice varieties are
in the breeder seed production (BSP) chain. Among these, 63 varieties have maxi-
mum adoption with the farmers within one state or across several states in terms of
their spread. Based on their popularity among the farmers, consumers, some of these
varieties have achieved the status of mega-varieties. These include Jaya, IR36, IR64,
MTU7029 (Swarna), BPT5204 (Samba Mahsuri), MTU1010 and Pusa
Basmati 1121.

3.24 Emerging Challenges in Rice Breeding

Sustaining rice productivity in the face of climate change is one of the major
challenges in rice production not only in India but also across the world. Broadly,
the key issues to be addressed in rice research are the decline in arable land,
increasing irrigation water scarcity, global climate change, shortage of agricultural
labours, high labour wages for cultural operations and increasing consumer demand
for high-quality rice (which often comes from low-yielding varieties). The major
problems confronting rice production in India and other countries across the world is
the narrow genetic background and yield plateau. The increased incidence and rapid
changes in pest and disease populations as well as emergence of hitherto minor pests
and diseases as major ones is another major challenge for rice improvement.
Therefore, the rice improvement needs a paradigm shift from enhancing productivity
to profitability which considers several factors including:

(a) Economising the cost of cultivation through development of rice varieties with
inbuilt resistance to biotic stresses (major insect-pests, diseases and weeds) as
well as tolerance to abiotic stresses.
202 S. Gopala Krishnan et al.

(b) Improving the grain and nutritional quality and value addition.
(c) Development of rice hybrids for productive environment and enhancing area
under-hybrid rice cultivation.
(d) Improving the water productivity and sustaining soil health by developing
technologies suited for aerobic/limited water and nutrient environments includ-
ing herbicide tolerant rice varieties.
(e) Developing varieties suited for managing the rice value chain, effectively.

Overall, the focus of rice breeding should be on the development of improved rice
varieties with high yield potential with resistance to major diseases and insects, and
to major abiotic stresses such as drought, submergence and heat, and better grain and
nutritional quality. To do this effectively with limited resources, needs the adoption
of modern tools and techniques enabling rapid and precision breeding for improve-
ment of rice.

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Maize Breeding
4
Firoz Hossain, Vignesh Muthusamy, Jayant S. Bhat,
Rajkumar U. Zunjare, Santosh Kumar, Nitish R. Prakash,
and Brijesh K. Mehta

Abstract

Maize has emerged as an important crop for food, feed and various applications.
Utilization of hybrid technology has resulted in a quantum jump in grain produc-
tion worldwide. However, ever-increasing population pressure coupled with
climate change warrant many fold increase in productivity in a shorter time
frame. Emergence of newer diseases and insect-pests further pose a great chal-
lenge to even sustain the production. Malnutrition has become a major health
issue, thereby causing severe socio-economic losses. However, discovery of new
genes and quantitative trait loci (QTLs) for higher grain yield, plant architecture,
resistance/tolerance to various biotic and abiotic stresses, nutritional quality and
specialty traits, and also availability of suitable donors provide great opportunity
to breed improved hybrids with higher productivity, better resilience to biotic and
abiotic stresses, and higher nutritional quality. Genomics-assisted breeding, dou-
bled haploid and gene editing technology provide great impetus to further
accelerate the breeding cycle. Here, we discussed the present status, opportunities
and challenges in maize breeding.

F. Hossain (*) · V. Muthusamy · J. S. Bhat · R. U. Zunjare

ICAR-Indian Agricultural Research Institute, New Delhi, India
S. Kumar
ICAR-Indian Agricultural Research Institute, Gauria Karma, Jharkhand, India
N. R. Prakash
ICAR-Central Soil Salinity Research Institute, Regional Research Station, Canning, India
B. K. Mehta
ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 221
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_4
222 F. Hossain et al.

Keywords

Zea mays · Corn · Genomics · Markers · Gene · QTL · Specialty traits

4.1 Introduction

Maize assumes great significance as food, feed and raw material for diverse indus-
trial applications, thereby serving as a source of livelihood to millions of people
worldwide (Prasanna et al. 2020a; Hossain et al. 2021). Globally, maize is produced
to a volume of 1148 million metric tons with cultivation of 197 million hectares area
(FAOSTAT 2019). Maize is an important cereal crop in as many as 169 countries
across North America, South America, Africa, Asia and Europe. Maize grains are
consumed in various forms such as flat bread, porridge, boiled and roasted grains/
cobs (Hossain et al. 2019a). Besides, maize possesses diverse usage as food in the
form of sweet corn, baby corn, popcorn, waxy corn, high amylose maize and high oil
maize (Hossain et al. 2019b; Pal et al. 2020; Chhabra et al. 2021). Maize, together
with rice and wheat, provides at least 30% of the food calories to more than 4.5
billion people in 94 developing countries (Shiferaw et al. 2011). Considering the
share of calories among all-staple crops, maize contributes 61% in Mesoamerica,
45% in Eastern and Southern Africa, 29% in the Andean region, 21% in West and
Central Africa and 4% in South Asia (Shiferaw et al. 2011). The contribution to
protein by maize is also in the similar tune (Mesoamerica: 62%, Eastern and
Southern Africa: 43%, Andean region: 28%, West and Central Africa: 22% and
South Asia: 4%). Maize grains are the principal component of animal feed, espe-
cially in the poultry and piggery industry (Gao 2002; Panda et al. 2013; Rajasekhar
et al. 2020). Besides, it serves as a source of raw material to corn syrup, emulsifier,
textile, paper and adhesive industries (Bao et al. 2012; Devi et al. 2017). To meet the
requirement of ever-increasing population and growing animal feed industry, the
demand for maize will be doubled by 2050 in the developing world (Rosengrant
et al. 2009).
Gradual progression from open pollinated (OP) varieties to single cross hybrid
technology helped to realize the highest potential for grain heterosis (Andorf et al.
2019). Furthermore, modification in plant architectural traits from wide leaf angle to
shorter leaf angle enabled the maize hybrids to grow under high density, thereby
further enhancing the grain yield. Maize production is increased by two-fold during
the past 40 years due to enhanced grain yield resulting from improved crop cultivars
coupled with the better responsiveness to fertilizer, water and pesticides (Evenson
and Gollin 2003). However, climate change quite often increases frequent crop
failures and decreases grain production. Lack of well-distributed rainfall pattern
would further lead to water scarcity and eventually occurrence of drought stress
which may lead to complete failure of the crop (Brown and Funk 2008; Funk and
Brown 2009). Increase in heat has become a major issue to healthy crop production
as each degree day spent above 30
C reduces the final yield by 1% under optimal
rain-fed conditions and by 1.7% under drought conditions (Lobell et al. 2011).
4 Maize Breeding 223

Incidence of biotic stress has also become a major limiting factor to maize
production.
Of various biotic stresses, fall army worm (FAW) has recently caused havoc
throughout the world, causing as much as complete loss of crop (Israni et al. 2020).
Considerable loss has also been attributed to diseases like grey leaf spot (GLS) and
maize lethal necrosis (MLN). Post-harvest loss up to 80% has been reported in the
tropics due to infestation by grain weevils and grain borers (Hossain et al. 2007;
Zunjare et al. 2014, 2015a, b, c, 2016). Malnutrition caused due to consumption of
unbalanced diet has emerged as one of the major health concerns particularly in the
developing and under-developed world (Bouis et al. 2019; Virk et al. 2021).
Globally, around two billion people suffer from malnutrition (Global Nutrition
Report 2020). Nearly 45% of deaths among children under age 5 are linked to
malnutrition (Global Nutrition Report 2018). Globally, 149.2 million (22.0%) chil-
dren (<5 years) are stunted, while 45.4 million (6.7%) children (below 5 years)
possess child wasting (UNICEF-WHO-WB 2021). Malnutrition contributes to loss
in 11% gross domestic product (GDP) in Asia and Africa, while malnutrition in all
its forms could cost society up to US$3.5 trillion per year (Global Nutrition Report
2016, 2018). Among various avenues, breeding for improved maize hybrid would
remain as the most sustainable and cost-effective avenues to combat the combined
challenges of increasing demand, frequent occurrence of biotic and abiotic stresses
and nutritional disorders.

4.2 Origin of Maize

Maize, as a crop is documented to be grown for 10,000 years (Schnable et al. 2009).
Adult plant morphology of maize is very unique among all cereals, having single
culm, separate male and female inflorescence and human-dependent seed dispersal,
which are thought to have been evolved through few major mutations (Doebley
1992). Morphological resemblances and cytological studies have confirmed its close
relatedness to teosinte (Doebley and Stec 1991). Role of humans in developing and
establishing maize as a crop species has also been documented because of presence
of great variability in maize and continuous selection by ancient people (Yu and
Buckler 2006). Establishing the scientific theory of origin and domestication of
maize was a daunting task because of absence of very close and morphologically
similar plant species (Wang et al. 2017a). Several theories regarding origin of maize
have been proposed and described below.

4.2.1 Tripartite Hypothesis (Mangelsdorf and Reeves 1938)

This hypothesis states that maize originated from an unknown plant which was
having similar ear morphology. Such unknown plant is now extinct. Accordingly,
teosinte is the offspring of maize and Tripsacum.
224 F. Hossain et al.

4.2.2 Catastrophic Sexual Transmutation Hypothesis (Iltis 1983)

According to this hypothesis, sudden sexual transmutation in teosinte was responsi-

ble for development of maize plant. The ear of maize is result of morphological
change in central spike of teosinte resulting from a phenomenon called “genetic
assimilation”.

4.2.3 Tripsacum–Zea Diploperennis Hypothesis (Eubanks 1995)

It is the modified version of tripartite hypothesis. According to this hypothesis,

maize plant evolved from the cross between Zea diploperennis and Tripsacum
dactyloides.

4.2.4 Teosinte Hypothesis (Beadle 1939)

According to this hypothesis, ancient people cultivated teosinte and selected the
morphologically useful plant forms. Maize plants arose due to major mutations in
few loci of teosinte.
Of these, teosinte hypothesis is the most accepted and validated, using modern
genomics associated studies (Doebley 1990; Doebley and Stec 1991; Dorweiler et al.
1993; Matsuoka et al. 2002; Wang et al. 2005; Dong et al. 2019). Beadle (1939) had
predicted teosinte as a sole progenitor of maize and carried out a planned experiment
using a very large recombinant population (F2) derived from crossing teosinte with a
primitive maize landrace. He reported that at least five major mutations were
responsible for converting teosinte into maize. Later on, during the 1990s, a research
group led by Prof. J.F. Doebley at University of Wisconsin, Madison, United States,
had redeveloped and studied the recombinant mapping population using the same
parent as done by Prof. Beadle in the 1930s. They also confirmed the role of at least
five major mutations in developing maize from teosinte in a series of selection events
practiced by ancient cultivators. Several studies have now been carried out to
understand the molecular basis of domestication of maize (Dong et al. 2019).
The mutation present in teosinte glume architecture1 (tga1) gene found in
chromosome 4S was responsible for development of naked kernels (Dorweiler
et al. 1993). This gene encodes a SBP (SQUAMOSA promoter binding protein-
like) family transcription factor. A single nucleotide polymorphism (SNP) at posi-
tion 18 of the ORF in this protein caused a gain-of-function mutation acting as
transcriptional repressor responsible for naked kernel in maize (Wang et al. 2015).
Similarly, single culm developed in maize with respect to tillering habits in teosinte
was found to be governed by teosinte branched1 (tb1) gene (Doebley et al. 1997).
The gene tb1 is a TCP-domain containing transcription factor whose higher expres-
sion in maize reduces the branching and tillering habits. The higher expression is due
to the presence of “Hopscotch” and “Tourist” transposon at ~58–69 kb upstream of
coding region (Studer et al. 2011). Similarly, other genes such as grassy tiller1 (gt1),
4 Maize Breeding 225

enhancer of tb1.2 (etb1.2), barren stalk1 (ba1), barren stalk2 (ba2) have been found
to be associated with branching habits in teosinte and maize intercross populations
(Prakash et al. 2020).

4.3 Species Distribution

Genus Zea consist of five species, that is, Zea diploperennis (diploperennial teosinte,
native of Western Mexico), Zea luxurians (Florida teosinte or Guatemalan teosinte,
native of Mexico, Guatemala and Honduras), Zea mays (Southern Mexico, include
cultivated maize, grown across the world), Zea nicaraguensis (Nicaraguan teosinte),
and Zea perennis (perennial teosinte, native of western Mexico). Among these, Zea
mays include four sub-species Zea mays ssp. mays (cultivated corn), Zea mays ssp.
parviglumis (Balsas teosinte), Zea mays ssp. mexicana (Mexican teosinte), Zea mays
ssp. huehuetenangensis (found on western highlands of Guatemala) (Hossain et al.
2016; Prakash et al. 2020). Among all the species documented under the genus Zea,
maize (Zea mays ssp. mays) is the only one which is being cultivated. The other
sub-species under Zea mays along with other species under Zea is collectively
considered as ‘teosinte’. It is now well established that maize is originated from
Zea mays ssp. parviglumis (also known as balsas teosinte). All the teosinte species
are commonly found in Mexico and northern part of South America.
However, maize has lost many variations present in these teosintes and acquired
new variations arising out of mutations. Doebley (1990) has estimated 25% loss of
gene diversity in maize from balsas teosinte. Later on, through various mutation and
selection by indigenous people, several plant forms of maize were developed, such
as waxy corn, popcorn, sweetcorn, pod corn (Smykal et al. 2018). Cultivated maize
has spread to North America, Europe, Asia, Australia and Africa by European
travelers of the colonial era. After introduction of maize into a different continent,
the variations present in them had led to adaptation to local conditions, and temper-
ate and tropical varieties began to evolve (Prasanna et al. 2010).

4.4 Types of Grains

Maize is of the most produced grain crops on this planet, and this has only been
possible due to the presence of enormous diversity and mutant forms, making it
suitable to be cultivated across environments and ecological conditions (Prasanna
et al. 2012). The various maize forms used in cultivation are given below.

4.4.1 Flint Corn (Zea mays ssp. mays var. indurata)

Complete kernel including outer portion is made up of hard starch.

226 F. Hossain et al.

4.4.2 Dent Corn (Zea mays ssp. mays var. indentata)

Only kernel is made up of hard starch. It has dent-like structure on top of the grain.

4.4.3 Sweet Corn (Zea mays ssp. mays var. saccharata)

Sugar content is high at milking stage (up to 20% as compared to other maize types).

4.4.4 Flour Corn (Zea mays ssp. mays var. amylacea)

Kernel is made up of soft starch, and it is easy to grind and used in making chappatis.

4.4.5 Popcorn (Zea mays ssp. mays var. everta)

Small size kernel which burst and turn inside out after heating. The bursting during
heating is because of formation of steam in the grain.

4.4.6 Waxy Corn (Zea mays ssp. mays var. ceratina)

These are waxy grains which are sticky after cooking. The waxiness of kernel is due
to the presence of low amylose and high amylopectin content (almost 100%).

4.4.7 Pod Corn (Zea mays ssp. mays var. tunicata)

These are podded grains covered inside glumes.

The various forms of maize with specialized usage are a type of mutations
selection occurring in the natural population. Most commonly used corn is of flint
type. Sweet corn has evolved through mutation in genes regulating sugar metabo-
lism, such as sugary1 (su1) and shrunken2 (sh2). Waxy corn is developed by
mutation at waxy1 (wx1) locus in maize. Similarly, pod corn is having mutation at
tunicate locus (Yadav et al. 2015).

4.5 Floral Biology

Maize is a monoecious type of plant with separate female and male flowers borne on
single plant. The main shoot of plant terminates into male inflorescence referred to as
‘tassel’, while the female inflorescence is called ‘silk’ that develop into the ‘ear’. The
modified leaf sheaths of several layers that surrounds around ear are known as
‘husks’. Being protandrous in nature, male flowers mature before female flowers
4 Maize Breeding 227

with a gap of 2–3 days. The genetic mechanisms of monoecism and protandry are the
key factors for anemophily (pollination due to wind) in maize (Kumar et al. 2011;
Tripathi et al. 2011). There are two functional florets in each of the male flower
spikelet, and each floret is composed of pair of thin layers (lemma and palea), three
anthers, one rudimentary pistil and two lodicules. Kiesselbach (1949) has reported
about 2000 to 7500 pollen grains per anther per floret.
Nearly 14  106 pollen grains can be produced by each plant tassel considering
mean of 7000 anthers/tassel and 2000 pollen grains/anther (Kiesselbach 1949).
The pollen grains are very small, lighter in weight and easily carried away by
wind. The female flower formed in the row with development progresses toward
the tip of the ear. The elongated style into thread-like structure known as ‘silks’
covered with numerous small hairs on which pollen grains fall leading to the base of
the silk where fertilization occurs. The pollen grains germinate and enter the embryo
sac within 12–28 h. Self- and cross-pollination are two important practices in maize
breeding. In the breeding nursery, hand pollination is usually followed for
accomplishing self- and cross-pollination, thus it is a labour and cost-intensive
process for maize breeders. Self-pollination is required for development and main-
tenance of inbreds varieties, while cross-pollination is essential to generate
variability and hybrid seed production.
To accomplish self-pollination, ear of plant is covered with ‘silk bag’ before the
silk emerges out. The fresh pollen grains (yellowish in colour) from tassel of same
plant are collected in the morning through bagging tassel with a ‘tassel bag’ wrapped
the previous day evening. The collected fresh pollen grains are placed on silk hairs of
the same plant with no outside exposure to ensure proper self-pollination. For cross-
pollination, pollen grains collected from desired male parent is transferred to well-
covered silk of desired female parent. The proper record of parents involved in
crossing, date of crossing, and breeding scheme is to be clearly written with water-
proof pencil on the tag fixed on the female parent. The plant-to-plant crossing is
generally carried out for generation of genetic variability and introgression of genes.
However, the large-scale hybrid seed production, fixed ratio of female rows to male
rows sown in the field. Tassel of female plant is removed before initiation of pollen
shedding, so that the pollen of male parent is used in the seed production plot.
Removal of tassel as soon as it emerges out of flag leaf is called ‘detasseling’ and is
necessary to avoid selfing in female rows.

4.6 Varietal Development

Most of the U.S. maize production traces to the U.S. Corn Belt dent corn, which was
the product of hybridization between two corn races, Northern flints and Southern
dents (Anderson and Brown 1952). Decades before the Mendel’s laws of inheri-
tance, farmer-breeders in the United States cherished the benefits of out-crossing,
and by 1813, new cultivars were being developed through controlled pollinations.
Lorain (1814) was the first to describe the effect of crossing dent and flint corns, and
also elaborated the potential of crossed seeds for farmers. Later, corn producers and
228 F. Hossain et al.

breeders crossed the Northern flints corn and Southern dents corn to combine the
favourable traits of both, and several new varieties of corn were developed for a quite
long time. The new varieties were somewhat high yielding, early in flowering, more
tolerant to drought and were more adapted to local environments (Anderson and
Brown 1952). Sturtevant (1899) documented the popular use of 323 OP varieties of
dent corn and 69 varieties of flint corn. Robert Reid crossed ‘Gordon Hopkins’, a
semi-gourd dent corn and ‘Little Yellow’, a native Indian flint corn, and developed a
new cultivar known as Reid’s Yellow Dent (Troyer 1999). The OP varieties devel-
oped by farmers and corn breeders dominated the corn production in the U.S. Corn
Belt for over 50 years. The OP varieties were the source material for the develop-
ment of inbreds initially by successive generations of self-pollination/inbreeding.

4.7 Hybrid Development

In the early twentieth century, farmer breeders, U.S. public sector breeders and
private seed producers bred OP varieties but with little gain in maize yield (Hallauer
2008). W.J. Beal was the first to use detasseling in crossing plots to make hybrids in
1881 (Beal 1881). Shull (1908) proposed that the maize yield can be increased by
selfing of parental lines over several cycles to develop inbreds, and then crossing
between inbreds to generate hybrids, the phenomenon termed as ‘hybrid vigour’, or
heterosis (Crabb 1947). At the same time (1909–1912), Edward M. East also
discovered the hybrid vigour at Harvard University’s Bussey Institution in associa-
tion with Connecticut Agricultural Experiment Station. The discovery of hybrid
vigour proved to be a turning point for U.S. maize production and economy (Crabb
1947). Though the potential of hybrid breeding was known since eighteenth century,
no commercial hybrid was developed until 1921. The reasons behind non-popularity
of single cross hybrids were the parental inbreds with poor vigour, very low yield,
low weed competitive ability and susceptibility to corn pests (Hallauer 2008).
Furthermore, low yield of parental inbreds increased the cost of hybrid seed
production.
The major breakthrough came in hybrid maize breeding when Donald F. Jones
created double-cross hybrid ‘Burr-Leaming’ in 1918, which was first produced
commercially in 1921 (Jones 1927). The use of double-cross hybrids greatly reduced
the cost of hybrid seed production, making the hybrid technology feasible for
farmers. A double cross hybrid is essentially the progeny of two single cross hybrids.
The first-generation hybrids overcame the weaknesses of inbreds as they gave
significantly higher seed yield with fewer diseases, insect-pest infestation and
weed issues. At the same time that double cross hybrids were produced and
commercialized, a number of technological advances were adopted in corn produc-
tion viz., (1) use of chemical fertilizers such as inorganic nitrogen fertilizer since
1945 (Gardner 2009), (2) mechanization which facilitated uniform harvesting and
other cultivation practices, thus saved time and labour inputs, and (3) improved
agronomic practices which significantly improved maize productivity in the United
States (Crow 1998; Troyer 2003).
4 Maize Breeding 229

Adoption of these technologies resulted in rapid shift of farmers toward double

cross hybrids. In 1940, about 50% area of maize production in the United States was
under double-cross hybrids, which reached to about 90% by 1950 (Griliches 1957).
During the double-cross hybrid era, the U.S. national average production increased
by ~1 bu./acre every year (Crow 1998). There were other contributing reasons, such
as uniformity in flowering and plant stature, that were aesthetically pleasing and
suitable for machine harvesting, and their better adaptation to different habitats
(Crow 1998) and tolerance to drought than open pollinated varieties (Crabb 1947).
Eventually, breeders could generate inbred varieties with higher productivity and
adaptability which was enough to use them as seed producers to achieve commercial
viability, and single cross hybrids (based on two parental lines) become popular and
grown widely throughout the world (Crow 1998).
With the availability of more vigorous and high yielding inbred lines along with
technological advances in maize production, the production of single hybrids
became more feasible. This again shifted the trend from double cross hybrids to
single cross hybrids in the United States. In the 1950s, many small- and medium-
sized private seed companies were established, but initially dependent on the public
sector hybrids to build their business (Fitzgerald 1990). The adoption of single cross
hybrids resulted in significant increase in U.S. national annual yield by an average of
1.71 bu./acre (Crow 1998). It has now been established that the hybrids developed
from genetically diverse parents are more often highly heterotic than generated from
similar inbreds (Hallauer and Miranda 1988). Following this observation, geneti-
cally similar maize lines were grouped together to generate distinct diverse groups
called ‘heterotic groups’. A heterotic group denotes a group of related or unrelated
genotypes from the same or different populations, which display similar combining
ability and heterotic response when crossed with genotypes from other genetically
distinct germplasm groups (Melchinger and Gumber 1998; Ricci et al. 2007). The
inter-group hybrids typically display more heterosis than intra-heterotic group
hybrids. Several heterotic groups have been described in the United States, viz.,
Reid Yellow Dent, Lancaster Sure Crop, European flints and Minnesota 13 (Dubreuil
and Charcosset 1999; Troyer 2006).

4.8 Genetic Resources

Maize is bestowed with enormous genetic diversity, and several landraces are
reported across the globe that offer opportunity for genetic enhancement to meet
the growing challenges. Wide variation for yield, stress tolerance and nutritional
quality are present in a diverse array of landraces or populations worldwide.
Landraces are heterogeneous in nature and are selectively grown by farmers for
specific characteristics like adaptation, yield, use in a specific diet form, nutritive
value and stress tolerance (Louette and Smale 2000). Some of the notable global land
races of maize that have been used in maize improvement programmes include
Tuxpeno, Bolita, Jala, Chalqueno, Nal-Tel, Palomero, Suwan-1, La Posta Sequia,
Conica, Conica Nortena, Bolita, Oloton, etc., (Louette et al. 1997; Prasanna 2012).
230 F. Hossain et al.

Wide variation for landraces in maize has also been reported in India, particularly in
Sikkim and northeastern Region of the country (Prasanna 2010). Some notable
examples are Murli makai, Kaali makai, Rathi makai, Paheli makai, Seti makai,
Putali makai, Chaptey makai, Gadbade makai, Bancharey makai, Kukharey makai,
Kuchungdari, Kuchungtakmar, etc. (Prasanna and Sharma 2005). These landraces
from India have been well-characterised both at phenotypic and molecular level for
its effective use in the breeding programme (Sharma et al. 2010). One of the most
promising landraces that has been well characterised is Murli makai (Sikkim Primi-
tive) that possess prolificacy (more ears per plant) and stay green in character
(Dhawan 1964; Prasanna 2012; Prakash et al. 2019; Prakash et al. 2021).
The most important consideration is use of these unique land races in the breeding
programme for development of inbreds with specific target traits (Prakash et al.
2019). Broadening of germplasm offers novel trait combinations to the breeders, and
it must be a continuous process. One such example is GEM’ (Germplasm Enhance-
ment of Maize) project, a cooperative effort of United States Department of Agricul-
ture (USDA) with many institutions and industries that aim to utilise diverse maize
genetic resources from around the world to widen the germplasm base of the
commercial hybrid corn in the United States. Such efforts are required globally in
the breeding programmes across the continents for germplasm enhancement and
utilisation in maize.
Different methods have been used to improve germplasm and develop potential
lines. The most important procedure for maize breeding is the recurrent selection
scheme; wherein cyclical improvement of the lines can be achieved. Among recur-
rent selection schemes, the reciprocal recurrent selection (RRS) is the most useful in
inter population improvement. The RRS applied may be half-sib RRS (HS-RRS;
Comstock et al. 1949) or full-sib RRS (FS-RRS; Hallauer and Eberhart 1970) for
developing lines with high general combining ability (GCA) and specific combining
ability (SCA) and to develop heterotic pools. The homozygous lines developed by
this are crossed to opposite heterotic pools, and highly heterotic hybrids can be
commercialized. This traditional recurrent selection schemes are upgraded by
marker technologies and using genomic selection (RRGS) which have shown lot
of promise.
Once the improved lines are available, these lines can be utilized to produce an
array of maize varieties and hybrids that include composites, synthetics, conven-
tional hybrids (single cross, double cross, three-way cross, modified single and three
way cross, and multiple cross) and non-conventional hybrids (inter-varietal hybrids,
inter-family hybrids, top cross, double top cross, and poly cross). The procedure of
development of composites and synthetics are similar, but they differ in the compo-
nent lines used. Composites are the OP populations developed by inter-mating of
outstanding lines (germplasm inbreds, OPVs, hybrids, advance generation lines) and
subsequently maintained by mass selection from isolated plantings, while synthetic
varieties are OP populations derived from the inter-crossing of selfed plants (homo-
zygous lines) or lines and subsequently maintained by routine mass selection
procedures from isolated plantings (Lonnquist 1961) and are proposed by Hayes
and Garber (1919).
4 Maize Breeding 231

4.9 Key Loci for Economically Important Traits

4.9.1 Grain Yield and Component Traits

The ear and kernel related traits are the important contributing traits for maize yield.
Two major quantitative trait loci (QTLs) for kernel row number (KRN4 and KRN1)
(Chuck et al. 2014; Wang et al. 2019) and one major quantitative trait locus (QTL)
for kernel size and weight (qHKW1) (Raihan et al. 2016) have been cloned using
map-based approaches. The ear and kernel-related genomic regions have undergone
selection during maize domestication and improvement (Liu et al. 2015a; Wang
et al. 2019). In addition, many secondary traits like nutrient uptake, photosynthesis,
translocation, sink size, transpiration and respiration also influence the yield levels in
maize. Grain yield is also affected by maturity duration, standability, and resistance
to biotic and abiotic stresses (Gong et al. 2015). Besides, well-developed root
system, strong stem, short plant height, low ear placement, ability to stay green at
maturity, etc., contribute to good standability, which in turn contributes enormously
toward higher yield.
High density planting is a practical approach to increase maize productivity per
unit area. It is predicted that a gain of 20% in maize productivity is possible if
planting density is increased by 15,000 plants/ha. Hence, breeding varieties suitable
to high density planting by targeting leaf architectural traits is an important task.
Among the multiple leaf traits important for high density planting, leaf angle is an
important target trait (Li et al. 2015). Breeding for narrow leaf angle leads to more
upright leaves, which helps in increasing the leaf area index and improve photosyn-
thetic efficiency by reducing shade syndrome (Sakamoto et al. 2006). During the last
century, maize breeders placed higher emphasis on shoot phenotypes (York et al.
2015). The recent understanding on root architecture makes it possible to modify
root traits to make maize more water- and nutrition-efficient, and also suitable for
high density planting.
The narrower xylem vessel reduces the root hydraulic conductance, and thereby
saves soil moisture for later use (Meister et al. 2014). By controlling the expression
of root-water channel-related genes, such as aquaporin, the water channels in the
roots can be modulated (Hachez et al. 2012). Besides, QTL mapping has identified
the maize genomic regions that govern root architecture in water uptake (Zurek et al.
2015). In dry and nitrogen- (N) deficient soils, a deeper root, reduced maize lateral
root branching, a smaller number of crown roots would optimize N and water use
(Lynch 2013; Zhan and Lynch 2015; Saengwilai et al. 2014). The shallow axial root
growth angles many shorter laterals, and long root hairs will enhance phosphorus
(P) utilization by maize (Lynch 2013).

4.9.2 Plant Architecture

The genetic variation for morphological traits is of great importance for plant
breeders. The majority of the genes responsible for differences in morphology and
232 F. Hossain et al.

growth rate between maize and teosinte are either transcription factors or molecules
regulating transcription factors (Yang and Xu 2013). Several candidate genes with
regulatory function have been identified. The liguleless1 (lg1) and liguleless2 (lg2)
genes are associated with leaf ligule and auricle development in maize (Tian et al.
2011). ZmCLA4 is the functional gene for leaf angle QTL qLA4–1 in maize (Zhang
et al. 2014). qLA4–1 is the major QTL that negatively controls the leaf angle by ~15

with semi-dominant effect. Two QTLs, Upright Plant Architecture1 (UPA1) and
Upright Plant Architecture1 (UPA2), control the upright plant architecture in maize
(Tian et al. 2019). The brd1 (brassino steroid C-6 oxidase1) and ZmRAVL1 are the
underlying genes for these two QTLs.
The UPA2 functions by altering the protein binding affinity of another leaf angle
gene, drooping leaf1 (Strable et al. 2017). ZmGA3ox2 is the functional gene for plant
height QTLs, qPH3.1 and dwarf1 in maize (Teng et al. 2013). qPH3.1 is the major
QTL for plant height with a 10.0 cm additive effect and 3.7 cm dominant effect.
qPH1 is another major QTL for plant height explaining 17.7 cm additive and 7.8 cm
dominant effects (Xing et al. 2015). The presence of transposable element (TE) in
tb1 enhances its expression in maize which represses the axillary growth and leads to
formation of female inflorescence, besides promoting apical dominance (Doebley
et al. 2006). Another most important gene in maize domestication is tga1, which
codes for a SBP transcription factor, and is responsible for naked grain phenotype in
maize instead of kernels encased in a hardened fruitcase in teosinte (Wang et al.
2005). A single amino acid substitution (lysine to asparagine) at sixth amino acid of
tga1 changes its specificity to target site in maize leading to naked grain phenotype.

4.9.3 Flowering Time

Flowering time is a complex trait associated with adaptation of maize in different

climatic regions. A large number of QTLs for flowering time in maize has been
identified, of them three QTLs, vegetative to generative transition 1 (Vgt1),
ZmCCT10 (CCT transcription factor) and ZmCCT9, were mapped and cloned
(Salvi et al. 2007; Hung et al. 2012; Yang et al. 2013; Huang et al. 2018). Associa-
tion analysis identified significant association of three polymorphisms (G/A/
indel324, Mite and ATindel434) in Vgt1 with flowering time in maize (Salvi et al.
2007). The insertion of TE upstream of ZmCCT10 changes the promotor methyla-
tion levels that would alter the expression pattern of ZmCCT10 (Yang et al. 2013).
ZmCCT9 is the functional gene for days to anthesis QTL, qDTA9 which was
confirmed by knocking out of ZmCCT9 function resulted in earlier flowering
under long day conditions (Huang et al. 2018).

4.9.4 Nutritional Quality

Maize is an important source of carbohydrate, protein, lipids, minerals and certain

vitamins (Prasanna et al. 2001). Several genes involved in starch biosynthesis in
4 Maize Breeding 233

maize endosperm have been mapped and cloned using well-known starch mutants
(James et al. 2003). Among them, su1 and sh2 has been widely used in sweet corn
breeding (Lertrat and Pulam 2007). The sh2 gene encodes large subunit of
ADP-glucose pyrophosphorylase and accumulates six times more sugars compared
to ordinary maize (Bhave et al. 1990; Mehta et al. 2017). The su1 gene codes for
isoamylose-type starch debranching enzyme (DBE) and retains two to three times
higher sugar and ten times higher water-soluble phytoglycogens than ordinary maize
(James et al. 1995). Several maize mutants with reduced zeins and enhanced
non-zeins have been well-characterized (Gupta et al. 2015).
The mutant opaque2 (o2) located on chromosome-7 encodes less active leucine
zipper transcriptional factor leading to enhanced lysine and tryptophan in maize
endosperm (Schmidt et al. 1992). opaque16 (o16), another recessive mutant of
Robertson’s Mutator (Mu) stock, located on chromosome-8 was found to be
associated with enhanced lysine and tryptophan in maize endosperm (Yang et al.
2005; Hossain et al. 2008a, b, 2017; Sarika et al. 2017). These two genes have been
shown to enhance lysine and tryptophan content in the introgressed versions of high
yielding maize hybrids adapted to different climatic conditions (Sarika et al.
2018a, b; Prasanna et al. 2020a). Among the genes governing carotenoids biosyn-
thesis, the favourable alleles of lcyE (lycopene epsilon cyclase) and crtRB1 (-
β-carotene hydroxylase) have been found to be responsible for enhancement of
provitamin-A (proA) carotenoids in maize kernels (Harjes et al. 2008; Yan et al.
2010).
The favourable allele of lcyE reduces lycopene flux by 30% in α-branch, and
thereby diverts lycopene flux toward β-branch of the carotenoids biosynthesis
pathway, resulting in three-fold enhancements in proA (Vignesh et al. 2013; Zunjare
et al. 2017, 2018a, b). The favourable allele of crtRB1 enhances proA concentration
in maize kernels by limiting the enzymatic activity involved in β-carotene conver-
sion in β-branch (Muthusamy et al. 2016; Zunjare et al. 2018c). The ZmVTE4 and
ZmPORB2 encoding γ-tocopherol methyltransferase and protochlorophyllide oxido-
reductase, respectively, enhance kernel provitamin-E (proE) content in maize
(Li et al. 2012; Zhan et al. 2019). The favourable allele of diglyceride acyltransferase
(DGAT1–2) which encodes type I acyl-coenzyme A: diacylglycerol acyltransferase
leads to higher oil content in maize endosperm and embryo (Zheng et al. 2008). The
insertion of an extra amino acid (phenylalanine) at position 469 of DGAT1–2 causes
enhancement of its enzymatic activity and results in increased oil and oleic acid.
Zmfatb gene which codes for acyl-ACP thioesterase enhances palmitic acid content
in maize (Li et al. 2011). An 11 bp InDel in the last exon of Zmfatb affects the
enzyme activity by introducing a premature stop codon.
234 F. Hossain et al.

4.10 Specialty Traits

4.10.1 Sweet Corn

Two genes affecting the starch metabolism, viz., su1 (chromosome 4) and sh2
(chromosome 3), have been extensively used for development of sweet corn
cultivars, where the sh2 is located upstream of the pathway, while enzyme coded
by su1 affects step downstream of the pathway (Hossain et al. 2015; Chhabra et al.
2019a, b, 2020, 2021). Sugary varieties (su1su1) at the milky ripening stage contain
nearly three times more reducing sugar and sucrose, ten times more water-soluble
phytoglycan (WSP) and one-third of starch content of normal maize (Fisher and
Boyer 1983; James et al. 1995; Feng et al. 2008). Besides, sugary kernels have
creamy texture with good flavour and appear wrinkled and glossy upon maturity
(Creech 1965). However, the sugar level after the harvest declines much faster in the
su1 types (Garwood et al. 1976). On the other hand, the sh2-based sweet corn types
popularly called ‘super sweet’ or ‘extra sweet corn’ accumulate sugar in place of
starch.
At milky ripening stage, the content of reducing sugars and sucrose in the kernel
is about six-fold higher than the ordinary maize (Feng et al. 2008; Khanduri et al.
2011; Solomon et al. 2012). However, the content of WSP is similar to normal
maize, and starch content is about one-third of the ordinary maize. By virtue of
higher amount of sugars in sh2sh2 mutant, kernels contain decreased amount of total
carbohydrates at the mature seed stage, and the kernels get collapsed and look
shrunken with degree of opaqueness (Creech 1965). The depletion of sugar level
is much slower in sh2 type even without refrigeration; thus, varieties have extended
shelf life and are better suited for prolonged storage. Sweet corn cultivars with
combination of su1 and sh2 have often been used in commercial sweet corn
development (Lertrat and Pulam 2007). Furthermore, sugary enhancer1 (se1) (chro-
mosome 2), a modifier of su1, has been used in combination with su1 in sweet corn
development. Now, brittle2 (bt2) (chromosome 4) based sweet corn cultivars have
also been developed and commercialized worldwide. Furthermore, sweet corn has
now been biofortified with high lysine, tryptophan, proA and proE (Feng et al. 2015;
Mehta et al. 2020a, b, 2021; Baveja et al. 2021).

4.10.2 Popcorn

Popping percentage and popping volume are two most important characters for
popcorn (Pal et al. 2020). Several mapping studies have reported many major
genomic regions for popping traits with >10% phenotypic variance (Lu et al.
2003; Babu et al. 2006; Li et al. 2007a, b; Liu et al. 2007a; Yongbin et al. 2012).
Recently, Meta-QTL analyses revealed three QTLs located on chromosome
1 (metaQTL1_1, metaQTL1_5 and metaQTL1_7) and one QTL on chromosome
6 (metaQTL6_2) as significant QTL responsible for popping traits (Kaur et al. 2021).
4 Maize Breeding 235

4.10.3 Baby Corn

Among various genes, teosinte branched1 (tb1) has been identified as the key gene
(on chromosome 1) determining prolificacy (Doebley et al. 1995, 1997; Doebley
2004). Wills et al. (2013) identified a ‘prol1.1’ major QTL located on chromosome
1 for prolificacy. Prakash et al. (2021) identified a novel QTL ‘qProl-SP-8.05’ from
‘Sikkim Primitive’ on chromosome 8. It is a prolific maize landrace with five to nine
ears per plant. QTL mapping identified a major QTL (bin: 8.05) explaining 31.7%
and 29.2% of phenotypic variance in two mapping populations.

4.10.4 Waxy Corn

Waxy maize is originated from the cultivated flint maize through mutation in Wx1
locus (Fan et al. 2008; Zheng et al. 2013). Wx1 is mapped on the short arm of
chromosome 9 (Klosgen et al. 1986; Mason-Gamer et al. 1998). Wx1 codes granule-
bound starch synthase (GBSS-I) gene which catalyses amylose synthesis from ADP
glucose in amyloplasts of maize endosperm. Different types of mutation, such as
insertion of transposon, retroposon and fragments of few nucleotides and deletion of
nucleotides, result in mutant allele (wx1) (Devi et al. 2017; Hossain et al. 2019b).
These mutations create the synthesis of altered transcript with premature stop codon
or change in amino acids in key domain or splicing or translational errors that in turn
stops the activity of wild-type Wx1 allele or inhibits the activity of GBSS-I, which
results in lower amylose and higher amylopectin in grain (Bao et al. 2012; Zhang
et al. 2013). Generally, GBSS-I is highly active in non-waxy maize and its product
(amylose) cannot be fully changed into amylopectin by starch branching enzyme.
GBSS-I coded by recessive gene wx1 possesses reduced activity (Liu et al. 2007b).
Most of the amylose synthesized by low activity of GBSS-I are transformed into
amylopectin by starch branching enzyme. Amylopectin is only accumulated in
endosperm, and the phenotype appears as waxy (Wessler et al. 1986).

4.10.5 High Amylose Maize

The recessive amylose extender1 (ae1) mutation (present on chromosome 5) that

codes for starch branching enzyme (sbe2b) enhances amylose to a level of 50–60%
from 25 to 30% found in traditional maize (Li et al. 2008). The ae1.1 is a null allele,
also called ae1-ref, which does not produce a SBE2b protein product (Vineyard and
Bear 1952). A second variant ae1.2, known as ae1-Elmore, produces a catalytically
inactive and truncated protein (Liu et al. 2012). Increase in amylose content by ae1
was only 50%. Maize starch with amylose content of >60% is the result of high
amylose modifier genes in the maize ae1 background. A major modifier gene of ae1
has been reported to be SbeIa, which can increase amylose up to 70–80% in the
presence of ae1 (Garwood et al. 1976; Hedman and Boyer 1982). Second modifier
called modifier of amylose extender1 (mae1) has also been reported (Krzywdzinski
2016).
236 F. Hossain et al.

4.11 Biotic Stress Tolerance

Diseases are the most important factors for yield loss in maize. Many QTLs for
disease resistance in maize has been identified; however, only few genes have been
validated (Yang et al. 2017; Liu et al. 2020a). The maize Hm1 gene governing
resistance against maize leaf blight was the first gene to be cloned and elucidated at
molecular level in plants (Johal and Briggs 1992). It is a dominant gene which is
located on chromosome 1 and codes for NADPH-dependent HC-toxin reductase
which inactivates HC toxin. The Rp1-D is another resistance gene conferring
resistance toward common rust in maize (Collins et al. 1999). Six resistance genes,
viz., ZmWAK, ZmHtn1, ZmTrx, Rcg1, ZmCCT10 and ZmAuxRp1, with relatively
large effects have also been cloned in maize (Zuo et al. 2015; Hurni et al. 2015;
Wang et al. 2017b; Ye et al. 2019). The ZmWAK gene codes for a wall-associated
kinase-specific 730 residue receptor-like protein which represses the fungal growth
(Sporisorium reilianum) in above ground tissues (Zuo et al. 2015). The ZmHtn1
gene mapped on chromosome 8 also encodes wall-associated receptor-like kinases
to confer resistance toward northern leaf blight (Hurni et al. 2015).
The ZmTrxh mapped on chromosome 6 lacks two canonical cysteines in its
thioredoxin active-site motif required to reduce disulfide bridges and provide resis-
tance to sugarcane mosaic virus (Liu et al. 2017a). Rcg1 is a major QTL located on
chromosome 4 which encodes a NB-LRR domain and provides resistance to
anthracnose stalk rot (Frey et al. 2011). ZmCCT10, a gene that controls the flowering
time in maize is also associated with resistance to Gibberella stalk rot (Yang et al.
2013). The CACTA-like transposable element in ZmCCT10 is the causal variant,
which alters its DNA methylation and histone modification, and results in greater
disease resistance (Wang et al. 2017b). ZmAuxRP1 encodes DUF966 protein and
also confers resistance to Gibberella stalk rot by affecting the biosynthesis of both
IAA and benzoxazinoids (Ye et al. 2019). Among insect-pest, FAW severely limits
maize production by causing severe damage to the growing young leaves. Womack
et al. (2020) identified two major QTLs (bin: 4.06 and 9.03) that explained 35.7% of
the phenotypic variance over all environments.
Resistance sources to foliar diseases of maize including maydis leaf blight (MLB,
southern corn leaf blight, or SCLB) (Bhat et al. 2012), turcicum leaf blight (TLB,)
northern corn leaf blight, or NCLB) (Ayiga-Aluba et al. 2015; Bhat et al. 2017;
Kurosawa et al. 2017), gray leaf spot (GLS) (Dhami et al. 2015), polysora and
common rust, downy mildew (DM), some viral diseases, Aspergillus contamination
(Hooda et al. 2012; Badu-Apraku and Fakorede 2017) have been identified and are
incorporated successfully through conventional breeding. In addition, multiple dis-
ease resistance (MDR) in maize has been reported (Martins et al. 2019). International
Maize and Wheat Improvement Center (CIMMYT) has developed a multiple borer
resistance (MBR) source population utilizing diverse germplasm obtained from
different organizations.
MBR population was developed by adopting recombination and recurrent selec-
tion under artificial insect epidemics against Southwestern corn borer (SWCB),
sugarcane borer (SCB), European corn borer (ECB) and fall armyworm (FAW)
4 Maize Breeding 237

Table 4.1 Secondary and tertiary gene pool resources of maize for biotic stress tolerance
S. No. Biotic stress Germplasm Reference (s)
Secondary gene pool
1. Maize chlorotic dwarf virus Z. diploperennis Findley et al.
(1982)
2. H. turcicum, H. maydis Z. diploperennis Wei et al.
(2003)
3. Corn smut disease downy mildew Z. mays spp. mexicana Mammadov
et al. (2018)
4. H. turcicum, H. maydis Z. diploperennis Mammadov
et al. (2018)
5. Fusarium spp. Z. spp. mexicana Pasztor and
Borsos (1990)
6. Striga-parasitic weed Z. diploperennis Yallou et al.
(2009)
7. Northern leaf blight Teosinte Ott (2008)
8. Ustilago maydis Teosinte Chavan and
Smith (2014)
9. Corn borer Z. mays spp. mexicana Pasztor and
Borsos (1990)
10. Asiatic corn borer Z. mexicana, Ramirez
Z. diploperennis. Z. perennis (1997)
11. Corn rootworm T. dactyloides Prischmann
et al. (2009)
12. S. frugiferda Z. diploperennis Farias-Rivera
et al. (2003)
Tertiary gene pool
13. C. graminicola, H. turcicum, T. dactyloides Bergquist
H. maydis, E stewartii, P. sorghi (1979)
14. Rust disesase T. dactyloides Mammadov
et al. (2018)
15. H. turcicum (Ht gene) T. floridanum Hooker and
Perkins (1980)
16. P. sorghi (RpTd gene) T. dactyloides Bergquist
(1981)

(Mihm 1985). As teosintes are more resistant to insects and pathogen than the
improved maize cultivars, understanding the underlying defence mechanisms of
teosintes would present novel strategies to breed for biotic stress resistance in
modern maize. Exploring the genetic variation for resistance and other agronomic
traits among wild and landrace of maize has long been advocated (Flint-Garcia
2013). Over the years, many research efforts have been directed towards the
identification/development of resistant sources against various biotic stresses.
Besides primary gene pool, resistant sources from secondary and tertiary gene
pools have also been identified (Table 4.1).
238 F. Hossain et al.

4.12 Abiotic Stress Tolerance

Initial attempt of QTL mapping for drought tolerance in maize was executed using
Polj17 (drought-resistant) and F-2 (drought-sensitive) to generate F2 population
(Lebreton et al. 1995). In this study, QTLs for abscisic acid (ABA) content and
stomata conductance were mapped. Since then, numbers of studies have been
recorded on QTL mapping in maize for important morpho-physiological traits
drought stress condition. In different studies of QTL mapping, many QTLs were
identified for morphological traits like male flowering, female flowering, anthesis
and silking interval (ASI), yield and cob number (Ribaut et al. 1996; Ribaut et al.
1997; Agrama and Moussa 1996; Sari-Gorla et al. 1999). Later, considering the
importance of root and its related traits imparting the tolerance to drought, different
QTLs for root architecture and root-associated traits along with yield traits have been
identified, viz., one QTL for root trait (Landi et al. 2010), 22 QTLs for root-
associated traits, such as root density, root dry weight, sugar concentration and
leaf ABA content through composite interval mapping in F2:3 population (Rahman
et al. 2011). Similarly, Trachsel et al. (2016) identified a total of 17 QTLs for
stomatal conductance, leaf water content, ASI, and grain yield.
Besides, association mapping is another important approach for better resolution
of QTLs as it utilizes the historical recombination events in natural populations
known as association panel. Setter et al. (2011) conducted association mapping to
identify single nucleotide polymorphisms (SNPs) related to genes involved in
carbohydrate and ABA metabolite accumulation during drought stress. Aldehyde
oxidase gene is found to regulate silk ABA concentration under drought stress.
Later, SNP-based genome-wide association mapping was conducted using 5000
inbred lines as association panel (Li et al. 2016). The study revealed significant
association of SNPs with drought tolerance associated candidate genes. However,
most of the identified QTLs identified till date are of minor effect except few major
QTLs. The mQTL study conducted using three populations and several
environments revealed seven genomic regions for grain yield and one genomic
region for ASI. Among these, six mQTL on grain yield mapped on chromosomes
1, 4, 5 and 10 under moisture stress and optimal environments and hence classify as
stable QTLs.
Though hundreds of QTLs for drought tolerance have been mapped, only few of
them have been cloned (Liu and Qin 2021). Two large effects on genes SDG140 and
Hp322 were identified for drought tolerance in maize (Lu et al. 2010). SDG140 gene
which encodes a SET-domain protein is the underlying gene for HP71 haplotype of
drought tolerance. Hp322 includes two closely linked SNPs from a gene encoding
aldo-keto reductase and provides enhanced drought tolerance. Four genes,
ZmNAC111 ZmVPP1, ZmTIP1 and Zmabh2, have been identified to be responsible
for seedling drought tolerance in maize (Mao et al. 2015; Wang et al. 2016; Zhang
et al. 2019; Liu et al. 2020b). Two genes, ZmPYL8 and ZmPYL12, which encodes the
abscisic acid receptors, facilitate drought tolerance in maize (He et al. 2018). Maize
ABP2 (ABRE binding protein 2) gene codes for bZIP transcription factor which
4 Maize Breeding 239

enhances the expression of stress-responsive, and carbon metabolism-related genes

result in enhanced tolerance to both drought and salt (Na et al. 2018).
Several QTLs for heat stress tolerance in maize has been mapped using biparental
and genome-wide association mapping approaches, and few candidate genes have
also been identified (Frey et al. 2016; Gao et al. 2019; Inghelandt et al. 2019;
Longmei et al. 2021). Frey et al. (2016) identified two QTL hotspots separately on
chromosome 2 and 3 for heat tolerance with respect to grain yield, which explained
7–13% of the variance. The low variance of these QTLs explained the multigenic
inheritance of tolerance to heat in maize. Frey et al. (2016) also identified three heat
tolerance genes (GRMZM2G115658; GRMZM2G537291 on chromosome 2; and
GRMZM2G324886 on chromosome 3) in the above identified QTL hotspot regions.
The gene GRMZM2G324886 codes for calcicylin binding protein involved in
calcium signalling in response to stress condition. QTL for heat susceptibility
index (leaf scorching trait) has been found on chromosome 9 and QTL for heat
susceptibility index (grain yield) were reported on chromosome 2 and 3, which
suggested the involvement of different genomic regions in regulation of genetic
mechanisms for leaf scorching and grain yield (Frey et al. 2016).
Inghelandt et al. (2019) identified six QTLs for heat susceptibility index of the
five traits at the seedling stage which exhibited 7–9% of the phenotypic variance.
Eleven QTLs have been mapped for pollen germination and pollen tube (Frova and
Sari-Gorla 1994). The pollen germination ability is correlated with the cellular
membrane stability since QTLs for both the traits map to common region on the
short arm of chromosome 8 (Ottaviano et al. 1991). Qin et al. (2007) reported that
higher expression of ZmDREB2A gene in maize may induce heat responsive genes
which may further provide adaptability under high temperature stress. QTLs
controlling leaf temperature, ASI and grain yield have been mapped in maize on
chromosome 7 (Sanguineti et al. 1999).
Transcriptome study in maize in response to heat stress identified 1029
upregulated and 828 downregulated DEGs, and the analysis indicated the central
role of protein processing in endoplasmic reticulum in response to heat stress (Qian
et al. 2019). They also identified 167 putative transcription factors associated with
heat stress response of maize belonging to the TF family of MYB, AP2-EREBP,
b-ZIP, bHLH, NAC and WRKY. Heat stress triggers the endoplasmic reticulum
stress which causes heat-induced upregulation of ZmbZIP60, and study by Li et al.
(2018) concluded that upstream region of ZmbZIP60 is vital in its upregulation under
heat stress.
Waterlogging tolerance in maize is governed by complex genetic mechanism
with involvement of multiple genomic regions (Mano and Omori 2007). Mano et al.
(2005) reported two QTLs on chromosomes 4 and 8 governing adventitious root
formation under waterlogging condition. Mano et al. (2009) also identified three
QTLs for adventitious root formation under waterlogging condition on
chromosomes 3, 7 and 8 from the backcross population derived from the cross
Mi29  teosinte (Z. nicaraguensis). Composite interval mapping of F2 population of
cross between F1649 and H84 reported that a single QTL of chromosome 1 is
responsible for the severity of leaf injury due to waterlogging (Mano et al. 2015).
240 F. Hossain et al.

Qiu et al. (2007) reported chromosomes 4 and 9 as the hot spots for several QTLs
governing root dry weight, shoot dry weight, total dry weight and plant height. Zaidi
et al. (2015) identified 22 candidate genes from several identified QTLs located on
chromosome1, 3, 4, 5, 7, 8 and 10 for grain yield and other secondary traits
associated with waterlogging tolerance.
A total of 7 out of 55 uniformly distributed QTLs among all the 10 chromosomes
were identified as the candidate genes for waterlogging tolerance. These candidate
genes were lying on the previously identified QTLs located on chromosomes 1, 4,
6, 7 and 9 (Osman et al. 2013). Transcriptome analysis has identified the rapid
induction in TFs families bZIP, AP2/ERF, bHLH, NAC and MYB under
waterlogging condition (Yu et al. 2020). A genome-wide analysis in the inbred
line HZ32 revealed 38 out of 184 AP2/ERF genes identified in maize which
responds to waterlogging stress (Du et al. 2014). In addition to all these genes and
transcription factors, non-coding RNAs also play key role in making adaptive
changes in morphology and metabolism of plants in response to waterlogging stress
(Yu et al. 2020). The gene ZmEREB180 of the ERF-VII family in maize have been
found to play key role in regulating the adventitious root growth, and overexpression
of ZmEREB180 also enhances the tolerance level against waterlogging stress
(Yu et al. 2019).

4.13 Genomics-Assisted Breeding

Conventional breeding achieved success in developing maize varieties with

enhanced yield, quality and stress tolerance through crossing and selection over
years (Liu and Qin 2021). However, this is tedious, time-consuming and inefficient
for complex traits. Genomics-assisted breeding approaches, such as marker-assisted
backcross breeding (MABB), forward breeding (FB) and genomic selection (GS),
are considered to be efficient tools for accelerating genetic gain by increasing
selection intensity and reducing selection cycles by two to three years (Gilliham
et al. 2017; Prasanna et al. 2021). Bouchez et al. (2002) introgressed favourable
alleles of three QTLs for earliness and grain yield through three cycles of marker-
assisted backcrossing. Marker-assisted introgression of o2, crtRB1 and vte4 has been
used to improve protein quality (Gupta et al. 2013; Hossain et al. 2018, 2019a, c;
Sarika et al. 2018a; Jompuk et al. 2020), proA content (Muthusamy et al. 2014; Liu
et al. 2015b; Zunjare et al. 2018a) and proE content (Feng et al. 2015; Das et al.
2021), respectively, in maize. In recent years, multi-nutrient-rich inbred lines and
hybrids, especially combinations of quality protein maize (QPM), proA, proE and
low phytate, have been developed through MABB (Bhatt et al. 2018; Goswami et al.
2019; Mehta et al. 2020b; Baveja et al. 2021; Das et al. 2021; Singh et al. 2021).
Several proA-rich and three QPM + proA-rich hybrids developed by MABB have
been released for commercial cultivation worldwide (Prasanna et al. 2020a). MABB
have also been used for improving disease resistance and abiotic stress tolerance in
maize. Zhao et al. (2012) introgressed qHSR1 QTL into 10 inbred lines of maize
which resulted in significant improvement for head smut resistance. Marker-assisted
4 Maize Breeding 241

backcrossing of H5 haplotype of ZmCCT showed to enhance resistance to stalk rot in

maize inbreds and hybrids (Li et al. 2017). The marker-assisted pyramiding of
sugarcane mosaic virus (Scmv1) and Scmv2 QTLs into F7 maize line resulted in
complete resistance to sugarcane mosaic virus (Xing et al. 2006).
Yang et al. (2017) developed near isogenic lines with qMdr9.02 locus containing
multiple disease resistance genes via maker-assisted selection, which possessed
resistance to southern corn leaf blight and GLS. Using MABB, resistance to maize
lethal necrosis (MLN) has been introgressed into over 30 elite drought-tolerant
maize lines (Prasanna et al. 2020b). Similarly, Awata et al. (2021) introgressed
QTL for resistance to MLN into nine elite but MLN susceptible lines. Ribaut and
Ragot (2007) showed drought tolerance in MABB-derived test cross maize hybrids
over control hybrids. Wang et al. (2016) intogressed ZmVPP1 QTL into drought
susceptible inbred, Shen5003 through four cycles of marker-assisted backcrossing.
The improved progenies with homozygous ZmVPP1 showed enhanced drought
tolerance than Shen5003.
FB is a simple form of population improvement using molecular markers tightly
linked to genomic regions of high importance. FB is being used for improvement of
maize populations with favourable alleles of large effect genes/QTLs for disease
resistance, such as maize streak virus and MLN, and nutritional quality traits, such as
proA (Prasanna et al. 2020c). Duo et al. (2021) applied marker-assisted pedigree
selection (MAPS) for improvement of proA in sub-tropically adapted maize inbreds.
The resultant inbreds and hybrids showed significantly higher proA than traditional
hybrids indicating the feasibility of MAPS for improving nutritional traits. Marker-
assisted recurrent selection (MARS) is useful to accumulate favourable alleles from
several genomic regions within a single population. Abdulmalik et al. (2017) applied
MARS in a bi-parental population to increase the frequency of favourable alleles for
drought tolerance.
GS is a powerful tool to take account of all the major or minor QTLs spread
throughout the genome and is especially useful for complex traits (Santantonio et al.
2020). GS is conducted in a training population by combining genotypic and
phenotypic data to estimate the marker effects (breeding values) of the individuals
that have been genotyped but not phenotyped in a population to be tested
(Meuwissen et al. 2001). GS helps in population improvement by rapid cycling
and higher genetic gain per cycle through the use of markers. GS has been applied in
maize for improvement of grain yield (Beyene et al. 2015; Zhang et al. 2017),
drought and water logging tolerance (Vivek et al. 2017; Das et al. 2020), disease
resistance (Technow et al. 2013; Sitonik et al. 2019; Nyaga et al. 2019; Liu et al.
2020c; Kuki et al. 2020; Holland et al. 2020), and kernel oil (Hao et al. 2019) and
zinc content (Guo et al. 2020; Mageto et al. 2020).
242 F. Hossain et al.

4.14 Doubled Haploid Technology

Maize breeding exploiting the doubled haploid (DH) technology based on in vivo
haploid induction has gained wide significance and become an invaluable tool due to
the fastest and most efficient route to produce completely homozygous lines for
maize breeding programmes (Ren et al. 2017). DH lines in maize is produced in four
steps, viz., haploid induction using the haploid inducer line, identification of
haploids, chromosome doubling and selfing of the doubled haploid maintain DH
line (Chaikam et al. 2019). The natural occurrence of haploid maize plants (~0.1%)
laid the base for in vivo DH production (Chase 1969). Haploid inducers may be the
paternal (used as female parent and haploid produced retain genome from the male
parent) or maternal inducers (used as male parent and retain genome from the female
parent). Paternal haploid induction has been reported through mutation in the ig1
gene (indeterminate gametophyte1) (Kermicle 1969; Evans 2007). However, it is not
being commonly used due to low haploid induction rate (HIR) of 1–2%, as well as
presence of anomaly in the cytoplasmic constitution of the resulting haploid
(Kermicle 1973, 1994).
Maternal haploid induction is quite successful and is being frequently used in
maize DH production due to high HIR of around 8–10%, and the haploid produced
retain the cytoplasmic and nuclear genome of the female parent without any
differences. At present, all the haploid inducers being used have been deduced
from the ancestral haploid inducer line Stock6 (HIR of ~3% of maternal haploids).
The currently available haploid inducers have the HIR of around 10%. In maize, two
major quantitative trait loci, qhir1 in bin 1.04 and qhir8 in bin 9.01, govern
significant haploid induction (Prigge et al. 2012). Dong et al. (2013) identified a
243 kb region with significant effect on haploid induction by fine-mapping a
3.57 Mb region between markers umc1917 and bnlg1811, targeting the QTL
qhir1. Kelliher et al. (2017), Liu et al. (2017b) and Gilles et al. (2017) reported
mtl/pla1/nld is the gene underlying the qhir1. 4 bp insertion near the terminal end of
the mtl gene causes the haploid induction. Zhong et al. (2019) cloned the gene
underlying qhir8 and found a non-Stock6-originating gene, dmp. They exhibited that
SNP substitution in dmp from thymine (T) to cytosine (C), at 131 bp from the
initiation codon ATG leads to amino acid substitution from methionine to threonine.
Enhanced ability of HIR by five to six times of dmp was observed in the presence
of mtl/pla1/nld. The first identified inducer ‘Stock 6’ had HIR of 1–3%. Efforts have
been made to enhance the HIR and several inducers like PHI (Rotarenco et al. 2010),
RWS (Rober et al. 2005), UH400 (Prigge et al. 2011) and MHI (Chalyk 1999) were
developed with HIR of ~6–15%, but all of them were adapted to temperate environ-
ment. Later on, tropically adapted inducer lines with HIR of around 6–14% were
also developed with the efforts of CIMMYT and the University of Hohenheim
(Prigge et al. 2012; Prasanna et al. 2012; Chaikam et al. 2016; Chaikam et al.
2018). DH technology is now the order of choice to all the maize breeders as lengthy
6–7 generation of inbreeding is bypassed, and completely homozygous plants are
achieved in two to three seasons.
4 Maize Breeding 243

4.15 Gene Editing Technology

Mutagenesis through physical and chemical agents and through Targeting Induced
Local Lesions in Genomes (TILLING) has been used to create variability (Slade
et al. 2005). Site-directed mutagenesis systems are now available for targeted
genome editing. Present-day genome editing tools such as zinc finger nucleases
(ZFNs), transcription activator like effector nucleases (TALENs) and clustered
regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated (Cas)
systems (Georges and Ray 2017). ZFN technology has been used to reduce phytate
content in maize seeds by targeting one of the inositol phosphate kinase (IPK)
homologues (Shukla et al. 2009). TALENs approach has been used to generate
heritable changes in maize gl2 locus (Char et al. 2015). In maize, various traits such
as grain composition, male sterility, lignin biosynthesis, herbicide tolerance, second-
ary metabolism and drought tolerance have been modified through CRISPR tech-
nology (Chilcoat et al. 2017).
The first use of CRISPR technology was reported for the maize IPK gene (Liang
et al. 2014). In addition, Shi et al. (2017) used the native maize GOS2 promoter to
both replace and supplement the native ARGOS8 promoter to achieve altered
expression of ARGOS8 and yield gains under drought high yield levels under
well-watered conditions. CIMMYT has started the MLN gene editing project
which uses CRISPR/Cas9 with the goal of deployment of resistant cultivars by
2025. Besides, transgene-free semi-dwarf maize plants were generated using
CRISPR-Cas9 technology by editing GA20ox3 gene (GA biosynthetic gene). Qi
et al. (2020) edited waxy locus in genetic background of ZC01 genotypes using
in vivo CRISPR/Cas9 tool and successfully obtained progenies rich in kernel
amylopectin. Recently, Liu et al. (2021) obtained genetic gain in multiple maize
grain-yield-related traits by engineering quantitative variation for yield-related traits.
This was done by engineering weak promoter alleles of CLE genes (a family of
genes that act as a brake to stop stem cell growth) and a null allele of a newly
identified partially redundant compensating CLE gene, using CRISPR-Cas9 genome
editing. Very recently, a new genome editing technology that does not require
double-stranded break in the DNA has been developed and is termed as prime
editing. This can achieve different types of editing such as any transition and
transversion mutations, as well as small indels. As this technology has wide flexibil-
ity to obtain different types of edits in the genome, it holds a great promise for
developing superior maize varieties with high yield, resistance to various abiotic and
biotic stresses, and quality of plant products (Marzec et al. 2020).

4.16 Future Thrust

Significant progress in understanding the genetics and efforts toward adopting newer
breeding methodologies and effective integration of omics tools have led to a
substantial genetic improvement of maize both in terms of productivity and total
production. Continued yield enhancement in maize with newer varieties year-after-
244 F. Hossain et al.

year has led to an imperative growth in area under cultivation of the maize crop. The
primary challenge in the future is going to be further enhancement of yield with
increased adaptation to the newer challenges. Despite the persistent yield growth,
breeding for stress tolerance particularly biotic stress is continuing to be an area that
need immediate attention. Although efforts have been made to understand the
genetics and to identify the gene(s)/loci governing disease resistance, their actual
use in breeding for resistant cultivars is still to reach its full potential.
With the changing climatic conditions and evolution of new races of pathogen,
breeding for resistance to disease of greater concern in the region is highly important.
In the most recent times, outbreak and rapid spread of FAW have created havoc in
maize cultivation as delay in control measures has led to a greater reduction in yield
and sometimes complete failure of the crop. This has also necessitated excessive use
of chemicals which has increased cost of production besides posing serious environ-
mental pollution. Besides, tolerance to abiotic stresses, particularly drought, heat and
water logging are very important as maize crop is sensitive to both moisture stress
and excessive moisture. Thus, widening of germplasm for multiple stress resistance/
tolerance and their use in crop improvement programme to breed high yielding
maize hybrids coupled with stress tolerance is very important.
Recently, considerable success has been achieved in development of high yield-
ing hybrids with enhanced nutritional quality (with one or more grain quality traits).
This offers hope for simultaneous improvement of multiple traits, and these
germplasms also need to be improved for stress tolerance for its wider adaptation
and adoption. Weeds continue to remain as one of the major yield-reducing factors in
maize production. Development of herbicide-tolerant maize genotypes will greatly
facilitate use of herbicides for weed management anytime during the crop growth.
This requires large-scale screening of available germplasm for herbicide tolerance or
use of mutation as a tool to create variation for such economically important traits.
Until recent times, breeders have been largely practising inbreeding for development
of more and more inbreds from the source population. By the virtue of process and
associated genetic effects, complete homozygosity could never be achieved in the
inbreds. Use of DH technology in the maize-breeding programmes needs to be
strengthened for rapid development of completely homozygous productive inbreds.
This will help in greatly reducing the time taken for inbred development besides
maximum realisation of heterosis. With the availability of gene-editing technology,
accelerated development of genotypes with target traits is very much possible, and
this will greatly facilitate in plant breeding. Furthermore, ‘speed breeding’ needs to
be explored in maize to accelerate the breeding cycle and development of hybrids in
a much shorter time frame.

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Barley Breeding
5
Santosh Kumar Bishnoi, Madhu Patial, Chuni Lal,
and Ramesh Pal Singh Verma

Abstract

The importance of barley stemmed mainly from the diversified use of its grain
and the plant pertaining to food, feed and forage. In many countries around the
world, this crop is often considered the only possible rain-fed cereal crop under
low input and stressful environments, such as drought, heat and cold. Therefore,
this old crop is likely to have new future in current situations of climate change
and ever-increasing population pressure on food supply. During the early 1920s,
the barley improvement program was started in India using pure line selection
method. Most of the developed barley varieties are of six-row types and are
primarily used for feed purpose, while two-row malt-purpose barley varieties are
of recent origin. Globally, barley improvement programmes now see a great
potential as industrial crop, and barley breeding activities were directed to
develop malt-type barley varieties. Besides conventional breeding, the develop-
ment in the fields of barley genomics is rapid, and researchers are having more
choice to identify, characterize, clone, annotate and edit the genes of interests for
the development of better varieties.

Keywords
Biotic and abiotic stress tolerance · Breeding objectives · Coordinated system of
testing · Genetic resources · Hordeum vulgare

S. K. Bishnoi · C. Lal · R. P. S. Verma (*)

ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
e-mail: rp.verma@icar.gov.in
M. Patial
ICAR-Indian Agricultural Research Institute, Regional Station, Shimla, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 259
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_5
260 S. K. Bishnoi et al.

5.1 Introduction

Since the beginning of sedentary civilization, cereal grains have been the integral
part of human diet providing a major proportion of dietary energy (50% of the total)
and nutrients including carbohydrates and protein (Laskowski et al. 2019). During
the course of metamorphosis of early humans from hunter gatherers to agrarian
sedentary civilizations, an array of cereal species had been domesticated and brought
under organized cultivation mainly through persistent selection in the form of pick
and choose. Apart from maize, rice and wheat, barley (Hordeum vulgare L. emend
Bowden.) is one such cereal grain that was domesticated very early and eventually
assumed unprecedented importance in the survival and well-being of the early
settlers. Therefore, it is not only one of the first domesticated crops but also antique
among cereals. The use of barley in making of beer was discovered early on, which
is the third most popular beverage around the world after water and tea, even today.
In the Sumerian and Babylonian civilizations, barley grains were even used as a
currency.
Evolutionary progression of barley has rendered this crop to be accustomed to
diverse eco-geographical environmental conditions as compared to other crop spe-
cies because of its resilience to extreme environmental variations. The adaptability
of barley to extreme environments and marginal growing conditions has led to
extensive cultivation of this cereal all over the world (von Bothmer et al. 1995).
The cultivation of barley extends from the tropics to high latitudes (>60
N) in
Iceland and Scandinavia, as well as in high altitudes up to >4450 m above sea level
(masl) in the Himalayas (Ceccarelli et al. 2008; von Bothmer et al. 2003).
Barley is a nutritious cereal grain that contains many important nutrients and
vitamins. It is characterized by its rich nutty flavour and chewy consistency. This
versatility of barley use makes it a vital grain commodity in the international
markets.
Although the main uses of barley are in animal feed and brewing purposes, but
owing to its nutritional value, specially being rich in dietary fibre, it is also consumed
as a staple food in the North and Sub-Saharan Africa (SSA), hilly areas of Central
Asia, South-West Asia and Northern Africa. The projected increase in global
population, food consumption and dietary changes (Godfray et al. 2010; Tilman
et al. 2011) are expected to broaden the gap between supply and demand of the food
grains only to be aggravated by the shrinking acreage available for agriculture amidst
the rampant global climate change (Ray et al. 2015). The world agricultural produc-
tion needs to be doubled by the year 2050 to keep pace with the demographic
expansion that is unfolding on the world (Gerland et al. 2014).
The IPCC (Porter et al. 2014) reported that for the major crops (wheat, rice and
maize) in tropical and temperate regions, without adaptation, climate change will
result into serious consequences for production when local temperature would
increase by 2
C or more. Therefore, the climate change may gradually upsurge
the inter-annual variability of crop yields in some regions, resulting in an increased
risk of more severe impacts on food security (Porter et al. 2014; Ray et al. 2015). The
global climate change will cause few areas to experience high precipitation, while
5 Barley Breeding 261

Fig. 5.1 Year-wise global production statistics of barley

few others facing prolonged droughts. In such a scenario, barley is one of the
hardiest cereal crops that can adapt well to the hostile climates through its genetic
plasticity (Garstang et al. 2011; Ingvordsen et al. 2015).
In fact, this crop can thrive well in the regions such as arctic and subarctic zone to
subtropical regions where the other cereals such as maize, wheat and rice can hardly
be grown. It is considered as the only available alternative in the harsh deserts owing
to its ability to thrive in environments of limited moisture availability, heat and cold.
Even more, barley when displaced by wheat particularly in the irrigated areas has
found a new niche role in nutraceuticals, distillery and ethanol fuel production
making it a potential candidate as an industrial crop around the world. Owing to
its nutritional composition, the barley grains are up for being the next nutraceutical in
a scenario of people being more health-conscious day-by-day. Lowering blood
cholesterol, blood pressure and glycaemic index have been considered to be the
major health benefits of barley because of presence of high amount of soluble fibre
and beta-glucan (Baik and Ullrich 2008).
The largest proportion of the global barley production is utilized for animal feed,
followed by the use in malting industries and various food products (Blake et al.
2011). Currently, barley is the fourth most important food crop of the world after
maize, wheat and rice (FAO 2020; Shabrangy et al. 2021). During the year
2020–2021, 159.74 million metric tons of barley was produced globally as com-
pared to 156.41 million metric tons in the year 2019–2020. The year-wise global
production statistics are presented in Fig. 5.1. In 2020–2021, the top five barley
producing countries were the Russian Federation (20.63), Australia (13), Canada
(10.74), Turkey (8.1), and Ukraine (7.95) (https://www.statista.com/statistics/271
973/world-barley-production-since-2008/) with the production in million metric
tons. Figure 5.2 represents country-wise production of barley in the year
2020–2021. The largest consumer of barley is the European Union followed by
Russia and the consumption pertains mainly to malting purposes.
262 S. K. Bishnoi et al.

Fig. 5.2 Country-wise production statistics of barley during 2020–2021

The world barley trade in the form of exports and imports across the years has
been presented in Table 5.1 (export) and Table 5.2 (import). The barley export trends
are more or less similar across last 5 years where the European Union, Russia and
Ukraine have been the largest exporters barring the year 2020–2021 where Australia
held rank one among the barley exporting countries if European Union were to be
considered not as a single country. The total global barley exports were stable from
2017–2018 to 2019–2020 and then increased in 2020–2021 and have shown a stable
performance during the current period of 2021–2022.

Table 5.1 World barley export October/September year (thousand metric tons)
Country 2017/18 2018/19 2019/20 2020/21 2021/22
Argentina 2537 3001 2598 2900 3500
Australia 6088 3666 3231 6700 5000
Canada 1868 2269 2520 3800 4500
European Union 5894 5809 7579 7600 7300
Kazakhstan 1411 1762 1292 1000 1300
Russia 5661 4320 5141 5400 5200
Syria 0 0 300 250 150
Ukraine 3188 4407 4990 4300 5100
United Kingdom 896 1538 1397 1425 1000
Uruguay 12 62 41 200 150
Others 343 246 144 407 192
World Total 28,000 27,181 29,388 34,257 33,667
Source: https://apps.fas.usda.gov/psdonline/circulars/grain.pdf
5 Barley Breeding 263

Table 5.2 World barley import October/September year (thousand metric tons)
Country 2017/18 2018/19 2019/20 2020/21 2021/22
Algeria 439 467 503 800 700
Brazil 584 608 647 700 700
China 8144 5181 5969 10,000 10,600
Colombia 324 341 308 320 350
European Union 979 1762 1089 1400 1300
Iran 2700 3200 2300 2500 2400
Israel 234 236 358 300 350
Japan 1253 1158 1253 1150 1250
Jordan 788 928 564 700 800
Kuwait 521 474 522 350 500
Libya 438 888 891 900 700
Mexico 1 82 346 350 350
Morocco 363 299 1073 700 300
Qatar 229 288 349 400 450
Saudi Arabia 7700 5700 7300 7500 7500
Thailand 147 206 685 1150 600
Tunisia 674 487 751 800 700
Turkey 774 375 1007 650 1000
United Arab Emirates 263 476 443 470 500
Vietnam 177 133 198 750 400
Others 1551 1846 1309 1492 1344
World Total 28,000 27,181 29,388 34,257 33,667
Source: https://apps.fas.usda.gov/psdonline/circulars/grain.pdf

As already pointed out, the rich genetic diversity in barley enables this crop to
adapt to diverse conditions. This genetic diversity of barley has always been an
important subject of study for geneticists and breeders in order to identify new
characters that can help improve the sustainability of the crop. This allowed early
spring varieties suitable for environments with a prolonged cold weather and short
spring-summer seasons and tardier winter varieties able to fully exploit the produc-
tive potential of temperate climates.
The good resistance to drought has also allowed the species to adapt to the
environments such as those of North Africa and the Middle East. In fact, barley
has a vast area of cultivation, from the humid regions of Europe to South America
and the arid areas of Africa and Asia (Kling and Hayes 2004; Tricase et al. 2018).
Nevertheless, the barley yield depends upon the favourable climatic conditions, soil
characteristics and agronomic practices, and because of the deployment of high
yielding varieties and other associated technological innovations, world barley
productivity has increased from 1.33 t/ha in 1961 to 2.95 t/ha in 2018. Countries
such as Belgium, Netherlands, New Zealand, Saudi Arabia, Ireland, Chile,
Switzerland and France have recorded more than 6.0 t grain yields per hectare in
2018 (Fig. 5.3) (FAO 2020).
264 S. K. Bishnoi et al.

Fig. 5.3 Countries with high barley grain yields (q/ha) in 2018

5.2 Types of Barley and Versatility of Their Use

The genetic diversity in barley pertaining to morphological as well as agronomic

attributes is immense, and different barley types are cultivated in different parts of
the world depending on the climate buffering capacity and end use of the produce.
Accordingly, barley can be classified depending on various factors major being the
growth habit (spring or winter types), number of rows of grains in spike (two-row
and six-row barley), spike compactness, hull adherence (hulled, presence of an outer
husk attached to the grain or hulless/naked with removal of the outer husk during
threshing), presence/absence or size of awns (awned, awnletted or awnless varieties),
end-use (malting, feed or food) and aleurone colour (black, purple or white kernels)
due to the different level of anthocyanin (Arendt and Zannini 2013; Ciccarelli et al.
2008; OECD 2004).
The two-row is the original ancestral variant which was domesticated and six-row
is a mutant selected later on. In the two-row type, the lateral two florets are sterile
while only the central floret is fertile. In the six-row type, all the three florets in a
spikelet are fertile. The spike fertility is conditioned by a gene Vrs1. The two row
barley grains are plump and the size is more uniform and lower in protein and high in
starch, therefore considered suitable for malting purposes. The six-row barley is
mainly used for feed and food with some good varieties also being utilised for
malting because of its higher enzymatic activities. The hulless barley varieties in
which the lemma and palea do not adhere to the pericarp strongly are preferred as
food. The hulled condition is controlled by the Nud gene. In the malt barley varieties,
hulled types are preferred as the hull which helps in faster moisture absorption in
steeping, protection of growing plumule in germination stage of malting process, as
well as it acts as a natural filter during mashing and brewing. Same is the case when
the barley is meant for the feed purposes because of the yield advantage. The hulless
barley constitutes a very small fraction of the total world barley production and is a
5 Barley Breeding 265

staple food crop in the Himalayan region, the Andes, north African countries and the
Ethiopian highlands.
Barley can also be classified based on grain composition (normal, waxy or high
amylose starch types, high lysine, and high beta-glucan or pro-anthocyanin free).
Barleys of different classes often differ widely in both their physical and composi-
tional characteristics, and as a result they have different processing properties and
end uses. Globally, about 70% barley produce is used as animal feed and 6% as
human food, while around 25% have industrial use in malting industry (Tricase et al.
2018). As a feed, barley is used in both ruminant and non-ruminant livestock, as well
as in poultry and fish. For malt barley, mostly two-row types are used which
normally yield less than the six-row varieties used for feed and food, however in
recent years, several two-row malting barley varieties have been developed in India
with comparable yield levels under optimum management.
Early uses of barley pertained to human food only to be followed by the malt
purposes and its use as feed although came in the last but has become the most
important one in the present day. The use as feed is global across developing and
developed countries, while the use as food is in few developing countries of Africa
and Asia. The utilization of barley for production of renewable biofuels has added
tremendously to the versatility of the crop although the utilization data for the world
or countries is not available. The wide adaptability of barley crop has contributed in
its major part of production being animal feed apart from the quality considerations
of the grain. Barley can be grazed, made into hay or silage while still green and can
be used as straw after the grain is taken out. It grows up to 120 cm in height and due
to its broader leaves, the leaf: stem ratio is quite high, that is, 0.88. The awnless/
hooded barley varieties are considered to be safer and of higher nutritive quality as
forage, as sometimes the pieces of the awns cause injury in mouth while animals are
being fed the dry straw.
The grain protein generally ranges from 10 to 20% while that of the starch
component is 50–70%. This nutrient composition is ideal for the livestock as well
as for poultry and fish industries. The barley straw is also used as feed and contains
2–6% protein and 80–86% neutral detergent fibre (NDF). At flowering, the protein
and NDF content has been reported to be 12% and 63%, respectively, which
decrease to 9% and 56% at the time of dough formation stage, and also the forage
is low in cell walls, ADF and lignin compared to other cereal forages (Ditsch and
Bitzer 2005). In forage-deficient regions, which are usually the water-deficit areas,
barley can be grown for obtaining both the forage and grain in the same crop, and
this type of barley is called dual purpose barley. It is an alternative approach ensuring
the availability of forage as well as acceptable amount of grain yield (Moustafa et al.
2021). The first cut of forage can be taken after 6–7 weeks of sowing, that is, the first
node appearance stage, beyond that the yield of grain from regenerated crop is
drastically decreased.
In India, scarcity of feed and fodder is one of the major constraints particularly in
resource-poor, rural areas. Evidences indicate that feed-related problems accounted
for about 36% (per annum in value terms) in dairy animals, and losses due to scarcity
of dry and green fodder were estimated to be 11.6% and 12.3%, respectively (Birthal
266 S. K. Bishnoi et al.

and Jha 2005). The green fodder deficit of 65% and dry fodder deficit of 25% has
been predicted in India by the year 2025 (Singh et al. 2013). Given the nutritional
quality of barley, green fodder as well as straw and the ability of crop to withstand
poor soils and drought, barley seems to be the trouble-shooter crop in the Indian
context. These issues coupled with a rise in demand for dairy products due to
urbanization and human population growth have warranted research on development
of high yielding forage crop varieties with enhanced quality of feed and fodder.
Under these circumstances, 70% of the total barley grain production of which is
utilized as feed globally, as well as in India is an important feed and fodder crop
particularly in winter when supply of green fodder is in shortage.

5.3 The Indian Context

In India, barley ranks fourth after wheat, rice and maize among the cereal crops. In
1961, a total of 2.82 million tons of barley grains were harvested from 3.2 million
hectares with a yield level of 1.14 tons per hectare as compared to 1.78 m tons from
0.66 million hectares with yield of 2.7 tons per hectare in the year 2018 (FAO 2020).
Though there was about 37% fall in the total grain production of this crop during this
period, chiefly due to sharp decrease of 79% in its acreage brought about by
increased irrigation facilities in the country leading to replacement of barley area
by rabi crops mainly by wheat. It coincided with the green revolution, in which a
spectacular increase of 206% in the yield levels propelled mainly through the
development of high yielding barley varieties insulated with inbuilt resistance to
important biotic and abiotic stresses was witnessed (Table 5.3). However, the area
under barley consistently decreased since 1961 only to stabilize in the last two
decades and drifts around 0.67 m ha (Table 5.3).
In India, barley is cultivated in the plains (Rajasthan, Uttar Pradesh, Madhya
Pradesh, Punjab, Haryana and Bihar) and on the hills up to an elevation of around
4000 m (Himachal Pradesh, Uttarakhand and Jammu and Kashmir). In the
Himalayas, the six-row husked barley types are commonly cultivated while the
two-row types, both husked and huskless, are grown only to a limited extent.
Cultivation of the six-row husk less forms are confined to the higher Himalayan
ranges. In these areas, barley is generally a crop of marginal, low-input, drought-

Table 5.3 Decade wise % Period Area Production Yield

increase/decrease, for area,
1961–1970 13.7 3.6 11.7
production and yield in
India 1971–1980 30.7 41.7 15.9
1981–1990 45.2 35.2 18.2
1991–2000 24.7 11.4 17.7
2001–2010 19.8 5.3 18.0
2011–2018 6.3 7.0 14.2
1961–2018 79.4 36.9 206.2
Source: FAO (2020)
5 Barley Breeding 267

Table 5.4 Recent high yielding varieties developed in India

Areas
Production recommended
Type conditions Varieties for
Malt IRTS DWRUB52, RD2668, DWRB92, DWRB101, NWPZ
barley RD2849, DWRB123, DWRB160, DWRB182 (all
2-R)
IRLS DWRUB64, DWRB73(2-R), DWRB91 (2-R)
Feed IRTS BH902, BH946, DWRB137, K1055, PL891a NWPZ
barley IRTS DWRB137, HUB113 NEPZ
IRTS PL751, JB1, RD2715,b DWRB137, RD2786, Central zone
RD2899, BH959
RFTS RD2660 NWPZ
RFTS K603, JB58 (MP) NEPZ
IRTS NDB1173, NDB1445, RD2794, RD2907 NWPZ and
(saline NEPZ
soils)
RFTS BHS380,b BHS400, UPB1008, VLB118, VLB130,b NHZ
(hills) HBL713
IRTS irrigated timely sown, IRLS irrigated late sown, DP dual purpose, 2-R two-row type, NWPZ
North Western Plain Zone (Punjab, Haryana, Delhi, Rajasthan, Western Uttar Pradesh), NEPZ
Eastern UP, Bihar and Jharkhand, West Bengal (excluding hills), Central Zone Madhya Pradesh,
Gujarat, Kota and Udaipur division of Rajasthan, Jhansi division of Uttar Pradesh, NHZ
Uttarakhand, Himachal Pradesh and J & K
a
Huskless
b
Dual purpose

stressed environments. The landraces grown in these areas are favoured by farmers
for their quality, both as grain and straw. However, the area under the husk-less
barley landraces, which were very popular and widely grown in higher Himalayan
ranges about four decades ago, has declined considerably (Kant et al. 2016).
The barley improvement program in India was initiated in the early 1920s, where
pure line selections were followed. Thirty-one barley varieties were developed for
cultivation in different states, before the inception of AICBIP. The organised
breeding program was initiated with the inception of All India Coordinated Barley
Improvement Programme (AICBIP) during 1966–1967 and since then more than
105 barley varieties have been released in India for commercial cultivation so far
(Kumar et al. 2017). Majority of these varieties are six-row types, developed for feed
purpose while two-row barley varieties meant for malt purpose are of recent origin.
Most of the recently developed (last 15 years) varieties for different purposes,
regions and production conditions (Table 5.4) are in seed chain and are being
cultivated as per recommendations. However, a significant reduction in annual
breeder seed indents of barley has been recorded (Table 5.5), which might prove a
cause of concern for this crop considered to be a climate change crop (Fig. 5.4).
Indian barley improvement programme has been very successful in raising
genetic potential of feed barley from 35 q/ha grain yield recorded in the variety
‘Vijaya’ to 67.44 q/ha in the variety ‘DWRB137’ released in the years 1972 and
268 S. K. Bishnoi et al.

Table 5.5 Barley breeder Year DAC indent (q) Varieties Production (q)
seed indents and production
2015–2016 1138.43 36 1123.57
during last five cropping
season in India 2016–2017 1140.75 38 1521.86
2017–2018 1048.25 35 1452.20
2018–2019 827.85 29 1421.05
2019–2020 524.97 26 997.25
2020–2021 638.06 24 830.0

Fig. 5.4 Decadal average area, production and yield of barley in India (Source: FAO, 2020)

60
53.7
55 50.1 50.9 52.2
49.8 48.7 49.7
50 45.1
45
Yie ld (q/ ha)

41.4
40 36.8 38.1
35
30
25
20
Alfa93 BCU73 DWR28 DWRUB52 DWRB92 DWRB101 RD2849 DWRB123 DWRB160 DWRB182 DWRB137
(6-R)

Fig. 5.5 Genetic gain in two-row malt barley cultivars released between 1994 and 2020 in India

2018, respectively. Similarly, in case of two-row malt barley improvement

programme, the significant genetic gain has been made between 1994 (Alfa 93)
and 2020 (DWRB182) (Fig. 5.5) initially utilizing the two-row  six-row
hybridization program, which was initiated to improve the local adaptation of the
introduced superior malting quality two-row barley cultivars in India. The yield gap
between improved six-row feed barley and two-row barley has been almost bridged
in northern plains under optimum management conditions as evident in Fig. 5.5,
5 Barley Breeding 269

where the average yield of latest six-row barley variety DWRB137 and two-row
barley varieties is at par.

5.4 Origin and Evolution of Cultivated Barley

Belonging to the grass family Poaceae, barley is assumed to be domesticated circa

10,000 years ago, that is, the dawn of human civilization, making it one of the first
domesticated crop plant species providing an anchor for development of early
agriculture through the Neolithic period (Wang et al. 2015). Barley finds a mention
in the oldest text available, that is, the Rig Veda supposed to be authored circa
5000 years ago and Yavagu a sour gruel somewhat similar to the modern-day beer is
believed to be made from barley grains at that time as well (Nene 2012). The origin
of cultivated barley is not conclusively, known and there are many claims about it
having originated from the Fertile Crescent which is the Middle East and northern
Africa (Jordan, Israel, Lebanon, Syria, Turkey, Iraq and Iran) in the present day
(Zohary and Hopf 2000; Badr et al. 2000).
However, another hypothesis of origin of barley in the South-Eastern Asia
(present-day China and Nepal) has been propounded by Clark (1967) and was
later on supported by Bothmer and Komatsuda (2011). Azhaguvel and Komatsuda
(2007) proposed diffuse (polyphyletic) origin of H. vulgare, that is, oriental and
occidental barleys originating independent of each other. Moreover, the discovery of
hulless six-row barley in Mehrgarh (Pakistan) dating 7000 to 6500 BC has made the
subject matter of origin of barley highly debatable (Mehra 2007). The Central Asia
and Tibetan plateau are also candidates of independent domestication events of
cultivated barley narrowing down the debate that barley has multiple origins (Dai
et al. 2014). Using sequences for NAM-1gene and grain protein content (GPC),
Wang et al. (2015) concluded that Tibet is one of the origin and domestication
centres for cultivated barley. The wide adaptability of barley to different climates
and soils is one of the major factors why this crop was among the first ones selected
for domestication by the early human settlers. Barley can naturally tolerate a variety
of abiotic stresses including drought, soil salinity, high and low temperatures and can
be termed as a minimum effort cereal crop. Therefore, where cultivation of wheat is
not possible due to prevailing climatic stresses, barley can perform better.
For any crop to survive the onslaught of climate change and introduction of new
crops, the genetic base needs to be large enough to incorporate new adaptive and
agronomic alleles apart from the quality. This is true in case of the genus Hordeum
which comprises of 31 species as opposed to Triticum (wheat) with only 10 species.
The broad genetic base is at the core of very high adaptability of barley and its
eventual spread as successful crop plant species to new geographies. Barley is
cultivated from Scandinavia to Sub Saharan Africa to Central Asia to the Himalayas
and to the Thar Desert. The progenitor barley species remains unknown, and the wild
barley H. spontaneum is considered to be an intermediate stage frozen in evolution.
Although in some studies, H. spontaneum has been considered to be the progenitor
of cultivated barley (Wang et al. 2015). Ethiopia is considered to be the secondary
270 S. K. Bishnoi et al.

centre of diversity, while India is the regional centre of diversity for barley. The
western Himalayas exhibit significant barley diversity for cold and drought tolerance
and aleurone colours particularly variations of black–and–blue colours. The main
domestication syndrome traits in barley are non-brittle rachis, hull-less (free
threshing) grains and large seed size (Salamini et al. 2002).

5.5 Barley Wild Relatives

Crop and produce uniformity have become an essential requirement for modern
agricultural production systems and this has led to a decline in the genetic diversity
leading to increased susceptibility of the crop plants to abiotic and biotic stresses.
Barley is no exception to this. To this effect, the barley crop wild relatives are
potential donors of new genes for better adaptation (Rehman et al. 2019). Barley
wild relatives possess good diversity for agronomic traits, resistance to diseases,
physiological growth, salinity tolerance, water and nitrogen use efficiency.
According to the gene pool concept (Harlan and de Wet 1971), the genus Hordeum
has 33 listed species arranged in three gene pools. The primary gene pool (natural
crossing occurs and hybrids are vigorous and fertile) in barley is composed of
Hordeum vulgare (landraces and varieties) and the progenitor species
H. spontaneum (Vincent et al. 2019; Rehman et al. 2019). Therefore, in barley
breeding programmes, H. spontaneum or the wild barley is of very much importance
as donor of desirable alleles to the cultivated barley and had been a regular feature of
the barley breeding programmes aimed at both abiotic as well as biotic stresses. The
Rph16 gene conferring resistance to all the known races of leaf rust fungus Puccinia
hordei and Mla-6 and Mla-14 against powdery mildew were sourced from
H. spontaneum (Ivandic et al. 1998; Jørgensen 1992).
Currently, the species is having above 30,000 accessions in different gene banks
around the world. The secondary gene pool (natural crossing generally does not
occur and the hybrids are weak/non-fertile) in barley is composed of only one
species, i.e., H. bulbosum. H. bulbosum has been historically utilized in developing
of double haploids in barley, as well as wheat but no significant gene transfer
incidence has been reported. Different studies have reported H. bulbosum as a
valuable source of disease resistance genes. The remaining diploid, tetraploid and
hexaploidy, 31 species of the genus Hordeum make its tertiary gene pool which still
remains to be utilized in the breeding programmes. The fourth gene pool represents
no living species but includes individual genes that may be transferred to barley by
genetic transformation from any species including animals and microorganisms
(Hernandez et al. 2020).
As far as the distribution of wild barley species is concerned, they are spread in
the Americas, Europe, the Mediterranean, Central and Middle-Eastern Asia and
Africa. These species possess very strong barrier to successful crossing including
non-pairing of the chromosomes during meiosis and eventual hybrid non-viability or
breakdown. Therefore, H. bulbosum in the secondary gene pool assumes very high
importance as a donor of desired alleles to H. vulgare. The interspecific
5 Barley Breeding 271

incompatibility, chromosome elimination, endosperm degeneration, hybrid instabil-

ity and chromosome pairing, hybrid infertility, reduced recombination and linkage
drag are the major constraints of the H. vulgare  H. bulbosum crosses (Pickering
and Johnston 2005). In spite of these constraints, many important genes have been
identified from these interspecific crosses including biotic stresses such as leaf rust,
powdery mildew, stem rust, Septoria speckled leaf blotch, barley yellow dwarf virus,
barley mild mosaic virus, barley yellow mosaic virus and abiotic stresses such as
drought tolerance (Rehman et al. 2019).
The primary gene pool, therefore, seems to be the most obvious choice for
utilization in the breeding programmes and the landraces from this have been
successfully utilized to breed powdery mildew-resistant varieties possessing mlo11
gene (Jørgensen 1992). The H. spontaneum germplasm has also been reported to be
a rich source of resistance genes against major diseases (leaf rust powdery mildew,
scald), aphid (Rhopalosiphum maides) and abiotic stresses mainly the drought and
salinity, as well as quality. Although the linkage drag is a persistent nuisance here
also, still extensive use of H. spontaneum has been made as a donor of useful traits to
the cultivated barley. H. spontaneum could be a good source of cold tolerance and
novel lipoxygenase (LOX) alleles (Hirota et al. 2008). The International Center for
Agricultural Research in the Dry Areas (ICARDA) has the global mandate for barley
improvement and holds in-trust one of the largest collections of barley which
includes unique and rich collections of landraces (18,935) and wild Hordeum
(2392) species (Rehman et al. 2020).
The obstacles including cross incompatibility, infertility, reduced recombination
and introgression of undesirable alien genome segments resulting in linkage drag
have historically hampered the utilization of barley wild relatives in breeding
programmes. A deeper and more practical understanding of these valuable wild
relatives is necessary if these assets are to be used effectively in developing
improved varieties. In general, current varieties and potential varieties have a narrow
genetic base, making them prone to suffer the consequences of new and different
abiotic and biotic stresses that can reduce crop yield and quality. Therefore, to
achieve higher genetic gains in yield and quality in the changing climate scenario,
the adaptation of the newly developed varieties must be very high in order to cope up
with the prevalent abiotic and biotic stresses and the use of barley wild relatives in
the breeding programmes might be highly useful to broaden the genetic base and to
enhance the adaptation (Hernandez et al. 2020).

5.6 Barley Genetic Resources

Plant breeding requires sufficient genetic diversity for effective generation of novel,
valuable and improved combinations of alleles. The genetic diversity in cultivated
barley ranges from very low in regions of Europe (Garcia et al. 2003) to extremely
high in other continents mainly Asia and Africa (Khodayari et al. 2012). Numerous
factors such as mutations, selection (both natural and artificial), genetic drift, random
mating, etc. have caused the origin of different forms in barley. For example,
272 S. K. Bishnoi et al.

mutation of ancestral wild-type two-row barley led to a recessive six-row type after
domestication. Similarly, geographical separations and differential breeding for
vivid end use led to different varieties of two- and six-row, and their further
adaptation to different environments differentiated the spring and winter forms of
barley. In barley, vast germplasm collections are accessible but their use for crop
improvement has been historically limited and efficiently accessing genetic diversity
is still a challenge.
The diverse barley genetic resources which include modern cultivars (currently in
use), obsolete cultivars (often elite cultivars from the past that are frequently present
in the pedigrees of modern cultivars), landraces, wild relatives, genetic and cyto-
genetic stocks, as well as breeding lines are essentially required to develop quality
cultivars ensuring stable productivity. Therefore, it is imperative to collect, evaluate
and maintain genetic resources available from different geographical areas through-
out the world. The barley collection comprises accessions representing 20 species
including wild relatives, of which 98.5% of the accessions represent common barley
(Hordeum vulgare L.). Out of more than 400,000 accessions of Hordeum genus
stored in 108 gene banks spread across 64 countries worldwide, include wild
relatives (15%), landraces (44%), breeding materials (17%), genetic stocks (9%)
and cultivars (15%).
The use of genetic resources for barley improvement programme started more
than 70 years ago with the collection of local landraces. Landraces store a high level
of genetic diversity and possess high potential for adaptation to environmental
conditions, and thereby they are an important element of future breeding
programmes. Landraces of inbreeding crops including barley are genetically hetero-
geneous populations comprising inbreeding lines and hybrid segregates generated
by a low level of outcrossing (Nevo 1992). In barley, they represent the largest part
of germplasm conserved in gene banks worldwide. Historically, landraces constitute
important resource for introgression of different alleles into pure line varieties. In the
initial collections of landraces held in gene banks, at least 50–60% of the total
genetic variation captured resides within the landraces, the remainder being
accounted for by differences between landraces (Brown and Munday 1982). Seven
gene banks hold the largest landrace collections of barley with ICARDA (Morocco),
having more than 15,500 landrace accessions. Other gene banks for barley landraces
are Chinese Academy of Agricultural Sciences (CAAS), Institute of Biodiversity
Conservation (IBC, Ethiopia), PGRC (Canada), USDA (United States), IPK
(Germany), and Research Institute for Bioresources (RIB, Japan), each having
more than 10,000 accessions. These landraces have been useful for varietal devel-
opment for disease resistance, abiotic stress and root architecture features
(Dziurdziak et al. 2020; Friedt et al. 2011).
Breeding materials are the second most frequent category of barley germplasm
held in gene banks globally with 49,000 accessions. The largest collection of
breeding material is conserved at CIMMYT in Mexico with 11,000 accessions,
followed by PGRC (Canada), ICARDA (Morocco), USDA (United States), National
Institute of Agrobiological Research (NIAR, Japan), and Institut National de la
Recherche Agronomique (INRA, France).
5 Barley Breeding 273

As already mentioned, the crop wild relatives provide an important source of

allelic diversity and enhanced levels of resistance to multiple stresses. Wild
ancestors introduce new alleles from wild and old species to locally adapted germ-
plasm and providing useful traits. For example, gene for fungal resistance has been
introgressed from H. spontaneum in several barley cultivars released in Europe
(Schmalenbach et al. 2008; von Korff et al. 2005). The majority of the wild relative
collections are represented by the barley progenitor, Hordeum spontaneum (20,700
accessions), while out of 5900 accessions of wild barley species belonging to the
secondary and tertiary gene pool, the largest collections are maintained in Canada
and Sweden.
However, the alleles in barley wild relatives such as H. spontaneum and
H. gricrithon have linkage drags, and their exploitation for cultivar improvement
is limited by cross-incompatibility barriers and hence the potential of wild relatives
for improving quantitatively inherited traits is largely unexplored (Fischbeck et al.
1976; Moseman et al. 1981). Many major genes from wild relatives have been
transferred into the cultivated gene pools (Hajjar and Hodgkin 2007). The genetic
stocks of barley include morphological mutants, genetic male sterile stocks, and
various cytogenetic stocks, for example, trisomic, inversion and translocation stocks.
Recently, the mapping populations are added to the list of the genetic stocks. The
Nordic Genetic Resources Center or NordGen (formerly Nordic Gene Bank) in
Sweden has the most extensive collection of barley genetic stocks which comprises
about 10,000 accessions, and large collections of genetic stocks are also maintained
at PGRC (Canada), USDA (United States) and NIAR (Japan).
The cultivars refer to the finished products (both advanced and obsolete) having
desired traits and stability derived from plant breeding programmes. Numerous high-
yielding barley cultivars have been evolved through extensive plant breeding efforts
and strict selection approaches. Natural mutations in H. vulgare as well as mutations
induced by radiation or chemical treatments have also been used for cultivar
development. The largest cultivar collections of barley are held at N.I. Vavilov
Research Institute of Plant Industry (VIR, Russia) with 9600 accessions (Tables 5.6
and 5.7).
Moseman and Smith Jr (1985) classified barley germplasm collections as either
base or working/active collections. Base collections are maintained for long-term
storage and are used as a benchmark for monitoring changes in genetic diversity over
time due to genetic drift. The seed viability of accessions should remain at acceptable
levels for at least 50 years. Active collections are available for distribution to
scientists and are accessed frequently. Accessions in an active collection include
cultivars, selections, breeding lines and landraces, which do not require special care
for maintenance. The active collection is intended to preserve germplasm viability in
medium-term storage conditions for at least 20 years.
274 S. K. Bishnoi et al.

Table 5.6 Share of Hordeum accessions based on different classification

Percent
Species collection Species (%)
Genebank collections H. vulgare ssp. vulgare 88
(Bockelman and Valkoun H. vulgare ssp. spontaneum 10
2011) H. bulbosum 0.4
other wild species 1.7
Landraces 44
Breeding lines 17
Crop wild relatives 15
Cultivars 15
Genetic stocks 9
Natural v/s Created Germplasm evolved in long-term interaction with 59
(Bockelman and Valkoun local environments and farming practices
2011) Germplasm resulted from modern plant breeding 41
and research

Table 5.7 Sample specifications for storage in base and active collection
Minimum sample size for storage
Type Base collection Active collection
Cultivated barley Two packets of 25 g each. 1500 seeds (L flag)
Wild relatives One packet of 25 g. 1500 seeds (L flag).
Source: https://cropgenebank.sgrp.cgiar.org/index.php/crops-mainmenu-367/barley-mainmenu-
250/conservation-mainmenu-368/storage-mainmenu-448

Table 5.8 Composition of the barley core collection

SN Category Number of accessions
1 Cultivars 500–800
2 Landraces 500
3 H. spontaneum (Wild progenitor) 150
4 Other wild Hordeum spp. 50–80
5 Genetic stocks 150–200

5.7 Barley Core Collection

In order to facilitate the better access and utilization, development of Barley Core
Collection (BCC) was initiated by van Hintum (1994). The USDA-ARS National
Small Grains Collection (NSGC) is one of the largest collections of barley germ-
plasm in the world (Munoz-Amatriain et al. 2014). The NSGC comprises of 33,176
barley accessions that have been acquired and maintained over the past 100 years.
These include cultivars, breeding lines, landraces and genetic stocks from more than
100 countries (Bonman et al. 2011). The BCC has five (Table 5.8) proposed
components of germplasm that represent the entire diversity of barley having 1700
accessions from different categories.
5 Barley Breeding 275

5.8 Floral Biology of Barley: Emasculation and Pollination

Techniques

The barley inflorescence is called a spike and is composed of spikelets in triplets at

each node of rachis. It is an annual, diploid (2n ¼ 2x ¼ 14) self-pollinating species
with a genome of >5 Gbp in size. Barley is not only used as a model plant for genetic
studies but the genome of Betzes cultivar of barley is being used as a reference
genome for tribe Triticeae under family Poaceae. This is because of its large genome
size (4873–5096 Mbp) unlike rice and maize and diploid ploidy level unlike wheat.
The chromosome number of barley (2n ¼ 14) is also lowest as compared to 2n
chromosome numbers of wheat, rice and maize having 42, 24 and 20, respectively
(Ullrich 2010). Barley has an incomplete flower because it lacks sepals and petals.
The inflorescence of barley is known as spike, head, ear or panicle of spikelet. This
flowering and fruiting unit emerges from the “boot,” which is the sheath of the
uppermost leaf on the culm (the flag leaf) (Fig. 5.6).
The flowers, group together in a central axis or rachis which is composed of nodes
and internodes, which bears a group of three spikelets. Spikelets have only one
flower. Each barley floret comprises of lemma, palea, lodicules, androecium and
gynoecium in the model proposed by Forster et al. (2007). As described in the
section “types of barley” above, the spikelet varies in six- and two-row barley types
where all the spikelets develop grains in six-row while in two-row barleys, only the
middle spikelet produces a grain, the remaining two outer ones being abortive. Each
spikelet consists of a sterile boat-shaped bract called glume. At the end of each fertile
spikelet, there is a long bristle called awn. A spikelet is partially enclosed by two

Fig. 5.6 The barley gene

pools (Source: Hernandez
et al. 2020)
276 S. K. Bishnoi et al.

Fig. 5.7 Barley floral

formula

Fig. 5.8 Barley floral

diagram

long narrow sheaths called “empty glumes,” which do not get larger as development
takes place. These empty glumes have two broad membranous sheaths inside which
are enclosed all vital flower parts known as “flowering glumes” or “palea”. Just
within the base of the outer flowering glume are two small scale-like structures
briming with long hairs, known as “lodicules”. These lodicules have an important
role in the opening and closing of the flower.
The barley floret is “perfect,” meaning that it contains both male (stamen) and
female (pistil) floral components (Figs. 5.7 and 5.8). The male and female flower
parts are enclosed within the lemma and the palea. Barley is polyandrous and each
androecium consists of three male organs or stamens having long slender stalk called
“filament” and a two-lobed anther containing the pollen (Fig. 5.9).
The anther dehisces just after the emergence and shed pollen on feathery stigma.
Pollen loses the viability very shortly after dehiscence. The ovary is superior,
unilocular and has basal placentation, and the two stigmas are feathery and biforked.
The stigma catches the pollen grains during flowering and serves as a medium for
pollen germination. Stigma remains receptive at least for 2 days after anthesis. The
hairiness of stigma varies among barley genotypes from completely covered to very
few hairs (smooth awned barley). In the lateral spikelet of two-row barley, the ovary
remains undeveloped. The ovary of barley encloses a single ovule. The seeds of
barley are called caryopsis and are endospermic monocotyledonous. The upper
flowers of the spike never develop and die off thereby, giving the barley ear its
characteristic truncated appearance.
5 Barley Breeding 277

Fig. 5.9 Barley inflorescence (https://in.pinterest.com/pin/120400990013798413/visual-search/)

5.9 Mode of Pollination in Barley

Barley has hermaphrodite/bisexual flowers and is mostly autogamous (self-

pollinated) crop, where the pollen from an anther shed within the floret on stigma
of the same flower and fertilization takes place just before the opening of florets, and
the phenomena is called chasmogamy. However, sometimes barley can be open
pollinated, as the glumes open during flowering and the anthers are pushed outside
the flower allowing the pollen to become wind-borne. The pollen can travel a few
metres where it can land on an awaiting stigma of a neighbouring plant and cross-
pollination then occurs. Cross-pollination may occur ranging from 1 to 5% in barley.
In either case, once the pollen reaches the stigma, the fertilisation process begins and
the fertilised cells begin their journey to become a grain. The cleistogamous state in
barley is recessive and under the control of a single gene at the cleistogamy 1 (cly1)
locus, which maps on the long arm of chromosome 2H (Turuspekov et al. 2004).

5.9.1 Selfing and Crossing Techniques

The generation and exploitation of new combinations of allelic variants at genetic

loci is the fundamental step for getting superior recombinant progeny or in under-
standing the genetic control of key characters. As already pointed out, cultivated
barley (Hordeum vulgare L.) is a diploid hermaphrodite where anthers tend to ripen
and shed pollen inside the spikelet making barley a natural inbreeder with low rates
278 S. K. Bishnoi et al.

of outcrossing. The crop has cleistogamous behaviour where anthesis occurs before
the anthers are exposed. In order to ensure complete selfing in barley, the inflores-
cence is covered with a butter paper as soon as it comes out of the boot and kept
undisturbed till the flower opens completely. For crossing and development of
hybrids, the following steps are generally adopted by the breeders:

5.9.1.1 Sowing
Plants for crossing programmes are grown in the field or in glasshouses. Crossing in
field is advantageous in terms of cost reduction; however, one has to restrict to a
limited crossing window and effect of weather. In contrast, crossing in the glass-
house is easier with flexibility of timing, no adverse weather effect and crossing
success is often better as compared to that in fields. All entries are labelled
containing information on the variety/nursery name and line number or code.
Some of the winter barley lines require vernalization treatment therefore knowledge
of the vernalization requirement has to be taken into consideration in a crossing
schedule. Also staggered sowing should be practiced for matching of anthesis and
pollination programme.

5.9.1.2 Tools Used for Crossing

To accomplish the selfing and controlled pollination, breeders need specific
instruments such as sharp fine-pointed scissor, fine-pointed forceps, jewellers tags,
glassine/cellophane/paper packets approximately 4 cm wide by 15 cm long and
special magnifying glasses (to see spikelets and their anthers), a hollow tube
approximately 2–3 cm internal width and 10–15 cm of length.

5.9.1.3 Emasculation
Removal of stamens/anthers or killing the pollen of a flower without affecting the
female reproductive organ is known as emasculation. In bisexual flowers such as in
barley, emasculation is essential to prevent self-pollination. Emasculation must start
at 1–2 days before anthesis, when anthers are green. If the anthers near the centre of
the spike appear pale yellow, the spike is too old to emasculate. Emasculation may
be done normally before 10 AM in morning to avoid any chance of anther rupture in
process. For emasculation, select the spike which is still enclosed in flag leaf sheath.
The leaf sheath should be visibly swollen but the degree of swelling will be greater in
a six-row parent than in a two-row one. Remove the flag leaf, lateral florets and very
small florets at the base and at the tip of the spike. This is because the lateral spikelets
under certain conditions can produce anthers that shed pollen and thus could
potentially self-fertilize the emasculated spikelets.
With fine-pointed scissors, clip the top of the lemma and palea in an “egg-
topping” approach. The idea is to cut at the top of the anthers (one can generally
see the anthers through the lemma as a dark shadow against it). Remove the three
anthers with a fine-pointed forcep from each spikelet without accruing any damage
to the stigma. Bag the emasculated spike with glassine bag to prevent the contami-
nation from the foreign pollen. Pickering (1982) observed significant improvement
in seed quality and weight in barley when spikes were covered with brown paper
5 Barley Breeding 279

bags as compared to glassine and polyethylene. Attach a tag to the emasculated spike
with information such as name of variety, date of emasculation and name of breeder.
Emasculation of barley is labour-intensive and tedious, and usually requires skilled
workers. Hot water emasculation is also another commonly used method for
deactivating pollen. It is an easy method and does not necessarily require skilled
labour (Tong and Yoshida 2008). The female emasculated spike will be ready to
pollinate when the spikelets open showing a gap between the lemma and palea.

5.9.1.4 Pollination
Before pollination, check spike to determine if any of the spikelets has already set
seed, these should be removed. Pollination is most successful if done with in 1–3
days following emasculation, when the stigma has maximum receptivity. Chose the
male parent and find a spike that has not shed pollen where the anthers are pale
yellow and are still at the base of each spikelet. Since anthers dehisce early in the
morning, it is best to look for pollinating spikes as early in the day as possible. Clip
the spikelets above the anthers, and after 5 min the anthers start to puff
up. Thereafter, the filaments start elongating and force the anthers upward. One
can check the shedding of pollen by gently tapping the spike and a cloud of pollen
grains should fall from the anthers, these anthers are used for pollinating female
parent. Barley pollination can be done by the twirl method or by anther transfer. In
anther transfer method, the anthers are removed and placed above the open female
spikelet and are broken. Since each anther contains numerous pollen grains, each
anther can be used to pollinate 2, 3, or more female flowers. In twirl method, a
10–15 cm long tube that is 2–3 cm wide is placed over the emasculated female
parent.
The spike with the extruded anthers is then held upside down over the top of the
tube and is twirled and inserted into the tube simultaneously to shed pollen over the
female spike. After the pollination, the glassine bag is replaced over the female spike
and female parent and date of pollination is written. Sometimes there is no pollen
available, so the emasculated spike may be kept in cold storage for up to 42 days.
Similarly, non-emasculated detached spikes can produce viable pollen after up to
26 days in cold storage in barley (Pope 1939). If the cross is successful, the
developing caryopses (kernels) will begin to be visible around 5 days after pollina-
tion and emerges from the cut spikelets by 7 days after pollination. The spike can
then be left to complete drying and the F1 hybrid seed picked off and packeted for
subsequent sowing to produce F1 plants. To reduce the time between crossing and
sowing of F1 hybrid seeds, the developing F1 embryos can also be cultured.
Other crossing methods have also been tested by researchers such as male and
female spikes are fastened together and enclosed in a bag. The bag is tapped or
shaken periodically to disperse pollen (Hamilton 1953); or in the field, the approach
method may be adopted for crosses between nonadjacent plants by cutting off the
male culm and placing it in a bottle of water beside the female plant; or emasculated
barley spikes can be cross-pollinated if male and female parents are planted in
alternate rows and female spikes are emasculated (Omarov 1973).
280 S. K. Bishnoi et al.

5.9.2 Enhancing Crossing in Barley

• Crossing in barley can be accelerated by growing parent plants in control

conditions.
• In winter barley, vernalization of seeds is needed for flowering to occur which can
be accomplished by exposing germinating seeds to temperatures slightly above
freezing.
• Tissue culture techniques such as embryo culture can be used for getting success
in some wide crosses.

5.10 Barley Breeding Objectives

Framing breeding objectives to the targeted area and population for development of
superior barley varieties is one of the most important planning steps in a breeding
program. As in other crop breeding programs, barley breeding also involves the
development and identification of short, intermediate and long-term objectives. The
short-term objective aims at development of improved high-yielding cultivars in
shortest possible duration, while intermediate and long-term objectives include
development of germplasm for future use and involves programmes for
incorporation of stable resistance genes to different biotic and abiotic factors,
introduction of exotic germplasm and selection for adaptation. However, at times,
most barley breeders are concerned primarily with short-term objectives (Wych and
Rasmusson 1983). Also, breeding efforts on other aspects such as semi-dwarf plant
development, lower protein content, higher malt extract are also equally important.
Winter barley breeding programs involve improved hardiness, lodging resistance
and disease resistance that are also suitable for harvesting as whole plant silage, thus
having a place in double cropping systems.
Several breeding objectives depend on consumer preference and environment,
and therefore is location-specific, for example, tolerance to acid soils and excess
moisture at harvest time is essential in some areas, whereas drought resistance and
suitability for irrigation are essential in other parts. Therefore, breeding objectives
should not be rigid and should provide continuity of developing improved barley
cultivars. In addition to high yield potential, barley breeding for yield stability, cold
resistance in areas where non-hardy plants would be injured, resistance to drought in
the dry areas, sturdy straw to prevent loss from lodging, resistance to soil stress in the
presence of excess aluminium or toxic salts, or resistance to disease pathogens and
insect pests that affect the plant’s health are other very important barley breeding
objectives. The major barley breeding objectives are described briefly in the sections
which follow.
5 Barley Breeding 281

5.10.1 Increased Yield

Development of high-yielding cultivars of grain and forage is the primary objective

of most barley breeding programmes because it directly affects the economic return
to the growers. Success of breeding programme is measured by comparing modern
cultivars with the older ones in terms of yield. In barley, substantial yield increase
from 1.09 tonnes per ha in 1971 to 2.92 tonnes per ha in 2020, growing at an average
annual rate of 2.55% have been demonstrated in India (https://knoema.com/
atlas/India/topics/Agriculture/Crops-Production-Yield/Barley-yield). Similarly, in
the Midwest, malting barley yields have increased at the rate of 2% per year over
the past 40 years (Wych and Rasmusson 1983). This increase has been attributed to
the yield contributing components including number of plants per unit area, number
of heads per plant, number of kernels per head, and kernel weight (Woodworth
1931). Yield potential is generally expressed phenotypically through complex plant
morphological, physiological functions and genetically complex quantitative char-
acter that interacts with the environment in which the plant genotype is grown.
Many studies in barley reported a positive correlation between grain yield and
number of grains m2 (Drikvand et al. 2011; Jabbari et al. 2010; Ruzdik et al. 2015).
However, Purl et al. (1982) reported that the increase in grain yield was associated
more with the weight than with the number of grains. Grafius (1965) described the
plant yield increase in barley as the product of three components, viz., number of
heads per unit area, number of kernels per head and kernel weight and proposed that
performance of a cross could be predicted geometrically from parental yield
components. Donald (1968) suggested uniculm ideotype for barley with a short,
strong stem, high harvest index, few small erect leaves, erect spike and awns. Later,
Casey-Common and Klinck (1981) suggested that the uniculm type is too restrictive,
and as an alternative, proposed a limited-tillering ideotype.
The association of physiological traits such as increased vegetative biomass
(Wych and Rasmusson 1983), harvest index (Martintello et al. 1987; Riggst et al.
1981) for improvement of the genetic potential of barley has also been highlighted.
However, very fewer studies on yield gains were associated with increase in harvest
index and grain number m2 in barley. Nonetheless, these studies highlighted the
genetic improvement contributed to the grain yield at the rate of 16 kg/ha/year in the
United States (Boukerrou and Rasmusson 1990), from 18 to 20 kg/ha/year in Canada
(Bulman et al. 1993; Jedel and Helm 1994) 19 kg/ha/year in the United Kingdom
(Riggst et al. 1981) 41 kg/ha/year in Spain (Munoz et al. 1998), 74 kg/ha/year in
Italy (Martintello et al. 1987), 41 kg/ha/year in Argentina (Abeledo et al. 2003),
21 kg/ha/year in Norway (Lillemo et al. 2010), 60 kg/ha/year in United Kingdom
(Mackay et al. 2011) and in the Netherlands (Rijk et al. 2013).
However, Austin (1978) and Riggst et al. (1981) suggested that harvest index of
barley may have reached a ceiling and that further increases in grain yield may have
to come from increases in the biomass. A greater physiological efficiency by
reductions in respiratory losses, increases in grain-filling duration, improved photo-
synthetic efficiency rate and greater pre-anthesis contribution to grain yield are the
major suggested interventions in this regard. Breeding for high-yield potential in
282 S. K. Bishnoi et al.

barley is normally accomplished by crossing among genotypes with complementary

genes to generate transgressive segregants with superior yield. Most selection for
yield potential at early stage is based on the breeder’s knowledge and experience,
and the accuracy of his observations. In the early segregating generations, single
plants are selected, which are then evaluated for yield potential by progeny tests.
While constantly striving to improve the potential yielding ability in barley, it is also
necessary to stabilize production by breeding for resistance to the adversities that
may limit the final harvest.
Apart from genetic factors, environment may be responsible for positive pheno-
typic associations; therefore, the yield components should be evaluated in the
environment in which selection is practiced. Most yield gains in barley have been
achieved by selecting for yield itself, or for other factors which reduce yield-like
resistance to lodging, shattering, disease resistance, etc.

5.10.2 Improved Malting Quality

Malting quality is a genetically complex trait, comprising of a series of different

quality parameters and traits which follow a complex mode of inheritance (Schmidt
et al. 2016). Malt quality is defined by the following specific criteria: Kolbach index,
that is, enzyme activity (high), extract difference (low), extract content (high) and
protein content (low). The trait, malting, is influenced not by genotype but by the
environment and also the malting and brewing process. Hence, for a reliable
description of this complex trait and its stability, multilocation trials are necessary,
which need to be confirmed over several years of cultivation. Of different traits
reported for malting improvement, the grain test weight (hectolitre weight) is
important for achieving higher malt extract (Verma et al. 2008) followed by grain
husk and protein content and can be used as a good selection criterion for large-scale
germplasm evaluation and varietal improvement.
MacLeod (2000) reported negative correlation between malt extract yield and
protein which is primarily due to hordeins. Diverse techniques based on multivariate
analysis, principal component plots, etc. have been suggested for malting barley
evaluation in breeding (Nielsen and Munck 2003), which give an easy-to-interpret
picture about the correlation structure of the components for malting quality. The
hulled barley is preferred by the malting and brewing industries, because the hulls
are used as natural filters during the brewing process (Newman and Newman 2008).
There has been a modest genetic gain for malting quality due to the development of
few crosses and ultimately testing a limited number of advanced lines (Munoz-
Amatriain et al. 2014). However, a new phase of breeding for high malting quality
began with the introduction of the micro-malting method in the 1960s, which
allowed a directed selection for processing quality based on small samples (Baumer
et al. 2000). Because of the economic importance of malting barley, there has been a
major effort to identify genes controlling malting traits and several references are
available in the Barley Genetics Newsletters and in the Proceeding of the Interna-
tional Barley Genetics Symposia.
5 Barley Breeding 283

5.10.3 Resistance to Biotic Stresses

Resistance breeding is an important strategy for reducing crop losses caused by

different biotic stresses. Genetic resistance is the most eco-friendly, durable and
affordable method for low-income farmers, therefore, forms the major objective of
most plant breeding programmes worldwide. Breeding for biotic stresses resistance
involves different approaches based upon the economic importance of stress, the
genetics of resistance, availability of resistance sources, expertise and the facilities
available, etc. Also, effective selection depends on number of available genes and
the screening environments. A list of major biotic stresses of barley is presented in
Table 5.9. There are numerous successful examples wherein the conventional
breeding approaches have done wonders; some of these include the resistant
varieties against the rusts, smuts, powdery mildew, etc. Biotic stress in barley,
specifically fungi, viruses, bacteria, nematodes, insects, arachnids and weeds,
hinders the potential yield performance of the elite barley cultivars to a huge extent.
These stresses cause varying degree of losses to the barley yield and quality. These
agents can also cause minor reaction and loss below economic threshold level,
however, sometimes devastating loses occurs that can cause epidemic by spreading
to larger areas, even continent, forcing to famine-like situations. These biotic agents
directly deprive their host of its nutrients leading to reduced plant vigour, and in
extreme cases, death of the host plant. Therefore, breeding for biotic stress
(Table 5.9) resistance is an important objective of barley improvement programmes.

5.10.3.1 Breeding for Disease Resistance

Under biotic stress, for most of the diseases, the genetics of resistance is relatively
well known. For example, for barley yellow dwarf viruses, at least 40 major genes
for resistance have been mapped till date. The QTL for resistance to all major
diseases have also been discovered (Williams 2003). In barley breeding, for host
resistance to different diseases each disease is treated as a separate breeding objec-
tive and based on severity of losses caused, the breeder establishes priorities on
developing resistant cultivars. The breeding strategy depends on number of factors
such as the resistance sources available, the number of loci involved, their mode of

Table 5.9 Major diseases and insect pests of barley

Type Name of diseases/pests
Diseases Net blotch (Pyrenophora teres), stripe rust (Puccinia striiformishordei), brown rust
(Puccinia hordei), stem rust (Puccinia graminis f. sp. hordei), powdery mildew
(Blumeria graminis f. sp. hordei), Scald (Rhynchosporium commune), head blight
(Fusarium heterosporium), spot blotch (Bipolaris sorokiniana), covered smut
(Ustilago hordei), loose smut (Ustilago nuda hordei)
Bacteria Bacteria blight (Xanthomonas campestris, Pseudomonas syringae)
Virus Barley yellow dwarf virus (BYDV), barley stripe mosaic virus (BSM)
Nematode Cereal cyst nematode (Heterodera avenae)
Insects Barley shoot fly (Delia arambourgi Seguy, D. flavibasis Stein.), Russian wheat
aphid (Diuraphisnoxia mordvilko), and corn leaf aphid (Rhopalosiphum maidis)
284 S. K. Bishnoi et al.

inheritance and whether the objectives are for short-term or long-term protection.
Generally, long-term resistance should be the ultimate objective of breeders, how-
ever, based on urgent need short-term breeding objectives may be taken on priority.
Disease-resistant cultivars are developed by identifying resistant genes for the host
species, or related wild species, and transferring it into adapted cultivars and
breeding lines, normally by hybridization, tissue culture or chromosome engineering
techniques. Quantitative resistance, which is durable (the chance of breaking the
resistance genes due to changes in the pathogen over time is lower) is generally
determined by multiple minor genes, should be chosen. Gene pyramiding approach,
involving the introgression of different major and/or minor genes for resistance into
one agronomically best cultivar is a useful strategy to assure long-term prevalence of
the resistance.
In barley, the qualitative resistance conditioned by one major gene has also been
durable, for example, the Rpg1 gene (also known as T gene), is still functional and
has provided resistance to stem rust for more than 60 years (Zhang et al. 2006).
Given the high significance of the disease, much of the work with disease resistance
in barley is done in powdery mildew. Outstanding in this regard are the mutations
induced at the ml-o locus. Multiline varieties and varietal mixtures offer another
possibility that may be considered in extreme situations for decreasing vulnerability
to attack from various pests of barley. For example, in the Netherlands, barley
cultivar ‘Grand Prix’ was released as a mildew-resistant multiline based on ‘Aramir’
Ml-ar germplasm. The multiline is composed of three backcross derived lines with
dominant mildew resistance genes from ‘Monte Cristo’ (C.I. 1017)- MI-a, ‘Nepal’
(C.I. 595)- MI-n, and ‘Engeldow’ (C.I. 9.3.1
7555)-MI-a.S.
Breeding objective for disease such as barley rust where the physiologic race
specialization is present involves race-specific genes. These genes confer major
resistance to a particular race and have simple inheritance. However, race
non-specialization resistance in the host genotype is conferred by non-race-specific
polygenes which are inherited quantitatively, each contributing a small increment
toward resistance to the disease pathogen. Also, reduction in disease damage can be
achieved by breeding for plant characteristics that enable the plant to escape or avoid
disease infection.

5.10.3.2 Breeding for Resistance to Insect Pests

Host plant resistance is used to control insect pests that are difficult to control
through cultural practices or use of pesticides. Breeding for host plant resistance is
economical and environmentally safe method. The breeding methods employed for
resistance breeding to an insect are generally similar to those used in breeding for
resistance to disease pathogens. Resistance sources to the insect species are first
identified and transferred to susceptible host genotypes by hybridization. During the
selection process, the breeding lines are exposed to natural or artificial insect
populations for efficient screening and to distinguish between resistant and suscepti-
ble genotypes. Breeding for genetic resistance to insects-pests has not been much
emphasised because of availability of highly effective insecticides. However,
5 Barley Breeding 285

identification of resistance sources has been done since long. For example, feed
barley with greenbug resistance has been grown widely since 1965 without break-
down of its effectiveness (Anglade 1978).
Aphid is a major insect problem in barley which causes heavy loss to the crop as
well as reduces grain quality. Also, the cereal cyst nematodes cause heavy losses by
reducing the tillering and ear head formation. Use of resistant varieties is generally
encouraged to control the damage by nematodes. Lines resistance to aphids
(Mornhinweg 2011); over 5000 cultivars resistance to Hessian fly Hill et al.
(1952); ‘Modjo’ (CI 3212) to seed transmission of BSMV (Carroll et al. 1979)
were reported early on. Improved resistance to different biotic stresses in barley
through composite cross breeding has also been attempted, e.g., scald resistance
(Zhang et al. 2019) and resistance against powdery mildew (Dreiseitl 2020) and
blotch (Visioni et al. 2020). Resistance sources for different biotic stresses in barley
are characterized and available (Lundqvist et al. 1997; Sharp 1985) and can be
requested from gene banks. Also, the global barley improvement program of
ICARDA provides diverse germplasm with resistance sources. Some of these
resistant sources are in agronomically non-adapted backgrounds; however, to
avoid the genetic gap, the barley breeders generally use the resistance genes already
incorporated into adapted varieties.

5.10.3.3 Abiotic Stress Resistance, vis-a-vis, Climate Change

Climate change poses a major threat to global food security and also affects barley
production. These climatic issues are very difficult to predict and their precise future
effects on crop yields are unpredictable. The climate change parameters include:
(1) physical parameters such as temperature, rainfall patterns and carbon dioxide;
(2) changes in agricultural environmental systems such as loss of pollinators and
increased occurrence of biotic stresses and (3) the adaptive responses of human
systems (FAO 2016). Under changing climatic conditions, barley has emerged as a
model plant mainly because of the broad and well-formed collections of landraces,
wild genotypes and other Hordeum species which are important sources of new
alleles (Dawson et al. 2015). Also, barley yield suffers less variation under climate
change conditions than those of wheat and most other small grains, and therefore it is
grown widely in semiarid regions (Cossani et al. 2009).
As far as drought stress is concerned, barley tends to mature earlier than other
cereal crops and may escape drought during anthesis or early grain-fill. Also, plant
might avoid drought stress by maintaining high internal moisture content. However,
an optimum duration for barley maturity should be maintained because if a cultivar is
too late in maturity, it may suffer from drought stress and if it is too early, it may fail
to take advantage of available moisture. Therefore, breeder’s job is to match the
growth pattern of the crop to seasonal availability of moisture without disturbing the
yield. Under field conditions, usually heat and drought stresses are correlated. Injury
from heat stress is critical during the flowering period reducing pollen viability,
stigma receptivity and seed formation.
Soil salinity also limits crop productivity in many arid and semiarid regions.
Barley is, however, one of the most tolerant cereal crops and it is even used in
286 S. K. Bishnoi et al.

reclamation of saline soils and considerable variability for this trait has been
reported. The resistance to soil salinity, generally referred to salt tolerance, is
primarily due to avoidance mechanisms such as salt exclusion and salt dilution in
barley (Levitt 1972). Initial breeding programme for salt tolerance involves a
germination test in saline solution. Seedlings that survive this screening are then
transplanted and grown to maturity with saline irrigation water. Breeding for resis-
tance to deficient and toxic levels of aluminium and other minerals (boron, manga-
nese or heavy metals) has received little attention in barley breeding programmes till
now. Barley genotypes differ in their ability to take up and use nutrients (Perby and
Jensen 1983).
Cultivars and breeding lines may be screened for aluminium tolerance in the
laboratory by growing seedlings in a nutrient solution containing a high concentra-
tion of aluminium ions and selecting for plants with longest root and top growth.
Minerals also affect other traits, aluminium, for example, inhibit root development
and indirectly affect drought resistance, winter hardiness and nutrient uptake. Alu-
minium resistance (sometimes measured as resistance to low pH) is heritable in
barley and may be screened for in soil or in nutrient solution cultures (McNeilly
1982).
Breeding for abiotic stress involves testing the germplasm at a specific or multiple
growth stages on a particular climate. For example, at floral initiation, drought
reduces the number of florets per spike and suppresses tillering, while after anthesis
it reduces seed set (kernels per spike) and kernel weight. After identifying tolerant
genotypes, a breeding programme starts by crossing the selected genotypes as donor
parents. The trait (morphological or physiological or yield related) to improve
drought tolerance must discriminate between drought-tolerant and drought-
susceptible lines, should have high heritability estimates and positive significant
correlation with final grain yield. The morphological and physiological traits such as
plant height, kernel plumpness, harvest index, tillering capacity, root growth
patterns, seedling vigor, stomatal size and density, stomatal control, diffusive resis-
tance, transpiration rate, water potential, desiccation tolerance and proline accumu-
lation may be associated with drought avoidance and tolerance.
There is interaction among these traits, and drought-resistant genotypes may
obtain their resistance from a favourable combination of traits. Apart from tolerance
to the abiotic stresses described above, the barley cultivars with inbuilt tolerance to
lodging are also needed particularly in the areas prone to heavy rainfall, hail and
windstorms. Lodging causes yield losses in barley, hence breeding to improve
resistance to lodging is important breeding objective which involves changing the
architecture of the plant. Breeding for lodging resistance involves developing plants
with short culms, sturdy straw, a root system capable of anchoring the plant in the
soil and acquiring resistance to diseases and insects as the later weakens the plant
making it more susceptible to lodging.
Lodging resistance is a quantitative character with complex inheritance, although
some of the plant characteristics associated with a reduction in lodging, such as
dwarfing genes, or resistance to disease and insect pests, are often simply inherited.
Improvement in lodging resistance of barley has been achieved through selection for
5 Barley Breeding 287

reduced plant height. For example, the Swedish cultivar ‘Pallas’ is an erectoides
mutant and, in general, Japanese cultivars are semi dwarf ert-k.32 mutants which are
resistant to lodging. Lodging-resistant semi-dwarfs are sometimes inferior to normal
lines, and thereby incorporation of the short-straw trait into agronomically useful
cultivars may require a long-term breeding effort.
Resistance to shattering (whole spikes or individual seeds) is imperative to
prevent loss of yield before and during harvest in barley. Resistance to shattering
is inherited as a complex quantitative character and depends upon environmental
conditions such as wind velocity, timing and method of harvest. Klinner and Biggar
(1972) observed that in certain environments, most shattering losses of barley result
from breaking off of whole spikes. Harlan and Pope (1921) observed a positive
association between rachis ash content and shattering. They found that awnless and
hooded cultivars tended to shatter easily and that the rachis was more brittle and
higher in ash than the rachis in awned cultivars. Therefore, they concluded that
selection should be effective for this trait.

5.11 The Conventional Approaches of Barley Improvement

Barley is a self-pollinated crop and the breeding methods developed for such crops,
for example, the pedigree and single seed decent apply and have been used for
development of improved cultivars in barley as well. These conventional approaches
of barley improvement have been the mainstay of barley breeders for almost whole
of the breeding history. Both the techniques are based on the introgressive breeding
plan which has been one of the most important methods of barley improvement since
its domestication. The introgression has been defined as ‘the transfer of one or
several novel, favourable alleles from un-adapted germplasm to adapted germplasm’
by (Hernandez et al. 2020).
As already mentioned, the domestication trait syndrome was used to determinate
growth habit, high seed set percentage, more number of grains per spike, non-brittle
rachis, bold seed and early germination (Harlan et al. 1973). These primary traits
hold significant importance even in modern-day technologically advanced breeding
programmes. The domestication lead to creation of locally adapted heterogeneous
mixtures of nearly homozygous lines called landraces. These landraces evolve
through artificial selection based on desired phenotype and 2% natural outcrossing
in barley. Therefore, landraces are very important sources of genetic diversity that
can be readily utilized to correct a specific defect of an otherwise good variety
through introgressive breeding. For example, gene Rpg1 providing resistance against
the Puccinia graminus f.sp. tritici induced stem rust was sourced from “Chevron”
(Steffenson 1992) and Russian Wheat Aphid (Diuraphis noxia) resistance was
sourced from PI 366450 from Afghanistan (Bregitzer et al. 2005). Based on the
source of starting genotypes, barley breeding can be elite  unadapted germplasm or
elite  elite lines.
288 S. K. Bishnoi et al.

5.11.1 Pedigree Method

The pedigree method by far remains the most used method of breeding improved
barley varieties. The pedigree method is hybridization-based and requires identifica-
tion of better combining parents with complimentary traits. Therefore, there is a
component of pre-breeding in utilization of pedigree method whose objective or
outcome is a pureline having the desired traits from both the parents. In this method,
phenotype-based plant selection is exercised from F2 generation onwards until the
segregating generations show no intraprogeny variations. In F2 itself, the plants
outperforming both the parents’ transgressive segregants are selected. Ear-to-row is
a basic pedigree method employed in case of barley improvement (Greveniotis et al.
2019).
The method is used in barley for improvement of a specific defect in a good
genotype such as resistance to a particular abiotic or biotic stress, quality trait or any
other trait contributing to the adaptation of the variety. From the F6 generations
onwards, the progenies are tested in the preliminary yield trails/multilocation trials
vis-a-vis the best local checks and the superior progenies having performance
significantly higher than the check are identified. Unlike wheat, the shuttle breeding
method (raising two generations in a year in geographically) is not successful in
barley because of the vernalization requirement. Shuttle breeding is utilized to make
the segregating lines homozygous in half of the period that will be required for
developing a variety. In barley, the technique of double haploids is utilized for the
same purpose which is described earlier.

5.11.2 Modified Bulk Pedigree Method (ICARDA/CIMMYT)

When the number of crosses to be handled in the segregating generations is in

thousands in the international breeding programmes targeted for different mega
environments then it becomes difficult to exercise individual plant selection in the
early generations through pedigree method. Therefore, a modification of the pedi-
gree method called modified bulk pedigree method was introduced and adopted at
the CG centres, mainly the CIMMYT and the ICARDA for barley and wheat. It is in
fact a local hybrid modification that combines the characteristics of both the bulk and
pedigree methods, in that it involves individual plant/spike selection in F2, F6 and F7
(pedigree) generations and bulking in F3, F4 and F5 (bulk) generations. The
individual head to row plots from F2 generation are sown to raise F3 plots in
which inter-plot selection is exercised for morphological, agronomic and disease
resistance traits.
A total of 10–15 healthy spikes from the selected plots are harvested and bulked
to raise F3. In the similar fashion, the generation is advanced up to F5. From F6
onwards, the selection is made for individual plants and head rows are planted in the
F7. The main advantage of the method is that as the selection is omitted in the three
generations, the logistic handling of the crosses becomes considerably easier and the
resource inputs in the form of time, labour, expenditure on nursery preparation, land,
5 Barley Breeding 289

etc. are significantly reduced. Also, the early generation rejection probability of a
potential line in this method is reduced because of bulking in the three consecutive
generations. Therefore, it preserves considerable diversity up to F5 generation from
which selection can be made. From F7 onwards, the lines are handled in pedigree
method (Van Ginkel et al. 2002; Wang and Pfeiffer 2007).

5.11.3 Mutation Breeding in Barley

Improvement through mutagenesis (physical and chemical) has been an unparallel

success story of barley breeding and some of the very popular varieties have been
bred this way. The superior varieties have been successfully targeted to generate
mutants which are more resistant to prevalent diseases, tolerant to various abiotic
stresses, having bold grains with better malting quality, improved protein, starch and
mineral composition and phenotypically having more number of effective tillers,
number of grains per spike, dwarf type and an improved root structure leading to
enhanced nutrient use efficiency. The extent of mutation research in barley has made
it a model species for studying mutation genetics and breeding in plants. The IAEA-
MVD Mutant Variety Database has listed a total of 316 barley varieties developed by
mutagenesis (https://mvd.iaea.org/#!Search?Criteria[0][val]¼barley%20 accessed
4 September 2021) including direct mutants and hybrids. The database also provides
information on the pedigree of the varieties and their country of origin. The database
includes direct mutants and their hybrids. The information includes the parent name,
country and year of development among others.
Pallas the first mutant variety was developed using X-rays and registered in the
United States in 1960 while the first chemically induced (diethyl sulfate) mutant
barley variety, Luther was released in 1966 in the United States. Pallas has high
lodging tolerance and higher yield to the parent variety Bonus. In the present times,
Golden Promise (γ-irradiation of Maythorpe) released in the year 1960 and Diamant
(Valticky irradiated by X-rays) released in the year 1965 remain two of the most
popular barley varieties globally. The Golden Promise is characterized by short and
stiff straw, salinity tolerance, high yield and good malting quality. On the other hand,
the main characteristic of Diamant is dwarf type, high number of effective tillers and
12% yield advantage over the parent variety with good malting quality. These
varieties have been part of different local breeding programmes, and thus form a
part of pedigree of some of the latest barley varieties across the countries.
IZ Bori is a Bulgarian winter feed barley variety and was developed through
chemical mutagenesis (sodium azide) and released in the year 2009. It is a variety
with wider adaptation, disease resistance (powdery mildew and rusts), with a yield
advantage ranging from 15 to 17%. It is frost resistance and nutritionally superior
(high protein and lysine content). In India, the barley mutation research began in
1970s and the first variety RDB1 (mutant of RS17) was released in 1971 followed by
PL56 (mutant of C164), HBL316 (mutant of HBL98). Presently, the mutation
research in barley in India has taken a backseat and the tide has turned in the favour
of utilization of available natural genetic diversity and the molecular tools.
290 S. K. Bishnoi et al.

5.11.4 Single Seed Descent (SSD)

In single seed decent method, one seed is taken from individual plant after F1
generation and bulked together to raise the F2 generation. This method was origi-
nally developed by Goulden (1939) for handling of the F2 onwards generations of a
cross made in self-pollinating crops. Basically, this method was devised to handle a
greater number of crosses at any one given time but it suffers from lack of selection
upto F5 generation. In an interesting study, Lalic et al. (2003) compared pedigree
method to the SSD in winter barley cross Timura* Osk.4.208/2–84. It was found that
grain yield per plot was higher under two planting densities for pedigree method,
however, upon comparison of top five lines from the crosses for both the methods,
the lines developed by SSD had advantage. The lines, though, were poor in inheri-
tance of traits with low heritability (yield per plant and effective tillers) which can be
understood in terms of loss of variability and lack of selection in SSD. Conversely,
the traits with high heritability such as grain weight and number of grains per spike
were better preserved in case of SSD compared to the pedigree method.

5.11.5 Doubled Haploids (DH) in Barley

Genetic uniformity is the prerequisite of a line to be registered or released as a variety

and in the pedigree and SSD methods, selfing and selection are the tools of achieving
this uniformity. However, this is a very long and economically intensive process and
usually takes no less than six generations to achieve this. On the contrary, the
doubled haploid system is one of the quickest methods to achieve homozygosity
in a line. In barley, the DH development was started by Clapham (1973) and since
then it has come a long way contributing in not only the development of high
yielding and genetically uniform barley cultivars as selection is easier among the
lines but also making the barley plant a genetic model for the cereal crops because of
the amenability of the DH for genetic studies, mutation and selection at the single
cell level in cultures as well as in studying embryo development. ‘Mingo’ was the
first cultivar developed and released in Canada in the year 1979 through DH
technique based on bulbosum method which is described in the subsequent
sub-section. The DH method is an alternative to the shuttle breeding method and
makes all the loci homozygous in one single generation (Singh et al. 2021). Now the
DH development has been taken up commercially by some institutes (e.g. Institut de
Genech, France) or companies, following anther culture procedure of the F1 plant.

5.11.6 Barley Haploid Development Techniques

5.11.6.1 Bulbosum Method

This method, discovered by Kasha and Kao (1970), is also called chromosome
elimination method. This technique is based on the fact that in a H. bulbosum (Pollen
donor) x H. vulgare (recipient) the chromosomes of the H. bulbosum are selectively
5 Barley Breeding 291

eliminated during the development of the embryo which eventually becomes haploid
retaining only the chromosomes of H. vulgare. These embryos are then rescued
some 2 weeks after pollination and cultured on artificial medium which is B5 minus
2,4-D and plus sucrose (20 g l1) and agar (7 g l1) (Gamborg et al. 1968) (Kasha
and Kao 1970). This is followed by the colchicine treatment to make the DH fertile
through doubling of the chromosomes. This method became an important tool of
barley breeding soon after its discovery and was utilized to achieve homozygosity in
the breeding pipelines and resulted in release of many cultivars across the world. At
present, this method is utilized when DH from hybrids are to be developed particu-
larly in the spring-type barley. It also has a utility in mapping, providing a random
sample of gametes. Bulbosum method is an example of in vivo DH production and
soon it was replaced by the in vitro methods including anther culture and isolated
microspore culture. The major disadvantage of the method is that only a limited
number of DH lines can be developed in a specific time.

5.11.6.2 Anther Culture

Guha and Maheshwari (1964, 1966) for the first time reported that anthers of Datura
metale could be raised into haploid plants if cultured artificially. Soon, it was applied
to barley by Clapham (1973). In anther culture, the anthers are taken from the
spikelets which are already surface sterilized. The acetocarmine staining is used to
identify the right stage of pollen development. In barley, the right stage is when the
microspores within the anther are at uninucleate stage which coincides with plant
developmental stage when the flag leaf and penultimate leaf is at a distance of
3–6 cm. This are then transferred to induction/nutrient media. The sporophytic
stage is induced by both cold shock at 4
C for 28 days or sugar starvation for
3–4 days in a 0.3–0.7 M solution of mannitol (Roberts-Oehlschlager and Dunwell
1990; Cistue et al. 1999), or alternatively with some macronutrients (Hoekstra et al.
1997). The culture plates are maintained at a 16:8 h of light:darkeness at 26
C. After
three to five weeks, the young embryos developing from the callus are transferred to
the regeneration medium containing the basal medium plus sucrose and minus
maltose. At the three to four leaf stage, the plants are transferred to glasshouse in
pots. The frequencies of the spontaneous DH, polyploidy and haploids in barley is
60–80:8:remaining, respectively.

5.11.6.3 Pollen Culture (Isolated Microspore Culture)

The anther culture is a relatively easy technique to generate double haploids because
of the high frequencies of spontaneous DH, but it suffers from the generation of
polyploid plants from the anther tissue other than the microspores. This drawback is
taken care by the pollen culture being high throughput (production of embryos in
large numbers) and easier to undertake. The spontaneous chromosome doubling also
reaches upto 80% making it a method of choice without the need of purposeful
doubling through colchicine. However, the dependency of the IMC on genotype is
major limiting factor restricting its routine use for development of DH in barley
(Touraev et al. 2009).
292 S. K. Bishnoi et al.

5.12 Exploitation of Heterosis and Hybrid Development

in Barley

Commercial barley hybrid production depends upon the degree of heterosis,

frequencies of cross-pollination, availability of a practical system for inducing
male sterility and (or) restoring fertility, and achieving acceptable quality for product
end use. The initial release of hybrid barley was at the United States which was
hindered by two major constraints; the balanced tertiary trisomic system allowed a
few male-sterile plants in commercial fields, and ergot disease was a problem in the
sterile heads. However, there are increased research efforts on hybrid barley because
of a cytoplasmic male-sterile source found in H. spontaneum C. Koch (Ahokas
1980) and the availability of gametocides for inducing male sterility (Foster 1984).
Numerous genes for genetic male sterility in barley have been documented (Hockett
and Eslick 1968). Cytoplasmic male sterility in barley has been obtained from
H. jubatum and H. spontaneum (Schooler 1967). Fertility restoration of the
H. spontaneum source of cytoplasmic male sterility has been reported. The cyto-
plasmic male sterility and fertility restoration found in H. jubatum crosses were
difficult to use because of extreme lateness (Schooler 1967). Inadiverse material
from crosses of spring and winter barleys, over 100% heterosis was reported (Fejer
and Fedak 1975). Yield advantage of 26% over five high-yielding varieties was
reported by Foster and Fothergill (1981). Lehman (1981) found that two-row hybrids
yielded 86 and 119% of the control cultivar during 1979 and 1980, respectively.

5.13 Application of Biotechnologies (Marker-assisted Selection,

QTL Identification, Introgressive Breeding) in Barley
Improvement

Most agronomic traits are inherited quantitatively and the loci controlling these are
called quantitative trait loci (QTL). The identification of QTL for major traits and
abiotic and biotic stress resistance is at the core of marker-assisted selection (MAS)
and marker-assisted introgressive breeding in barley. The major techniques adopted
when the QTL being explored are unlinked are the standard interval mapping (SIM)
and multiple imputation (IMP) and when the QTL are linked on a chromosome then
composite interval mapping (CIM) is used. The QTL discovery process is inherently
statistical in nature and the calculated logarithms-of-odds (LOD values) are used to
consider a region on genome to be a QTL controlling a specific trait.
The identified QTL are the main targets of MAS and introgressive breeding (Riaz
et al. 2021). With the advent of the next-generation sequencing based on the SNPs,
the process of QTL discovery has received a major, boost and its resolution has
improved manifold compared to the RFLP and SSR markers. The major application
of the MAS has been in the field of disease resistance in barley (Wang et al. 2019). In
MAS, a particular phenotype is associated with presence/absence of a molecular
marker at DNA level in the genome of barley, and once characterized, it circumvents
5 Barley Breeding 293

the necessity of field evaluation each single time, thus saving the time and resources
apart from being highly accurate.
Powdery mildew was the first disease against which a QTL was reported (Heun
1992). It was followed by QTL for other diseases such as spot blotch by Steffenson
et al. (1996). The identification of major genes is a straightforward approach for
development of cultivars with inbuilt vertical resistance to major disease. The ym4
gene conditioning yellow mosaic disease in barley from Franka cultivar was suc-
cessfully introgressed into Igri by Ordon et al. (1995). Similarly, the Rph7 gene
conditioning leaf rust resistance in barley was also discovered by marker technology
(Graner et al. 2000), and it was followed by genes conditioning other disease
resistance such as powdery mildew, spot blotch and the rusts as well. A list of
major QTL discovered for major barely diseases is presented in the Table 5.10.
The abiotic stresses such as drought and heat are becoming increasingly impor-
tant for barley cultivation particularly in the tropical, sub-tropical and arid regions in
the climate change scenario. Here also the marker technology has come into play for
development of tolerant varieties suitable for a wide range of climatic regimes. QTL
on different chromosomes have been identified for drought component traits such
relative water content (RWC), Osmotic adjustment, Carbon isotope discrimination
(CID) and proline accumulation (Visioni et al. 2020). The QTL identified for dry
root weight under field conditions by Reinert et al. (2016) was later associated with
the genes HvCBF10A and HvCBF10B. Other genes such as HvNCED2, HVA1 and
cer genes were also discovered and were found to regulate abscisic acid synthesis,
leaf wilting and wax synthesis, respectively (Saade et al. 2018). Soil salinity impacts
the barley productivity adversely in a significant area around the world and research
efforts had been directed towards identification of markers associated with this
complex trait in barley. The tolerance to soil salinity is conditioned by the loci
regulating osmotic adjustment, generation of reactive oxygen species, ion transport
and signal transduction transcriptional factors. The QTL controlling ionic action on
root and shoot were identified by Nguyen et al. (2013), and in a later study, Saade
et al. (2016) observed a 30% increase in salinity tolerance upon introgression of a
wild 2H allele. Therefore, as far as tolerance to soil salinity is concerned, the role of
barley wild relatives could not be underestimated. Similarly, the QTL conditioning
the tolerance to frost have been reported on 5H chromosome. The tolerance to low
temperatures (Fr-H1and Fr-H2) has been observed to be correlated with vernaliza-
tion (HvBM5A) and flowering time. The genes HvCBF2A and HvCBF4 in high copy
numbers are responsible for imparting tolerance to frost in barley (Francia et al.
2016).
The improvement in quality traits constitutes a very important aspect of barley
breeding. Malting quality is one of the most important barley quality traits and more
than 200 QTL have been discovered for this. However, the utilization aspect of the
discovered QTL is still lagging behind mainly because of the low phenotypic
variation explained by the QTL and linkage drag. Cu et al. (2016) identified
63 QTL for 10 important quality traits in a barley DH population. The QTL on
1HS and 7HL chromosomes were found to be associated with α-amylase, soluble
protein, Kolbach index, free amino acid nitrogen, wort β-glucan and viscosity.
294 S. K. Bishnoi et al.

Table 5.10 Disease resistance genes mapped in barley

Chromosome Marker type/linked
Disease/pathogen Gene location marker Reference
Leaf rust Rph27 4H DArT-Seq Rothwell
Puccinia hordei et al. (2020)
Rph26 1H CM_1194 Yu et al.
(2018)
Rph24 6H 3,999,875, 3,265,068, Ziems et al.
3,272,559, and (2017)
3,272,930
Rph23 7H bPb-8660 and Singh et al.
bPb-9601; Ebmac0603 (2015)
Rph22 2H H35_26334 & Johnston
H35_45139 et al. (2013)
Rph21 4H GBM1044 & Sandhu et al.
GBM1220 (2012)
Rph16 2H GBR 1185 Perovic
et al. (2004)
Rph13 3H HvKASP_Rph13plus Jost et al.
(2020)
Rph7 3H TC2863–12.4 and Mammadov
Rph5 3H ABG70 et al. (2007)
Rph6 3H MWG2021 & BCD 907 Zhong et al.
(2003)
Rph3 7H EBmac755 Park et al.
(2003)
RphMBR1012 1H GMS021 & GBS546 König et al.
(2012)
RphC 5H DART4872 and Dracatos
DART7508 et al. (2014)
Stripe rust Rdg2a 7H MWG2018 Arru et al.
Puccinia (2003)
striiformis Tacconi
et al. (2001)
Stem rust Rpg1 7H ABG704-MWG036B Kilian et al.
Puccinia graminis (1994)
Rpg4 5H ABG391 Kilian et al.
(1997)
Erysiphe graminis 6H DArT markers Piechota
f. sp. hordei (4,793,171, 3,258,880 et al. (2020)
(powdery mildew) 3,264,002 & 3,432,488)
Mla 7H GBM1126 & Soldanova
GBM1060 et al. (2013)
GBMS192 &
GBM1060
Leaf scald Rrs1 3H 11_0010 and 11_0823 Hofmann
Rhynchosporium et al. (2013)
commune
(continued)
5 Barley Breeding 295

Table 5.10 (continued)

Chromosome Marker type/linked
Disease/pathogen Gene location marker Reference
Yellow mosaic Rym17 3H ABG070 Kai et al.
virus (2012)
Polymyxa graminis Rym 18 4H Bmag0490 Kai et al.
(2012)
Rym13 4H HVM67 & GBM1015 Humbroich
et al. (2010)
Loose smut Un8 Un8 SNP4; Zang et al.
Ustilago nuda 0498 L15 F8/R8 (2015)
Wheat stripe rust Rps6 7H FPC 320 Dawson
et al. (2016)
Spot blotch Scs6 1H Bc183711 and Bc13291 Leng et al.
Cochliobolus (2018)
sativus
Spot blotch Rbs7 6H M13.06 and M13.37 Wang et al.
Bipolaris (2019)
sorokiniana

Similarly, for the trait hot water extract, QTL were located on the 1H, 2H, 4H, 5H,
and 7H chromosomes. Two large effect QTLs explaining 48% phenotypic variation
in the malt extract were identified by Wang et al. (2015) in a DH population. Before
this, Zhou et al. (2012) identified major effect QTL explaining up to 53% phenotypic
variation in malt extract. Other workers have reported QTL for KI, FAN, α-amylase,
beta amylase and diastatic power on different barley chromosomes (Cu et al. 2016;
Mohammadi et al. 2015; Panozzo et al. 2007; Wang et al. 2015; Zhou et al. 2016).
The forage quality traits such as crude fiber (CF), acid detergent fiber (ADF), dry
matter digestibility (DMD), crude protein (CP), dry ash (DA) and neutral detergent
fiber (NDF) have also been subjected to marker analysis and QTL have been
reported on different chromosomes explaining variable quantum of total phenotypic
variance.

5.13.1 Genome-wide Association Studies in Barley

The genome-wide association study (GWAS) or linkage disequilibrium mapping

takes the advantage of historical recombination events which occurred during the
course of evolution. Generally, for gene mapping and marker trait association, the
mapping populations such as RILs, NILs or DH have to be developed which are
eventually subjected to the field evaluation for the trait in question. The development
and maintenance of mapping populations is a time and resource-intensive endeav-
our, and given the limited recombination events that occur during the course of
development, these studies suffer from low resolution as far as mapping of the
QTL/gene is concerned. The GWAS takes care of these disadvantages in that any
296 S. K. Bishnoi et al.

random set of genotypes can be subjected to mapping and the resolution that is
achieved is quite high. The invention of high-throughput genotyping (SNP, DArT)
has enabled the researchers to scan any given set of barley genotypes for the trait of
interest.
This accelerated growth in DNA-based research has been felt in both basic and
applied studies for biotic/abiotic stresses resistance and quality in barley during last
two decades. The GWAS has been applied to identify marker trait association for
abiotic and biotic stresses and other agronomic and quality traits as well. A total of
five QTL conditioning resistance for barley yellow dwarf virus were reported by
Kraakman et al. (2006) in a set of 148 spring cultivars. Large and medium effect
QTL for spot blotch resistance, leaf spot disease and net blotch have been reported
by different workers using the GWAS (Adhikari et al. 2020; Gyawali et al. 2018;
Tsai et al. 2020). In a recent study, Qian et al (2021), utilizing the latest version of
barley genome discovered largest number (468) of NLR genes with chromosome
7 harbouring the most number (112) of genes present in multigene clusters. Such
studies have immense implications as far as molecular breeding of barley is
concerned. Among the abiotic stresses, significant marker trait associations have
been reported for heat stress by Abou-Elwafa and Amein (2016), identification of
nine haplotypes of HSP17.8 genes by Xia et al. (2013), heat and drought tolerance
and stay green trait by Gous et al. (2016) drought tolerance at germination and
seedling stage by Mwando et al. (2020) and drought tolerance under field conditions
(Thabet et al. 2020) in diverse barley panels.

5.13.2 Genomics in Barley Improvement

As such the QTL mapping and GWAS are also the tools of genomics; however, here
we consider the whole genome information as genomics for the sake of simplicity.
The whole genome sequence of barley is published and molecular markers for
different traits have been mapped in genetic and physical maps (Mascher et al.
2017). The genome sequence data is available in the public domain and is being used
for deciphering gene function and identification of genes underlying the major traits
by a myriad of researchers. The whole genome sequencing of barley has ushered the
era of genomics-based breeding in barley. At present, there are several genomic
databases such as EnsemblPlants, Nord-Gen, BARLEX, MorexGenes, GrainGenes,
HvGDB, Bex-DB, BarleyDB and BarleyVarDB which are used to map genes/
regions of interests in the whole genome. The major use of the reference genomes
is to conduct a bulk segregant analysis (BSA) of different genotypes to analyse the
extent of sequence variability resulting in identification of different alleles of the trait
in question. Apart from the reference genome-based genomics, the bulk segregant
ribonucleic acid (RNA) sequencing (BSR-seq) and specific-length amplified frag-
ment sequencing (SLAF-seq) are also being standardized for barley. The
transcriptome sequences are proving to be very useful for understanding of the
gene function based on expression analysis of the candidate gene. The directional
approach of the CRISPR/Cas9 technology is a futuristic tool for editing of the barley
5 Barley Breeding 297

genes to make them express-desired proteins. Collectively, the techniques of

genome sequencing, genomic selection, GWAS and gene editing and cloning should
cater to the challenge of molecular information not being efficiently translated into
end products that is high yielding cultivars with desired quality traits and tolerant to
the hostile environment and local diseases and pests mainly because of the complex
regulatory framework of the traits and dispersal of genes across the seven barley
chromosomes (Feng et al. 2019).

5.14 Coordinated System of Testing, Status of Varietal

Development and Maintenance Breeding in India

The barley research was initiated way back during the nineteenth century in India
and several improved varieties, such as NP13, NP21, BR22, BR32, C251, CN292
and CN294, were developed by pure line selection from indigenous landraces. Prior
to inception of a national system of testing, the improved barley lines across the
country in a coordinated pattern, about 31 barley varieties were already developed
mostly through selection from the local germplasm. All India Coordinated Barley
Improvement Project (AICBIP) was launched in 1966–1967 at IARI, New Delhi,
which gave impetus to barley improvement programmes in different barley cultiva-
tion states. AICBIP was merged with wheat improvement programme in 1997 and a
common coordinated programme for these two important cereals as All India
Coordinated Wheat and Barley Improvement Project (AICW & BIP) came into
existence.
Based on the agro-climatic conditions, barley cultivation regions have been
divided into four zones, namely, North-western Plain Zone (NWPZ), North-eastern
Plain Zone (NEPZ), Central Zone (CZ) and North Hill Zone (NHZ). The advanced
lines found to be promising in the station trials conducted at the originating centre of
the line are evaluated in the two-tier system of evaluation. All the entries are first
evaluated in Initial Varietal Trial (IVT) across the zones except the NHZ where
separate IVT is constituted. Based on the performance in a zone, the test entries are
promoted to Advanced Varietal Trials first year (AVT I) to be conducted in that
particular zone. Again, based on the performance in the AVT I, the entries are
retained for second year of testing (AVT II). In each trial, the test entries are
compared with the latest suitable zonal checks. Based on the superior performance
across the yield evaluation trials (IVT and AVT), performance in the agronomic
trials and their resistant reaction to diseases like yellow rust and leaf blights, the
entries are identified for release by the Variety Identification Committee during the
annual workshops of wheat and Barley. If all the requirements are met, the Central
Sub-committee on Crop Standards, Notification and Release of Varieties of Agricul-
tural Crops (CVRC) of Department of Agriculture Cooperation and Farmers’ Wel-
fare release this test entry as variety and notify it in its Gazzet for commercial
cultivation. The originating centre of dropped test entries in the AICW & BIP
testing, if are promising in their state, has option to release these as varieties for its
298 S. K. Bishnoi et al.

state through State Variety Release Committee (SVRC). After release by the SVRC,
this is also notified in the central gazette of DAC & FW.
The centres namely IARI, New Delhi, Ludhiana, Kanpur and Sabour contributed
significantly and developed several improved barley varieties, which paved the way
for yield maximization, especially under rain-fed cultivation. Dolma a naked barley
variety for food purpose was released in 1982. Barley improvement efforts have
largely been concentrated on feed barley development, and a good number of feed
barley varieties have been developed. The dual purpose varieties RD2715, BH380
and VLB130 have also been developed for feed and fodder purpose, while RD2035
and RD2552 released as normal feed barley were also found to be good dual purpose
types. During the last decade of twentieth century, more efforts to improve naked
barley for food purpose were made which led to the development of food barley
varieties like Geetanjali, Sindhu, Norbo, NDB943, Karan16, HBL276, BH352 and
PL891. Similarly, the barley improvement programme of the country envisaged
huge potential of barley as industrial crop and barley breeding activities were steered
to develop malt barley verities.
These efforts led to the release of malt barley varieties namely Clipper, Alfa
93, Rekha, DWR28, BH885, DWRUB52, RD2668, DWRB73, DWRUB64,
DWRB91, DWRB92, DWRB101, RD2849, DWRB123, DWRB160 and
DWRB182. Majority of the released barley variety are six row types. To utilize
the grain-boldness of two-row barley for grain yield maximization, two-row barley
varieties (Clipper, BH885, Alfa93, Rekha, DWR28, RD2668, DWRB73, UPB1008,
DWRB91, DWRB123, DWRB160, DWRB182 and PL891) have also been
released. As of now, 105 barley varieties have been released by CVRC (56) and
SVRC (49) since 1966–1967, the year of launching AICW & BIP.

5.14.1 Maintenance Breeding

After release and notification, genetic purity of a variety is maintained by the

originating institution. Seed from single spike of a variety is grown in a single
row. Rows having doubtful plant characters deviating from the original variety
characters are removed before flowering. Based on heading and maturity time
also, the doubtful rows are rejected. At maturity also screening of rows is done for
any deviation in the spike and awn characters. These rows are harvested separately
and are evaluated for their grain characters. Only those rows which qualify for
characters of the variety are taken as Nucleus Seed Stage I (NSS I). From the
produce of a row, small seed plots are raised. Seed (NSS2) from only those plots
is bulked which qualify for the variety characters. Genetic purity of all the varieties
which are under cultivation is also maintained through grow-out tests. Seed samples
of barley varieties under seed chain are sent from the originating institutions to
ICAR-IIWBR, Karnal, where the seed unit arranges for the grow-out test of these
varieties. At the end of the season, feedback about the genetic purity of a variety is
sent to the concerned breeder who, in turn, takes need-based curative action.
5 Barley Breeding 299

5.15 Future Thrust and Conclusion

Barley is an ancient crop with inbuilt climate change buffering making it a food and
feed crop of seemingly hostile future. The multifacet uses of barley in food, feed,
forage, malt and other industrial uses make it a crop where the breeding efforts need
to be invested for food and energy requirement of the demographically expanding
world. The recent progress in barley genomics and particularly the whole genome
assembly of the Golden Promise barley cultivar have been a morale booster of the
researchers who now can more efficiently target and improve specific traits. These
advances including the assembly of barley reference genome can well be utilized in
understanding of the barley genetics and the trait which are being sought in the
cultivar development programmes around the world. The understanding of genetics
of important traits related to diseases, drought, heat and quality, etc. is not complete
and functional characterization of the identified genes and their annotation in the
reference genomes are still a challenge to the researchers. In this context, sequencing
of additional genotypes including the barley wild relatives, landraces and
segregating generations will bring to light more information available for uses by
the barley workers. The conventional breeding approaches might be benefitted by
these technologies in making the selection more rapid and accurate. They might also
be very useful in identification of the parental material with the gene of interest. The
CRISPR/Cas9 gene editing technology promises a plethora of theoretical advantages
of which the practical and deliverable aspects remain to be seen in case of barley.
With this technique, any gene of interest can be targeted for understanding of gene
function in a non-transgenic fashion and thus the regulatory hurdles applied to the
transgenic cultivars will not come into play in this case.

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Pearl Millet Breeding
6
C. Tara Satyavathi, S. Mukesh Sankar, Sumer Pal Singh,
Chandan Kapoor, S. L. Soumya, and Tripti Singhal

Abstract

Pearl millet is a rainfed crop grown and distributed worldwide over tropical zones
covering nearly 30 countries. Globally, India is the leader both in terms of area
under pearl millet cultivation and production. Due to unpredicted nature of
weather, low seed cost, and more resilience for various abiotic and biotic stresses,
open pollinated varieties are still very popular among the pearl millet farmers of
India and arid regions of Africa. Pearl millet is often considered to be a ‘super
cereal’ due to its rapid growth, high photosynthetic efficiency, balanced
nutritional profile, and tolerance properties to extreme climatic conditions.
Besides, pearl millet grains have immense medicinal value and have been
encouraged by dieticians and nutritionists as a super food for the benefit of a
large section of society. With the rise in some of the key global issues like
malnutrition, climate change, global warming, pearl millet has received special
attention amongst farmers, consumers, and policymakers during recent years as a
crop of choice. This chapter mainly deals with the basics of pearl millet as a crop,
its breeding strategies, variety developmental procedure, and also the key future
researchable areas.

Keywords

Nutritional properties · Gene pool · Breeding techniques · Hybrid development ·

Biotic and abiotic stresses

C. T. Satyavathi (*)
ICAR-All India Coordinated Research Project on Pearl Millet, Jodhpur, Rajasthan, India
S. Mukesh Sankar · S. P. Singh · C. Kapoor · S. L. Soumya · T. Singhal
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 309
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_6
310 C. T. Satyavathi et al.

6.1 Introduction

Pearl millet [Pennisetum glaucum (L.) R. Br. syn. Cenchrus americanus (L.)
Morrone] is the world’s sixth most important cereal and the primary food source
in the dryland farming systems of semi-arid and arid tropical environments. In India
and Africa, it is primarily grown for food and forage, while in the American
continents it is a main component of poultry and livestock sector (Serba et al.
2020). Pearl millet was domesticated over 4000 years ago in the West African
Sahel, spreading later to East Africa and India (Sharma et al. 2020b). Now it is
being cultivated over 30 million ha worldwide, with the majority of the crop grown
in Africa (>18 million ha) and Asia (>10 million ha) (Raheem et al. 2021). Around
90 million people in the Sahelian region of Africa and northwestern India consume
pearl millet grain as a staple food (Srivastava et al. 2020a). It is traditionally served
as a thick porridge (toh), or to prepare unfermented breads and cakes (roti), steam-
cooked dishes (couscous), fermented foods (kisra and gallettes), and snacks. In
India, flour made out of it is used to make chapattis, porridge, boiled or roasted
food, and even weaning mixtures (Pattanashetti et al. 2016).
In northern Nigeria, Masa, a popular fried cake is prepared from pearl millet
(Ajeigbe et al. 2020) and its grains are also locally brewed to produce non-alcoholic
or alcoholic beverages in Asia and Africa (Dwivedi et al. 2012). Alternative uses
have increased (55%) mainly as animal feed for dairy both as a green fodder and dry
stover for cattle. Green fodder is high in protein, calcium, phosphorus, and other
minerals, with lower levels of oxalic acid. Stover has excellent forage quality with
lower hydrocyanin content (Kumar et al. 2020a). Apart from its utility in human
consumption and in livestock sector, it is used in industries for alcohol and fuel
industry, starch industry, processed food industry, and has great export demand
(Punia et al. 2021).
Pearl millet is often considered to be “super cereal” with respect to its rapid
growth even with least input, high photosynthetic efficiency, inheritably good and
balanced nutritional profile, tolerance to extreme climatic conditions and biotic
stresses (Chandra et al. 2021). Pearl millet has C4 photosynthetic pathway which
is very efficient in energy production (50% higher photosynthesis efficiency than C3
crops) in hot and dry climate (Wang et al. 2018). It is usually grown under the most
adverse agro-climatic conditions where other staple cereal crop like rice and wheat
fail to survive. The high dependency of people, mainly in arid and semiarid regions,
on pearl millet is due to grain production capability even in the harshest conditions,
including low soil fertility, high soil pH, high soil Al3+ saturation, low soil moisture,
high temperature, high soil salinity, and scanty rainfall (Varshney et al. 2017). Pearl
millet is more nutritious than commonly consumed staple crops such as wheat, rice,
maize, and sorghum (Kumar et al. 2021a) and offers gluten-free grains with high and
better protein in terms of quality and quantity. It is the only cereal whose flour is
alkaline in nature with a low glycemic index (~55) making it a diabetic-friendly
food. Also, it is filled with resistant starch, vitamins, antioxidants, essential
micronutrients such as iron and zinc, and more balanced essential amino acid profile
than maize or sorghum (Goswami et al. 2020; Punia et al. 2020). Because of its high
6 Pearl Millet Breeding 311

nutritional and nutraceutical value, it is renamed as ‘Nutricereal’ by Govt. of India

through gazette No. 133 dated 13th April 2018 for production, consumption, and
trade and included in Public Distribution System (PDS).
With the emergence of global issues such as malnutrition, climate change, global
warming, a rise in lifestyle-related diseases, need for green fuel sources, and so on,
millets have received more attention amongst farmers, consumers, and policymakers
during recent years. According to Lesk et al. (2016), adverse climatic conditions
such as a dramatic rise in temperature, drought, and other factors have reduced cereal
crop production by 9–10% in recent years. Its effect can be seen not only in terms of
quantity but also in terms of quality reduction. Many nutrient rich crops experienced
to have 3–17% lower concentrations of protein, iron, and zinc in its grain. According
to estimates, India will have a 2.2% increase in protein-deficient people (with 38.2
million new protein-deficient people) and a 2.9% increase in zinc-deficient people by
2050. About 106.1 million children and 396 million women would become iron-
deficient (Beach et al. 2019; Moore et al. 2020). In all these context, millets can be
saviour to mankind as it has lower carbon footprint than commonly consumed cereal
like wheat, rice, and maize (Kritee et al. 2013; Saxena et al. 2018) and can provide
food and nutritional security even in the hardest situation (Anuradha et al. 2017).
Hence, millet is rightly termed as nutricereal. In addition, to include millets into the
mainstream and exploit its nutritionally superior qualities and promote its cultiva-
tion, Govt. of India has declared Year 2018 as the ‘Year of Millets’ and FAO
Committee on Agriculture (COAG) forum had declared Year 2023 as ‘International
Year of Millets’. With the importance of pearl millet in bringing food security and
nutri-revolution to resource-constrained regions of Asia and Africa in mind, the
following sections explain the various aspects and past and on-going pearl millet
improvement programmes.

6.2 Origin, Domestication, Taxonomy, and Distribution

6.2.1 Origin and Domestication

Pennisetum violaceum (Lam.) Rich. [syn. P. americanum subsp. Monodii (Maire)

Brunken] has been described as the wild progenitor of the cultivated pearl millet
species, occurs in the Sahel zone in Africa from Senegal to northern Sudan (Brunken
et al. 1977; Sharma et al. 2020b; Fuller et al. 2021). It was hypothesized that the
origin of cultivated form of pearl millet occurred near Taoudeni Basin in western
Sahara (6.61
E, 23.58
N). Burgarella et al. (2018) reported that in the Sahel zone,
both cultivated and wild Pennisetum species coexists along with intermediate
morphologies, and genotypes supported a Saharan cradle of pearl millet domestica-
tion. Wild pearl millet dating back to the middle Holocene (~5000 BC), was being
exploited in northern Mali in the fifth millennium BC and that pre-domestication
cultivation was probably established sometime in the fourth millennium
BC. Domestication of pearl millet has been suggested to have occurred through
single or multiple events between regions of Niger and Mauritania. By the middle of
312 C. T. Satyavathi et al.

the third millennium BC, morphological domestication traits had become well-
established.
The domesticated pearl millet was introduced to adjacent regions, including the
Hodh depression of Mauritania and the Lower Tilemsi Valley in Mali toward the end
of the third millennium BC; and southern Mali, northern Ghana, and by the first half
of the second millennium BC at the Lake Chad region. Domestication is said to have
resulted in the first early maturing cultivars (Tostain and Marchais 1989). By
3000 BC, these early maturing forms of domesticated pearl millet were introduced
to eastern Africa (Tostain and Marchais 1993; Tostain 1998) facilitated by their
efficient adaptation to arid conditions (D’Andrea and Casey 2002) and then to India
(D’Andrea et al. 2001; Khairwal et al. 2007).
India is regarded as the secondary diversity hotspot (Brunken et al. 1977). Around
2000 years BC, photoperiod-sensitive varieties were selected for further diffusion in
the region near Lake Chad (on the Nigerian side) (Klee et al. 2004). This led to the
development of a secondary center of diversity in this region. These late-maturing
lines were transported further into the Sudanian zone of southwest Africa from
northern Nigeria to southern Senegal (Tostain et al. 1987; Tostain and Marchais
1993). Further these lines were tailored to adapt under the humid conditions in the
southern Sudanian zone (Tostain 1998; D’Andrea and Casey 2002). About
1000 years BC, pearl millet was extended towards the plateau of southern Africa
via Uganda and to Namibia (Tostain and Marchais 1993; Tostain 1998). The United
States and Brazil were the most recent countries to introduce this crop; records of its
cultivation date back to the 1850s in the United States and the 1960s in Brazil
(National Institute of Plant Health Management 2014).
Pearl millet shares many of the same morphological changes known for other
cereal domestications. The domestication process of pearl millet is associated with
frequent morphological changes such as suppression of spikelet shedding, size
reduction of bristles and bracts, increase in seed size, increase in spikelet pedicel
length, loss of dormancy, decrease in the number of basal tillers, and increase in
spikelet length (Fuller et al. 2021).

6.2.2 Taxonomic Classification and the Gene Pool

The genus Pennisetum Rich. belongs to the family Poaceae, the subfamily
Panicoideae, and the tribe Paniceae. This genus is closely related to the genus
Cenchrus L. (Stapf and Hubbard 1934; Boer et al. 2007) and both are placed within
the bristle clade in the tribe Paniceae along with 23 other genera (Ixophorus
Schltdl., Paspalidium Stapf, Setaria P. Beauv., and others) (Doust and Kellogg
2002; Bess et al. 2005). The characteristics such as degree of fusion of the bristles,
the presence of pedicellate spikelets, and type of bristles (flat or stiff), are commonly
used to separate Pennisetum from Cenchrus (Clayton and Renvoize 1982, 1986;
Watson and Dallwitz 1992); however, none of them can be effectively used to
segregate the two genera (Webster 1988). Kellogg et al. (2009) also placed the
6 Pearl Millet Breeding 313

genus Odontelytrum, harbouring only a single species, O. abyssinicum, in this clade

along with two genera: Pennisetum and Cenchrus.
A study based on a combined nuclear, plastid, and morphological analysis
proposed the unification of the three genera Pennisetum, Cenchrus, and
Odontelytrum (Chemisquy et al. 2010). Similarly, based on the chromosomal and
genomic characteristics along with phylogenetic relationships, Robert et al. (2011)
favoured the inclusion of Cenchrus species in the genus Pennisetum. Therefore, it
has been proposed to reconsider the taxonomic position of the Cenchrus species and
to rename them into genus Pennisetum as previously known (Robert et al. 2011).
The genus Pennisetum comprises 80–140 species (Brunken 1977) with different
basic chromosome numbers (x ¼ 5, 7, 8, or 9) (Jauhar 1981), ploidy levels (diploid to
octoploid), reproductive behaviour (sexual or apomictic), and life cycle (annual,
biennial, or perennial) (Martel et al. 1997). Phylogenetic analysis suggested that the
chromosome complement in Pennisetum has evolved from a basic chromosome
number of x ¼ 9 with a short length (Martel et al. 2004). Species with basic
chromosome numbers of x ¼ 5, 7, and 8 appear in the most recent divergent clades,
suggesting that the genome structure in Pennisetum may have evolved towards a
reduced chromosome number and an increased chromosome size (Martel et al.
2004), which is consistent with the chromosome evolutionary trend generally
observed in grasses (Martel et al. 2004).
Based on morphological characteristics, genus Pennisetum is classified into five
sections (Stapf and Hubbard 1934): Brevivalvula Döll (pan-tropical), Eupennisetum
(tropical and subtropical Africa and Asia), Gymnothrix (P. Beauv.) Steud (pantropi-
cal), Heterostachya Schumach. (northeastern Africa), and Penicillaria (Willd.)
Benth and Hook.f. nom. Superf. (tropical Africa and India), each having a variable
number of species with variable basic chromosome number. The annual diploid
cultivated pearl millet, P. glaucum (L.) R. Br. [former P. americanum (L.) Leeke;
syn. P. glaucum ssp. glaucum] along with its diploid wild species, P. glaucum ssp.
monodii (Maire) Br., the diploid weedy species, P. glaucum ssp. stenostachyum
(Klotzsch ex Müll. Berol.) Brunken (all species with 2n ¼ 2x ¼ 14) and the
reproductively isolated perennial tetraploid P. purpureum Schumach (2n ¼ 4x ¼ 28)
are placed in the section Penicillaria (Martel et al. 2004).
Based on the cross-compatibility relationship between cultivated pearl millet and
crop wild relatives, these species can be put in three genepools: primary (GP1),
secondary (GP2), and tertiary (GP3) as per Harlan and de-Wet (1971). Details of
each member included in each genepool are provided in Table 6.1. Under sympatric
conditions, members of GP1 could easily cross to each other resulting fertile F1
showing normal chromosome pairing (Harlan and de-Wet 1971). Hence the
members in GP1 have higher possibility for successful introgression of genes from
crop wild relatives (CWR) into cultivated ones. Cultivated diploid species,
P. glaucum ssp. glaucum, its wild progenitor, P. glaucum ssp. monodii with two
ecotypes (1) Pennisetum violaceum (Lam.). L. Rich. (also known as P. glaucum ssp.
monodii forma violaceum) and (2) Pennisetum mollissimum Hochst. (also known as
P. glaucum ssp. monodii forma mollissimum Hochst.)] and a weedy form known as
shibras [¼ P. glaucum ssp. stenostachyum Kloyzesh ex. Müll. Berol. Brunken]
314 C. T. Satyavathi et al.

Table 6.1 Details of species coming under different genepools in Genus Pennisetum
Life cycle
Common Gene and
Species name name Section pool Ploidy reproduction
P. glaucum ssp. Cultivated Penicillaria GP1 2n ¼ 2x ¼ 14 Annual,
glaucum (L.) R. Br Pearl millet Sexual
P. monodii (Maire) Wild Pearl Penicillaria GP1 2n ¼ 2x ¼ 14 Annual,
Brunken, Ecotype: millet Sexual
P. violaceum
P. monodii (Maire) Wild Pearl Penicillaria GP1 2n ¼ 2x ¼ 14 Annual,
Brunken, Ecotype: millet Sexual
P. mollissimum Hochst.
P. glaucum ssp. Shibras Penicillaria GP1 2n ¼ 2x ¼ 14 Annual,
Stenostachyum Sexual
(Klotzsch ex Müll.
Berol.) Brunken
P. purpureum Schum. Napier/ Penicillaria GP2 2n ¼ 4x ¼ 28 Perennial,
elephant Vegetative/
grass Sexual
P. schweinfurthii Heterostachya GP1 2n ¼ 2x ¼ 14
Pilger.(¼
P. tetrastachyum)
P. squamulatum Fresen Heterostachya GP2 2n ¼ 6x ¼ 54 Perennial,
or Apomixis
2n ¼ 8x ¼ 56
P. alopecuroides (L.) Swamp Gymnothrix GP3 2n ¼ 2x ¼ 18 Annual,
Spreng. foxtail Sexual
grass
P. hordeoides Steud Brevivalvula GP3 2n ¼ 2x ¼ 18 Annual,
Sexual/
Apomixis
P. pedicellatum Trin. Deenanath Brevivalvula GP3 2n ¼ 4x ¼ 36 Annual,
grass Sexual
P. polystachion Mission Brevivalvula GP3 2n ¼ 6x ¼ 54 Annual/
L. Schult. grass Perennial,
Sexual/
Apomixis
P. ramosum (Hochst.) Gymnothrix GP3 2n ¼ 2x ¼ 10 Biannual,
Schweinf. Sexual/
Apomixis
P. cenchroides Rich. Unknown GP3 2n ¼ 4x ¼ 36 Perennial,
Sexual
P. ciliare L. Mant. Syn: Buffel Unknown GP3 2n ¼ 4x ¼ 36 Perennial,
Cenchrus ciliaris grass Sexual/
L. Mant. Apomixis
P. clandestinum Kikuyu Eu- GP3 2n ¼ 4x ¼ 36 Perennial,
Hochst. Ex Chiov. grass Pennisetum Vegetative/
Sexual
P. divisum (Forssk.) Unknown GP3 2n ¼ 4x ¼ 36 Perennial,
Ex. Gmel. Sexual
(continued)
6 Pearl Millet Breeding 315

Table 6.1 (continued)

Life cycle
Common Gene and
Species name name Section pool Ploidy reproduction
P. flassidum Griseb. Unknown GP3 2n ¼ 4x ¼ 36 Perennial,
Sexual/
Apomixis
P. hohenackeri Hochst. Moya Gymnothrix GP3 2n ¼ 2x ¼ 18 Perennial,
Ex Steud grass Sexual/
Apomixis
P. lanatum Leeke. Unknown GP3 2n ¼ 2x ¼ 18 Perennial,
Apomixis
P. macrostachyum Unknown GP3 2n ¼ 7x ¼ 63 Perennial,
(Brongn.) Trin Sexual
P. macrourum Trin. Needle Gymnothrix GP3 2n ¼ 4x ¼ 36 Perennial,
grass Vegetative
P. mezianum Leeke. Gymnothrix GP3 2n ¼ 4x ¼ 32 Perennial,
Sexual/
Apomixis
P. orientale L.C. Rich. White Heterostachya GP3 2n ¼ 4x ¼ 36 Perennial,
Fountain Sexual/
grass Apomixis
P. setaceum (Forssk.) Fountain Eu- GP3 2n ¼ 3x ¼ 27 Perennial,
Chiov. grass Pennisetum or Sexual/
2n ¼ 6x ¼ 54 Apomixis
P. thunbergii Kunth. Gymnothrix GP3 2n ¼ 2x ¼ 18 Perennial,
Sexual
P. villosum Fresen. Feather top Eu- GP3 2n ¼ 5x ¼ 45 Perennial,
grass Pennisetum Sexual/
Apomixis/
vegetative

forms GP1 members of the pearl millet. Napier grass (Pennisetum purpureum) and
P. squamulatum are the members of GP2 in case of Pennisetum. P. purpureum, also
known as Napier grass or elephant grass (2n ¼ 4x ¼ 28 with A0 A0 BB genome), and
the apomictic and octaploid species P. squamulatum Fresen (2n ¼ 8x ¼ 56)
(Kaushal et al. 2007). The GP2 includes an allotetraploid rhizomatous perennial
species, which can be easily crossed with members of GP1 but their hybrids are
highly sterile.
The GP3 includes the remaining species that are cross-incompatible with
cultivated pearl millet. There are strong reproduction barriers between the members
of GP3 and GP1 or GP2, and gene transfer is only possible by radical manipulations
involving in vitro techniques or by using complex hybrid bridges. In GP3,
P. schweinfurthii (¼ P. tetrastachyum) Pilg. is the only Pennisetum species to
have 2n ¼ 2x ¼ 14 large chromosomes with an annual growth habit (Martel et al.
2004) but its chromosomes are nonhomologous (Hanna and Dujardin 1986) with
316 C. T. Satyavathi et al.

different genomic localizations of rDNA probes (Martel et al. 1996). Tertiary gene
pool species with a basic chromosome number of 9 (x ¼ 9) are more likely to cross
with pearl millet than those with x ¼ 5 [P. ramosum (Hochst.) Schweinf] or x ¼ 8
(P. mezianum Leeke).

6.2.3 Distribution

Pearl millet is a warm season millet grown as rainfed crop, and it prefers to grow in
light-textured (sandy or light loam), well-drained soils. Pearl millet is distributed
worldwide over tropical zones covering more than 30 countries and occupies an area
of 27 million ha (Varshney et al. 2017) (Fig. 6.1). It serves as a significant crop in the
arid and semiarid regions of South Asia particularly India and Africa. It occurs in
Africa from north to south mainly concentrated in the west/central Africa (WCA)
region (Nigeria, Niger, Chad, Mali, and Senegal) and east/southern Africa (ESA)
which includes Sudan; rarely being found in the southern portions of the Arabian
Peninsula, Spain, and the South-eastern United States (Brunken et al. 1977). The
Sahel zone of West Africa exhibits the most significant share of genetic diversity,
whereas the arid sections of India exhibit the highest hectarage. Western and Central
Africa (WCA) is the largest pearl millet producing region in Africa and the world
accounting for 95% of the total area in WCA (Jukanti et al. 2016). India occupies
32% of world pearl millet area followed by Niger (23%) and Nigeria (8%) of total
cultivated area. The West and Central Africa (WCA) region has large areas under
millets (15.7 million hectares), of which more than 90% is pearl millet. The crop is
cultivated on more than two million hectares in the eastern and southern Africa
region.

Fig. 6.1 Distribution of pearl millet in the world in which yellow regions indicate zone of pearl
millet cultivation. (Source: Global Biodiversity Information Facility Network)
6 Pearl Millet Breeding 317

Jammu & Kashmir

Himachal Pradesh
Punjab
Chandigarh
Uaranchal

Haryana
Delhi Arunachal Pradesh

Sikkim
Rajasthan Uar Pradesh
Assam
Nagaland
Bihar
Meghalaya
Manipur

Jharkhand Tripura
Gujarat West Bengal Mizoram
Madhya Pradesh
Chasgarh

Daman & Diu Orissa

Dadra & Nagar Haveli
Maharashtra

h
des
a pra
dr
ka

Goa An
ata

% to all India pearl millet area

rn
Ka

< 1%
u

Andaman & Nicobar

ad

Pondicherry 1-10%
il N

Lakshadweep
m

10.1-20%
Ta

Kerala

> 20.1%

Fig. 6.2 Distribution of pearl millet in the India in which percentage area coverage indicated by
strength of green shade. (Source: AICRP-PM 2021)

India has the distinction of being the largest producer of the crop, both in terms of
area and production in the world. It is grown in 7.41 million hectares area with a
production of 10.3 million tons during 2020–2021 (Directorate of Millets Develop-
ment 2021). The major pearl millet growing states are Rajasthan, Maharashtra,
Gujarat, Uttar Pradesh, and Haryana which account for more than 90% of pearl
millet acreage in the country (Fig. 6.2). Amongst Indian states, Rajasthan ranks first
in total pearl millet area of cultivation (57%) followed by Uttar Pradesh (13%) and
Maharashtra (10%) with a production contribution of 45% from Rajasthan, 20%
Uttar Pradesh, and 7% from Madhya Pradesh.
318 C. T. Satyavathi et al.

6.3 Nutritional and Nutraceutical Importance

Pearl millet, generally considered an orphan crop, is often regarded as ‘powerhouse

of nutrients’. It forms a good source of energy, carbohydrate, protein, fat, dietary
fiber, vitamins, and minerals, especially iron and zinc in right quality and quantity
required by human beings in order to fulfil their dietary requirement. Table 6.2

Table 6.2 Nutrient composition of major cereals (per 100 g) edible portion
Contents Pearl millet Sorghum Maize Rice Wheat
A. Proximate composition
Moisture (%) 12.40 11.90 14.90 13.00 12.80
Carbohydrates (g) 61.8 67.7 64.8 78.2 64.7
Energy (Kcal) 347 334 342 356 321
Protein (g) 10.9 9.9 8.8 7.9 10.6
Fat (g) 5.43 1.73 3.77 0.52 1.47
Dietary fibre (g) 11.5 10.2 12.24 2.8 11.2
B. Micronutrients
Calcium (mg) 27.4 27.6 8.9 7.5 39.4
Phosphorus (mg) 289 274 279 96 315
Magnesium (mg) 124 133 145 19 125
Iron (mg) 6.4 3.9 2.5 0.6 3.9
Zinc (mg) 2.7 1.9 2.8 1.2 2.8
Copper (mg) 0.55 0.55 0.54 0.72 0.49
Sodium (mg) 10 7 4.4 3 18
Potassium (mg) 402 321 291 110 349
Thiamine (mg) 0.25 0.35 0.33 0.05 0.46
Riboflavin (mg) 0.20 0.14 0.09 0.05 0.15
Niacin (mg) 0.90 2.10 2.69 1.70 2.70
Folic Acid (μg) 36.1 39.4 25.81 9.32 30.1
β-Carotene(μg) 293 212 893 16.87 3.03
Vit E (mg) 0.24 0.06 0.36 0.06 0.77
C. Amino acids + (g/16 g N)
Lysine 3.19 2.31 2.64 3.7 2.6
Tryptophan 1.33 1.03 0.7 1.27 1.4
Methionine 2.11 1.52 2.1 2.6 1.75
Threonine 3.55 2.96 3.23 4.36 3.01
Isoleucine 3.45 3.45 3.67 3.28 3.83
Leucine 8.52 12.03 12.24 8.09 6.81
Cysteine 1.23 1.06 1.55 1.84 2.35
Phenylalanine 4.82 5.1 5.14 5.36 4.75
Valine 4.79 4.51 5.41 6.06 5.11
Arginine 4.54 3.96 4.2 7.72 5.13
Histidine 2.15 2.07 2.7 2.45 2.65
Tyrosine 2.67 3.61 3.71 4.36 3.12
Source: NIN Hyderabad, 2017 and 2018
6 Pearl Millet Breeding 319

summarizes the nutritional composition of pearl millet grains compared to other

staple cereals. Pearl millet is a rich source of energy (350 Kcal/100 g) comparable
with sorghum, wheat, rice, and maize. The carbohydrate content of pearl millet is
61.8 g/100 g; with 60–70% starch comprising 28.8–31.9% amylose amongst which
14.6–17.2% form complex with native lipids. It encompasses a comparatively higher
water absorption capacity and swelling index than the other cereal starches (Kajla
et al. 2020). Free sugar, such as sucrose, glucose, fructose, and raffinose, forms
2.6–2.8%. Pearl millet contain adequate amount of dietary fibers (11.5 g/100 g)
amongst which most of them belong to insoluble form, when compared with other
grains (National Institute of Nutrition 2017). It helps to overcome acidity due to its
alkaline nature. Pearl millet is having low glycaemic index score of ~55 and
significantly rich in resistant starch. Hence, pearl millet can be excellent diet for
diabetics, constipations, obesity, and celiac diseases (Nambiar et al. 2011).
The protein content of pearl millet is about 11 g/100 g, comparable to wheat but
higher than rice. The amino acid profile of pearl millet protein includes most of the
essential amino acids, which is comparatively higher than wheat and maize proteins.
Similar to other cereals, lysine is one of the limiting amino acid. It is rich in
methionine but poor in other sulphur containing amino acids. With low prolamin
fraction, pearl millet is a gluten-free grain and is the only grain that retains its
alkaline properties after being cooked which is ideal for people with gluten allergy.
Pearl millet is rich in fat content (5–7 mg/100 g) with better fat digestibility as
compared to other grains. Pearl millet grains have proportionally very large germs
than other cereals where most of the lipids are located. It is rich in unsaturated fatty
acids (75%) with higher content of nutritionally important omega-3 fatty acids such
as oleic acids (25%), linoleic acid (45%), and linolenic acid (4%) than other cereal
grains.
The ash content of whole pearl millet grain ranges between 1.6% and 3.6%. In
terms of actual minerals, pearl millet grain, like other cereal grains, is an adequate
source of dietary minerals, such as phosphorus, calcium, magnesium, iron, zinc, and
copper (Serna-Saldivar 2016 and Pujar et al. 2020). Most of these minerals were
located near to pericarp, and dehulling of the grain will lead to considerable loss of
these mineral nutrients. Pearl millets are a rich source of phosphorus which is an
important mineral for energy production. It is an essential component of ATP, the
energy currency of the cell. It also forms a part of the nervous system and cell
membranes. A well-cooked cup of millet gives 26.4% daily need for magnesium and
24% daily need for phosphorus.
Magnesium from pearl millets helps in relaxing blood vessels and maintains the
blood pressure, enhances nutrient delivery by improving the blood flow, and thus
further protects the cardiovascular system. Magnesium increases insulin sensitivity
and lowers triglycerides. It also acts as a cofactor for more than 300 enzymes. Iron
(Fe) and zinc (Zn) deficiency affects 50% of the world population resulting in
anaemia, diarrhoea, impairment of physical growth, and suppressed immune func-
tion. Pearl millets are rich in these minerals can reach up to 5.5 mg/100 g and 3.2 mg/
100 g, respectively (Minnis-Ndimba et al. 2015). However, like all cereals, pearl
millet contains phytate, an anti-nutrient that chelates with minerals forming
320 C. T. Satyavathi et al.

complexes hence reducing their effective absorption and utilization by humans (Kent
1994). The typical ranges of phytate content in pearl millet are 443–1076 mg
phytate/100 g (El-Hag et al. 2002).
Even though phenolic acids of pearl millet have detrimental effect on micronutri-
ent bioavailability, they have considerable interest due to their impacts on human
health through important biological and pharmacological properties, such as anti-
hyperlipidemic against cardiovascular diseases and anti-carcinogenic activities
against cancer. It is rich in brain cell promoting factors which can alleviate
Parkinson’s disease such as galic acid (15.3 μg/g), chlorogenic acid (16.0 μg/g),
syringic acid (7.4 μg/g), p-coumaric acid (1350.88 μg/g), ferulic acid (199.56 μg/g),
cinnamic acid (41.30 μg/g), ellagic acid (14.47 μg/g), querctin (5.9 μg/g), and
apigenin (9.08 μg/g) sample of pearl millet flour. Furthermore, pearl millet has
plenty of health-promoting attributes owing to its nutritional composition and
hence has an immense potential toward medicinal uses. As for example, its high
fibre content can make it a potential component in the diets of patients suffering from
constipation, obesity, and gallstones (Ambati and Sucharitha 2019). Further due to
its anti- or hypo-allergic properties, it can be safely incorporated in the diets of celiac
patients, pregnant women, infants, lactating mothers, elderly, and convalescents.
Thus, pearl millet grains have immense medicinal value and should be aggressively
promoted by dieticians and nutritionists so that a large section of society could be
benefited.

6.4 Botanic Description and Floral Biology of the Crop

Pearl millet is a diploid (2n ¼ 2x ¼ 14) annual monocot grass (Family-Poaceae) with
a short life span of 75–100 days. It can achieve a height of 1.5–3 m tall but can grow
up to 5 m. However, improved cultivars such as OPVs and hybrids are reportedly
shorter. Culms can have a simple or branching habit with either slender or stout girth
having a smooth or hairy surface. Leaf sheaths, collars, and blades may also be
smooth or hairy. Its leaf blades are simple, minutely serrated, alternate, flat, green
can be up to 1.5 m long and 8 cm wide. Generally, panicle emerges around ~35 to
70 days from the day of sowing depending on the maturity type in pearl millet (early/
medium/late). Panicle emergence is marked by the rapid elongation of the peduncle
and the inter-node below it and by the appearance of the flag leaf or boot leaf which
requires nearly 6 days emerging from the leaf sheath (Fig. 6.3a). The inflorescence,
usually regarded as panicle or spike are mostly cylindrical to conical in shape, stiff,
and very dense and usually range from 10 to 45 cm long and up to 7–9 cm. Typical
feature of Pennisetum spp. can be seen in case of involucres with bristles each of
which enclosing 1–9 spikelets (Brunken et al. 1977).
Spikelets are short pediceled, come two in a fascicle, and are 3.5–4.5 mm long,
ovate, and turgid. Spikelets on a panicle can vary between 500 and 3000 in number
depending upon the genotype. Each spikelets have two kinds of flowers, staminate
floret which is sessile in nature with single lemma and 3 stamens and is borne below
6 Pearl Millet Breeding 321

Fig. 6.3 Floral biology of pearl millet (a) Booting of panicle (b) Stigma emergence stage (c)
details of floral organs in pearl millet (d) Anthesis (e) Staminate spikelet (f) Hermaphrodite Spikelet
(g) Pollen from the anther

shortly pedicelled hermaphrodite (bisexual) ones (Fig. 6.3e). Hermaphrodite floret

comprises 1 pistil, 2 feathery style, and 3 anthers enclosed between the lemma and
palea (Fig. 6.3f). Pearl millet seeds are small wedge-shaped to spherical, can be of
various colours ranging from white or yellow, brown or even grey, and size can vary
between 0.5 and 3 mm long and could weigh between 3 and 25 g/1000 seed. After
50% flowering, seeds could reach physiological maturity in 27–30 days.
It is a highly allogamous (cross-pollinated) crop with outcrossing rate more than
85% mainly because of its protogynous nature. Hence, a natural population of pearl
millet genetically represent heterozygous and heterogeneously. The main mode of
pollination is due to anemophily (wind pollination). The panicle emerges around
10 weeks after sowing; the styles begin to protrude 2–3 days later first at the top of
the inflorescence and proceeds downwards. They take 2–3 days to complete the
entire spike (Fig. 6.3b). Exerted stigma remains receptive for 12–24 h. Anthesis
commences from one-third of the apex of spike and proceeds upwards and down-
wards (Fig. 6.3c). Bisexual flowers appear 2–3 days earlier than staminate flowers.
Hence, the first male phase in which the anthers from perfect floret commence
followed by second male phase from the staminate florets emerge and anthesis is
over within 2–3 days. This is followed by the first male phase in which the anthers
from the perfect florets emerge out. Second male phase commences on the fifth day
of anthesis. Usually, anthesis lasts throughout the day and night with the peak
between 8.00 p.m. and 2.00 a.m.
322 C. T. Satyavathi et al.

6.4.1 Selfing and Crossing Techniques

To ensure selfing, spikes may be bagged before emergence of the stigmas at boot leaf
stage. Care should be followed to cover the lowermost spikelet using selfing bag in
an elongating spike. Another procedure is to enclose within a bag two full spikes
from the same plant, 1 day (or) 2 days older than the other and ready to shed pollen as
the stigmas are emerging form the younger spike. Since the spikelet in pearl millet is
small, emasculation in pearl millet is very difficult and laborious and due to overlap
of the female flower with the male phase at the tip of spike, about four-fifths of the
upper portion of the spike is removed and the rest is bagged before the styles appear
to prevent contamination. Flowers are pollinated by dusting them with fresh pollen
obtained from the desired male plant or by shaking a spike which is shedding pollen
over the exposed stigmas.

6.4.2 Controlled Cross-pollination

Pearl millet does not require emasculation for making crosses. The female line will
be covered before stigma emergence with butter paper bag. Without removing the
butter paper bag, one could observe the emergence of stigma. After most of the
stigma has emerged, pollen from desired male parent is collected and dusted on to
the female line. Pollination is usually made in the morning. The crossed heads are
labelled. Another method is instead of removing the selfing bag of female and
dusting, the top of the cover clipped of desired male parent inflorescence in the
process of pollen bursting is inserted to burst the stigma. Then the clipped top of the
bag is folded and stapled. The crossed heads can be collected after 30–35 days.

6.5 Cytogenetics

Rao (1929) from root tip studies, determined the chromosome number of pearl millet
as 2n ¼ 14. Later Rangaswamy (1935) studied the chromosomes in dividing cells of
the microsporangium and confirmed the chromosome number as 2n ¼ 14. Reader
et al. (1996) was the first to use fluorescence in-situ hybridization (FISH) for detailed
characterization of the somatic complement of pearl millet. Pantulu (1958) studied
the chromosomes at pachytene and grouped them into four classes on the basis of
relative length and position of centromere (1) two pairs (Chromosome 1 and 2)
which had the greatest length and median centromere (2) two somewhat shorter pairs
(Chromosome 3 and 4) with median to submedian centromeres (3) two pairs
medium-sized (Chromosome 5–6 with submedian centromeres; and (4) the shortest
pair (Chromosome 7) with the nucleolus organizer. Most lines of pearl millet have
one pair of nucleolus-organizing chromosomes (Pantulu 1960). Karytopic
measurements of an inbred I–55 of pearl millet revealed that the seven pairs of
chromosomes were numbered 1–7 according to their descending total length, chro-
mosome 1 being the longest (5.51 μ) and chromosome 7 being the shortest (3.24 μ)
6 Pearl Millet Breeding 323

as recorded by Tyagi (1975). The shortest chromosome was the SAT chromosome
(Pantulu 1960). Some African origin varieties have one or two of the longer pairs
that reveal secondary constrictions in their long arms. The shortest chromosome pair
of the complement carries the nucleolar organizer in the short arm. B-chromosomes
occur only in pearl millet populations of African origin. These B-chromosomes
exhibited nucleolus-organizing activity (Burton and Powell 1968; Pantulu 1960;
Powell et al. 1975).
Jauhar (1970) suggested that chromosome complement of P. glaucum has been
derived from a basic set of x ¼ 5 chromosome based on the meiotic paring behaviour
in haploids, interspecific hybrids, and autotetraploids where two bivalents per cell
(some with two chiasmata each) were observed suggesting duplication of two
chromosomes in the species. Jauhar (1968) also considered inter and intra-genomic
chromosome pairing in an interspecific hybrid and its bearing of the basic chromo-
some number in Pennisetum. Manga and Pantulu (1971) did not report any bivalent
in haploid plants, whereas Gill et al. (1973) considered that the occurrence of
bivalents was the result of segmental homologies amongst some chromosomes.
Powell et al. (1975) also reported pairing of chromosomes in haploids and attributed
the pairing to the duplicate loci.

6.6 Breeding Objectives

Pearl millet breeding strategies have evolved over several decades, considering to
meet ever-changing human needs and knowledge gained with respect to production
constrains, access to novel germplasm, and accumulated knowledge in the fields of
genetics, physiology, pathology, and so on. Even though various farmers participa-
tory pearl millet breeding surveys conducted across globe over different periods had
pointed out similar set of traits to be focused for future improvements (Ipinge et al.
1996; Christinck 2002; Basavaraj et al. 2015; Angarawai et al. 2016; Thangapandian
et al. 2017; Drabo et al. 2019). Major trait to be focused was maturity earliness and
drought resilience under low rainfall conditions. Farmers preferred the plant type
(e.g., HHB 67 and RHB 177) as they could mature within 70–75 days, before the
available moisture got exhausted. Early maturity is a preferred trait for fitting in any
cropping system and also helps from the menace of bird damage. Under irrigated
conditions, farmers preferred high yielding cultivars with bold grains (>10 g/1000
grains), medium tillering nature, long, thick, and compact panicles. Most of the
farmers, particularly the women, preferred to select those cultivars which have good
grain quality traits such as light or white grain colour, shape, ease to mill, sweetness,
good keeping quality, and least prone to staling or firming (maintenance of softness)
in bread once prepared. Since pearl millet is a part of subsistence farming, they also
preferred to grow stay green, non-lodging cultivars with good stover yield and
disease resistance (e.g., foliar blast). In African countries, farmers pointed out the
infection was due to striga as major biotic factor followed by head miner infestation,
whereas in India, downy mildew and foliar blast was reported as major biotic
constrains. Even though chemical control is available for above mentioned biotic
324 C. T. Satyavathi et al.

constrains, it will add to the cost of production which is undesirable for farmers with
poor resources.

6.7 Centres Involved in Pearl Millet Breeding

6.7.1 Genesis of AICRP (Pearl Millet)

In the early 1940s, efforts were initiated by the Indian Council of Agricultural
Research for pearl millet crop improvement in India. ICAR-All India Coordinated
Millet Improvement Project (AICMIP) was established in the year 1965 with its
headquarters at the Indian Agricultural Research Institute, New Delhi. Headquarter
of the project was shifted to Pune in 1977. Later on, pearl millet was separated from
the rest of the millet crops, and the All India Coordinated Pearl Millet Improvement
Project (AICPMIP) was established in 1985 with its headquarters at Pune as an
independent coordinated project. Later in July 1995, the headquarters of AICPMIP
was shifted to Jodhpur in the state of Rajasthan, the state which occupies nearly half
of pearl millet area of the country. AICPMIP has a network of 12 centers in
Rajasthan, Maharashtra, Uttar Pradesh, Karnataka, Andhra Pradesh, Madhya
Pradesh, Punjab, Haryana, Tamil Nadu, and Gujarat (Table 6.3). The All India
Coordinated research project on Pearl Millet (AICRP) centers pursue mandated
activities in pearl millet improvement, production, and protection. AICRP on pearl
millet has played a pioneering role in developing a diverse range of improved
breeding lines and parental lines of hybrids. These lines have been used extensively
to develop and commercialize a large number of hybrids.

6.7.2 Role of ICRISAT in Pearl Millet Research

International Crop Research Institute for the Semi-Arid Tropics (ICRISAT) started
during 1972 had key role in pearl millet improvement programmes taken up in
Indian and African countries. They conduct inter-disciplinary and partnership-based
research for the genetic improvement of its mandate crops including pearl millet.
Initial emphasis was given on: (1) developing a diverse range of trait-specific
composites, based on the germplasm largely from the Western and Central Africa;
(2) improving them by the process of recurrent selection, principally for grain yield
and downy mildew (Sclerospora graminicola [Sacc.] Schroet) resistance; and
(3) developing open-pollinated varieties (OPVs). The improved composites,
OPVs, and breeding lines derived from them were disseminated for worldwide
utilization. In 1990s, pearl millet improvement programme at ICRISAT adopted a
regional strategy, by aligning its research and breeding product development
priorities with the priorities of the regional players. In case of India, public sector
breeding programmes in the National Agricultural Research System (NARS) were
largely directed towards hybrid breeding as well as private seed companies, which
6 Pearl Millet Breeding 325

Table 6.3 List of AICPMIP centres involved in pearl millet research and extension in India
Year
S. no Name of start Research areas
1 AICRP coordinating unit Mandor, Jodhpur 1965 Breeding, Agronomy,
(Rajasthan) Pathology, statistics
2 Agricultural Research Station, SK Rajasthan 1974 Breeding, Agronomy,
Agricultural University, Jaipur (Rajasthan) Pathology, Physiology,
Entomology
3 Agricultural Research Station, SK Rajasthan 1994 Breeding, Agronomy
Agricultural University, Bikaner (Rajasthan)
4 College of Agriculture, Mahatma Phule Krishi 1995 Breeding, Agronomy,
Vidyapeeth, Dhule (Maharashtra) Pathology
5 Regional Research station, Marathwada 1974 Breeding, Agronomy,
Agricultural University, Aurangabad Pathology
(Maharashtra)
6 Millet Research Station, Junagarh 1965 Breeding, Agronomy,
Agricultural University, Jamnagar (Gujarat) Pathology, Physiology,
Entomology
7 Department of Plant Breeding, CCS Haryana 1965 Breeding, Agronomy,
Agricultural University, Hisar (Haryana) Pathology, Biochemistry
8 Regional Research Station, University of 1978 Breeding, Agronomy
Agricultural Sciences, Vijayapura (Karnataka)
9 Downy Mildew Research Laboratory, 1978 Pathology
University of Mysore, Mysore (Karnataka)
10 Agricultural Research Station, Acharya 1971 Breeding
N.G. Ranga Agricultural University,
Anantapur (Andhra Pradesh)
11 Department of millets, Tamil Nadu 1965 Breeding, Agronomy
Agricultural University, Coimbatore (Tamil
Nadu)
12 College of Agriculture, Rajmata Vijayaraje 1986 Breeding, Pathology
Scindia Krishi Vishwa Vidyalaya, Gwalior
(Madhya Pradesh)
13 Department of Plant Breeding, Punjab 1978 Breeding
Agricultural University, Ludhiana (Punjab)

were rapidly emerging as dominant players and were engaged only in the hybrid
development.
Thus, pearl millet breeding at ICRISAT, Patancheru, made a strategic shift
towards developing and disseminating a diverse range of high-yielding and downy
mildew (DM) resistant, trait-based breeding lines, and hybrid parents (seed parents
and restorer parents) while their utilization in hybrid development and commerciali-
zation was taken up by the NARS and private seed companies. Significant research
progress made in achieving genetic gain in grain and fodder yield of hybrids through
development of diverse parental lines with good agronomy and high combining
ability, utilization of alternate male sterile cytoplasm and restorers, minimizing the
severity of DM epidemics, biofortication of pearl millet with regard to grain
326 C. T. Satyavathi et al.

micronutrients, building genomic resource platform and development of basic,

strategic and applied research methodology related to pearl millet improvement.

6.7.3 Other Centers

The details of other centers and their specific research objectives are listed in
Table 6.4.

6.8 Breeding Achievements and Cultivar Development

Initially, its emphasis was on organizing research activities and conducting multilo-
cation experimental trials to identify cultivars with high grain yield and broad
adaptation OPVs by using simple plant selection and mass selection. Later, during
the l 970sand 1980s, the focus spread to the development of cultivars resistant to
biotic and abiotic stresses along with yield enhancement. After discovery of cyto-
plasmic male sterility (CMS), the focus of NARS research shifted to development of
hybrids to overcome downy mildew infestation and yield enhancement. The
AICPMIP has played a significant role in developing a diverse range of improved
breeding materials and parental lines of hybrids. These lines have been used
extensively to develop and commercialize a large number of hybrids. List of hybrids
and varieties released in India for commercial cultivation by farmers can be accessed
through the link given http://www.aicpmip.res.in/pearl%20millet%20hybrids%20
and%20varieties.pdf

6.8.1 Population Improvement and OPV Development

Due to unpredicted nature of weather, low cost of seeds, longer seed replacement
period, and greater resilience towards abiotic and biotic stresses, open pollinated
varieties (OPVs) in pearl millet are still popular amongst the farmers of India and
arid regions of Africa despite of 25–30% less yield potential to corresponding hybrid
developed for that area. In contrast to single cross hybrids of pearl millet, the intra-
population variability in pearl millet OPVs contributes to greater resilience to a
multitude of biotic and abiotic stresses. The genetic heterogeneity of OPVs offers
genetic plasticity to adjust itself against the pressure by the limiting environments
and disease epidemics (Freshley and Delgado-Serrano 2020). The genetic improve-
ment of OPVs started in the 1930s and largely concentrated on improving the yield
by mass selection and progeny testing and could not progress beyond a certain limit
because of a narrow genetic base (Yadav et al. 2013, 2021).
ICRISAT during the 1970s, introduced African germplasms especially from
Western Africa, and introgressed them with Indian germplasm to enhance the
genetic diversity of this crop. Due to such focused efforts, composites and OPVs
were developed largely based on these germplasm lines. These populations were
6 Pearl Millet Breeding 327

Table 6.4 List of some other major institutes relevant to pearl millet research
Sl.
no. Research Centre Specific objectives related to pearl millet
International level
1 Consultative Group for International Research to improve food security and
Agricultural Research, France nutrition, natural resources, and ecosystem
2 Institute of Biological, Environmental and Genome-wide association mapping of
Rural Sciences Aberystwyth University, genes related to abiotic stress, grain quality
Aberystwyth, Ceredigion SY23 3DA
3 International Atomic Energy Agency, Crop improvement by mutation breeding;
Vienna, Austria Publication of protocol for mutation
breeding in plants
4 International Center for Agricultural Germplasm characterization and
Research in the Dry Areas Beirut, Lebanon development of heat-tolerant lines
5 International Center for Tropical Maintenance of crop biodiversity;
Agriculture, Cali, Colombia co-ordination of HarvestPlus programme
6 International Food Policy Research Research on impact on various economic
Institute Washington, DC 20005–3915 policies on agricultural crops
USA
7 International Institute of Tropical Maintenance of crop biodiversity;
Agriculture, Oyo State, Nigeria networking of food and nutritional
programmes
8 International Centre for Genetic Research related to cloning and
Engineering and Biotechnology, New identification of plant genes related to
Delhi, India abiotic stress
9 Kansas State University Studies on abiotic stress tolerance in pearl
millet
10 University of Georgia, Tifton, USA Development of pearl millet cultivars,
Basic work related to fertility restoration,
apomixes, etc.
11 University of Florida and National Exploration of plant materials for deep
Aeronautic Space Agency (NASA), USA space acclimatization
12 Senegalese Institute of Agricultural Development of pearl millet cultivar for
Research (ISRA) (Institut sénégalais de drought prone areas of Senegal
Recherche Agricole), Dakar, Senegal
13 Environmental Institute for Agricultural Development of pearl millet cultivars for
Research (INERA) Institut de drought-prone areas of Burkina Faso
l’Environnement et de Recherches
Agricoles, Burkina Faso
14 Institut d’Economie Rurale (IER), Bamako, Development of pearl millet cultivars for
Mali drought-prone areas of Mali
15 Centre d’étude régional pour l’amélioration Development of pearl millet cultivars for
de l’adaptation à la sécheresse (CERAAS), drought striga and downy mildew-prone
Senegal areas of Senegal
16 Institut National de la Recherche Development of pearl millet cultivars for
Agronomique du Niger (INRAN), Niger drought striga and downy mildew-prone
areas of Niger
(continued)
328 C. T. Satyavathi et al.

Table 6.4 (continued)

Sl.
no. Research Centre Specific objectives related to pearl millet
17 Institut de Recherche pour le Basic research work on domestication
Développement (IRD), Montpellier, traits, earliness, root Phenotyping studies
France. for drought tolerance in pearl millet.
18 Beijing Genomics Institute (BGI)- Generation of genomic resources in pearl
Shenzhen, Shenzhen, China millet
19 Leibniz Institute of Plant Genetics and Generation of genomic resources in pearl
Crop Plant Research (IPK), Gatersleben, millet; wide hybridization studies in pearl
Germany millet
National level
1 Central Arid Zone Research Institute, Research
Jodhpur, Rajasthan, India
2 Central Institute of Post-Harvest Development of processing-related
Engineering and Technology, Ludhiana, protocols
India
3 Central Research Institute for Dry land Research on agricultural technology related
Agriculture, India to drylands
4 Indian Institute of Millets Research Developing improved production and crop
Rajendranagar, Hyderabad-Telangana, protection technologies in millets
India
5 Indian Agricultural Research Institute, New Research, training, extension on pearl
Delhi, India millet
6 Indian Grassland and Fodder Research Research in fodder pearl millet and related
Institute, Jhansi, India species
7 National Bureau of Plant Genetic Exploration, evaluation, conservation,
Resources, New Delhi, India genetic fingerprinting of plant genetic
resources
8 National Institute on Plant Biotechnology, Biotechnological aspects of pearl millet
New Delhi, India

also a source for the breeding lines, which were widely used over the years by both
the public and private sectors (Andrews and Kumar 1996; Rai et al. 2014). The Iniadi
germplasm, acquired from western Africa, has been extensively used in India, the
United States, and other places worldwide. Soon after their release, OPVs like
WC-C75, Raj 171, ICMV 155, ICMV 221, ICTP 8203, Pusa composites-383,
443, 612, 701, CZP 9802, and JBV 2 became very popular with farmers (Reddy
et al. 2021). In Maharashtra, a substantial proportion is still occupied by a
biofortified OPV, Dhanshakti for its grain iron content.
However, the OPV option allows only partial exploitation of heterosis. Sustain-
able improvement in grain and fodder yield through OPVs faces a major dilemma.
On the one hand, crosses between morphologically similar genotypes or lines
generate little genetic variability to sustain significant genetic gains, though the
pace in development of the OPVs will be rapid with having acceptable phenotypic
uniformity. On the other hand, utilization of genetically dissimilar lines in crossing
will create more heterotic combination and huge variability in subsequent
6 Pearl Millet Breeding 329

generations, but the population will take more generations to achieve desired
phenotypic uniformity.

6.8.2 Hybrid Development in Pearl Millet

Pearl millet displayed high degree of heterosis for grain and stover yields (Virk
1988) and attempts were made to exploit heterosis in the 1950s utilizing the
protogynous nature of flowering of this crop. The usual method at that time for
production of hybrid seeds was growing the parental lines in mixture and allowing
them to cross-pollinate. The resultant seed contained approximately 40% hybrid
seed when the two parental lines had synchronous flowering at about same time.
These chance hybrids thus produced, out-yielded local varieties by 10–15%. How-
ever, they could not become popular due to their limited yield advantage over OPVs,
narrow range of adaptation and lack of seed production programmes. Exploitation of
heterosis is the most efficient means for enhancing the productivity. Work on hybrid
development in India started in the early 1950s and chance hybrids were released in
Maharashtra and Tamil Nadu in the 1950s. Due to limited hybrid seed production,
hybrids could not be cultivated at commercial scale. This limitation was overcome
by the discovery of cytoplasmic male sterility by Burton in 1958.
The first male sterile line, Tift 23 A, was developed using Tift 23 B as a recurrent
parent and was released in 1965 (Burton 1965). The above-mentioned limitations in
the exploitation of heterosis were circumvented with the discovery of cytoplasmic
nuclear male sterility and release of male-sterile lines Tift 23A and Tift 18A in early
1960s at Tifton Georgia, USA. These lines were made available to Indian breeding
programmes. The male-sterile line Tift 23A containing Tifton male sterile cytoplasm
(A1) was extensively utilized, both at the Punjab Agricultural University and the
Indian Agricultural Research Institute, because of its short stature, profuse tillering,
uniform flowering, and good combining ability. This laid the foundation of pearl
millet hybrid breeding in India. The demonstration of the first commercial pearl
millet grain hybrid HB-1, developed by Punjab Agricultural University (PAU),
Ludhiana, and released in India in 1965, had twice much grain yield as the then
improved OPVs (Athwal 1965) boosted the shift in research and adoption of the
single cross hybrids over the OPVs.

6.8.3 Different Phases of Pearl Millet Hybrid Improvement in India

There have been four conspicuous phases in hybrid development in India in which
rate of improvement in grain yield in kg/ha/year during each phase (Singh et al.
2014; Yadav et al. 2019) is given by Fig. 6.4. The details regarding the four phase of
pearl millet improvement is given below.
330 C. T. Satyavathi et al.

Fig. 6.4 Snapshot depicting increasing trends in pearl millet grain productivity during India’s four
phases of hybrid improvement, with numbers inside the figure indicating the rate of grain yield
improvement in kg/ha per year for each phase

6.8.3.1 Pre-hybrid Phase (1950–1966)

The Indian Council of Agricultural Research (ICAR) was the first institution to take
up the responsibility of pearl millet crop improvement in India. During the early
1940s and 1950s, research was sporadic and mainly aimed to improve productivity.
Some periodic efforts were made in the 1940s towards varietal improvement through
simple mass selection from locally adapted material aimed at improvement of yield.
As a result, varieties like Vansari, Kopargaon Local, N 28–15–1, Co 1, K 1, Co 2, Co
3, AKP 1, AKP 2, RSJ, RSK and T 55 were developed and released. The same
method was used with African populations, which resulted in the development of S
530 and Pusa Moti. In order to exploit heterosis, attempts were made to breed chance
hybrids: The hybrids thus produced were released in India in the early 1950s (X1,
X2, X3) and they outperformed local varieties by 10% in terms of yield. But these
hybrids and improved varieties did not become popular because of their limited
productivity, narrow range of adaptability, and lack of seed production programmes.
Overall, there have been four phases in the development of pearl millet improved
cultivars in India, covering a period of 60 years. During the pre-hybrid phase
(1950–1966), improvement efforts largely concentrated on local traditional landrace
materials and carried out simple mass selection. This resulted in the development
and release of a total of 13 improved cultivars (3 hybrids and 10 OPVs). The average
6 Pearl Millet Breeding 331

improvement in pearl millet productivity during this period was 4.5 kg/ha per
annum.

6.8.3.2 Second Phase (1967–1983)

During this phase, hybrid breeding received a major impetus when cytoplasmic male
sterility (CMS) was discovered. Broadly, there have been three conspicuous phases
of pearl millet hybrid development in India. ICAR established the AICMIP in 1965
to conduct intensive and systematic research on millets. The project played a
pioneering role in developing a diverse range of improved breeding lines and
parental lines of hybrids, conducting multilocation trials and commercializing a
large number of hybrids. Later, the project also developed production and protection
technologies specific to agro-ecological regions in different states. Male sterile lines
Tift 23A and Tift 18A were released in the early 1960s. This laid the foundation for
pearl millet hybrid breeding in India. At the same time, two additional male sterile
lines, L 66A and L 67 A, were developed at Ludhiana. The male sterility line Tift
23A was extensively utilized because of its short stature, profuse tillering, uniform
flowering, and good combining ability. The first hybrid HB 1 was released in 1965
followed by HB 2, HB 3, HB 4, and HB 5.
During this period, 16 hybrids and 13 varieties were developed, and India
enjoyed the privilege of being the first country to release pearl millet hybrids.
Most of the hybrid releases dominated the cropped acreage during that period.
Amongst the hybrids of the HB series, HB 3 became the most popular because of
its shorter maturity, bold grain, and adaptability to moisture stress conditions.
Adoption of these hybrids led to a 75–100% increase in yield over local cultivars
and boosted production from 3.5 million tons in 1965 to a record 8.0 million tons in
1970. In the initial years of pearl millet research after ICRISAT was established in
1972, the emphasis was more on population improvement and development of OPVs
rather than hybrids and hybrid parents (Kumara et al. 2014). Overall, there was only
a modest increase (6.6 kg/ha per year) in pearl millet productivity during this phase.

6.8.3.3 Third Phase (1984–2000)

In third phase of the development of pearl millet improved cultivars in India, the
recurring problem of downy mildew epidemics that had been affecting hybrids till
1980 led to strengthening of research on genetic diversification of hybrid seed
parents. As a result, large number of genetically diverse male sterile lines were
developed and utilized in hybrid breeding programmes. With hybrids based on Tift
23A succumbing to downy mildew, another male sterile line 5071A, bred at IARI,
Delhi, by mutational change from Tift 23A and showing less downy mildew
incidence, was utilized. Three hybrids, NHB 3, NHB 4, and NHB 5, were developed
from this line but they did not become popular because of their low yields and
continued susceptibility to downy mildew. They were cultivated for not more than a
year or two. Two more male sterile lines were developed and made available from
Tift 23A. These lines, 5141A and 5054A, had good downy mildew resistance and
were widely used. The hybrids BJ 104 and BK 560 (5141A) and CJ 104 (5054A)
332 C. T. Satyavathi et al.

were widely cultivated during 1977–1984. Hybrids based on 5141A were phased out
in 1985 due to susceptibility to the downy mildew.
From the mid-1980s, the private sector started participating actively in pearl
millet crop development and seed distribution. A major driver of this spurt in private
sector participation was the strong public sector research support programme and
supply of breeding material from national and international institutions. However,
the partnership between ICRISAT, national institutes, and the private sector
remained informal and passive. It was in the 1990s that ICRISAT changed its
research focus from OPV development to hybrid parent development in alignment
with the regional priorities of the NARS and the rapidly expanding private seed
sector. A total of 38 hybrids and 16 OPVs were released during this period. Downy
mildew was largely contained by using the genetic diversity of pearl millet. A critical
analysis of the situation reveals that the absence of long-lasting resistance to downy
mildew amongst hybrids was primarily due to the lack of diversity in their parental
lines. This was due to the fact that most of the hybrids were based on Tift 23A and
then on 5141A and 5071A.
Similarly, the same pollinators were also repeatedly used in combinations with
different male sterile lines. For example, J 104 was used in four hybrids, K 560–230
in three, and K 559 in two hybrids. Thus, the outbreaks of downy mildew in hybrids
were due to the use of a limited number of parental lines in hybrid breeding rather
than the cytoplasm linked susceptibility (Yadav et al. 1993). Much greater efforts are
now being made in developing genetically diverse male sterile lines. As a result, a
large number of male sterile lines with A1 source of cytoplasmic male sterility
(CMS) have been used in hybrid breeding. In addition, CMS sources other than
A1 have also been used. The average productivity has been enhanced to about
19.0 kg/ha per annum during this period.

6.8.3.4 Fourth Phase (2001–2020)

During the fourth phase, greater emphasis was placed on genetic diversity by using a
larger number of highly diverse seed and pollinator parents in hybrid development
and targeting adaptation to specific niches in different zones. The highest number of
cultivars (81 hybrids, 20 varieties) was released during this period. The hybrids
released during the last decade were based on more than 12 generally diverse male
sterile lines and a large number of diverse pollinators. Moreover, several hybrids
developed by the private sector in its sound and well-established research and
development programmes further helped in diversifying the genetic base of hybrids.
Consequently, the problems of downy mildew epidemics were kept largely under
control. As a result, improvement in grain productivity further increased to 31.1 kg/
ha per year.

6.8.3.5 Hybrid Development at a Glance from 1950 to 2021

One-hundred-eighty hybrids were released in India from 1950 to 2021. Forty-two
hybrids during 2015–2021; 35 hybrids during 2009–2014, 14 during 2004–2008,
17 during 1999–2003, 22 during 1994–1998, 11during 1989–1993, 14 during
1984–1988, 7 during 1979–1983, 10during 1974–1978, 5 during 1969–1973, and
6 Pearl Millet Breeding 333

3 hybrids during 1950–1957 were released by both public and private sector (Kumar
et al. 2020b).

6.8.4 Search for New Sources of CMS and Male Fertility Restorers
in Pearl Millet

Large-scale use of the single A1 CMS source during the 1960s in all the hybrids had
raised concern regarding its potential vulnerability to diseases and insect pests. As a
result, continuing efforts were made to search for alternate CMS sources. This led to
identification of A2 and A3 CMS sources from genetic stocks and their derivatives
(Athwal 1961, 1966); Av and A4 CMS sources from P. glaucum sub-species
monodii (violaceum) accessions (Marchais and Pernes 1985; Hanna 1989); and
Aegp and A5 CMS sources from gene pools (Sujata et al. 1994; Rai 1995). Based
on the differential male fertility restoration of hybrids using common restorers, it has
been established that the A1, A2, A3, Av, A4, and A5 were distinctly different CMS
system. Enormous differences in downy mildew incidence amongst male sterile
lines based on Tift 23A, cytoplasm indicates that the cytoplasm is not associated
with downy mildew susceptibility, and that it is nuclear gene resistance which is
important. Experimental evidence confirms this assumption (Kumar et al. 1983).
Thus, at present, there is no need to be alarmed about the vulnerability of Tift 23A1
cytoplasm to downy mildew. However, in the long run, the large scale and continu-
ous use of a single cytoplasm source runs the risk of it becoming vulnerable to
existing or unforeseen diseases. Hence, there is a need to diversify the cytoplasmic
base of male sterile lines. Later discovery of A4 and A5 CMS system marked new
landmark in heterosis breeding in pearl millet. These CMS systems were found most
stable and imparting better fodder yield than corresponding counterparts. But their
utilization is limited by shortage of their restorer lines. Later mapping of theses
restorer genes were carried out (Pucher et al. 2018; Thribhuvan 2020) using molec-
ular markers. Theses gene linked markers can serve as tool for diversification of
pearl millet parental lines.

6.8.5 Breeding for Climate Change Resilience in Pearl Millet

Pearl millet meets the food and nutritional securities for resource-poor farmers of
arid and semi-arid tropics. It is such a hardy crop that other major cereals fail to grow
and survive. Usually such areas are affected by low soil moisture stress due to
limited level and untimely rainfall, poor soil nutrient status, salinity, high
temperatures, crust formation, etc. which badly affects the productivity of the crop
and its grain quality. Looming climate changes makes environmental stresses even
more prominent (Porfirio et al. 2018). Since, each environmental stress mentioned
below have different genetic basis, proper breeding strategies need to encompass to
address them.
334 C. T. Satyavathi et al.

6.8.5.1 Breeding for Drought Resistance

Drought is the most serious abiotic stress limiting the pearl millet productivity. Even
though pearl millet has low water requirement of 350 mm when compared to other
main cereal crops, rice (1250 mm) and wheat (450 mm) (Ullah et al. 2017), low soil
moisture at seedling stage can result in poor crop establishment and at reproductive
stage can results in spikelet sterility leading to reduction in grain number and grain
size reduction due to reduction in grain filling period which ultimately reflects in
reduced grain and fodder yield (Meena et al. 2021; Gupta et al. 2015). Studies on
drought tolerance are very complicated because of uncertain nature of duration and
intensity of dry spells and due to control under quantitative traits (Shivhare and Lata
2017). Hence, devising the screening methods for breeding for drought should be
simple and reproducible for the target environmental conditions. Several drought
screening methods such as screening germplasm using in vitro techniques with PEG
treatment (Govindaraj et al. 2010), split plot technique/pot experiment in which a set
of lines were given ample irrigation and withholding irrigation in another set
containing same genotypes (Kholová et al. 2016; Choudhary et al. 2020), use of
lysimeter (Vadez et al. 2013) and LeasyScan facility (Chaudhary 2020), employing
rainout shelters (Ausiku et al. 2020) and multilocation screening of germplasms and
breeding lines across drought-prone areas (Varshney et al. 2017). Various indicator
traits are identified which are associated which explains the drought resilience in
pearl millet such as high seedling growth and rapid canopy development (Vadez
et al. 2015), early flowering (Bidinger et al. 1987), low threshing percentage and
panicle harvest index (Bidinger 2002), low transpiration rate at high atmospheric
evaporative demand (Kholova et al. 2010; Choudhary et al. 2020), involvement of
specific aquaporins (Tharanya et al. 2018), high level of leaf abscisic acids and
proline content (Vadez et al. 2015; Jaiswal et al. 2018), etc. Researchers could
identify various genotypes and germplasms could serve as donor for imparting
drought tolerance in pearl millet. The most studied and exploited one is PRLT
2/89–33 (Serraj et al. 2005) harbouring DT-QTL at LG-2 regulating the ionic uptake
Na+ by roots. Others were CZP 9802, 863B, ICMP 83720, ICMV 9413, and ICMV
94472 (Shivhare and Lata 2017) which serves as promising genotypes for breeding
for drought tolerance in pearl millet.

6.8.5.2 Breeding for Seedling and Terminal Thermotolerance

Optimum temperature required by pearl millet for its germination, seedling emer-
gence and for photosynthesis is ~35
C (Garcia-huidobro et al. 1982) which indicates
its inherent capacity to survive in hot regions of Sahel and Thar deserts when
compared to other staple food crops. But high soil temperatures higher than 45
C
lead to heat girdling in pearl millet which apparently block the phloem prevent the
channelling of carbohydrate to roots (Peacock et al. 1993). Further, the high temper-
ature of seedbed has been established as a major cause of poor plant stand in pearl
millet (Ong 1983). Various studies suggested existence of huge genetic variance for
seedling thermotolerance in pearl millet (Sankar et al. 2014; Yadav et al. 2011;
Sankar et al. 2021a). Field screening techniques for heat tolerance include the
6 Pearl Millet Breeding 335

seedling thermo-tolerance index (STI) (Peacock et al. 1993) and seed-to-seedling

thermo-tolerance index (SSTI) (Yadav et al. 2011, 2013).
Howarth et al. (1997) developed laboratory-based screening methodology based
on membrane stability index (MSI) for identification of thermo-tolerant genotypes
amongst large number of germplasm and breeding lines. Accessions IP 3201
(Howarth et al. 1997), inbreds H77/833–2, 99HS-18, CVJ-2-5-3-1-3, 96AC-93,
Togo-II, G73-107, and (77/371  BSECT CP-1) (Yadav et al. 2014), MS 841B
(James et al. 2015; Maibam et al. 2020), and WGI 126, TT-1 (Sankar et al. 2021a)
are screened as heat tolerant at seedling stage. There is growing trend in summer
cultivation of pearl millet in regions of Gujarat, Rajasthan, and Uttar Pradesh where
high temperatures (>42
C) are of common occurrence during flowering. As similar
to seedling thermotolerance, variation for supra-optimal temperature tolerance was
observed while screening lines at reproductive stage. Genotypes such as ICMB
92777, ICMB 05666, ICMB 02333, IP 19877 showed less spikelet sterility (Gupta
et al. 2015) and PI526279 and PI307704 showed higher pollen germination under
high temperature stress given under growth chamber (Djanaguiraman et al. 2018). A
few hybrids from some of the seed companies (e.g. 86M64 and Proagro 9444) were
found to have good yield under summer cultivation in India.

6.8.5.3 Breeding for Salinity Tolerance

Soil salinity as well as irrigation with brackish water affects large areas of West Asia
and North Africa (WANA) zones and in India, especially states of Rajasthan,
Haryana, Punjab, and UP. It can cause around 33% reduction in grain yield. As
compared to other cereal crops, only limited information is available on response to
soil salinity in pearl millet. Reduced shoot N content and increased K+ and Na+
content is usually associated with salinity tolerance in pearl millet (Dwivedi et al.
2012). According to Krishnamurthy et al. (2007), shoot-biomass ratio associated
with salt tolerance and shoot Na+ concentration could be used as potential selection
criteria for screening of pearl millet germplasm at vegetative stage.
Accessions such as 93,613, KAT/PM-2, Kitui, Kitui local, 93,612; 10,876,
10,878, 18,406, 18,570; IP 3757, 3732; Birjand pearl millet; IP 6112; IP 3616,
6104, 6112; ZZ ecotype found to be tolerant to salinity (Pattanashetti et al. 2016).
Raipuria (2012) conducted pot experiments with 21 genotypes of pearl millet, in
which 10 seeds of each genotype were planted in pots 12 cm high and 8 cm diameter
(12  8 cm). The pots were irrigated at with varying NaCl solutions levels (50, 100,
150, and 200 mM) on alternate days. Observations were taken for shoot length,
germination percentage, root length, root shoot length ratio, fresh and dry root and
shoot weight, root shoot dry weight ratio, and seedling vigour index (Fig. 6.5a, b). Of
the 21 genotypes studied, genotypes D 23 and DPR 18 exhibited salinity tolerance
with good seedling vigour index and other seedling parameters tested (Fig. 6.5c, d).
Pearl millet variety ‘HASHAKI 1’ is a good forage variety and has been released in
2012 for saline areas like Uzbekistan (Fig. 6.5e).
336 C. T. Satyavathi et al.

Fig. 6.5 Salinity stress tolerance studies in Pearl millet (a) Screening of pearl millet at different
level of NaCl induced salinity under controlled conditions (b) Performance of salinity tolerant pearl
millet genotype DPR-18 seedlings at different concentrations of NaCl. (c) Field view of DPR-18 (d)
Field view of D-23 (e) Field view of “HASHAKI 1”. (Photo source: Kristina Toderich)

6.8.5.4 Breeding Pearl Millet for Better Nutrient Use Efficiency

Semi-arid and arid regions are characterized by poor soil conditions with either
limiting plant nutrients or present in unavailable form. Application of excess fertil-
izer to a nutrient irresponsive genotype makes economic loss to farmers as well as
lead to various environmental concerns (Móring et al. 2021). Moreover, the sources
of fertilizers especially phosphorus and potassium are under depletion (Manschadi
et al. 2014). Hence, breeding effort needs to concentrate in research and develop-
ment towards highly yielding and nutrient-efficient genotype. Nutrient use efficiency
(NUE) is defined as the ability to produce economic yield per unit soil nutrients
applied. NUE mainly depends on the results of two main processes, such as uptake
efficiency and utilization efficiency. The understanding of grain yield response and
its associated NUE traits performance is still largely lagging in the pearl millet
diversity panel. However, few studies have explored genotypic variations for NUE
at different levels of nutrients. In one such report, 20 diverse pearl millet genotypes
and few high-yielding hybrids were screened under field conditions at two Nitrogen
levels (Alagarswamy and Bidinger 1987). Recently, ICRISAT screened the germ-
plasm panel to identify the genotypes and QTLs associated with higher NUE, could
identify 25 Nitrogen-insensitive genotypes. Amongst which, Genotypes IP 10820,
6 Pearl Millet Breeding 337

IP 17720, ICMB 01222-P1, IP 10379, ICMB 89111-P2, IP 8069, ICMB 90111-P2,

ICMV-IS 89305, and ICMV 221 proved to be the most efficient genotypes in terms
of grain yield at low and high N2 levels, and indeed shows their inherent genotypic
plasticity toward N2 application (Pujarula et al. 2021). Similarly, strategic research at
ICRISAT in the Western and Central African region has been initiated to identify
QTLs for enhanced phosphorous efficiency and to examine the stability of their
expression across the genetic backgrounds and the environments (Gemenet et al.
2015, 2016).

6.8.6 Addressing Emerging Biotic Constraints

In comparison to other major cereals, pearl millet is a very hardy crop with few
diseases and insect pests. The diseases that affect pearl millet, on the other hand, are
capable of wreaking havoc. Amongst 111 diseases reported on pearl millet in India
and Africa, downy mildew, foliar blast, rust, smut, ergot, and damage due to Striga
are important. Downy mildew is important in India and to some extent in western
Africa, and Striga is important in western Africa. Being a crop grown by resource-
constrained farmers, diseases and pests can be best managed through host plant
resistance (HPR).

6.8.6.1 Downy Mildew

Downy mildew or ‘green ear’ caused by Sclerospora graminicola (Sacc. Schroet.) is
one of the most devastating disease of pearl millet causing maximum yield loss in
India and Africa (Kumar et al. 2013). Downy mildew attacks plants results in general
stunted and often undergo a transformation of flower organs into leaves (phyllody or
witches’ broom), and their effects may range from mild symptoms to catastrophes
when large fields have been destroyed (Fig. 6.7a). The disease was first reported in
India and was considered of minor importance till 1970 when HB3, a popular Indian
pearl millet hybrid suffered severe yield loss from approximately 8.2 million metric
tons in 1970–1971 to 4.6 million metric tons in 1971–1972 due to downy mildew
epidemic (Dwivedi et al. 2012; Kumar et al. 2013). There is clear evidence that the
A1 cytoplasm is not associated with susceptibility or resistance (Kumar et al. 1983).
There is ample evidence for nuclear genes controlling resistance to this disease.
Except in one case, where resistance was reported to be recessive (Singh et al. 1978),
reports generally confirm that resistance is inherited as a dominant trait and variation
in segregating populations is continuous (Singh 1995). In a few cases where clear
Mendelian segregations has been observed, the number of dominant genes
governing resistance has been one or two (Deswal and Govila 1994). Quantitative
inheritance studies have been more successful, and non-additive gene action is
responsible for much of the heritable variability (Tyagi and Singh 1989; Deswal
and Govila 1994; Kataria et al. 1994). Such non-additive gene action can contribute
substantially to general combining ability (GCA), since parents having dominant
resistance can be expected to have high GCA for this trait when compared to more
susceptible parents.
338 C. T. Satyavathi et al.

Due to concentrated effort done by ICRISAT towards diversification of nuclear

background with periodic monitoring of advanced breeding progenies with the help
of glass house and field sick plot methods, finally derived B-lines and R-lines
resistant to this disease (Rai et al. 2014). Several putative QTL have been identified
that determine a significant proportion of DM resistance in pearl millet (Jones et al.
1995; Breese et al. 2002; Jones et al. 2002; Satyavathi et al. 2016; Chelpuri et al.
2019). Integrated conventional and marker-assisted back-crossing was taken up to
introgress DM resistance QTL from sources IP 18293 and P 1449-2 into the genetic
backgrounds of maintainer lines 81B, 843B, and PT 732B advanced by a generation
following screens against highly virulent pathogen isolates from Patancheru and
New Delhi. Resistance alleles at two DM QTL, one each on linkage groups 1 (LG1)
and 4 (LG4) were added to the male parent (H77/833-2) of widely grown hybrid
HHB 67 through marker-assisted back crossing from the resistance donor ICMP
451, and a DM resistant version was released as ‘HHB 67 improved’ (Yadav and Rai
2013).

6.8.6.2 Foliar Blast

Foliar blast caused due to Magnaporthe grisea took over as the major and top
priority disease in case of pearl millet in India (Sankar et al. 2021b). It is widespread
in different pearl millet-growing ecologies of India but became a very serious threat
in both A1 and A zones, where early- to medium-maturing cultivars are preferred
(AICRP-PM 2020). The disease starts out as a small speck or lesion that grows larger
and necrotic, causing widespread chlorosis and premature death of young leaves
(Fig. 6.6). Lesions can appear as diamond-shaped white to gray or reddish-brown
lesions near the leaf tips or margins, or both with reddish to brown borders that
extend down and may enlarge, coalesce, and kill entire leaves (Nayaka 2021).
Inheritance studies suggest the foliar blast resistance is governed by single dominant
gene in P glaucum (Gupta et al. 2012; Mallik et al. 2021). But wild accession of
P. glaucum subsp. monodii is reported to have three independent dominant resis-
tance genes (Hanna and Wells 1989), and four landraces from Burkina Faso each had
independent dominant resistance genes (Wilson et al. 1989). Sharma et al. (2020a)
identified 17 accessions belonging to P. violaceum (Lam.) Rich found as highly
resistant to foliar blast. Amongst two blast resistant accessions, namely IP 21544 and
IP 21720, and four cultivated pearl millet genotypes [one germplasm line (IP 22269),
one forage variety (ICMV 05555), and two hybrid parents (ICMB 94555 and ICMB
97111)], four advanced backcross populations were developed for multi-institutional
evaluation of blast-resistant breeding lines (Sharma et al. 2020b).

6.8.6.3 Breeding for Striga Resistance

Striga spp., S. hermonthica (Del.) Benth. and S. asiatica (L.) Kuntze, known as
witch weeds, are one of the most troublesome and damaging weeds affecting pearl
millet in western and central Africa (Parker 2009). About 40% of the cereal
producing area is severely infested with Striga and grain yield losses can go up to
100% in sub-Saharan Africa (Kountche et al. 2013). Similar to other biotic
constraints, breeding for striga-tolerant genotypes is most economic and central
6 Pearl Millet Breeding 339

Fig. 6.6 Symptoms of foliar blast on infected pearl millet plants. (a) Infected leaves. (b) Sheath
and stem infection. (c) Infected plants along with resistant lines. (d) Conidia of Magnaporthe grisea.
(Photo source: Sankar et al. 2021b)

approaches in their management. Only vague information on inheritance of striga

tolerance in pearl millet is existing and mostly suggests the partial dominance nature
(Wilson et al. 2000, 2004). Since 2006, the ICRISAT in Niger, in partnership with
the national agricultural research programme in Mali (Institut d’Economie Rurale,
IER), has conducted recurrent selection in a diversified pearl millet genepool to
increase the frequency of desirable alleles for Striga and downy mildew resistance
and panicle yield (Kountche et al. 2013) thereby considerable improvement in the
striga resistance in landraces such as M141, M239, M029, M197, M017, and KBH
were made possible. Moumouni et al. (2015) constructed genetic linkage map of
SNP markers together with SSR markers using a segregating population derived
from a cross between a wild relative, resistant to Striga (Wilson et al. 2004), and a
cultivated-susceptible pearl millet parent and the underlying QTLs were identified.
This material will serve as excellent breeding source for the development of Striga-
resistant genotypes through marker-assisted selection.

6.8.6.4 Other Minor Biotic Constraints

Other biotic constraints have received relatively low priority in breeding
programmes targeted at the semi-arid tropical regions of Asia and Africa. These
can be grouped into two categories. The first category includes ergot (Claviceps
340 C. T. Satyavathi et al.

fusiformis Lov) and smut (Moesziomyces penicillariae [Bref.] Vánky), diseases of

pearl millet; for these, good resistance sources and effective screening techniques
have been developed (Thakur et al. 2011). However, these have been shown not to
have as large an impact on yield, on as large a geographical scale. Also, some of
these can, to some extent, be managed by other means, for instance, by breeding for
improved male fertility restoration in hybrids and by resorting to alternative cultivar
options (e.g. OPVs, top-cross hybrids, and protogyny-based single-cross hybrids
wherein seed is produced using protogynous flowering rather than by male-sterile
seed parents) can be effective in reducing ergot and smut severity in pearl millet).
Simply inherited recessive ‘tr’ allele, which conditions trichomelessness to most
aboveground parts, including stigmas, confers a useful degree of smut resistance.
Rust of pearl millet is of minor importance as it generally occurs after the grain-
filling stage. Rust resistance has been demonstrated to be under the control of a
single dominant gene (Andrews et al. 1985). One major QTL present on LG1
explaining 58% of total phenotypic variance has been identified for rust resistance
but their deployment in the parental lines is yet to begin (Ambawat et al. 2016).
The second category includes stem borers of pearl millet (Coniesta ignefusalis
Hampson); and head miner (Heliocheilus albipunctella de Joannis) for which con-
firmed sources of good resistance are not available and (or) the trait inheritance is too
complex to permit its effective utilisation in breeding. This category has received
little attention in breeding programmes in Asia and Africa. The details of biotic stress
resistant pearl millet genotypes are given in Table 6.5.

6.8.7 Development of Genetic and Genomic Resources in Pearl

Millet

Genetic and genomic resources and tools will be the raw materials for futuristic pearl
millet improvement approaches towards mitigating the crisis of ever-increasing food
and fodder yield, nutritional security, and sustainable crop production. Some of such
genetic and genomic resources and tools are briefly discussed relating to its devel-
opment and utilization in understanding pearl millet genetics and their use in pearl
millet improvement.

6.8.7.1 Markers, Mapping Population, and Genetic Linkage Maps

Genomic resources such as DNA-based molecular markers, genetic linkage maps,
and sequence information on gene are a prerequisite to conduct any genetic studies
or marker-aided breeding programme in any crop. The first key milestone was laid
with the use of RFLP as molecular tool for the development of a linkage map of pearl
millet (Liu et al. 1994). In subsequent years, AFLP, RAPD, expressed sequence
tag-based (EST) markers, sequence-tagged sites (STSs), simple sequence repeat
(SSRs/microsatellites), DArTs, CISP, SSCP-SNP, and NGS-based SNP genotyping
have been developed to distinguish genetic variability, linkage map analysis, and
marker-assisted screening to expedite the breeding programmes (Devos et al. 1995;
Allouis et al. 2001; Gale et al. 2001; vom Brocke et al. 2003; Qi et al. 2004; Bertin
6 Pearl Millet Breeding 341

Table 6.5 Biotic stress-resistant genotypes available in pearl millet

Biotic agents Resistant genotypes References
Downy mildew ICML 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 Thakur et al. (1982, 1992),
(Sclerospora ICMPE 13-6-30, 134-6-9, 134-6-34, Willingale et al. (1986), Thakur and
graminicola) 13-6-27, 37, 71; ICMA 92666, King (1988a, b), Rai et al. (1998a),
ICMB 92666, ICMA 91333, 91444, Khairwal and Yadav (2005),
91555 (resistant to downy mildew, Satyavathi et al. (2016) and Chelpuri
smut and ergot), WGI 52, WGI et al. (2019)
148, ICMR 09999, ICMB 89111-
P6  ICMB 90111-P6
Blast IP 7846, IP 11036, IP 21187, IP Sharma et al. (2013, 2020a, b) and
(Magnaporthe 4291, IP 15256, IP 22449, IP 5964, Sankar et al. (2021b)
grisea) IP 11010, IP 13636, IP 20577, IP
5964, IP 11010, IP 13636, IP 21525,
IP 21531, IP 21536, IP 21540, IP
21594, IP 21610, 21,640, IP 21706,
IP 21711, IP 21716, IP 21719, IP
21720, IP 21721, IP 21724, IP
21987, IP 21988, IP 22160, IP
21544, IP 21720, IP 22269, IP
21544, IP 11353, IP 22423, IP 7941
Rust (Puccinia IP 16438, IP16762; P310-17, P1449- Singh et al. (1997), Khairwal and
spp.) 3; IP18292, IP18293, IP700651; Yadav (2005), Thakur et al. (2006),
ICML 12 to 16, 22; ICMP 312, 423, Sharma et al. (2007, 2020b) and
85410; 7042S; 841A; IP 9, 55, Ambawat et al. (2016)
104, 262, 253, 346, 336, 498,
545, 558; landraces like Desi Bajri-
Chomu, Dhodsar local, Ardi-Beniya
Ka Bas, 81B-P6, ICMP 451-P8, IP
21629, 21645, 21658, 21660, 21662,
21711, 21974, 21975, and 22038
Smut ICML 5 to 10; ICML 17 to 21; Tif Bourland (1987), Thakur and King
(Moesziomyces leaf 3; Tift 3 (PI 547035) and Tift (1988a), Wilson and Burton (1991),
penicillariae) 4 (PI 547036); Tift 65 (resistant to Burton and Wilson (1995) and
leaf spot and rust) Hanna et al. (1997)
Ergot ExB 46-1-2-S-2, ExB 112-1-S-1-1, Thakur and King (1988c), Yadav
(Claviceps ICMV 8282, 8283; ICMA 88006A and Duhan (1996), Rai et al. (1998b)
fusiformis and 88006B (resistant to downy and Khairwal and Yadav (2005)
mildew and smut); ICMA 91333 to
91555; ICML 5 to 10; SSC FS
252-S-4, ICMPS 100-5-1, 700-1-5-4,
900-1-4-1, 900-3-1, 900-9-3, 1300-
2-1-2, 1400-1-6-2, 1500-7-3-2,
1600-2-4, 1800-3-1-2, 2000-5-2; ICI
7517-S-1, ExB 132-2-S-5-2-DM-1,
P-489-S-3; SSC 46-2-2-1, SC 77-7-
2-3-1, SSC 18-7-3-1

et al. 2005; Senthilvel et al. 2008; Supriya et al. 2011; Sehgal et al. 2012; Rajaram
et al. 2013; Srivastava et al. 2020a, b; Singhal et al. 2021). Currently, application of
NGS-based sequencing platform such as GBS, RAD-seq, etc. are gaining popularity
342 C. T. Satyavathi et al.

for its rapid, high density genome coverage and low-cost marker development, and
genotyping platform (Shivhare et al. 2020a, b). These genetic tools have also been
used for diversity assessment (Liu et al. 1992; Bhattacharjee et al. 2002), studying
recombination rates (Busso et al. 1995; Liu et al. 1996), analysing domestication
syndrome (Poncet et al. 2000, 2002), and comparative genetics (Gale and Devos
1998).
Another key genomic resource is mapping population and the molecular linkage
maps. A mapping population is a genetic tool used to develop genetic maps, which
can be used later for gene/QTL mapping studies. Different types of mapping
populations may be used for linkage map development and QTL mapping, each
population type having advantages and disadvantages (Singh and Singh 2015). The
first linkage map based on RFLP marker used an inter-varietal F2 population (Liu
et al. 1994). The first integrated map was constructed using four F2 populations
developed from LGD  ICMP 85410, 81B  ICMP 451, ICMB 841  863B, and
PT 732B  P1449-2 crosses (Qi et al. 2004). The F2 population of the ICMB
841-P3  863B-P2 cross was also used to integrate a newly developed SSR marker
in previous maps (Senthilvel et al. 2008).
Subsequently, RILs were used for genetic linkage mapping of pearl millet
genome. RILs developed from Tift23DB x PI536400 cross (Pedraza-Garcia et al.
2010), H 77/833-2  PRLT 2/89-33 (Supriya et al. 2011), H77/833-2  PRLT 2/
89-33 (Sehgal et al. 2012) crosses were used for genetic linkage mapping. Four RILs
populations developed from ICMB 841-P3  863B-P2, H 77/833-2  PRLT 2/89-
33, 81B-P6  ICMP 451-P8, and PT 732B-P2  P1449-2-P1 were used to construct
a consensus linkage map (Rajaram et al. 2013). An F2 population of a cross between
wild pearl millet (116_11-(PS202-14)-121) and a cultivated pearl millet (SOSAT-
IBL-197) was also used to map high density map (Moumouni et al. 2015). Two
downy mildew QTLs were mapped using genome-wide SSR and AFLP markers
while phenotyping a RIL mapping population derived from the parents, WGI 52 and
WGI 148, against S. graminicola Delhi isolate (Sg561). Similarly, the RIL popula-
tion derived from the parents WGI 148 X ICMR 09999 exhibited four QTLs on
LG1, 3 and 5 and two QTLs imparting resistance when screened against the
Rajasthan isolate (Sg384) and the Gujarat Banaskanta isolate (Sg445), respectively
(Fig. 6.7b–e; Satyavathi et al. 2016). Punnuri et al. (2016) developed 96-plex ApeKI
GBS library from the 186 RILs and from their parents (‘Tift 99D2B1’ and ‘Tift 454’)
and F1 population. DNA of these populations was sequenced and the results were
used for the development of reference genetic map using 150 RILs that contained a
total of 16,650 SNPs and 333,567 sequence tags spread across all seven pearl millet
chromosomes.
The final map has a genetic distance of 716.7 cM with 23.23/cM overall average
density of SNPs and 1.66 unique linkage bins per cM. This map was further used in
mapping QTLs for flowering and resistance to Pyricularia leaf spot disease in pearl
millet. Kumar et al. (2018b) used another population to construct a genetic linkage
map with DArT and SSR markers using 317 RIL progenies derived from the (ICMS
8511-S1-17-2-1-1-B-P03  AIMP 92901-S1-183-2-2-B-08) cross. Recently, same
mapping population was utilized to agronomic traits by Kumar et al. (2021b) on
6 Pearl Millet Breeding 343

Fig. 6.7 QTL mapping for downy mildew resistance and MAS in pearl millet. (a) Symptoms of
downy mildew on infected pearl millet plants. (b) Sporangia on infected leaves. (c and d) Screening
biparental population for DMR through artificial inoculation. (e) Linkage map construction and
QTL mapping (Satyavathi et al. 2016) (f) Field view of HHB 67 improved at ICRISAT

seven linkage groups. To circumvent the problems of segregation distortion and

masking of minor-effect alleles/QTLs, a set of chromosome segment substitution
lines (CSSLs) for all the seven LGs was developed by introgression of overlapping
chromosome segments from 863B line into the genetic background of elite ICMB
841 line (Kumari et al. 2014). These are valuable genetic stocks for minor-effect
QTL detection, fine mapping, and trait mechanism studies, especially for complex
traits in pearl millet. The second-generation mapping populations such as nested-
association mapping (NAM) and multi-parent advanced generation inter-cross
(MAGIC) populations are derived from multiple elite breeding lines with a combi-
nation of useful traits. These populations are useful for precise QTL mapping and for
use in cultivar development. However, their development in pearl millet is not yet
realized.

6.8.7.2 Mapping of Trait for Marker-Assisted Breeding

The molecular markers and linkage maps discussed above have been used to identify
and map QTLs for terminal drought (Yadav et al. 2002), reduced salt uptake (Sharma
et al. 2011, 2014), grain and stover yield (Yadav et al. 2002, 2003, 2004), and for
downy mildew resistance (Jones et al. 1995, 2002; Breese et al. 2002; Gulia et al.
344 C. T. Satyavathi et al.

2007; Satyavathi et al. 2016), rust and blast resistance (Morgan et al. 1998, Punnuri
et al. 2016), fertility restorer genes (Yadav 2005; Pucher et al. 2018;), grain
micronutrient enrichment (Kumar et al. 2018b; Singhal et al. 2021). However,
linkage analysis in most of these studies suggest presence of genes/QTLs at a
distance of 10–40 cM from the closest markers making it difficult for MABB or
functional validation of candidate genes (Dwivedi et al. 2012). Until now only a few
reports showing that either fine mapping or validation of candidate genes associated
with a particular trait have been identified in this crop-like drought tolerance QTL on
LG2 (Sehgal et al. 2012), validation of grain Fe-Zn candidate genes, etc.
(Mahendrakar et al. 2020; Singhal et al. 2021).
Molecular markers flanking identified QTLs and genes have successfully been
deployed in MABC to further improve ‘HHB 67 Improved’ and GHB 538 hybrids
from India. In fact, the first molecular marker-assisted cultivar released for commer-
cial cultivation belongs to pearl millet hybrid ‘HHB-67 Improved’ (Hash et al.
2006). HHB 67 pearl millet hybrid was released in 1990 and soon became a
farmer-preferred hybrid owing to its extra-early maturity that helped the plant escape
end season drought. However, this hybrid became susceptible as the incidence of
DM increased in western India, warranting improvement. The parental lines of HHB
67, namely ICMB 843 and H77/833-2, was improved for their DM resistance in
which the former through conventional backcross breeding and latter through
marker-assisted backcross breeding and the new reconstituted hybrid, with DM
resistance, was released in 2005 in the name ‘HHB 67 improved’ (Fig. 6.7f).
Researchers at ICRISAT partnered with Chaudhary Charan Singh Haryana
Agricultural University (CCSHAU) and ICAR-All India Coordinated Research
Project on Pearl Millet (AICRP-PM) for the second cycle improvement of HHB
67 Improved hybrid. Using genome-wide simple sequence repeat (SSR) DNA
markers, three DM resistance QTLs were stacked along with drought resistance
QTLs at LG-2. The latest improvement has been christened HHB 67 Improved 2–7
(meaning HHB 67 Improved second cycle improvement, seventh version). It
completed testing in Essentially Derived Variety (EDV) multi-location, multiyear
trials of AICRP-PM in A1 and A (dry) zones of India. The new version hybrid shown
to have around 58% improvement over downy mildew resistance and 11% over blast
incidence, keeping the maturity earliness at par with earlier version HHB-67
improved (Srivastava, personal communication). Based on yield superiority of
15% in grain yield and 21% in fodder yield, with very low DM incidence (% disease
incidence ¼ 2.6%) in EDV trials, the HHB 67 Improved 2–7 (MH 2545) was
identified for release for cultivation in Rajasthan. Haryana, and Gujarat under rain-
fed conditions in Kharif season (VIC proceedings on Pearl millet, AICRP-PM
2021).

6.8.7.3 Draft Pearl Millet Genome Sequence

With the effort of a global participation of various international institutes, a draft
pearl millet reference genome sequence made available to public which serves as a
valuable genomic resource for pearl millet improvement (Varshney et al. 2017). A
global reference genotype, Tift 23D2B1-P1-P5 has been chosen to develop its draft
6 Pearl Millet Breeding 345

genome sequence through whole genome shotgun and Bacterial artificial chromo-
some (BAC) sequence approaches. The genome size is roughly 1.79 Gbp and has
around 38,579 genes. Along the draft reference genome, a set of 994 germplasm
lines including its wild genotypes were re-sequenced and were also made available
to public which harbours around three million SNPs. The genome sequence and
resequencing data will facilitate the successful marker–trait association studies,
defining heterotic pools, and predicting hybrid performance in future programmes.
The data can be accessed through following weblink, http://cegsb.icrisat.org/ipmgsc/
and http://gigadb.org/dataset/100192.
While addressing any biotic constraints, the availability of genome sequence
information of pathogen will complement the understanding on host–pathogen
interaction. It provides a way and means for biotechnological manipulation of host
(through gene editing via CRISPR-Cas) for their successful management. In this
direction, whole genome sequencing was successfully conducted in two major
pathogens in pearl millet, namely Sclerospora graminicola (causing downy mildew)
and Magnaporthe grisea (causing foliar blast). The draft genome sequence of
S. graminicola pathotype 1 had 299,901,251 bp length and was assembled having
N of 17,909 bp with minimum of 1 kb scaffold size and overall coverage of 40
(Nayaka et al. 2017; Chakravartty et al. 2017). Draft genome sequence of
Sclerospora graminicola, the pearl millet downy mildew pathogen. It had 47.2%
GC content with 26,786 scaffolds and scaffold size of 238,843 bp was found to be
longest amongst these. The genomic sequence and other related data of
S. graminicola can be retrieved from NCBI through link given, https://www.ncbi.
nlm.nih.gov/bioproject/PRJNA325098/. Similarly, Prakash et al. (2019) sequenced
genome of Magnaporthe grisea strain PMg_Dl and generated 13.1 Gb PE reads
(number of reads, 43,962,401), 3.4 Gb mate-paired reads (number of reads,
17,160,010), and 1.1 Gb PacBio reads (number of reads, 148,768). M. grisea strain
PMg_Dl genome sequence and relevant information can be found at NCBI through
following link, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA494483/. These
genomic resources would potentially benefit in deciphering the pathogen’s evolu-
tionary pattern and effector evolution in order to develop successful durable resis-
tance breeding programme in pearl millet.

6.8.7.4 Transcriptomics, Proteomic Approaches, and Genomic Database

of Pearl Millet
Transcriptome database is available for large number of crops but no such database
has been developed for orphan crop like pearl millet to be used as genomic resources
in crop improvement research (Kumar et al. 2020b). Few researchers have attempted
to unravel the molecular basis of drought, salinity, and heat tolerance in pearl millet
using whole transcriptome approach (Jaiswal et al. 2018; Dudhate et al. 2018;
Shivhare et al. 2020a, b; Shinde et al. 2018; Sun et al. 2020; Maibam et al. 2020).
Mapping of sequenced reads against the foxtail millet genome, which has been
relatively well-annotated, led to the identification of several differentially expressed
genes under drought stress. Pathway and gene function analysis by KEGG online
tool revealed that the drought response in pearl millet is mainly regulated by
346 C. T. Satyavathi et al.

pathways related to photosynthesis, plant hormone signal transduction, and

mitogen-activated protein kinase signalling. They also identified 34,652 putative
markers (4192 simple sequence repeats, 12,111 SNPs and 6249 InDels).
Transcriptome has been used in the area of pearl millet for the development of first
web-based genomic resource (http://webtom.cabgrid.res.in/pmdtdb/) which can be
used for candidate genes-based SNP discovery programmes and trait-based associa-
tion studies.
Recently, using transcriptomic studies, the key candidate genes, viz. PglZIP,
PglNRAMP, PglYSL, and PglFER family genes were candidates for grain Fe content
and grain Zn content were discovered for grain Fe and Zn metabolism in pearl millet
(Mahendrakar et al. 2020). Ferritin-like gene (PglFER-1) was found to be the
strongest most potent candidate gene for grain Fe Content. Expressed genes were
correlated with major QTL co-localized on LG7 for grain Fe content and grain Zn
content (Mahendrakar et al. 2020). Also, in order to dissect the molecular basis of
flour rancidity, denovo transcriptome sequencing was carried out in contrasting
genotypes of pearl millet to identify involvement of lipase towards hydrolysis of
unsaturated fat present in pearl millet flour (Kumar et al. 2021a). The study provided
a useful understanding of different Fe and Zn metabolism gene homologs and laid a
foundation for functional dissection. Also, the role of small RNA towards abiotic
stress was investigated by Shinde et al. 2020 and Kumar et al. 2018a.
Detailed studies of pearl millet with respect to whole genome proteomics is much
limited than that of transcriptomics. A few literatures related to whole proteomics is
available related to identification of key genes involved in drought tolerance
(Anatala et al. 2015; Ghatak et al. 2021), downy mildew resistance (Anup et al.
2015), and grain quality (Bugs et al. 2004; Marcellino et al. 2002). Analysis of pearl
millet lines using SDS-PAGE for the storage protein pattern profiling in popular
pearl millet showed the appearance of most of the band in the range of 25–65 KDa.
The alcohol soluble fraction of the storage protein was also separated on SDS-PAGE
and observed very intact and prominent bands of prolamins in all the fractions of
different genotypes of pearl millet.
Biophysical methods and structural modelling techniques have been used to
characterize the prolamins from maize and pearl millet. The alcohol-soluble prola-
min from pearl millet was extracted using a simple protocol and purified by gel
filtration in a 70% ethanol solution. Two protein fractions were purified from seed
extracts of pearl millet with molecular weights of 25.5 and 7 kDa, as estimated by
SDS-PAGE. The high molecular weight protein corresponds to pennisetin, which
has a high a-helical content both in solution and the solid state, as demonstrated by
circular dichroism and Fourier transform infrared spectra. Fluorescence spectros-
copy of both fractions indicated changes in the tryptophan microenvironments with
increasing water content of the buffer. Low-resolution envelopes of both fractions
were retrieved by ab initio procedures from small-angle X-ray scattering data, which
yielded maximum molecular dimensions of about 14 nm and 1 nm for pennisetin and
the low molecular weight protein, respectively, and similar values were observed by
dynamic light scattering experiments (Kumar et al. 2020b).
6 Pearl Millet Breeding 347

6.8.8 Increasing Nutritional Value Through Biofortification

Biofortication of pearl millet with iron (Fe) and zinc (Zn) initially by ICRISAT
supported by the HarvestPlus conducted in partnership with public and private sector
research organizations, has become a role model to be adopted for the improvement
of the nutritional profile in other staple food crops. Biofortification Priority Index
(BPI) given by IFPRI indicates pearl millet is a major target crop for iron and zinc
biofortification (Herrington et al. 2019). Screening the existing germplasms for Fe
and Zn indicated a huge variability for Fe (31–125 ppm) and Zn (35–82 ppm)
content whereas not a single popular cultivar is having grain Fe content more than
HarvestPlus baseline of 77 ppm to be considered as High Fe Pearl millet cultivars.
Hence, there was a good prospect of developing cultivars with higher levels of these
micronutrients. In pearl millet biofortification programme, the initial strategy was to
select and improve the existing OPVs to improve yield and grain micronutrient
simultaneously through recurrent selections as the grain Fe and Zn content in pearl
millet is under additive gene action. Most of the high Fe and Zn accessions were
from Togo and Ghana that had Fe content of 95–121 ppm and Zn content of
59–87 ppm indicating iniadi germplasm as a valuable germplasm resource for
genetic improvement of Fe and Zn contents in pearl millet.
First systematic breeding effort to develop a high Fe cultivar resulted in a world
first high-Fe pearl millet variety ‘Dhanashakti’ was developed by utilizing the intra-
population variability within ICTP 8203, an early-maturing, large-seeded, disease-
resistant and high-yielding open-pollinated variety, was released in 2014 as
Dhanashakti, which has been rapidly adopted by the farmers. The improved version
of variety ICTP 8203, having an Fe content of 71 mg/kg without any change in Zn
content. Likewise, variety ICMV 221Fe11-2, a better version of variety ICMV
221, has been developed with high Fe (81 mg/kg) and Zn (51 mg/kg) content.
Simultaneously, ICRISAT had utilized the existing high-Fe hybrid parents in devel-
opment of high-yielding and high-Fe hybrids which resulted in two hybrids, namely
ICMH 1201 and ICMH 1301 with Fe content of 75 and 77 mg/kg, respectively.
These hybrids had a yield advantage of 36% and 33% over variety ICTP 8203,
respectively (ICRISAT, India). Later with the effort of AICRP partners, biofortified
pearl millet hybrid HHB 299 was developed by CCSHAU, Hisar with an Fe content
of 73 ppm and average grain yield of 39.5 q/ha, which was notified in 2018 (AICRP-
PM 2020). Also, five biofortified hybrids, namely AHB 1200Fe, RHB 233, RHB
234, HHB 311, and AHB 1269, have been released during 2018–2020. These
biofortified cultivars mark the first milestone in the mainstreaming of the grain
mineral traits in the cultivar development process (Fig. 6.8; Table 6.6). With the
great support of partners, especially MPKV-Dhule, AICRP-PM, Mandore and
Nirmal seeds Pvt. Ltd., first high-iron variety Dhanashakti reached regular seed
systems that annually send 200–300 kg of breeder seed to national partners; so far,
they have reached >60,000 farmers in peninsular India. The truthfully labelled seed
(TLS) production of Shakti-1201 is being undertaken by Shaktivardhak Seed Com-
pany for commercialization, and it has been adopted by 20,000 ha, mostly in
Maharashtra and Rajasthan (Govindaraj et al. 2019). The significant progress
348 C. T. Satyavathi et al.

Fig. 6.8 Biofortified pearl millet cultivars released by ICAR for cultivation by Indian famers

made by AICPMIP regarding development and release of biofortified cultivars in

India (Satyavathi et al. 2021) can be accessed through the link http://www.aicpmip.
res.in/Micronutrient%20Pearl%20Millet.pdf
ICAR-AICRP on Pearl millet (AICPMIP) constructed a special module to test
and release biofortified pearl millet cultivars in India (AICPMIP 2017). Furthermore,
ICAR has endorsed a landmark decision on inclusion of the minimum levels of iron
(42 ppm) and zinc (32 ppm) in varietal promotion criteria for future pearl millet
 6

Table 6.6 List and salient features of biofortifed cultivars developed and cultivated in India
Grain Grain
Grain Fodder Fe zinc
Sl. Hybrid/ Breeding Notification Days to Days to yield yield content content
no variety Station details Area of adoption Salient features flowering maturity (kg/ha) (q/ha) (ppm) (ppm)
1 Dhanshakti ICRISAT, S. O 1146 Maharashtra, Early maturing 45 76 2199 53 81 43
India and (E) 24.04.2014 Karnataka, AP, bold, globular,
MPKV, Tamil Nadu, shining slate grey-
Pearl Millet Breeding

Dhule Rajasthan, coloured seed

Haryana, MP, resistant to downy
Gujarat, UP and mildew disease
Punjab
2 HHB 299 CCS HAU, S. O 1379 Rajasthan, Medium maturing, 50 81 3274 73 73 41
Hisar (E) 27.03.2018 Haryana, Gujarat, compact panicle
Punjab, Delhi, greyish hexagonal-
Maharashtra and shaped grain and
Tamil Nadu resistant to major
diseases
3 AHB 1200 NARP, S. O 1379 Rajasthan, Medium maturing, 47 78 3170 70 77 39
Aurangabad (E) 27.03.2018 Haryana, Gujarat, cylindrical panicle
Punjab, Delhi, resistant to downy
Maharashtra and mildew and highly
Tamil Nadu, AP, responsive to
and Telangana fertilizers
4 AHB 1269 NARP, S. O 1498 Rajasthan, Medium maturing, 50 81 3168 74 91 43
Aurangabad (E) 01.04.2019 Haryana, Gujarat, long cylindrical type
Punjab, UP, Delhi, panicle, bold grain
Maharashtra, Tamil and resistant to
Nadu, AP, major diseases
Telangana, and
Karnataka
349

(continued)
Table 6.6 (continued)
350

Grain Grain
Grain Fodder Fe zinc
Sl. Hybrid/ Breeding Notification Days to Days to yield yield content content
no variety Station details Area of adoption Salient features flowering maturity (kg/ha) (q/ha) (ppm) (ppm)
5 HHB 311 CCS HAU, S. O 3220 Rajasthan, Medium maturing, 50 81 3173 72 83 39
Hisar (E) 06.09.2019 Haryana, Gujarat, compact panicle
MP, Punjab, Delhi, having grey-
Maharashtra, and coloured hexagonal-
Tamil Nadu shaped grain, Highly
resistant to downy
mildew and other
diseases
6 RHB 233 SKNAU, S. O 3220 Rajasthan, Medium maturing, 49 80 3157 74 83 46
Jobner (E) 06.09.2019 Haryana, Gujarat, grey globular-
MP, Punjab, Delhi, shaped grain;
Maharashtra, and Highly resistant to
Tamil Nadu blast and downy
mildew diseases
7 RHB 234 SKN AU, S. O 3220 Rajasthan, Medium maturing, 49 81 3169 71 84 41
Jobner (E) 06.09.2019 Haryana, Gujarat, conical shaped
MP, Punjab, Delhi, compact panicle
Maharashtra and with greyish
Tamil Nadu coloured
hexagonal-shaped
grain, Highly
resistant to downy
mildew
C. T. Satyavathi et al.
6 Pearl Millet Breeding 351

varieties to be released in the country which is the first of its kind in the world. Thus,
along with yield improvement, focus on the nutritional improvement was also taken
care in pearl millet and in order to develop biofortified varieties/hybrids with
enhanced Fe and Zn. With visionary breeding strategies along with proper policy
intervention results in much greater progress in adopting high-Fe hybrids with a
high-grain yield is seen in pearl millet.

6.8.9 Breeding Pearl millet for Better End-Use Consumer

Acceptability

In spite of better nutrition profile the main constraints in utilization of pearl millet as
whole or in multigrain food products has been the problem of rapid development of
rancidity or bitterness in the flour after milling, poor flour rheological properties,
presence of various anti-nutrients like phytate and polyphenol and typical grey
colour of the pearl millet. The understanding regarding the genetics related to
these traits are only preliminary. Extensive work related to reduction of flour
rancidity in pearl millet was carried out by researchers of IARI, New Delhi, and
CCS, HAU, Hisar. High-fat content coupled with highly active lipases causes
hydrolysis of pearl millet fats to fatty acids. The typical fat content in pearl millet
is about 5.1% on a dry weight basis. Pearl millet fat contains 74% unsaturated fatty
acids, predominantly linoleic (C18:2) and oleic (C18:1). Lipase enzyme is
concentrated in the pericarp, aleurone layer, and germ gets released upon grinding
and accounts for the stepwise hydrolysis of these fatty acid fractions resulting in free
fatty acids and acyl glycerols (Satyavathi et al. 2017). Rancidity results from the
hydrolysis of these free short chain fatty acids and glycerols when exposed to air,
light, moisture, or bacterial activity, leading to unpleasant odour and taste. Rancidity
reflects the storage ability of pearl millet grain flour and its products affecting its
nutrient composition. Sharma and Saharan (2006) reported that the rancidity devel-
opment in pearl millet flour is caused by higher phenol contents and higher peroxi-
dase activity. Enzymes such as polyphenol oxidases act on the phenolic compounds
like C-glycosyl flavones resulting in browning of flour and the activities of
peroxidases results in off odour in flour. Based on the degree of rancidity indicators
such as comprehensive acid value (CAV), comprehensive peroxidase value (CPV),
and activities of lipase and lipoxygenase (LOX), a rancidity matrix was generated
using 93 pearl millet genotypes which can further help the pearl millet breeders in
designing low rancid pearl millet cultivars (Goswami et al. 2020).
Even though pearl millet is considered as ‘powerhouse of nutrients’ their bio-
availability is low, due to the presence of certain antinutritional factors. These
antinutritional components are mainly found in the bran layer. There exists a
negative correlation between the presence of antinutrients and in vitro protein
digestibility. One of the antinutrients of pearl millet grains is phytate, with a range
of 172–327 mg/100 g (Taylor 2004). Phytate binds multivalent metal ions such as
calcium and iron, thereby interfering with their absorption in the gut (Lestienne et al.
2007). Several studies have investigated the phytate content of pearl millet grain. A
352 C. T. Satyavathi et al.

panel of 145 pearl millet inbred lines analysed for phytic acid phosphorus (PAP)
revealed a large genetic diversity PAP content ranged between 0.198  0.034 and
0.410  0.036 g/100 g of seed flour with a relative standard deviation amongst the
lines of 12.8% and an average PAP content of 0.281 g/100 g (Boncompagni et al.
2018). Two studies so far analysed the genetics of phytic acid content in pearl millet
using diallel cross (Satija and Thukral 1985; Shanmuganathan et al. 2006). They
showed highly significant differences amongst parents as well as the hybrids and
demonstrated that both additive and non-additive gene effects were significant. It is
advisable to follow a population improvement programme using recurrent selection
to breed for low phytic acid content.
IARI identified a low phytic acid line, PPMI 1161 (TPR-14-12-4-5-3-B) having
low PAP of 0.001 g/100 g of seed flour while screening 68 advance breeding lines
and test single cross hybrids for grain Fe/Zn along with PAP (IARI-Annual Report
2020). Polyphenols are yet another factor that limits protein and starch utilization
either by binding with proteins or by inhibiting digestive enzymes, especially
trypsine and amylase. Polyphenols also form insoluble complexes with iron and
cause inhibition of iron absorption (Brune et al. 1991; Cercamondi et al. 2014).
Yadav et al. (2010) reported a lower concentration (50.87 mg/100 g) of polyphenol
in cultivar HTP 94/54. The variability for grain minerals and its bioavailability traits
in this crop opens the opportunity for breeding high bioavailable micronutrient-rich
breeding lines and hybrid parents, and thereby high-iron cultivars for improved
human nutrition in millet consuming regions.
Most of the hybrids and varieties available in commercial market are either grey
or brown grain colour, due to the presence of a thick pericarp and the presence of
pigments in the aleurone layer. Akingbala (1991) reported the presence of the
phenolic compounds, C-glycosyl flavones concentrated in the outer layers of the
grains, and they contribute to the grey grain colour (Taylor 2004). Grey colour in
food products made out of pearl millet imparts undesirable consumer acceptance
towards them. Pearly white grained genepool amongst pearl millet were first
reported by Patel 1939. Later Mangath (1987) developed white grain inbred lines
from segregating germplasm lines through selections. But these lines have heavy
incidence of downy mildew which further hampered the development of white grain
hybrids. Thinh (2011) reported that white grain lines were higher in reducing sugar
level which may be the reason for its susceptibility to downy mildew disease.
Satyavathi et al. (2015) developed 126 white grain pearl millet inbred lines with
downy mildew resistance along good agronomic features that could be utilized for
developing white grain hybrids. Lakkawar and Govila (1998) reported inheritance of
white grain colour in pearl millet is under the control of single dominant gene. Now
efforts were undergoing to map the gene responsible for the trait and to introgress
them into elite parental lines.
6 Pearl Millet Breeding 353

6.9 Future Research Thrust Areas

6.9.1 Improvement of Grain Yield

The impressive use of hybrid technology in India is evidenced by continuing genetic

gains of over 31.1 kg/ha/year in grain yield. Single-cross hybrids will continue to be
the only commercial option, given the private sector’s increasingly dominant role in
hybrid development and seed production. As a result, parental line development with
high-yield potential, DM and blast resistance, and regional adaptation should be
prioritized. Hybrid development should prioritize better-endowed environments,
while strategic research for marginal environments should be prioritized.

6.9.2 Diversification of Parental lines and Utilization of Alternate

CMS Systems

Development of heterotic pool and diversification of different heterotic pool is

crucial for developing the good heterotic hybrids. Various approaches (pedigree
breeding, backcross breeding, mutation breeding, and population approaches) can be
effectively employed for diversification of parental lines amongst pool. Also, A4 and
A5 based CMS resources are found to have better stability and concern-linked
markers were known and can be deployed through rapidly through marker-assisted
backcrossing in diverse genetic background to exploit their commercial potential.

6.9.3 Exploitation of Pre-breeding Programmes

Past-breeding efforts utilized only the narrow genetic diversity existing in pearl
millet found mostly in the cultivated types. Wild and wild relatives are the rich
sources of novel traits for pearl millet improvements. Exploitation of wild types and
wild relatives should be incorporated along with regular pearl millet breeding
programmes to identify new gene sources of biotic and abiotic stresses. Novel
breeding and biotechnological approaches like somatic hybridization, embryo res-
cue, speed breeding, gene editing techniques, etc. can put synergistic effect towards
creation of new genetic material for further improvements in this crop.

6.9.4 Quality Trait Focus

Till date, breeding efforts was mainly concentrated on improving grain yield,
earliness, and imparting biotic and abiotic resistance. Emphasis should be given
for the development of biofortified pearl millet with high consumer acceptance.
Success on iron-zinc biofortified hybrids in India can be kept as a role model for
improvement of other grain quality traits such as protein content, pro-vitamin A,
vitamin E, Niacin, etc. Recent research on improving the bioavailability of nutrients
354 C. T. Satyavathi et al.

and improvement of up-keeping quality of pearl millet flour is also impressive.

Despite the fact that pearl millet has a high protein content of 11.6%, key amino
acids such as lysine and tryptophan are deficient from these proteins. As a result,
research into quality protein pearl millet (QPPM) should commence, following the
advances made in quality protein maize (QPM). However, incorporation of con-
sumer or end-use preferred traits into elite cultivars need to be emphasized.

6.9.5 Marker-assisted Breeding

Development of molecular markers tightly linked to economic traits is of prime

importance in pearl millet. Identification of gene-based markers enable rapid intro-
gression of target traits into parental lines belongs to different heterotic groups.
Recent developments in sequencing technology and bigdata analytics provide a way
to identify and utilize such trait-linked markers and pyramid them together against
multi-disease complexes, abiotic stress, improvement of grain nutritional and
up-keeping quality and ultimately the yield.

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Sorghum Breeding
7
Prabhakar, R. Madhusudhana, and C. Aruna

Abstract

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop
after wheat, rice, maize, and barley across the world. It is mostly cultivated in the
arid and semi-arid tropics for its better adaptation to drought, heat, salinity, and
flooding. It is the main staple food for the poorest and most food-insecure people
of the world. In sorghum, commercial exploitation of heterosis has been possible
owing to availability of a stable and heritable CMS mechanism enabling large-
scale, economic hybrid seed production and sufficiently high magnitude of
heterosis across a range of production environments for economic characters.
The greater contribution of hybrids to yield, compared to improve and landrace
varieties, has been demonstrated in almost every situation/condition. The hybrids
besides being superior for grain yield and other traits of interest are stable across
environments. In India, many improved high yielding hybrids and varieties of
kharif, rabi, forage, and sweet sorghum, suitable to different zones/states, have
been released for cultivation, which resulted in higher production and productiv-
ity. Trait-based approach for the genetic improvement of sorghum has been
adopted by use of cutting-edge technologies of plant biotechnology and molecu-
lar biology to develop genotypes with improved performance under stress during
crop growth and enhanced quality of the produce with extended shelf life of seed,
grain, and novel sorghum products. Genomics has made rapid advances during
the past decade. The sorghum genome has been sequenced, and important gene
transcripts and regulatory mechanisms are being deciphered on a large scale
worldwide.

Prabhakar (*)
(Small Millets), ICAR, New Delhi, India
R. Madhusudhana · C. Aruna
ICAR-Indian Institute of Millets Research, Hyderabad, Telangana, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 367
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_7
368 Prabhakar et al.

The genetic diversity in sorghum provides an opportunity to search for new

genes and alleles that are responsible for conferring desirable phenotypes.
Genome profiling using molecular markers would provide a large number of
DNA markers. Genomic selection programs would pave way for effective utili-
zation of sorghum germplasm for crop improvement. The chapter on sorghum
starts with introduction to the crop, history, its origin, evolution, and distribution
of species and forms, wild relatives, and plant genetic resources. Information on
floral biology, emasculation, and pollination techniques, insight into molecular
cytogenetics and breeding, and genetic studies on qualitative and quantitative
traits are exhaustively covered for the benefit of users. Breeding objectives
including yield, quality characters, biotic and abiotic stresses, exploitation of
heterosis, and development of hybrids and varieties through conventional and
non-conventional breeding including genomics-assisted breeding are given
exclusively for the students and sorghum researchers to serve as reference and
use in crop improvement.

Keywords
Genetic resources · Germplasm · Hybridization · Purity maintenance · Varietal
development · Genomics

7.1 Introduction

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop after
wheat, rice, maize, and barley across the world. It is mostly cultivated in the arid and
semi-arid tropics for its better adaptation to drought, heat, salinity, and flooding. It is
the main staple food for the poorest and most food-insecure people of the world.
Sorghum is reported to be cultivated across 105 countries representing 41.1 million ha
with an average production of 58.6 million, with productivity hovering around
1.60 tons/ha. With exceptions in some regions, it is mainly produced and consumed
by poor farmers. India contributes about 16% of the world’s sorghum production.
Sorghum is the fourth most important cereal crop in India. This crop was one of
the major cereal staples during the 1950s and occupied an area of 17.36 million ha
but has come down to 4.48 million ha in 2020. The decline has serious concern on
the cropping systems and the food security of these dry land regions of the country.
However, the productivity has increased from 387 kg/ha in 1955–1956 to 1018 kg/
ha in 2019–2020, with threefold increase (Figs. 7.1, 7.2, 7.3, and 7.4). The total
sorghum production in India has registered a constant growth rate of 0.10% per
annum during the period from 1969–1970 to 2015–2016. Though, kharif sorghum
yield growth rates were relatively higher, it could not offset the declining growth
rates in production, as the growth rates in kharif sorghum area were negative and
high. Just opposite is true in case of rabi sorghum where the area decline was not
sufficient to undermine the yield growth, thus resulting in positive production
growth rates. The overall increase in productivity of kharif is far more than rabi
7 Sorghum Breeding 369

Fig. 7.1 Area and Production of Sorghum in India from 1955–1956 to 2019–2020 (Area,
million ha; production, million tons)

Fig. 7.2 Yield of Sorghum in India from 1955–1956 to 2019–2020 (Yield, kg/ha)

sorghum. However, the loss in both area and production is greater in kharif sorghum
than in rabi.
If we consider the recent 6 years, the area in kharif reduced from 2.3 million ha in
2014–2015 to 1.69 million ha in 2019–2020 and from 3.15 to 2.79 million ha in rabi
in the same period, with percent change of
26.5% in kharif and
11.4% in rabi.
However, there was improvement in productivity in both kharif (28.6%) and rabi
(24%). The coverage with high yielding varieties (HYVs) of sorghum is nearly 80%
in kharif, and potential under moderate input is also high (4–6 tons/ha). The area loss
may be due to the expansion in irrigation which has made other crops such as rice,
370 Prabhakar et al.

Fig. 7.3 Area and production of sorghum in kharif and rabi seasons in India from 2014–2015 to
2019–2020 (Area, million ha; production, million tons)

Fig. 7.4 Yield of sorghum in kharif and rabi seasons in India from 2014–2015 to 2019–2020
(Yield, kg/ha)

sugarcane, cotton, etc. more attractive and remunerative thus rendering sorghum to
be less competitive. The decline in consumption demand of sorghum grain was also
a major factor for the decline in area. The increased productivity of sorghum has not
been able to compensate the loss in area turning the production to be negative.

7.2 Origin, Evolution, and Distribution of Species and Forms

and Wild Relatives

Origin and early domestication of sorghum is hypothesized to have taken place

around 5000–8000 years ago in northeastern Africa or at the Egyptian-Sudanese
border. There is no argument against the African origin of sorghum, with the largest
7 Sorghum Breeding 371

diversity of cultivated and wild sorghum also found there (De Wet and Huckabay
1967; Doggett 1988; Kimber 2000). The secondary center of origin of sorghum is
the Indian subcontinent, with evidence for early cereal cultivation discovered at an
archaeological site in western parts of Rojdi (Saurashtra) dating back to about 4500
before 1950 AD (Kimber 2000).
Murdock (1959) has suggested that the Mande people around the headwaters of
the Niger river might have domesticated sorghum. Doggett (1965) indicated that
archaeological evidence suggests that the practice of cereal domestication was
introduced from Ethiopia to Egypt about 3000 BC It is possible that domestication
of sorghum began about that time. de Wet et al. (1970) studied archaeological reports
but found only meagre information about sorghum. They suggested that sorghum
had a diverse origin and probably arose from Sorghum verticilliflorum.
S. arundinaceum is a grass of the tropical forests, and S. aethiopicum and S. virgatum
are found in desert regions. These habitats are outside the major sorghum areas and
probably contributed less to its domestication. S. verticilliflorum is usually found in
areas where sorghum is cultivated. There is tremendous variation in
S. verticilliflorum: and it, as well as the other wild species, readily crosses with
cultivated sorghum. The races durra, guinea, and caffra are closely allied and may
have arisen from S. aethiopicum, S. arundinaceum, and S. verticilliflorum, respec-
tively. Murty and Govil (1967), using several different statistical procedures, classi-
fied the genus sorghum into nine groups: S. roxburghii, S. conspicuum, S.
arundinaceum, S. nervosum, S. durra, S. subglabrescens, S. sudanense, S.
halepense, and S. virgatum (OECD 2017).

7.2.1 Domestication

Sorghum, a grass of the steppes and savannas of Africa, was probably domesticated
in the northeast quadrant of Africa, an area that extends from the Ethiopia-Sudan
border westward to Chad (Doggett 1970; De Wet 1978). From there, it spread to
India, China, the Middle East, and Europe soon after its domestication (Doggett
1965). The great diversity of S. bicolor has been created through disruptive selection
(i.e., selection for extreme types) and by isolation and recombination in the
extremely varied habitats of northeast Africa and the movement of people carrying
the species throughout the continent (Doggett 1988). It has been diversified into a
food source, sugar source, and construction material. Harvesting of entire panicles of
sorghum by people altered the selection process (Kimber 2000). The basic morpho-
logical difference between a domesticated and a wild sorghum is the presence or
absence of an abscission zone at the rachis, panicle, or spikelet nodes (Harlan 1972).
The process of domestication involved a change in several characteristics of the
plant. A tough primary axis (rachis) and persistence of sessile spikelet were
introduced early in the process. It is likely that the transformation of a loose and
open inflorescence into a compact type involved several changes: (1) an increase in
the number of branches per node, (2) an increase in the number of branches per
primary inflorescence branch, and (3) a decrease in the internode length on the
372 Prabhakar et al.

rachis. An increase in seed size was also probably a product of domestication, the
seed becoming large enough to protrude from the glumes (House 1985).

7.2.2 Classification and Nomenclature

The word “sorghum” typically refers to cultivated sorghum (Sorghum bicolor [L.]
Moench subsp. bicolor), a member of the grass family Poaceae, tribe
Andropogoneae, and subtribe Sorghinae, which is grown for its grain (grain sor-
ghum) and its sugary sap (sweet sorghum) or as a forage (forage sorghum). A variety
of common names are used in different regions to refer to cultivated sorghum,
including great millet, guinea corn, broomcorn, kaffir corn, durra, mtama, milo,
jowar, or kaoliang (OECD 2017).
Cultivated sorghum is only one member of the genus Sorghum, made up of
25 species and separated into five taxonomic sections: Chaetosorghum,
Heterosorghum, Parasorghum, Stiposorghumand, and Eusorghum. Eusorghum spe-
cies are agronomically important, which include cultivated sorghum and its wild
progenitor (Sorghum bicolor [L.] Moench). The nomenclature of cultivated sorghum
and its wild and weedy relatives was thoroughly reviewed by Wiersema and
Dahlberg (2007). Competing names and priorities were considered, and three sub-
species were validated for S. bicolor: S. bicolor subsp. bicolor, S. bicolor subsp.
verticilliflorum, and S. bicolor subsp. drummondii. S. bicolor subsp. bicolor
comprises the cultivated sorghums; S. bicolor subsp. verticilliflorum comprises
annual wild relatives of cultivated sorghum native to Africa, Madagascar, and the
Mascarenes and introduced varieties to India, Australia, and the Americas; S. subsp.
drummondii comprises annual weedy derivatives arising from hybridization of
cultivated sorghum and S. bicolor subsp. verticilliflorum. A complete listing of the
names of all known subspecies plus homotypic species names is provided by
Wiersema and Dahlberg (2007).
Section Eusorghum also includes the rhizomatous taxa Johnson grass and
S. propinquum (de Wet 1978). Although Johnson grass is native to southern Eurasia
and India, its introduction to temperate regions and introgression with cultivated
sorghums has caused it to become a troublesome weed (de Wet 1978).
S. propinquum is generally restricted to Sri Lanka, southern India, and Burma east
toward Southeast Asia (de Wet 1978; Doggett 1988). By natural crossing with
cultivated sorghums in the Philippines, S. propinquum has also become a geograph-
ically isolated noxious weed (de Wet 1978).
Of the 25 recognized species of Sorghum, 17 are native to Australia and Southeast
Asia, of which 14 are endemic to Australia (Lazarides 1991). Basic chromosome
numbers vary from 10 to 40, and in some cases, such as within S. timorense (Kunth)
Buse, there are multiple ploidy levels. These species are not within the Eusorghum
section and previously were regarded as sufficiently distant to be sexually incompat-
ible with cultivated sorghum. Recent studies have demonstrated that
S. bicolor  S. macrospermum crosses are not only possible but that there is
7 Sorghum Breeding 373

significant genomic introgression of the wild germplasm into the cultivated species
after backcrossing the hybrids (OECD 2017).

7.2.3 Description

Cultivated sorghum is a cane-like grass with diverse morphology. Plant height

ranges from 0.5 meters (m) to 6 m. Culms (stalks) are erect and range from slender
to stout. Tillers (adventitious stems originating from the plant base) can range in
quantity from none to profuse. Leaf blades vary from linear to lanceolate and can be
smooth or hairy, measuring up to 100 centimeters (cm) long and 10 cm wide with
smooth to thinly pilose sheaths. The inflorescence consists of a single panicle with
many racemes. Panicles may be either compact or open up to 50 cm long and 30 cm
wide; panicle branches are stiffly ascending or spreading and pendulous, with the
bottom branch being almost half as long as the panicle. At maturity, racemes have
one to eight nodes and can be either fragile or tough. Spikelets may be glabrous or
hirsute, elliptic to obovate, and up to 6 mm long (Fig. 7.5). Glumes (bracts) range
from leathery to membranous, often with winged keels. Lower lemmas are approxi-
mately 6 mm long, while upper lemmas are slightly shorter and often awned. Both
upper and lower lemmas of sessile spikelets are somewhat ciliate and translucent
(Doggett 1988).
For many years, sorghum breeders have classified cultivated sorghum into races
or working groups (Murty and Govil 1967) according to morphological
characteristics. de Wet et al. (1970) described the various groups of cultivated
sorghum and identified their historical geographic distribution. A system was then

Fig. 7.5 Spikelet types of the five races of cultivated sorghum

374 Prabhakar et al.

developed dividing cultivated sorghum into five basic inter-fertile races (Bicolor,
Kafir, Caudatum, Durra and Guinea) and ten intermediate races, based on floral
morphology (Harlan and de Wet 1972). This classification system was widely
adopted. An integrated classification of cultivated sorghum was proposed by
Wiersema and Dahlberg (2007) following the morphological guidelines outlined
above and simplifies their classification systems by presenting working groups
numerically. A more detailed description of the characteristics of each of the five
main races of cultivated sorghum can be found.
For cultivated sorghum, Harlan and de Wet (1972) have developed a simplified,
informal classification useful to plant breeders for the cultivated sorghums and their
closest wild relatives. The classification is based on five fundamental spikelet types.

7.2.3.1 Bicolor
Grain elongate, sometimes slightly obovate, nearly symmetrical dorso-ventrally;
glumes clasping the grain, which may be completely covered or exposed as much
as 1/4 of its length at the tip; spikelets persistent.

7.2.3.2 Guinea
Grain flattened dorso-ventrally, sub-lenticular in outline, twisting at maturity 90
between gaping involutes glumes that are nearly as long to longer than the grain.

7.2.3.3 Caudatum
Grain markedly asymmetrical, the side next to the lower glume flat or even some-
what concave, the opposite side rounded and bulging; the persistent style often at the
tip of a beak pointing toward the lower glume; glumes 1/2 of the length of the grain
or less.

7.2.3.4 Kafir
Grain approximately symmetrical, more or less spherical, not twisting, glumes
clasping and variable in length.

7.2.3.5 Durra
Grain rounded, obovate, wedge-shaped at the base and broadest slightly above the
middle; the glumes very wide, the tip of a different texture from the base and often
with a trans-verse crease across the middle.
Harlan and de Wet (1972) developed a simplified classification of cultivated
sorghum into five basic and ten hybrid races (Table 7.1) that proved to be of real
practical utility for sorghum researchers. The 15 races of cultivated sorghum are
identified by mature spikelets alone, although head type is sometimes helpful.
Sorghum is classified under the family Pinaceae, tribe Andropogoneae, subtribe
Sorghinae, and genus Sorghum Moench. The genera is divided into five subgenera:
Eu-sorghum, Chaetosorghum, Heterosorghum, Para-sorghum, and Stiposorghum.
Chaetosorghum and Heterosorghum are found in single species primarily in
Australia and the South Pacific. Para-sorghum includes seven species found in the
eastern hemisphere and Central America, while Stiposorghum contains ten species
7 Sorghum Breeding 375

Table 7.1 Fifteen races of Basic races Intermediate hybrid races

cultivated Sorghum bicolor
1. Race bicolor (B) 6. Race guinea-bicolor (GB)
subsp. bicolor
2. Race guinea (G) 7. Race caudatum-bicolor (CB)
3. Race caudatum (C) 8. Race kafir-bicolor (KB)
4. Race kafir (K) 9. Race durra-bicolor (DB)
5. Race durra (D) 10. Race guinea-caudatum (GC)
11. Race guinea-kafir (GK)
12. Race guinea-durra (GO)
13. Race kafir-caudatum (KG)
14. Race durra-caudatum (DC)
15. Race kafir-durra (KO)
Source: Harlan and de Wet (1972)

endemic to Australia. Lazarides (1991) present an excellent overview of the species

in each of these four subgenera. The basic chromosome number of sorghum is
5, although striking differences in chromosome number, modes of origin, chromo-
some size, and geographic distribution of species are observed. Five is hypothesized
as the lowest chromosome number in the Para-sorghum and Stiposorghum species,
with polyploid proposed as autopolyploidy building by units of 10. S. bicolor spp.
contain all the cultivated sorghums and are described as annual, with stout culms up
to 5 m tall, often branched, and frequently tillering (Doggett 1988). The International
Plant Genetic Resources Institute (IPGRI) Advisory Committee on Sorghum and
Millets germplasm has accepted and recommended this classification to be used in
describing sorghum germplasm.
Harlan (1972) reported that in Africa, the distribution of indigenous materials is
rather consistent. Guinea is primarily West African with a secondary center in
Malawi-Tanzania. Caudatum is most abundant from east Nigeria to eastern Sudan
and southward into Uganda. Kafir is primarily a race of East Africa, south of the
equator and southern Africa. Durra is dominant in Ethiopia and westward across the
continent in the driest zones of sorghum culture near the Sahara. The hybrid races are
found rather consistently in the expected places: e.g., guinea-caudatum occurs where
guinea and caudatum overlap (Nigeria. Chad, Sudan), durra-caudatum occurs in
northern Nigeria and parts of Sudan where durras and caudatums are also found, etc.
The bicolor race occurs on a minor scale almost everywhere in Africa. The sweet
types used for chewing are usually bicolors, and some are used for beer. On the other
hand, the highland Ethiopian sorghums belong to the durra-bicolor race and are
grown very extensively. Bicolor races are frequently reconstituted locally through
introgression between grain sorghums and wild and weedy sorts that are very
abundant in central and eastern Africa (OECD 2017).
Indian sorghums are mostly durra, guineas, and guinea-kafirs, with some bicolors
grown on a minor scale. The American grain sorghums are now almost entirely kafir-
caudatums. The Nigerian Kau-ras are durra-caudatums; the Zera zeras and Hegaris
are caudatums. What is called Feterita in Sudan ranges from guinea-caudatum
through caudatum to durra-caudatum. Broom corns, sorgos, and sudan grass fall
376 Prabhakar et al.

under race bicolor. Cultivated sorghums are more variable than the wild-weed
complexes.

7.2.4 Wild Sorghum

The weedy and wild relatives of the grain sorghums, earlier classified primarily in
series Spontanea Snowden, are now listed in subsp. drummondii and subsp.
arundinaceum (de Wet 1978). The wild relatives included in the classification of
Harlan and de Wet (1972) as races arundinaceum, aethiopicum, virgatum, and
verticilliflorum are now included in subsp. arundinaceum; and propinquum has
been recognized as a separate species of the genus Sorghum. The weedy taxa of
subsp. drummondii are stable hybrids of the cultivated races and the wild taxa in
Sorghum bicolor. These “species” have less tough racemes. The wild “species” have
fragile racemes, and the plants usually inhabit natural grass vegetation but may
invade cultivated fields.
Ng’uni et al. (2010) published a phylogenetic analysis showing the relationships
between the taxonomic sections based on four regions of the chloroplast DNA (trnY-
trnD, psbZ-trnG, trnY-psbM, and trnT-trnL) and the internal transcribed spacer
region of the 18S-5 ∙ 8S-26S nuclear ribosomal DNA from 21 sorghum species
(Fig. 7.6). Germplasm accessions used in their study include wild sorghum species
and several cultivated sorghums obtained from the Australian Tropical Crops
Genetic Resource Centre, Biloela, Queensland, Australia, and the Zambian National
Plant Genetic Resources Centre.

7.3 Plant Genetic Resources

Plant genetic resources are defined as the “genetic material of plants that is of value
as a resource for the present and future generations of people.” The importance of
genetic resources was recognized at the intergovernmental platform under the
umbrella of the Food and Agricultural Organization (FAO) of the United Nations
as the “common heritage of mankind,” which should be made available without
restriction. Genetic resources have evolved as a product of domestication, intensifi-
cation, diversification, and improvement through conscious and unconscious selec-
tion by countless generations of farmers. These landraces and improved cultivars
provide the basic and strategic raw material for crop improvement the world over for
present and future generations.
Sorghum has an immense range of genetic resources with much of the genetic
variability available in the African regions where domestication first occurred and in
the Asian region as an introduction. In Africa, the genetic variability occurs as
cultivated species, wild crop progenitors, and wild species (de Wet and Harlan
1971). Landraces and wild relatives of cultivated sorghum from the centers of
diversity have been rich sources of resistance to new pathogens, insect pests, and
other stresses, such as high temperature and drought, as well as sources of traits to
7 Sorghum Breeding 377

Fig. 7.6 Phylogenetic analysis of 21 sorghum species based on four regions chloroplast DNA and
internal transcribed spacers of nuclear ribosomal DNA. *Clades are indicated by letters below the
branches. Bootstrap values 50%, indicating the percentage likelihood that subgroups differ, are
located above the branches. (Adapted from Ng’uni et al. 2010)

improve food and fodder quality, animal feed, and industrial products. However, this
natural genetic diversity is by the adoption of improved varieties. To prevent the
extinction of landraces and wild relatives of cultivated sorghum, the collection and
378 Prabhakar et al.

conservation of sorghum germplasm were accelerated about four decades ago. Since
then, germplasm collection and conservation have become integral components of
several crop improvement programs at both national and international levels.

7.3.1 Status of Genetic Resources

At the global level, sorghum germplasm collections consist of approximately

168,500 accessions; the largest collection (21% of global total) is held at the
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT),
Patancheru, India. The total accessions consist of 18% landraces, old cultivars,
21% advanced cultivars breeding lines, and 60% mixed categories of unknown
material, while very few are wild relatives.

7.3.2 Genetic Resources at ICRISAT, Hyderabad

The gene bank at ICRISAT, India, that serves as a world repository for sorghum
germplasm conserves 39,234 accessions from 93 countries, including 6249 from
seven South Asian countries: Afghanistan (6), Bangladesh (9), India (6101), the
Maldives (10), Nepal (8), Pakistan (90), and Sri Lanka (25). A total of 5340
geo-referenced accessions were used to identify gaps, and 5322 accessions that
were characterized at ICRISAT were used to assess the diversity in the collection.
Accessions of basic races varied widely than those of intermediate races for
flowering in the post-rainy season, plant height in both rainy and post-rainy seasons,
panicle exertion, panicle length and width, seed size, and 100 seed weight.
Landraces from India were late flowering and tall and produced stout panicles and
larger seeds. Landraces from Pakistan flowered early in both seasons and produced
stout panicles, and those from Sri Lanka were late flowering and tall in both seasons,
produced more basal tillers and stout panicles. A total of 110 districts in 20 provinces
of India, 13 districts in three provinces of Pakistan, three districts in Bangladesh and
five districts in four provinces of Sri Lanka were identified as geographical gaps.
Sorghum bicolor subsp. verticilliflorum, S. halepense, and S. propinquum were
identified as taxonomic gaps in the collection. Therefore, it is suggested to explore
the districts identified as gaps to enrich the variability in the world collection of
sorghum at ICRISAT (Reddy et al. 2008a, b; Upadhyaya et al. 2009).

7.3.3 Core and Mini Core Collections at ICRISAT

Core and mini core collections representing diversity in the entire collection of the
germplasm of a given species preserved in the gene bank are an ideal resource for
efficient conservation and utilization of plant genetic resources in crop improvement
programs. Both core and mini core collections are available in sorghum. The core
collection consisting of 2277 accessions constituted about 10% of the accessions of
7 Sorghum Breeding 379

the entire collection of a given species preserved in gene bank, while the mini core
collection consisting of 242 accessions constituted 1% of the accessions of entire
collection or 10% of the accessions of the core collection representing diversity of
the core collection and entire collection of a given species preserved in a gene bank.
Core and mini core collections served as resource to discovering new sources of
variations. Research to date suggests that core and mini core collections or genotype-
based reference sets have been found useful in extracting germplasm with
agronomically beneficial traits for use in crop improvement programs. The
researchers at ICRISAT and elsewhere have extensively evaluated these subsets
for resistance to abiotic and biotic stresses and for agronomic and nutritional traits
and reported a number of germplasm accessions with agronomically beneficial traits.
New sources of variations for resistance to abiotic and/or biotic stresses and of
agronomic and nutritional (oil and protein, Ca, Fe and Zn, O/L ratio) traits have been
reported for use in crop breeding. More importantly, a number of accessions with
multiple resistance and nutrient dense types, some with specific adaptation (rainy
and/or post rainy seasons), are available in ICRISAT gene bank, which can be
accessed after signing with ICRISAT the Standard Material Transfer Agreement
(www.icrisat.org/icrisat-ip-mta-htm). With the availability of abundant genomic
resources on these crops, it is visualized that there will be increased use of
genomics-based germplasm analysis to enhance use of germplasm and make impact
in breeding programs in the near future.

7.3.4 Genetic Resources at ICAR-IIMR, Hyderabad

ICAR-Indian Institute of Millets Research (IIMR) is one of the National Active

Germplasm Sites (NAGS) to act as a national repository for sorghum germplasm in
India. The objectives of the Millets Gene bank are collection, augmentation, conser-
vation, characterization, evaluation, documentation, distribution, and utilization of
millets genetic resources (Elangovan 2020). A total of 43 explorations were
undertaken and 1372 acc. of sorghum collected from 13 states, viz., Andhra Pradesh,
Karnataka, Tamil Nadu, Maharashtra, Gujarat, Uttar Pradesh, Rajasthan,
Uttarakhand, Madhya Pradesh, Odisha, Chhattisgarh, Bihar, and Jharkhand. For
assembling, a total of 76,329 accessions of sorghum and other millets augmented
from other national and international centers, in which 7708 acc. received from
ICRISAT and 57,319 acc. from NBPGR. A total of 57,663 acc. of millets germplasm
were characterized for different morpho-agronomic traits (25–27 traits). This
includes Sorghum (39,974 acc.). Besides, as of 1 December 2020, the gene bank
has 53,562 accessions of millets in bulk and 18,513 accessions in voucher sample.

7.3.4.1 Distribution
A total of 90,752 acc. were distributed to bonafide users during 2000–2020, which
includes sorghum (70,645 acc.), wherein NRCS/DSR/IIMR received 49,776 acc.
followed by AICRP on Sorghum (23,466 acc.), distributed to 16 State Agricultural
Universities, 2724 acc. to ten ICAR institutes and two KVKs, etc. On utilization part,
380 Prabhakar et al.

the compilation from the published annual reports of NRCS/DSR from 2000–2001
to 2013–2014 revealed that 3585 accessions have been identified based on their
uniqueness of trait. The compilation from the published AICRP on Sorghum reports
from 2004–2005 to 2013–2014 revealed that 17,794 sorghum genotypes have been
identified based on their uniqueness of trait in the AICSIP trials.

7.3.4.2 Database
Database on collection (passport), augmentation, characterization, evaluation, mul-
tiplication, conservation, distribution, utilization, and registration of all the millets
germplasm accessions are maintained at MGB-IIMR-Hyderabad as primary data-
base. Besides, it also maintains the passport and characterization database of millets
germplasm maintained at ICAR-NBPGR-New Delhi and ICRISAT-Hyderabad as
secondary database. Pedigree database of sorghum (1975–2017) are also available.
The database of potential genetic stocks identified for utilization in sorghum under
AICRP on sorghum (2004–2014), sorghum under NRCS/DSR (2000–2014), and
millets under ICAR-IIMR (2014–2019) are also published. A total of 35 final
products contributed using the ICAR-IIMR germplasm through selection/breeding
by the AICRP on Sorghum trials during 2007–2020. There were a maximum of
18 rabi sorghum varieties followed by six sweet sorghum varieties, six kharif
sorghum varieties, and three single-cut forage varieties. One each of sweet sorghum
hybrid and dual-purpose varieties contributed to the trials.

7.3.4.3 Registration
Registration with ICAR-NBPGR-New Delhi: 16 genetic stocks were registered with
ICAR-NBPGR in which 15 are sorghum for shoot fly resistance, good roti quality,
multiple-disease resistance, high grain yield and biomass, MS line with bold seed,
early MS line with compact ear head, yellow pericarp, and scented sorghum. The
Institute facilitated ten Import Permit from NBPGR-New Delhi, 67 Standard Mate-
rial Transfer Agreement (SMTA) from ICRISAT, and 931 Material Transfer Agree-
ment (MTA) of NRCS/DSR/IIMR.

7.3.4.4 Mobile App Development for Germplasm Characterization

The Institute customized the free android mobile application “Field Book” devel-
oped by CIMMYT-Mexico and Kansa State University-USA for characterization of
70 agri-horticultural crops which include sorghum, pearl millet, finger millet, foxtail
millet, barnyard millet, proso millet, little millet, and kodo millet germplasm. Also,
the Institute developed spatial mapping for all the millet germplasm collection and
merging of characterization data of sorghum germplasm and developed webpage
with information on 5000 acc. of sorghum germplasm characterization for 25 traits
along with panicle photos under CRP-Agro-biodiversity (Elangovan 2020).
7 Sorghum Breeding 381

7.4 Floral Biology, Emasculation, and Pollination Techniques

Sorghum is primarily a self-pollinated crop; however, outcrossing does occur. In

varieties with compact or semi-compact panicles, selfing can be up to 90–95%, with
5–10% outcrossing (occurring more frequently at the tips of the panicles) (Doggett
1988). Varieties with loose or open panicles have higher rates of outcrossing:
30–60% (House 1985). In nature, the rate of outcrossing is affected by the wind as
stigmas are most receptive during the first 3–5 days after their emergence, but can
remain receptive up to a week or more after anthesis, depending upon temperature
and humidity (Doggett 1988).
Hybridization, or crossing, of sorghum on a field scale is made feasible through
genetic, cytoplasmic, and cytoplasmic-genetic male sterility systems (Ayyangar and
Ponnaiya 1937; Stephens and Holland 1954). Limited scale crossing can be carried
out through (1) emasculation with hot water and plastic bag technique or (2) hand
emasculation and pollination techniques. Emasculation using hot water and plastic
bags is cumbersome and requires a lot of preparation. It is safer to use hand
emasculation, which can easily be done by unskilled staff with some training
(House 1985).
Sorghum is normally self-pollinated, but some florets are protogyny resulting in
cross-pollination averaging about 6%. So, it is classified as often cross-pollinated.
The amount of natural cross-pollination varies from 0.6% to 50% in different
varieties and places. The cross-pollination is more in loose panicles than in compact
ones. Anthesis starts from tip to downward at the rate of 2–5 cm/day and completes
within 7–10 days, with anthesis time 3–6 A.M. The pollen grains are viable only for
short period, and stigma is receptive for 8–16 h.

7.4.1 Selfing

Head bagging becomes efficient for selfing the ear heads. Once the decision to bag
heads has been made, all heads in a row should be covered. If a head has already
begun to flower, the flowering portion should be cut off. During head bagging, boot
leaf of the plant is usually removed prior to placing the bag.

7.4.2 Emasculation

7.4.2.1 Hand Emasculation and Pollination

Conventional crossing or hybridization of different sorghum varieties is carried out
by simple hand emasculation of normal bisexual florets and then transferring the
pollen from the chosen male parent (which usually is a pure line but not necessarily
always) to the stigmas of the emasculated florets (Reddy 1997).
For this we need a pair of scissors, a secateur or a manicuring clipper, a blunt
needle or a pencil, a pair of forceps, 7 cm  3 cm  15 cm butter paper bag, paper
clips or a stapler, and a marking pen.
382 Prabhakar et al.

The steps are as follows:

• From the desired parental line, choose a panicle that has just started anthesis.
• Clip off the florets which have completed anthesis, with a secateur or scissors.
• Remove primary- or secondary- and tertiary-branch rachises in the lower portion
of the panicle, leaving about 200–300 florets in the central portion of the panicle
just below the clipped florets.
• Clip off all the pedicellate (sterile) florets from the central portion, leaving only
the sessile (fertile) florets.
• Thin out the sessile florets by clipping off some of the tertiary rachises to make it
easier to hold the sessile florets during emasculation.
• Grasp the sessile floret to be emasculated between the thumb and forefinger.
• Insert a blunt needle between the glumes below the middle portion of the floret,
and move it slowly around the inner surface of the glumes so as to break the
stamen filaments.
• Lift the needle out and upward, slowly pushing the detached anthers out of the
floret.
• After emasculating the florets as described above, cover them with a butter paper
bag, and clip or staple it as explained earlier in the selfing process. These bags
should have the date of emasculation recorded on them.
• Inspect the emasculated panicles on the following day for any remaining anthers
that might have emerged from the florets. Remove these florets along with the
anthers, and once again cover the emasculated panicles with bags.
• On the third/fourth day after emasculation, take the pollen from the chosen parent
into another butter paper bag. Slowly insert the emasculated panicle into the bag
with the pollen, and with a hand over the bag clasping the peduncle at the base of
the panicle, shake the panicle so that the pollen in the bag stick to the stigmas that
would have emerged from the emasculated florets.
• Staple/clip as in selfing with the folded corners of the mouth of the bag clasping
the peduncle. Make sure that the bag carries information on the date of emascula-
tion, date of pollination, and the male parent used in crossing. It is useful to
pollinate a second time on the following day to ensure pollination of all the
florets.

When the seed is harvested from the pollinated panicle, make sure that the bag
containing the seed is properly labeled and the male and female parents and the
crosses are clearly indicated. The cross is usually denoted as follows:
Name of the parent female  male, where “” denotes the cross. For example, IS
3541 IS 1052 means that IS 3541 as female has been crossed with IS 1052 as male.
Care should be taken that the glume closest to the pedicellate spikelet is held facing
away from the worker. Trimming should be done so that the individual sessile florets
remain uniformly spread.
7 Sorghum Breeding 383

7.4.2.2 Emasculation with Hot Water and Plastic Bag Technique

This requires plastic sleeves, a pair of scissors, string, butter paper bags, paper clips
or a stapler with staples, hot water in a thermos flask, and a thermometer.
The steps are as follows:

• Cut and trim the florets at the tip of the panicle. Take a bag made out of a plastic
sleeve and, tie it closely around the peduncle to surround the panicle.
• Pour hot water (42  C) into the closed plastic sleeve, and leave it for 10 min,
soaking the panicle in hot water.
• The water is drained after 10 min, and the sleeve is tied over the panicle.
• The florets at the top of the panicle open after 2–3 days, and anthers emerge but do
not dehisce and do not shed pollen; knock these anthers free from the panicle by
tapping it.
• Remove the remaining unopened florets from the lower portion of the panicle.
• Get pollen from another panicle of the desired line in a butter paper bag, and put it
over the emasculated panicle, tying it around the peduncle as in the selfing
process.
• Before collecting the pollen, write the name of the pollen parent and the date of
crossing/pollination on the bag.
• On the fourth day after pollination, check for selfed florets; these can be
recognized by their distinctively superior size compared with the rest. Remove
the selfed florets and rebag.

(Note: This is a cumbersome method and requires a lot of preparation. It leaves

some selfs in the F1 which need to be thoroughly checked and rogued out. It is
always safer to follow the hand emasculation method which can be easily done by
unskilled staff with some training.)
In this method, the panicle flowered tip and lower panicle branches are removed.
About 50 florets (in clusters of two or three) are immersed in hot water at 48  C for
10 min.

7.4.2.3 Plastic Bag/Mass Emasculation Technique

In this method, sorghum panicle is covered with plastic bag. This creates high
humidity inside the bag. Under such humidity, the florets open, and the anthers
emerge but shed no pollen. The anthers are knocked free of head by tapping. In this
method, some selfing occurs. Therefore, marker genes are needed to identify the
plants arising from selfed seed.
On a dry morning when pollen shedding is occurring between 6 and 7 A.M., the
hand pollination may begin around 9.30 A.M. In rainy days, the operation may be
started at 11.30–12.30 A.M. The pollen is collected in paper bags. Sorghum pollen
kept in bags is viable for 10–20 min. For collection, appropriate heads may be
selected and bagged in the previous night itself.
The selected male parent panicle will be covered with brown paper bag the
previous day evening before dehiscence of anthers. Next day, the pollen will be
collected by tapping the bag. The collected pollen will be dusted on to the
384 Prabhakar et al.

emasculated head and covered with butter paper bag labeled properly. Dusting of
pollen is done for 2–3 days continuously.

7.4.3 Importance of Selfing and Crossing

Selfing and crossing are essential tools in the regulation of variability in plant
breeding programs. The breeder must therefore know these techniques. When a
flowering panicle is tapped with a finger, a cloud of yellow pollen grains can be seen.
The wind carries the pollen grains to the stigmas, and pollination is achieved. Pollen
is normally viable for 3–6 h in the anther and 10–20 min outside. In nature,
occurrence of outcrossing varies from 1% to 10%; in wild types with loose/open
panicles, it may be up to 30%. In normal compact or semi-compact panicles in
improved cultivars, selfing can be up to 90–95%, with 5–10% outcrossing, occurring
more frequently at the tips of the panicles.
Selfing and crossing or outcrossing are processes with opposite effects. Selfing
promotes homozygosity and preserves the linked gene complexes, which helps
maintain pure stocks of cultivars. Outcrossing or crossing promotes recombination
and creation of new linkage gene complexes, leading to variability, which provides
an opportunity to the breeder to select upon.
Outcrossing, referred to as crossing here, is a process of transferring pollen grains
from a floret of one panicle to the stigma of a floret of another panicle. In nature, it is
usually effected by the wind as stigmas remain receptive up to a week or more after
blooming, depending on the temperature and humidity. Lower temperatures favor a
longer period of receptivity of stigmas. However, stigmas are most receptive during
the first 3–5 days after their emergence.
Hybridization of sorghum on a field scale is made feasible through the use of the
genetic and cytoplasmic genic male sterile (CMS) system. There are a number of
genes (ms1, ms2, ms3, ms4, ms5, ms6, ms7, ms8) which individually contribute in
homozygous condition to male sterility. Also, another system, independent of the
genetic system, called the CMS system, creates male sterility because of the interac-
tion of genes in the cytoplasm with those in the genome.

7.4.4 Fertilization

Pollen grains germinate as soon as they come in contact with a receptive stigma; the
pollen tubes grow through the stigmatic papillae down to the ovary through the stylar
region. Only one pollen tube succeeds in reaching the micropyle. The sperm nucleus
divides into two, one of which fertilizes the egg cell to give rise to the embryo
(2n ¼ 20 chromosomes in sorghum), while the other joins the two polar nuclei to
form the endosperm (3n ¼ 30 chromosomes, i.e., 20 from the female parent and
10 from the male parent). This process of embryo formation by the union of egg
nucleus and sperm nucleus is called fertilization. The glumes close shortly after
pollination. The ovule begins to develop as a light green, almost cream-colored
7 Sorghum Breeding 385

sphere, and about 10 days after pollination, it becomes bigger and turns dark green.
The development of the embryo and endosperm continues for another 30 days when
the seed reaches physiological maturity with the hilum region (a spot on the seed
through which the seed receives nourishment of the plant) becoming black. During
the development, the seed passes through milk, early-dough, and late-dough stages.
The dried-up style may persist in some seeds up to physiological maturity (House
1985).

7.5 Techniques of Maintaining Genetic Purity of Seed Stocks

Various techniques are followed in breeding programs to maintain/enhance the

purity of seed stocks. The choice of the methods depends on the quantity of seed
required, the resources available, and the extent of genetic purity and trueness to type
required for the given material. These methods are described briefly here.

7.5.1 Roguing

Before flowering, all odd plants or “rogues” are removed. The panicles, after
trimming the tips (top quarter of the panicle), are harvested and bulked from the
plots in breeding blocks. This method does not assure genuine purity of the stocks.
Therefore, when a crop is raised from seed multiplied in this manner, roguing should
be repeated.

7.5.2 Isolation

When one or two stocks need to be multiplied in large quantities, sowing in isolation,
field plots away from other sorghum plots, with or without variable sowing times, is
desirable to maintain a high level of genetic purity. Isolation with variable sowing
times is risky as there is a chance of overlapping of flowering between different
plots. Isolation that physically separates plots is considered more useful. A minimum
distance of 200 m between sorghum plots is recommended for multiplying varieties
or pure lines with the required standards of genetic purity. Generally, in India, seed
certification standards call for 99.5% genetic purity. Roguing of “odds” or “rogues”
before and during flowering is essential, and plants with trueness to type should be
retained/harvested.

7.5.3 Selfing by Bagging

Sorghum is a perfect-flowered plant (i.e., it has both sexes in the same floret). Self-
pollination or selfing is the process of ensuring the transfer of pollen of a floret to the
stigma of the same floret or of another floret within the same panicle. This is usually
386 Prabhakar et al.

accomplished in a breeding program by using kraft paper bags. In addition to kraft

paper bags, the other things required for selfing are a pair of scissors, paperclips or a
stapler, watchmaker tags, and a marker. The steps involved in selfing are:

• Remove odd or off-type or rogue plants from the plot before they reach the boot
leaf stage.
• When a few florets have opened at the tip of the panicle, snip off the
• flowered florets.
• Cut the flag leaf at the base.
• Record the date of selfing on the selfing bag.
• Put the bag (with the date) over the panicle, taking care to see that the whole of the
panicle is covered by the bag and that the bag also covers about 5–8 cm of the
peduncle.
• Make sure the peduncle stays in the center of the mouth of the bag wrapped over
by the folded corners of the paper bag on either side.
• Either staple the folded corners of the paper bag or put a paper clip, taking care to
see that the bag holds the peduncle tightly.

Ten to 15 days after bagging, the bags can be removed from the panicle. The same
bags or watchmaker tags can be stapled around the peduncles to mark selfing. The
number of plants to be bagged in a plot to ensure selfing depends on the purpose of
developing materials (in case of segregating lines) and the quantity of seed needed
(in case of near uniform lines). Care should be taken to harvest individual plants
separately in case of segregating generations, and bulk harvest the true-to-type
panicles only in case of uniform lines.

7.5.4 Precautions

Bags can be blown away by the wind or can be damaged by rain. Care must be taken
to replace them immediately, recording the information originally written on the
bags. Periodic inspection of the selfed plots is essential to detect damaged bags.

7.6 Molecular Cytogenetics and Breeding

Sorghum bicolor has a haploid chromosome number of 10, and it is classified as a

diploid (2n ¼ 2x ¼ 20). Most species within Sorghum are diploid (2n ¼ 20), but
several species, most notably Sorghum halepense, are tetraploid (2n ¼ 4x ¼ 40). As
the basic chromosome number in the Sorghastrae is 5, it has been hypothesized that
sorghum may be of tetraploid origin. Earlier studies on the meiotic chromosome
pairing analysis did not provide evidence for the tetraploid origin of S. bicolor, and
the information on the existence of homologous segments in the chromosomes of
S. bicolor is poor; therefore, the chromosomes were regarded as distinct. Recent
studies provide limited evidence about tetraploid origin of sorghum (Lazarides
7 Sorghum Breeding 387

1991). Duplicated loci were found on the map, suggesting that sorghum has tetra-
ploid origin. However, Subudhi et al. (2000) contended that these evidences of
tetraploidy are not satisfactory. They argued that in both analyses, the duplicated
loci found on the mapped genome are only to an extent of 8% and 11%, respectively.
The cultivated sorghum could be considered a diploid from the perspective of
genome organization (Subudhi et al. 2000; Rooney 2000; OECD 2017).

7.7 Interspecific Hybridization

The genus Sorghum consists of 25 species that are classified into five taxonomic
subgenera or sections, Eu-sorghum, Chaetosorghum, Heterosorghum, Parasorghum,
and Stiposorghum. Cultivated sorghum belongs to the Eu-sorghum section, and
19 sorghum species belonging to sections other than Eu-sorghum are distributed
primarily in Australia, southern Asia, and Africa and comprise an untapped tertiary
gene pool. Most of the undomesticated sorghum species having agronomically
important genes fall within the tertiary genepool, making gene transfer to
domesticated species very difficult due to strong sterility barriers (Harlan and de
Wet 1972). Tertiary wild species of sorghum carry many desirable traits for resis-
tance to pests, diseases, and drought. Pollen-pistil interactions are the primary
reasons why S. bicolor will not hybridize with divergent Sorghum species. The iap
(inhibition of alien pollen) allele was identified to allow hybridization; however, it is
patented and is under restricted use. Interspecific hybridization in sorghum was
initiated as early as 1930s, but was not successful due to pollen pistil inhibitions
(Ayyangar and Ponnaiya 1937; Rooney 2000).
Compared with interspecific hybridization, intergeneric pollination is more diffi-
cult to accomplish because of the lack of homology between chromosomes of the
two parental genotypes that causes irregular meiosis. Intergeneric pollination plays a
key role to generate extensive stochastic genomic and epigenomic variations that can
be translated into phenotypic novelties. Their progenies show various genomic,
epigenomic, and transcriptomic differences compared with the parental genotypes.
It was demonstrated that introgressive hybridization between rice Oryza sativa ssp.
japonica cv. Matsumae and its incompatible counterpart, Zizania latifolia Griseb,
has provoked genome-wide, extensive genomic changes in the rice genome, and
some of which have resulted in important phenotypic novelties. Several genome-
wide homozygous single nucleotide polymorphisms (SNPs) and insertion/deletions
(InDels) were identified in a typical rice-Zizania introgression line RZ35. Pollination
by pollen from an incompatible species causes massive activation of silent TEs, thus
acting as a “genome shock,” resulting in the transcriptional activation of the TE
mPing. Introgression line RZ35 had several TEs transcriptionally activated or
mobilized that led to enhance the resistance to blast fungus (Rooney 2000; OECD
2017).
388 Prabhakar et al.

7.8 Genetic Studies on Qualitative and Quantitative Traits

7.8.1 Maturity

Quinby (1967), who has pioneered research on maturity and height in sorghum,
identified factors at four loci that influence maturity, Ma1, Ma2, Ma3, and Ma4.
Generally tropical types are dominant (Ma-) at all four of these loci, and a recessive
condition (mama) at any one of them will result in more temperate zone adaptation.
In fact, the great bulk of lines used in the temperate zone have been found to be
recessive at locus 1. Lines in a program to convert tropically adapted lines to
temperate zone adaptation are likely recessive at locus 1 and dominant at the other
three loci. Genes at these loci interact: when dominance occurs at the Ma1 locus, the
dominant and recessive classes at the Ma2, Ma3, and Ma4 loci can be identified in an
F2 population. When the recessive condition (ma1ma1) occurs, variation in time to
flowering will diminish, making it difficult to separate genotypes (52.4–56.7 days’
variation, compared to variation of 64.6–90.5 days when dominance occurs at locus
1). If Ma1 is dominant, Ma2, Ma3, and Ma4 demonstrate dominance (lateness), but
if the gene at locus 1 is recessive (ma1ma1), then the recessive ma2ma2, ma3ma3,
and ma4ma4 may express dominance. There is an exception: when the gene at locus
1 is heterozygous (Ma1ma1) and that at locus 2 is recessive (ma2ma2), maturity is
later than if both alleles at the Ma2 locus are dominant (Ma2Ma2) (Quinby 1974).
Most of the lines from the tropical-to-temperate conversion program are recessive
(ma1) and dominant at the other loci. Yet the time to flowering varies from 60 to
85 days. Early-maturing tropical varieties tend to be early after conversion, and late-
maturing tropical lines tend to be late.

7.8.2 Height

Genes at four loci in sorghum are important in the control of plant height. These
genes are assigned the symbols Dw1, Dw2, Dw3, and DW4. Tallness is partially
dominant to dwarfness. The dwarfing effect of recessive genes (dwdw) at any of
those four loci is brachytic in nature (i.e., the length of the internode is reduced, but
not the peduncle length, head size, or leaf number, and the maturity is not changed).
The zero-dwarf type (dominant [DW-] at all loci) may reach a height of 4 m. The
change from four to three dominant genes may result in a height change of 50 cm or
more. If genes at one or more of the loci are recessive, the difference in height
resulting from the recessive condition at an additional locus may have a smaller
effect in reducing plant height. The difference between a 3-dwarf (recessive genes
[dwdw] at three loci) and a 4-dwarf type may be only 10 or 15 cm. There is variation
in height between different varieties with the same genotype. This is thought to be
due to an allelic series at a particular locus and not to modifying factors at other loci.
There is instability at the Dw3 locus; a dw3 allele mutates to the dominant allele at a
high rate (one mutation in 1209 gametes). Thus, some sorghum fields may have a
ragged appearance due to a greater frequency of tall plants. Some instability has also
7 Sorghum Breeding 389

been found at the Dw4 locus, but not at Dw1 or Dw2. Tall hybrids can be produced
from shorter parents using complementary factors. For example, 2-dwarf hybrid
(dw1Dw2Dw3dW4) can be produced from two 3-dwarf parents (dw1Dw2dw3dw4
and dw1dw2Dw3dw4).

7.8.3 Male Sterility

Genetic male sterility is caused by single recessive genes. Of these, ms3 is most
widely used because its expression of male sterility is good and it is stable over many
environments. Male sterility caused by the recessive condition for ms2 has been
useful; also male sterility caused by the anther-less gene (al) has been found useful.
Genetic male sterility is used primarily in composites to enhance the level of
recombination.
Cytoplasmic genetic male sterility in sorghum makes possible the commercial
production of hybrid seed. Male sterility results from an association of Milo cyto-
plasm with sterility genes found primarily among kafirs but also in some varieties of
other races. The genetics involved is not completely clear, but two genes (msc1 and
msc2, when recessive in the presence of Milo cytoplasm) result in male sterility.
There are other factors that influence the sterility reaction, possibly having a
modifying effect on the level of partial fertility. Most of the information in this
section is adapted from Doggett (1970).

7.8.4 Disease Resistance

Kernel smut (Sphacelotheca sorghi)—three races of this disease are known, and
resistance to each is controlled by an incomplete dominant, Ss1, Ss2, and Ss3. Head
smut (Sphacelotheca reiliana)—in most varieties, resistance is dominant to suscep-
tibility. Reaction to milo disease (Periconia circinata) is controlled by a single locus
(Pc). Susceptibility is partially dominant; F1 is intermediate. Anthracnose
(Colletotrichum graminicola) susceptibility on the leaf is controlled by a simple
recessive gene (I). Susceptibility to the stalk rot phase of this organism is controlled
by the simple recessive (Is). Rust (Puccinia purpurea) susceptibility is controlled by
a simple recessive gene (pu). For leaf blight (Exserohilum turcicum), most grain
sorghums are resistant. Susceptibility in sudan grass is inherited as a simple domi-
nant. In charcoal rot (Macrophomina phaseolina), the inheritance of resistance is
recognized but has not been analyzed completely; apparently, more than one gene is
involved. Downy mildew (Peronosclerospora sorghi) resistance is inherited as a
recessive character. A number of types, including most of the kafirs, are resistant.
Sudan grass is susceptible. Maize dwarf mosaic virus resistance is dominant.
390 Prabhakar et al.

7.8.5 Insect Resistance

The genetics of insect resistance are not well understood. Generally, it appears to be
multigenetic, and complete resistance is seldom found. Shoot fly (Atherigona
soccata) resistance is found at a low but useful level. There are apparently three
aspects: (1) non-preference for oviposition; (2) antibiosis (i.e., plant resistance per
se); and (3) recovery resistance (tillers form after the main stem is destroyed and
survive to make a crop). Recently, the presence of trichomes (microscopic hairs on
the lower surface of leaves) has been found to contribute to oviposition
non-preference. The presence of trichomes is controlled by a single recessive gene.
Stem borer (Chilo partellus): Variation in resistance is generally found at a
relatively low level. Storage insects: small corneous grains store better than large
soft ones.

7.8.6 Stalk Dryness and Sweetness

Dry stalks are controlled by a simple dominant gene, D; juiciness is recessive. Dry
stalks have a white leaf midrib; juicy stalks have a dull green leaf midrib (possibly
with a narrow white strip in the middle). An insipid stalk is controlled by a single
dominant gene, , sweetness being recessive. There is apparently no linkage
between the genes at loci controlling the dry juicy and insipid sweet characters.
There is no clear evidence favoring either sweet or non-sweet stalks for forage;
livestock eat both.

7.8.7 HCN Content

Sorghum produces HCN, which may be dangerous when the crop is used for feed.
The problem is particularly acute in seedlings or on re-growth of a ratoon crop and is
aggravated by drought and low temperatures. Inheritance seems to be controlled by
more than one factor, and in many cases low HCN content shows partial dominance.

7.8.8 Plant Colors

Genes for plant color influence the green portions of the plant—leaves, stems, and
glumes. The gene P produces a purple color, and recessive plants (pp) are tan. The
shade of purple pigmentation is influenced by alleles at the Q locus; purplish-black is
due to the allele q, and reddish-purple is due either to the Q or q0 alleles.
7 Sorghum Breeding 391

7.8.9 Glume Color

This is controlled by the same two loci (P and Q). Black and red glumes are
dominant (P-), and mahogany or sienna glumes are recessive (pp). There appear to
be inhibitors causing the glume colors in some plants to fade. A red pigment appears
in dead leaves and sheaths in red-seeded varieties, but not in white-seeded ones.
Genes R-yy are responsible for red pericarp color and for this effect in dead leaves.
The Q gene influences color in plant sap (spots on white-seeded varieties are red in
red-pigmented plants and purple black in purple-pigmented plants.)

7.8.10 Grain Color

This is determined by pigmentation of the pericarp, testa, and endosperm. Color in

these tissues is controlled by different sets of genes. Genes for grain color are the
following:

Ce. Plant color is present in the testa and the glume cup (Q is expressed).
B1, B2: Cause a brown testa (when both genes are found in presence of Ce).
B1b2, b1B2, B1B2, and Ce B1B2 have colorless testas.
S1: Testa spreader, in the presence of B1 and B2, results in brown color in the
epicarp (outer layer of the pericarp).
Y: Epicarp is yellow color (in rrY-condition) versus white (yy condition).
R: Epicarp is red if Y is found; otherwise it is yellow or white.
I: Intensifies color of the pericarp (epi-carp).
Bw1 and Bw2 are complementary factors; when both are found, there is a brown
wash on the seed.
M: Causes a colored wash on the seed.
Pb: Causes purple blotching of the seed.
Pt: Causes a purple tip on the grain.

7.8.11 Endosperm Characters

Wx (waxy) results in a starch with a normal amylose-amylopectin balance; when

homozygous, the recessive allele wx results in a waxy endosperm, i.e., a predomi-
nance of amylopectin. Su (sugary) gives normal sugar content, while the recessive
(su) condition results in high sugar content. Seeds are usually dimpled, and the stems
are usually sweet. Z causes greater endosperm hardness than the homozygous
recessive z, which produces a chalky condition. Yellow pigment in the endosperm
is not well understood, but it appears that more than one major gene or modifier is
involved. The yellow color is due to xanthophylls and carotene pigments.
392 Prabhakar et al.

7.9 Breeding Objectives

7.9.1 Yield, Exploitation of Heterosis, and Hybrid Development

Sorghum is one of the crops in which heterosis could be exploited. In sorghum,

commercial exploitation of heterosis has been possible owing to (1) the availability
of a stable and heritable CMS mechanism (Stephens and Holland 1954), enabling
large-scale, economic hybrid seed production, and (2) sufficiently high magnitude of
heterosis across a range of production environments for economic characters. The
greater contribution of hybrids to yield, compared to improve and landrace varieties
has been demonstrated in almost every situation/condition. The hybrids besides
being superior for grain yield and other traits of interest are stable across
environments. The adoption of the first commercial hybrid (CSH 1) in India over
much of the rainy season sorghum area, while local varieties confining to fairly
narrow specific environmental niches, is a testimony to the wide adaptability of
hybrids over the varieties (Rao 1970, 1982).
Indian public sector agricultural research agencies have been breeding improved
sorghum genotypes since the early part of the twentieth century. In this article, the
status of research on grain sorghum hybrid development under All-India Coordi-
nated Sorghum Improvement Project (AICSIP) is reviewed. Hybrid sorghum
research in India started in the early 1960s, with the establishment of hybrid breeding
programs at a number of agriculture research centers and the SAUs in Maharashtra,
Karnataka, and Andhra Pradesh with Indian Institute of Millets Research (IIMR)
(Formerly Directorate of Sorghum Research and National Research Centre for
Sorghum) as the nodal agency dealing with all aspects of sorghum research and
development including coordination and consultancy. The Indian Institute of Millets
Research is mandated with organizing and coordinating sorghum research at all
India levels through AICSIP with a network of 18 centers located in states having
major sorghum-growing areas. Through these coordinated efforts, the Indian
national program over the years released 41 hybrids and 42 open pollinated varieties
under the kharif sorghum (rainy season), rabi sorghum (post-rainy season), sweet
sorghum, and forage sorghum. Release of more than 40 hybrids at national level and
several at state level is a standing testimony to the success of Indian sorghum
improvement program (Prabhakar et al. 2015). So far, outstanding and significant
progress has been achieved in case of kharif hybrids. But a great deal is yet to be
done to exploit heterosis in breeding hybrids for rabi cultivation.

7.9.2 Kharif Sorghum

In spite of the decrease in the area of kharif cultivation, there has been impressive
enhancement of productivity of sorghum from 560 kg/ha in 1970 TE to 1000 kg/
hectae in 2000 TE which has actually kept production levels relatively stable despite
constant erosion of area under kharif sorghum. This increase in productivity is due to
introduction of short duration dwarf high yielding hybrids which are especially well
7 Sorghum Breeding 393

adopted in the state of Maharashtra, a major kharif-growing area in the country.

Sorghum improvement program though initially followed wide adaptability as the
basis for breeding strategy, as the time goes by, considering the demands of local
conditions; it is now following specific adaptation as the breeding strategy. For
kharif sorghum, the different zones have been identified.
The discovery of cytoplasmic genetic male sterility in sorghum and its use for
hybrid-seed production made the commercial exploitation of heterosis possible.
Though the Indian sources of cytoplasm such as Maldandi (M 31-2A and M
35-1), Vijayanagaram (VZM 2A), and Guntur (G1) are well-known, the milo
cytoplasm discovered in the USA has been most extensively utilized in the entire
hybrid program of our country. The hybrid program in India was initiated in the early
1960s by attempting crosses of Indian tall cultivars as well as temperate dwarf
parents as male parents on exotic CMS lines. Combined Kafir (CK) 60A is one
such CMS line, which was extensively utilized in developing two commercial
hybrids (later released as CSH 1 using IS 84 as restorer in 1964 and as CSH
2 (1965) with IS 3691 as the male parent). The male parents of CSH 2 and CSH
3 were shorter than respective CMS lines. Therefore, they imposed restriction on the
spread of these hybrids. The next commercial hybrid, CSH 4, was based on CMS
1036A and Swarna as a male parent.
With the breeding efforts in the Indian sorghum improvement program, improved
and promising parental lines became available, and hybrids such as CSH
5 (2077A  CS 3541) and an early hybrid, CSH 6 (2219A  CS 3541), were
developed. These hybrids released in 1975 (CSH 5) and 1976 (CSH 6) showed a
quantum jump in grain yields. Both hybrids were widely adapted in the country with
acceptable grain and fodder yields as well as tolerance to grain molds and leaf
diseases (mainly attributed to the male parent CS 3541, converted zerazera line from
Ethiopian germplasm) compared to CSH 1. The next breakthrough came through the
release of CSH 9 (296A  CS 3541) based on improved parental lines. This hybrid
maintained 18–20% higher yield than CSH 5 and CSH 6 and became the best-selling
hybrid. CSH 10, a dual-purpose (grain + stover) hybrid, and CSH 11 could not find
popularity with farmers due to seed production problem and/or small seed size.
Another potential hybrid based on 296A was released as CSH 13 (296A  RS
29). It is adapted to both kharif and rabi seasons and also as single-cut fodder hybrid
and gives 45% higher dry fodder yield. As dependence on CMS 296 A increased,
diversification of CMS lines became a high priority in the late 1980s in addition to
genetic enhancement of R lines. These efforts helped to develop another set of four
hybrids, i.e., CSH 14 (AKMS 14A  R 150), CSH 16 (27A  C 43), CSH
17 (AKMS 14A  RS 673), and CSH 18 (IMS 9A  Indore 12) on new CMS
lines. The hybrids CSH 14 and CSH 17 are also known for earliness by 8–10 days
with grain yield potential of CSH 9. CSH 16 has 9% higher grain yield than CSH
9 along with bold seed and is tolerant to grain molds. The hybrid CSH 18 released by
Indore Center of AICSIP is 9% superior in grain yield than CSH 9; further it is a
dual-purpose hybrid yielding good amount of stover.
CSH 23 is another early maturing hybrid released in 2005 for the states of
Maharashtra, Karnataka, AP, MP, Gujarat, Rajasthan, and UP. It takes
394 Prabhakar et al.

101–103 days to mature and yields 43 q/ha of grain. One more medium maturing
hybrid, CSH 25, was released for zone II in 2008. It is developed from the parents
PMS 28A and C 43 and yields 43 q/ha of grain and 120 q/ha of fodder and was found
to have good tolerance to shoot fly and grain molds.
Another medium maturing hybrid, CSH 27, was released recently in 2012 for
zone I involving the states of Rajasthan, N. Gujarat, UP, AP, and Tamil Nadu. It is a
dual-purpose hybrid with 39 q/ha of grain and 136 q/ha of fodder yield. It was
developed based on the parents 279A  CB 11. It has better level of tolerance to
grain molds. The latest hybrid which has been recommended for release in zone II
comprising of the states of Maharashtra, Karnataka, MP, South Gujarat, and North
AP was CSH 30, which is an early maturing hybrid with good level of tolerance to
grain molds.
All these hybrids played a major role in pushing up productivity and production,
particularly in the case of kharif sorghum (Table 7.2). Among the kharif hybrids,
CSH 1, CSH 5, CSH 6, CSH 9, CSH 14, and CSH 16 need special mention as CSH
5 and CSH 6 had a yield potential of 34 q/ha which was raised to 40 q/ha in CSH
9 and further raised to 41.0 q/ha in CSH 16, CSH 23, CSH 25, and CSH 30 with
distinct superiority in grain and fodder quality.

7.9.3 Rabi Sorghum

Focused breeding on rabi sorghum was initiated in the early 1970s. These breeding
efforts led to the central release of varieties like Muguti. Heterosis breeding led to the
central release of hybrids like CSH-7R, CSH-8R, and CSH-12R. These cultivars
were notable in two respects: first, that none of these cultivars succeeded in gaining
consistent acceptability from farmers at a scale to effect a discernible impact and
second, there was problem of seed production of hybrids.
The second phase of rabi sorghum breeding with emphasis on hybrid cultivars
was initiated in the late 1980s. During this period, 250 experimental hybrids were
evaluated in the AICSIP trials. These trials resulted in the identification of two
hybrids, SPH 504 and SPH 677, for central release as CSH-13R and CSH-15R.
CSH-13R has significant yield superiority over M 35-1 but is highly vulnerable to
shoot fly and low temperature and has inferior grain quality. The case of CSH-15R
having a rabi based MS line (104A) developed at Mohol Centre is different from
CSH-13R which has a marginal yield advantage over M 35-1. Rabi sorghum hybrids
will have a tangible impact only when the male sterile and restorer lines having the
season adaptability and desired combining ability are developed (Rao 1970)
(Table 7.3).

7.9.4 Forage Sorghum

In the 1990s, multi-cut sorghum hybrid received much emphasis. At this juncture,
the private sector also came forward to join the efforts. Since then, many hybrids like
Punjab Sudex Chari, Pro-Agro Chari, MSFH3, Hara Sona, and Safed Moti and
Table 7.2 Nationally released kharif sorghum hybrids
7

Year
of Centre which
S. No. Hybrid/variety release Pedigree of the hybrid/variety developed Area for which recommended
1 CSH 1 1964 CK 60A  IS 84 NRCS (DSR), Hyd. Maharashtra, Karnataka, MP, Gujarat, UP,
(currently IIMR) Rajasthan, Tamil Nadu
2 CSH 2 1965 CK 60A  IS 3691 NRCS (DSR), Hyd. – do –
Sorghum Breeding

3 CSH 3 1970 2219A  IS 3691 NRCS (DSR) – do –

4 CSH 4 1973 1036A  Swarna NRCS (DSR) – do –
5 CSH 5 1975 2077A  CS3541 NRCS (DSR) – do –
6 CSH 6 1977 2219A  CS3541 NRCS (DSR) Maharashtra, Karnataka, AP, Gujarat,
Rajasthan, Tamil Nadu
7 CSH 9 (SPH 1983 296A  CS3541 NRCS (DSR) Maharashtra, AP, MP, Gujarat, Rajasthan,
61) UP.
8 CSH 10 (SPH 1984 296A  SB 1085 Dharwad Maharashtra, Karnataka, AP, MP,
196) Rajasthan, UP
9 CSH 11 (SPH 1986 296A  MR 750 ICRISAT Maharashtra, AP, MP, UP, Gujarat,
221) Rajasthan, Tamil Nadu
10 CSH 14 (SPH 1992 AKMS14A  AKR 150 Akola Maharashtra, Karnataka, AP, UP,
468) Rajasthan, Tamil Nadu
11 CSH 13K & R 1995 296A  RS 29 NRCS (DSR), Hyd. Maharashtra, AP, MP, UP, Gujarat,
(SPH504) Rajasthan, Tamil Nadu, Karnataka
12 CSH 16 (SPH 1997 27A  C43 NRCS (DSR) Maharashtra, Karnataka, AP, MP, UP,
723) Gujarat, Rajasthan, Tamil Nadu
13 CSH 17 (SPH 1998 AKMS 14A  RS 673 NRCS (DSR) Karnataka, Gujarat, MP, Tamil Nadu
660)
14 CSH 18 (SPH 1999 IM 9A  Indore 12 Indore Maharashtra, Karnataka, AP, MP, UP,
960) Gujarat, Rajasthan, Tamil Nadu
15 CSH 21 (SPH 2005 MLSA 848  MLR 34 Mahendra Hybrid For the zones I and II: Maharashtra,
1342) Seeds, Jalna Karnataka, Andhra Pradesh, Madhya
395

Pradesh, Gujarat, Rajasthan, Uttar Pradesh

(continued)
Table 7.2 (continued)
396

Year
of Centre which
S. No. Hybrid/variety release Pedigree of the hybrid/variety developed Area for which recommended
16 CSH 23 (SPH 2005 MS 7A  RS 627 NRCS (DSR) – do –
1290)
17 CSH 25 (SPH 2005 PMS 28 A  C43 Parbhani and DSR All major kharif sorghum areas of
1567) Maharashtra, Karnataka for sole crop
18 CSH 26 (SPH 2011 MLSA 848  R 400 Devgen Seeds & Crop Maharashtra, Karnataka, MP, South
1629) Tech Pvt. Ltd, Gujarat, North AP, and Tamil Nadu
Secunderabad
19 CSH 27 (SPH 2012 279 A  CB 11 DSR, Hyderabad Rajasthan, north Gujarat, UP, AP, and
1644) Tamil Nadu
20 CSH 28 (SPH 2013 NS 516A  NS444R Nuziveedu Seeds, Maharashtra, Karnataka, MP, south
1647) Secunderabad Gujarat, and north AP (zone II)
21 CSH 29 (SPH 2013 501A and 606R Mahodaya Hybrid Maharashtra, Karnataka, MP, South
1648) Seeds Pvt. Ltd, Jalna Gujarat, and North AP (zone II)
22 CSH 30 (SPH 2012 415 A  CB33 DSR, Hyderabad Maharashtra, Karnataka, MP, South
1655) Gujarat, North AP under rainfed kharif
cultivation
23 CSH 32 (SPH 2014 MLA 55 and R 421 Devgen Seeds Maharashtra, Karnataka, MP, South
1674) Gujarat, and north AP
24 CSH 33 (SPH 2015 NS 509A  NB 235 R Nuziveedu Seeds Rajasthan, UP, North Gujarat, South
1703) Andhra Pradesh, and TN
25 CSH 34 (SPH 2016 HTJP001 A  HTJP002 R Hytech Seed Maharashtra, Karnataka, MP, AP,
1702) Chhattisgarh Gujarat, and Rajasthan
26 CSH 35 (SPH 2016 AKMS 30 A  AKR 504 Akola Maharashtra, Karnataka, MP, South
1705) Gujarat, and Telangana
27 CSH 37 (SPH 2017 HTJP004A  HTJP007R Hytech Seed All India
1778)
Prabhakar et al.
 7

28 CSH 38 (SPH 2017 HTJP008A2X HTJP006R Hytech Seed All India

1779)
29 CSH 2018 296-1A  C43 IIMR All kharif sorghum-growing areas of MP,
41 (JAICAR Rajasthan, Gujarat, Maharashtra,
GOLD; SPH Karnataka, AP, TS, and TN
1820)
Sorghum Breeding

30 CSH 42 (SPH 2020 Single cross Hybrid: 2219A  SVD 1278 UAS-Dharwad Karnataka, Madhya Pradesh, Andhra
1883) SVD-1278 is a R line developed by Pradesh, and Gujarat
pedigree breeding from a NCB breeding
material code 09R-GQ-02
397
398 Prabhakar et al.

Table 7.3 Rabi sorghum hybrids released at national level

Year
of Pedigree of the Centre which Area for which
S. No. Hybrid release hybrid/variety developed recommended
1 CSH 7R 1977 36A  168 NRCS(DSR) Maharashtra,
IIMR Karnataka, AP
2 CSH 8R 1977 36A  PD3-1- Parbhani Maharashtra,
11 Karnataka, Gujarat,
AP
3 CSH 12R 1986 296A  M148- Dharwad Maharashtra,
(SPH 218) 138 Karnataka, Gujarat,
AP
4 CSH 13R 1991 296A  RS29 NRCS (DSR) Maharashtra,
(SPH 504) Karnataka, Tamil
Nadu, Gujarat, AP
5 CSH 15R 1995 104A  RS NRCS (DSR) Maharashtra, eastern
(SPH 677) 585 parts of Karnataka,
Tamil Nadu, Gujarat,
AP
6 CSH 19R 2000 104A  R354 Akola Maharashtra,
(SPH 1010) Karnataka, Gujarat,
(AKMS AP
9601(R))
7 CSH 31R 2013 MLSA Devgen All rabi sorghum-
(SPH 1666) 1426  6644R Seeds, growing states of
Secunderabad India
8 CSH 39 R 2017 AKRMS 66-2 PDKV Akola All India—deep black
(SPH 1801) XSPV 1359-3 soils

varieties like UPMCH 503 have been released. In addition to high green and dry
fodder yields and wide adaptability, these varieties have high seed production,
resistance to foliar diseases, and better-quality fodder. From an interspecific cross,
a multi-cut variety, Co(FS)29, was released from Coimbatore in 2001. Multi-cut
hybrids developed at Pantnagar, CSH 20MF and CSH 24MF, have improved fodder
yield and quality (Table 7.4).

7.10 Major Constraints of Hybrid Adoption

7.10.1 Kharif Sorghum

The yield levels of kharif sorghum hybrids and varieties are showing a tendency
toward plateauing, and critical studies are needed to get over this. This could be
accomplished through (a) wider exploitation of genetic resources in line improve-
ment, (b) refinement of breeding procedures, (c) diversification of male sterile
parents including the use of diverse cytoplasmic sources and restorers, and
 7

Table 7.4 Forage sorghum hybrids released at national level

Year
of Pedigree of the hybrid/
S. No. Hybrid release variety Centre which developed Area for which recommended
Sorghum Breeding

1 CSH 13 2000 296 A  RS 29 NRCS (DSR) All India cultivation

2 PCH 106 1997 MS 2219 A  PC 23 IARI, New Delhi All India cultivation
3 CSH 20MF (UPMCH 2005 2219 A  UPMC 503 Pantnagar All India cultivation
1101)
4 CSH 24MF 2009 467 A  UPMC 503 Pantnagar All India cultivation
(UTMCH1302)
5 CSH 36 F (SPH 1752) 2017 MLA0052  MLSFR0179 Syngenta India Ltd. Pune Single-cut forage for irrigated growing
(DFSH 109/Dairygreen) condition for medium to high soil fertility under
normal sowing window for spring and kharif
season for Delhi, Gujarat, Rajasthan,
Uttarakhand, Haryana, Uttar Pradesh, and
Punjab
6 CSH 40F (SPH 1797); 2017 11 A2  Pant Chari 5 G.B. Pant University of Delhi, Gujarat, Rajasthan, Uttarakhand,
(UTFSH 2) Agric. and Tech., Haryana, Uttar Pradesh, and Punjab
Pantnagar Maharashtra, Tamil Nadu, Karnataka, and
Madhya Pradesh for cultivation during rainfed
kharif season. Optimum temperature for good
crop growth 28–350  C
7 CSH 43 MF (SPH 1881) 2020 11A2  Pant Chari 6 G.B. Pant University of Haryana, Punjab, Rajasthan, Gujarat,
Agric. and Tech., Uttarakhand, Uttar Pradesh, Maharashtra,
Pantnagar Tamil Nadu, Telangana, and Karnataka
399
400 Prabhakar et al.

(d) incorporation of multiple resistance traits for insect pests, diseases, and striga.
The major constraints for hybrid in kharif are discussed below.

7.10.1.1 Lack of Demand for Kharif Sorghum as Food

Kharif sorghum is not preferred as food because of quality concerns. However, the
utilization of kharif sorghum grain as a raw material in various industries is increas-
ing, given the limited prospects of rainy season (kharif) sorghum for human con-
sumption. The main industries currently using sorghum in India are the poultry feed,
animal feed, and alcohol distilleries.

7.10.1.2 Poor Grain Quality of Kharif Sorghum

The kharif seed is not as remunerative as that of rabi produce because the seed is not
round and lustrous. Though grain yield was doubled by utilization of exotic breeding
material in hybrid program, this resulted in relatively poor grain quality (in turn led
to consumers’ non-preference and price differences between locals and hybrids). The
grain quality of the hybrids was inferior to that of local varieties as selection process
among temperate  tropical crosses was more on heterotic lines rather than on
quality of the grain. Efforts are underway to make kharif seed bold and lustrous by
using diverse germplasm lines from world collection.

7.10.1.3 Susceptibility to Grain Molds

Development of high yielding cultivars with relatively early maturity resulted in
coincidence of grain development with late rains during certain years. This increased
the incidence of grain molds that largely nullified the advantage of increased
productivity.

7.10.1.4 Susceptibility to Shoot Fly

High yielding cultivars of sorghum are also generally vulnerable to shoot fly
particularly under late sowing.

7.10.1.5 Yield Plateau in Kharif Hybrids

Looking over the years, whenever there was a change in male sterile line, the yield
increased. There is a need for developing new male sterile lines having better
combing ability in comparison to that of available MS lines. Till now, a lot of
germplasm of different botanical races have been utilized in the development of
parental lines. The grain yield levels of rainy season hybrids have reached plateau,
and there is a need to exploit unused germplasm. The yield genes are to be identified
from unexplored photosensitive germplasm lines from world collection, and these
lines are to be converted into photoinsensitive ones before proper use.

7.10.2 Rabi Sorghum

Difficulties in recombining grain and fodder yield, grain quality, and resistance to
biotic and abiotic stresses equivalent to popular variety Maldandi restricted genetic
7 Sorghum Breeding 401

improvement to a few varieties and hybrids only. Multiple trait selection is coupled
with low genetic advance in rabi sorghum. Both grain and fodder being of higher
value than that of kharif, building high grain yield and increased harvest index at the
expense of fodder yield could not be favored. This is one of the reasons why there is
low magnitude of heterosis in rabi compared to kharif.
Contrary to kharif hybrids, the heterosis in rabi hybrids is insignificant because
the landraces (which are low community performers) are used (mainly to maintain
the consumer-preferred grain size and luster) in the development of both parents. It is
envisaged that introduction of larger grain size and luster in the female parents of
kharif hybrids by novel methods and hybridizing such female parents with rabi based
R lines would increase the yield levels of rabi hybrids to fetch better farm incomes to
farmers.
Other constraints restricting the yield improvement in rabi sorghum include:

• Growing crop over large area in medium to shallow soils where the occurrence of
drought is much faster than the deep soils
• Susceptibility to shoot fly and charcoal rot
• Low temperature affecting growth
• Lack of appropriate hybrids with required traits of rabi adaptation and limited
response to applied nutrients under moisture stress situation. Low heterosis
because of using maldandi for the improvement of both parents

7.11 Biotic Stresses

In the early 1960s, the first organized sorghum improvement program was started in
India when the Indian Council of Agricultural Research (ICAR) initiated an
“Accelerated hybrid sorghum project” in 1962. The intensive research efforts of
this project resulted in the development of the first commercial hybrid, CSH1, in
1964. Thereafter, the development and release of new sorghum hybrids and varieties
marked a genetic breakthrough in the yield levels of sorghum in India. During the
1980s and 1990s, focus was shifted to insect and disease resistance breeding.
Initially, it was mainly concentrated on the screening of germplasm for insect and
disease resistance, identifying traits associated with resistance, inheritance of resis-
tance, and development and evaluation of segregating populations. As of now,
significant improvements have been made particularly in developing screening
techniques for major pest and diseases. New resistance germplasm lines have been
identified for shoot fly (Atherigona soccata), stem borer (Chilo partellus), midge
(Stenodiplosis sorghicola), aphids (Schizaphis graminum and Melanaphis sacchari),
shoot bug (Peregrinus maidis), and grain mold, charcoal rot, and foliar diseases (Das
and Padmaja 2016).
402 Prabhakar et al.

7.11.1 Breeding for Resistance to Diseases

Among the diseases of sorghum, grain mold is the most important during kharif
seasons followed by foliar diseases, viz., downy mildew, anthracnose, and ergot. Out
of these diseases, grain mold is one of the principal reasons behind reduction in
kharif sorghum area. Mechanism of resistance against grain mold and its inheritance
are very complex with significant genotype-environment interaction. The Guinea
and zera-zera races from West Africa have provided resistance against grain mold
and other foliar diseases. Through introgression program using these sources, which
were otherwise not agronomically desirable, 14 genetic stocks have been developed
and registered with the National Bureau of Plant Genetic Resources. Converted MS
lines with grain mold resistance helped in infusing resistance in the hybrids and
cultivars. In all of India, testing moderate resistance among test entries remained a
focused attention. Significant tolerance against grain mold was infused in CSH 16.
Integration of tan pigmented plant types in kharif program further helped breed
disease-resistant varieties and parental lines. Unlike kharif sorghum, grain mold or
other foliar diseases are not of major concern in rabi sorghum. Charcoal rot is a
major problem, which gets aggravated under water stress. Resistance among high
yielding rabi cultivars is low. Incorporation of drought tolerance is likely to infuse
charcoal rot tolerance, and this problem is handled accordingly.

7.11.1.1 Grain Mold

Grain mold is one of the most important biotic challenges to address in kharif (rainy
season) sorghum-growing areas. Overall the sorghum grain per hectare has
increased, but the total area under cultivation has been declining. There are several
reasons for this decrease such as low demand for sorghum, limited commercializa-
tion, limited yield gains, and grain mold susceptibility. The grain molds are caused
by complexes of fungi, predominantly by Fusarium moniliforme, Curvularia lunata,
F. semitectum, and Phomasorghina. Breeding grain mold-resistant sorghum hybrids
and varieties requires identification of useful resistance gene(s) in the germplasm or
defining other sources of such genes. Highly significant correlations between
measures of grain mold and seed hardness, seed phenol content in acid methanol
extract, and glume color indicated that they strongly affected grain mold response.
Harder grain, higher levels of seed phenols, and darker glumes contributed to grain
mold resistance. Weaker and less consistent correlations between measures of grain
mold and seed color, seed flavan-4-ol content, glume phenol and flavan-4-ol
contents, and glume cover indicated relatively less effect of these traits on grain
mold response.
Success in developing grain mold resistance in high yielding genotypes was
limited because of the fact that grain mold resistance is governed by multiple
mechanisms of resistance and many agronomically undesirable traits are associated
with the resistance (Aruna and Audilakshmi 2004). Moreover, resistance should be
incorporated in the genotype with acceptable grain quality, which is governed by
several major and minor genes showing significant genotype (G)  environment
(E) interactions. Due to this, breeding efforts in about three decades to develop grain
7 Sorghum Breeding 403

mold resistance in high yielding genotypes have not paid many dividends. The
complex genetics of mold resistance is due to the presence of different mechanisms
of inheritance from various sources. Evaluation of segregating population for resis-
tance and selection for stable derivatives in advanced generations in different
environments was found effective. The grain mold occurring before physiological
maturity (PM) is influenced by genetics and to some extent by the environment.
Efforts were made to assess the host plant resistance at pre-PM stage.
Along with conventional breeding, population breeding approach has been
initiated during 2000 to tackle grain mold problem. There is an improvement of
grain mold incidence over three cycles of random mating (personal communication).
Through random mating population, an improvement to the tune of grain mold score
7 in cycle I and score of 6.4 in cycle II was realized in B lines from the base score of
9.0. Similarly, improvement of 6.5 score in cycle I and 5.4 in cycle II was realized
over the base score of 8 in case of R lines.

7.11.1.2 Foliar Diseases

In sorghum, apart from grain mold, downy mildew, anthracnose, and ergot are the
major diseases during kharif season. Sorghum crop is also infected by several foliar
diseases like leaf spots, chlorotic stripe virus, and rust which are prevalent under
warm humid conditions and are highly destructive. These diseases reduce the
amount of green leaf area available for photosynthesis and affect the quality of
fodder by reducing the protein, zinc, and IVDMD (in vitro dry matter digestibility).
The use of host plant resistance is considered to be more practical and reliable for
managing foliar diseases. To develop resistant cultivars, plant breeders require a
detailed knowledge of the inheritance of resistance. Resistance can be complex,
controlled by a single or several genes depending on the source of resistance, plant
development stage, and the pathotype used. Recently, genes for anthracnose resis-
tance in sorghum have been mapped to chromosomes SBI-05 and SBI-08 (Perumal
et al. 2008). Mohan et al. (2010) reported QTLs (quantitative trait loci) conferring
resistance to foliar diseases. This information generated will be useful for transfer-
ring resistance into elite susceptible cultivar through marker-assisted selection
(MAS).

7.11.1.3 Charcoal Rot

Charcoal rot caused by Macrophomina phaseolina Tassi (Goid) is a stress-related
disease. The disease is prevalent in entire rabi (post rainy) sorghum-growing tracts.
Post-flowering lodging and poor grain filling indicate that the crop is infected by this
disease. There are studies on inheritance of this disease. It was noticed that domi-
nance of susceptibility governed by three major, one basic complementary, and two
duplicate complementary genes. Reports of partial dominance, non-additive with a
high degree of dominance (Indira et al. 1984), polygenic threshold character
governed by partial dominance, duplicate epistasis, and low heritability among the
crosses involving resistant and susceptible parents have been studied. Polygenic
nature of susceptibility was reported with dominance in the F1 generation. On further
investigations it revealed non-allelic interactions, like additive  dominance and
404 Prabhakar et al.

dominance  dominance with a major role in an inheritance of this trait. Dominance

gene action was observed for resistance with over-dominance and low heritability
values for number of nodes crossed and length of stem infected by the pathogen
(Garud and Borikar 1985). Phenolic compounds produced by sorghum plants also
attribute resistance against pathogens by inhibiting spread of fungus during the dry
period thus making sorghum plant tolerant to pathogen.

7.11.2 Breeding for Resistance to Insect Pests

Shoot fly is the most important insect pest of sorghum both in kharif and rabi
seasons, followed by stem borer and midge. Large-scale screening of germplasm
against shoot fly has led to identification of moderately resistant sources. However,
transfer of shoot fly resistance to cultivars has still remained elusive due to complex
nature of inheritance. IS 18551 is a proven source of resistance against shoot fly.
Major QTLs governing shoot fly resistance have been identified, and currently
efforts are being made to convert parental lines of popular hybrids through
marker-assisted selection. Against stem borer efforts are being made to use identified
sources of resistance like IS 2205 in breeding program and to screen the advanced
lines at hot spots. In case of both shoot fly and stem borer, simultaneous screening of
new cultivars under all India coordinated programme at the hot spots has led
to identification and release of cultivars with moderate tolerance. Transgenic
approaches are also being made to infuse resistance against stem borer using
Cry1b gene, and initial field evaluation of advanced events showed much promise.
Sources of resistance against midge have been identified. One midge-resistant
cultivar, DSV 3, has been released for the state of Karnataka, which is a selection
from ICSC 745. In recent past, aphid is emerging a major pest, particularly under
rabi sorghum. Sources of resistance have been identified, and currently, efforts are
being made to understand the genetics of aphid resistance for deciding effective
breeding strategies.

7.11.2.1 Shoot Fly

The major task of screening 10,000 germplasm and variety world collections was
systematically done at different locations. Initially, the “deadheart” was taken as the
parameter for evaluating resistance. This work resulted in the identification of a
number of varieties with comparatively less shoot fly damage. The identified lines
were from the rabi-growing areas. The genetic studies revealed that the shoot fly
resistance is a very complex trait and quantitative in nature with various mechanisms
of resistance (Dhillon et al. 2006). Resistance attributing traits like leaf glossiness,
trichome density on lower surface of leaves, and seedling vigor deter shoot fly from
egg laying and confer resistance (Dhillon et al. 2005). The inheritance studies also
revealed that the alleles for shoot fly resistance are contributed by both resistant and
susceptible parents and thus require methodologies to bring together the favorable
alleles present in the resistant and susceptible genotypes. Resistance exhibits partial
dominance under low infestation but appears to be partially recessive under high
infestation. Insect populations vary from location to location and season to season,
7 Sorghum Breeding 405

causing varying degrees of damage. In the absence of high levels of resistance,

persistence or stability of even a low level of resistance is of considerable value. This
can be handled by the application of advanced breeding technologies like marker-
assisted breeding (Aruna et al. 2011a, b, c). Identification of varieties with such
inherent genetic characteristics is useful for a resistance breeding program.
Subsequent screening in the All India Coordinated Sorghum Improvement Project
(AICSIP) has identified a number of resistant lines. During kharif 2009, 1321
experimental lines (1250 lines from National crossing Block, 26 advanced progenies
from MAS program, 24 shoot fly nursery lines, and 21 germplasm accessions) were
evaluated for shoot fly resistance. About 21 lines were selected that which showed
on a par performance with resistant check IS 2312.
Recently, in one of the novel approaches, field observations have suggested that
shoot fly-susceptible sorghum varieties emit attractive volatiles. Efforts are under-
way to identify plant-derived attractants for shoot fly in relation to breeding sorghum
varieties less attractive to this pest (Padmaja et al. 2010).

7.11.2.2 Stem Borer

Sources for stem borer resistance were reported by Trehan and Butani (1949). About
3953 germplasm lines from world collection were systematically screened. Plant
height, tassel percentage, stem thickness, number of leaves, leaf length, leaf width,
leaf thickness, and leaf strength are negatively correlated with deadheart formation.
Days to panicle initiation and shoot length are associated with resistance to stem
borers. Genotypes with early panicle initiation (IS 12308 and IS 13100) escape
deadheart formation due to inability of the larvae to reach the growing point. Faster
internode elongation is also associated with borer resistance. Shoot length, moisture
content, plant growth rate or seedling vigor, leaf glossiness, and ligular hairs are
associated with resistance. Antibiosis is a major factor associated with stem borer
resistance. A number of biochemical factors such as amino acids, sugars, tannins,
phenols, neutral detergent fiber, acid detergent fiber, lignins, and silica content also
contribute to resistance mechanism. Information on these factors is very important
for any breeding program. On the basis of general (GCA) and specific combining
ability (SCA), estimates revealed the additive type of gene action in governing
resistance to spotted stem borer. Presence of both antixenosis and antibiosis to
C. partellus in terms of reduced eggs per plant, larval survival, and development
was reported in the advance breeding lines developed (Padmaja et al. 2012). Results
indicate the transmission of characteristics responsible for resistance to the progeny
from the resistant parent.

7.11.2.3 Sorghum Midge

Sorghum midge, Contarinia sorghicola (Coquillett), is probably the most common
insect pest of sorghum in most of the sorghum-growing countries. Resistance
sources have been reported from several countries. Midge resistance is a
polygenically inherited trait and governed by both additive and non-additive gene
action. Knowledge about the traits attributing resistance is important for developing
screening techniques. Most of these traits are not present in single genotypes, so
406 Prabhakar et al.

there is need to club them in a common background to increase the resistance levels.
Use of random-mating populations appears to be ideal for accomplishing this task.
Patil and Thombre (1983) reported that both gca and sca effects were important for
midge resistance. They found additive genetic variance greater than non-additive
genetic variance. Also resistance has to be present in both parents of a potential
hybrid.

7.12 Abiotic Stress Resistance Including Climate Change

7.12.1 Genetic Improvement Against Abiotic Stresses

Among biotic stresses, drought is the main production constraint in rabi sorghum.
Though sorghum possesses excellent drought tolerance, post-flowering drought
causes extensive yield losses to the crop. Stay greenness is considered as an
important trait attributing drought tolerance in sorghum. Major QTLs contributing
toward stay-green trait has been identified and are being attempted to be transferred
to superior cultivars. Crossing between high yielding adapted lines and screening
under stress situation has yielded release of several rabi adapted cultivars both at
state and central level. The varieties are necessarily drought tolerant and were
released based on the performance under specific soil situations.

7.12.2 Breeding Approaches for Drought Tolerance

The development and use of crop cultivars adapted to water-stressed conditions is a

long-term solution for improving and stabilizing crop productivity. Sorghum will
likely become much more important in arid and semi-arid regions of the world as the
demand for limited fresh water and global warming trends increases. Drought
resistance in sorghum is a complex trait affected by several interacting plant and
environmental factors. The growth stage (GS) at which moisture stress occurs is very
important in determining the response or reaction of sorghum to water stress.
Strategies for genetic enhancement of crop plants for drought tolerance have been
widely discussed. It has been postulated that the genes for yield and tolerance to
stresses are different, at least at some of the loci, and therefore, drought tolerance can
be improved without sacrificing substantial yield.
Four basic approaches to the breeding for drought tolerance/resistance have been
proposed. The first is to breed for high yields under optimal conditions, i.e., to breed
for yield potential, and then to assume that this will provide a yield advantage under
suboptimal conditions. The second is to breed for maximum yield by empirical
selection in the field in the target drought-prone environment. The success of this
approach depends entirely on how variable the target environment is. It works well
in the Indian post-rainy season environment, which is very predictable, but not in the
rainy season environment, which is highly unpredictable. The third approach is to
incorporate the selected physiological and/or morphological mechanisms conferring
7 Sorghum Breeding 407

drought tolerance into traditional breeding programs. The fourth breeding approach
involves identifying key trait that confers drought tolerance at specific growth stages
and its introgression into the high yielding background. This method involved
selecting (through pedigree selection) breeding materials for specific traits such as
(1) longer mesocotyl length for emergence under crust and grain yield under
drought-prone and yield potential areas for early seedling stage drought; (2) for
grain yield under drought-prone and yield potential areas alternatively for
mid-season drought; and (3) for stay-green and non-lodging and grain yield under
drought-prone and yield potential areas alternatively for terminal drought.
Crosses were made between high yielding adapted lines, and lines were selected
for high yields under drought and/or with one or more drought-related traits.
Selections from F2 onward were made by evaluating the segregating material in
alternate generations under specified drought (early, mid-season, and terminal stage)
and in yield potential environments. The F5/F6 pure lines are evaluated for drought
yields, potential yields, and specific drought-related traits. Testing for yield under
mild stress was adequate as the rankings of genotypes for potential and drought
yields were similar, since the drought-tolerant lines selected under mild stress had
high yield potential in non-stress environments. However, breeding for drought
tolerance has been slow due to G  E interaction effects (Sajjanar et al. 2011).

7.12.2.1 Heterosis Breeding for Drought

Rao and Khanna (1999) reported the superiority of sorghum hybrids over their
parents for leaf area and dry matter production under both pre-flowering and post-
flowering drought stress. Potential for hybrid breeding for drought tolerance in rabi
sorghum was reported by Patil et al. (2013). The increased performance of hybrids
than their parents is due to greater growth rates and greater total biomass production
and higher harvest index with or without an apparent increase in leaf photosynthetic
rates. Bhale et al. (1982) found that some sorghum hybrids showed heterosis for
proline accumulation (known to confer drought tolerance) under moisture stress.
Evidences suggest that wider adaptability of hybrids is due to their relative tolerance
to a wide range of abiotic stresses including soil moisture stress and related factors
than varieties. The improvement of per se performance and combining ability of
parents for agronomic traits and grain yield under drought stress should be given
strategic importance, considering that parental per se performance and general
combining ability in sorghum are strongly correlated with hybrid performance
(Bhavsar and Borikar 2002).

7.13 Quality Characters Including Biofortification

7.13.1 Genetic Improvement for Grain Quality

Physical quality of sorghum refers to color, size, texture, and luster of grain.
Genetics of all these traits are quite complex. However, breeding efforts have
succeeded in developing hybrids with bold and round grains by having at least
408 Prabhakar et al.

one parent with desirable trait(s). In rabi sorghum, the breeding efforts always
revolved around grain quality in terms of physical appearance and roti-making
qualities. Among recently released varieties, CSV 22, Phule Vasudha, Phule Chitra,
and Parbhani Moti have very good roti-making qualities besides being high yielders.
Besides roti quality, sorghum is also used for other preparations as well like pop
sorghum, papad making, and hurda sorghum. Some such special sorghum varieties
are RSSGV 46 (hurda purpose), RPASV 3 (papad making), SMJ 1, RSJ 1, PKV
Ashwini (hurda purpose), AKJ 1 (flaking purpose), KMJ 1 (popping purpose), etc. In
terms of biochemical quality, starch and protein quality, protein digestibility, and
iron and zinc content are important characters. However, till recently, these traits
were not the focus of breeding efforts due to complexity of the trait. Currently
focused breeding efforts using biotechnological tools have been initiated at the
national level. Efforts are also being made to identify specific cultivars for specific
end uses. Grain sorghum can be processed to develop different end products, flours,
semolina, alcoholic beverages, pet foods, packaging materials, etc. (Aruna et al.
2018). A wide range of end use products that can be made from sorghum demand
different grain characteristics and altered crop ideotype. Lot of research is underway
at the Indian Institute of Millets Research on suitability of sorghum for different end
uses, and also a successful and sustainable value chain model has been furnished
through innovations in sorghum food processing assuring sustainable food and
nutritional security (Aruna et al. 2020a, b; Dayakar Rao 2018).
The rabi sorghum possess excellent grain quality and are characterized by bold
and round grains and have a characteristic luster. Among various sorghum food
preparations, the unleavened roti and bhakri are prepared and consumed tradition-
ally. Compared to hybrids, landraces/varieties possess superior quality traits and are
more suited for food purposes Dough and roti properties of hybrids were much
inferior to those of the local cultivars (Anantharaman 1968). Viraktamath et al. in
1972 reported differences among varieties for culinary properties in sorghum and
demonstrated that the traditionally grown cultivars possessed relatively superior
culinary properties over recently developed cultivars. During the 1960s in India,
several hybrid combinations superior for yield were developed; however, they were
reported non-acceptable. Anantharaman (1968) observed considerable variation for
roti quality among hybrids with pearly white grains. M 35-1 (Maldandi), a sorghum
cultivar, is known for its good quality of roti due to having pearly white grain color,
its flour having higher water-holding capacity and good organoleptic taste. However,
this cultivar is low yielder. To evolve sorghum high yielding genotype coupled with
these good roti qualities, systematic breeding program was planned and executed at
MPKV, Rahuri.
Local landraces RSLG 428-1, RSLG 1238, and RSLG 1275 and the genotypes
RSV 290, RSV 292, RSV 858, RSV 859, RSV 861, RSV 868, RSV 894, RSV
985, RSV 992, RSV 995, and RSV 999 were found to be promising for protein,
sugar, water absorption, and soluble protein content and were suggested for further
improvement in nutritional quality through breeding program. Among the latest
cultivars, Phule Vasudha (RSV 423), CSV 22, and Phule Chitra (SPV 1546) were
found to be the most promising for roti quality (Chavana et al. 2009). Bhakri
7 Sorghum Breeding 409

prepared from rabi sorghum is white and more palatable than that of kharif sorghum.
Apart from roti, several other food preparations like popping are prepared and
consumed in traditional sorghum-growing states. The popped sorghum grains were
found to have much flavor and to be as nutritious as popcorn (Subramanian 1956).
Popped sorghum grains are used in the preparation of sweet snacks, which are
commonly consumed in Maharashtra. It was reported that popping varieties of
sorghum belong to the Talavirchina group (S. roxburghii var. hians) characterized
by small grain with a dense and corneous endosperm (Ayyangar and Ayyer 1936).
Pelalujonna belonging to the Snowden species S. membranaceum was considered to
be good for popping (Reddy 1957).
Apart from its major use as food, the crop finds its potential for alternative uses
such as livestock and poultry feed, potable alcohol, and starch and ethanol produc-
tion. In India, rainy season produce is mostly used for industrial purposes due to
inferior-quality grains infected by molds. Mold-affected grains are generally not
used for food purposes, but recent efforts are being made to remove mold-affected
parts by decortication or pearling techniques and test its feasibility for food uses.

7.14 Breeding Approaches: Conventional

and Non-conventional Including the Use of Genomic Tools

7.14.1 Conventional Approaches

Sorghum is grown in a wide range of physical conditions in locations ranging from

the equator to over 50 N and 30 S. The crop is therefore subject to a wide variety of
temperature, day length, and moisture regimes. Development of improved sorghum
cultivars for a particular environment always involves breeding for adaptation to the
specific climatic conditions found there. This is usually indicated by the appropriate
crop duration for that environment and by acceptable and stable yield levels and
appropriate grain qual
The type of cultivar required for a target location also influences the objectives of
the plant breeder. For example, the height of a pureline variety for a specific
environment and the heights of the parental lines of a hybrid for the same environ-
ment are likely to be different.
In addition, improved cultivars for specific locations must possess resistances to
major constraints to production encountered and grain- and stover-quality factors
appropriate for sorghum there. These constraints include biotic such as diseases,
insects, and parasitic weeds and abiotic stresses, the requirements for which are
usually quite different from one location to another. Resistances to these constraints
are deliberately bred into cultivars by crossing resistant types with cultivars
possessing other desirable traits and selecting plants with both resistance and
desirable traits.
410 Prabhakar et al.

7.14.2 Trait-Based Approach

Trait-based approach for the genetic improvement of sorghum would make use of
cutting-edge technologies of plant biotechnology and molecular biology to develop
genotypes with improved performance under stress during crop growth and
enhanced quality of the produce with extended shelf life of seed, grain, and novel
sorghum products. Genomics has made rapid advances during the past decade. The
sorghum genome has been sequenced, and important gene transcripts and regulatory
mechanisms are being deciphered on a large scale worldwide. Our national program
has already begun implementing precision breeding using molecular marker-based
selection for traits under complex genetic control such as resistance to shoot fly,
post-flowering drought, and grain mold.
Efforts are on to identify genes and alleles associated with abiotic stresses and
quality using allele mining approach. The system has achieved a very high degree of
success in producing genetically transformed plants for an array of genes of interest
that add value to existing cultivars. In this background, it is necessary to explore and
attempt the new technologies for improving relevant traits. The traits of interest to be
addressed by new technologies include improving resistance to complex traits—
biotic (shoot fly, grain mold, stem borer, aphids, etc.) and abiotic (drought, salin-
ity)—improving quality (grain for food, poultry, and industry, fodder, stalk for
ethanol production) and novel bio-products. In addition, research aimed at predicting
heterosis and incorporation of apomixis needs to be pursued using new tools to help
farmers realize the maximum yield potential at minimum cost.

7.14.3 Nutritional Quality

In the past, the sorghum project carried out several genetic studies to transfer quality
protein/high lysine trait from Ethiopian sorghums with shriveled seeds and also a
purdue mutant. From the late, photosensitive Ethiopian sources, early dwarf high
lysine types with shriveled seeds and normal plump seed types were developed. The
transfer of high lysine to plump seeds was partially successful. Studies need to be
continued using modern biotechnology tools. β-carotene content in several yellow
endosperm types was analyzed, and the stability of carotene was also studied. The
studies need to be pursued.

7.14.4 Population Improvement

For incorporation of multiple traits and traits governed by quantitative genes and
population improvement procedures are ideal. Using the Maldandi source of cyto-
plasm and allowing 4–5 years of inter-mating and crossing with diverse types,
selfing was practiced, and fertile types were isolated. They were designated FR
lines. Some of them were agronomically good. When some of the FR lines were
crossed to male steriles, surprisingly, they did not restore fertility. We had a feeling
7 Sorghum Breeding 411

whether the restoration was apomictic. Development of improved populations for

incorporating multiple traits is certainly a useful adjunct.

7.15 Emerging Challenges at National and International Level

Various factors leading to the decline of sorghum crop in Indian agriculture are a
matter of concern. Sorghum-based agricultural systems need to withstand biotic and
abiotic stresses because of their cultivation mostly in unfavorable soil and climatic
conditions. Further, they also need to adjust to changing economic (prices and
income) and policy-induced stresses as has been the case in India where subsidized
wheat and rice are supplied through the public distribution system. With this
background in view, there is a need to embark on future approaches for improve-
ment. Promotion of genetic diversity, cropping system stability, and economic
advantage or parity will become the major criteria. Genetic approaches should
promote genetic diversity and cropping system performance and stability.

7.15.1 Kharif Sorghum

The higher order yield of the currently available hybrids and varieties is around
4–5 tons/ha. Average yields hover around 1 ton/ha only. The food use of kharif
sorghum is declining. Marginal yield improvements at the experimental level with-
out perceptible changes in grain quality or a major advance in insect resistance, etc.
do not make much difference. Areas under kharif sorghum have been substantially
reduced in the traditional sorghum areas due to the grain mold problem and compe-
tition from more remunerative crops (like cotton, maize, soybean, etc.), in spite of
the fact that high yielding hybrids of sorghum were developed, and their replacement
ratio had been very high (up to 90%). In view of the self-sufficiency in food grains in
the country (from other cereals) and changing food habits of the people, demand for
kharif sorghum grains as food has been substantially reduced. Hence, there is good
scope to divert kharif sorghum grain to cattle and poultry feed, biofuel, and value-
added food products as well as exports. Colored sorghums have good potential as
feed and also for export purposes.
Future program on kharif sorghum improvement should concentrate on
incorporation of resistance to grain mold by different tools, improvement of feed
value, and improvement in starch and other attributes of sorghum grain for higher
ethanol production and value addition for food products. Shoot fly resistance is being
incorporated in sorghum cultivars of economic worth. Quality standards of both
grain and forage to meet international standards need to be addressed Extension of
sorghum cultivation to non-traditional areas (e.g., rice fallows) will produce mold-
free grains, and hence it should be explored (e.g., in states like Andhra Pradesh,
Odisha, Jharkhand, Bihar, and West Bengal and in all other states).
Exploration of non-conventional areas, for harnessing favorable environmental
conditions for production of sorghum at highly cost-effective manner, is an avenue
412 Prabhakar et al.

for increasing sorghum production to compensate for lower production from kharif
sorghum. Rabi/summer conditions in rice fallows do not experience limitations from
biotic stresses like shoot fly and grain mold and therefore provide greater opportu-
nity to realize higher yields from lower investment in terms of external inputs and
natural resources (Prabhakar et al. 2015).

7.15.2 Rabi Sorghum

In view of the lack of significant progress in improving rabi sorghum yields, more
basic and fundamental genetic studies are warranted to understand the genetic
processes involved in the improvement of yield and the adaptation processes.
Studies on heterosis in diverse crosses, temperature implications, lodging, and
shoot fly and shoot bug resistance stability across early normal and delayed sowings
in the respective regions under receding soil moisture situations need to be achieved.
Terminal drought is one of the major production constraints for higher rabi
sorghum productivity and limits the use of purchased inputs like hybrid seeds and
fertilizers. Therefore, research on drought tolerance involving development of early
maturing rabi sorghum varieties and incorporation of stay-green and other drought
QTL/genes needs to be taken up. Another important issue is the lack of substantial
heterosis in rabi hybrids as landraces (which are low community performers) are
used (mainly to maintain the consumer preferred grain size and luster) in develop-
ment of both A/R parents. Breeding diversified A and R lines involving exotic durra
and other sorghum races can be of much help. However, the basic requirements of
grain quality, resistance to shoot fly, charcoal rot, and terminal drought, should be
kept in mind.
Program to develop genotypes for mechanical harvesting is required in the light
of non-availability, high cost of manual laborers, and difficulties due to crop loading.
More employment of genomic tools to dissect the complex traits of rabi sorghum per
se and its adaptability needs to be taken up in structured program involving all
AICRP centers. Programs to implement genomic selections and genome editing may
be planned as a long-term activity. In order to achieve higher genetic gains in rabi
sorghum, new tools of speed breeding can be taken up (Prabhakar et al. 2015).

7.15.3 Forage Sorghum

Forage sorghum improvement programs are beset with lack of information on

variability and useful genetic stocks for various traits. Therefore, concerted and
planned efforts are needed to collect, evaluate, catalogue, and maintain germplasm
exclusively for forage sorghum. Since sorghum is also important as a source of green
forage in the country, and the diary and livestock industry is growing in a faster pace,
strategies to develop efficient forage production systems are the need of the day.
Research on evolving high yielding cultivars with good-quality, management
practices to ensure fodder availability during lean seasons may be focused. More
7 Sorghum Breeding 413

hybrids and varieties with wider adaption are required for use across the country.
Use of wide hybridization to diversify the genetic base may be explored to incorpo-
rate desired traits.
Major areas of improvement required for forage sorghum production in India
include drought-tolerant high biomass single-cut types and high seed yielding multi-
cut hybrid parents. Another important area is to augment the protein content in all
types of forages, especially in the cultivars from public sector. The future emphasis
should be to increase per day dry matter production in single-cut cultivars. Drought-
tolerant types that can recover faster are preferred for both single- and multi-cut
types.
To get a regular supply of green fodder for a longer period of time, multi-cut
varieties having profuse tillering, quick regeneration, faster growth, and capability of
giving a minimum of 4–5 cuttings should be developed. The high yield and multi-cut
potential of Sudan grass should be further exploited in breeding program to develop
highly adapted and high yielding stable multi-cut variety of forage sorghum. Atten-
tion should be paid to stability in production of biomass and nutrient content through
resistance breeding. This can be achieved through tile incorporation of resistance to
biotic factors, improved tillering capacity, and quick growth (Prabhakar et al. 2015).

7.15.4 Sweet Sorghum

In the context of climate change, sweet sorghum outperforms other crops as an

attractive climate-resilient crop to produce ethanol, generate power, and reduce
carbon emissions produced from fossil fuel utilization. One of the obstacles to this
crop’s expansion as a biofuel feedstock is the fact that sugarcane has established
dominance over the production chain of sugar and ethanol, receiving the majority of
the investments. A limiting factor for its widespread cultivation is the availability of
varieties/hybrids adapted to different seasons and agroclimatic conditions with both
biotic and abiotic stress tolerance, including cold tolerance. Consequently, research
should address the optimization of sweet sorghum as an energy crop through
breeding for enhanced productivity under limited available resources. Genetic
improvement should focus on stalk sugar, biomass quantity and quality and general
agronomic traits, and adaption of sweet sorghum to rabi conditions and arid saline
and alkaline conditions.
Further improvement in brix juice volume and stalk yield (45 tons/ha with
hybrids) should be targeted in sweet sorghum to help improve the benefits to the
industry and farmers without any detrimental effect on grain yield. Efforts may be
made to improve the means of stabilizing the juice to minimize sugar loss during the
storage. Production of high value-added products from sweet sorghum juice may be
explored. Opportunities should be explored for the integration of sweet sorghum into
cropping systems without compromising sustainability and disruption of crop pro-
duction for other purposes including food. Sustainable value chains for sweet
sorghum for ethanol should be developed and popularized by waking with sugar
industry (Prabhakar et al. 2015).
414 Prabhakar et al.

Table 7.5 Sweet sorghum hybrids

Year of Pedigree of the Centre which Area for which
S. No. Hybrid release hybrid/variety developed recommended
1 CSH 22 SS 2004 ICSA 38  SSV NRCS (DSR) All India
(NSSH 104) 84 cultivation

The road blocks for large-scale cultivation of sweet sorghum are ethanol pricing,
limited availability of genotypes suited to different agroclimatic conditions with all
resistances, photoperiod sensitivity, and non-availability of required quantity of
feedstock suited to off-season crushing in sugar industries. There is a need to
develop sweet sorghum cultivars that produce high stalk yield per unit time, input,
energy, and land area in different agroclimatic areas of the country. These cultivars
should also be photo- and thermo-insensitive with desired levels of resistance/
tolerance to various stresses and should be of different maturities to widen the
harvest window which thereby ensures a continuous supply of feedstock to the
industry. The predominant role of non-additive gene action for most of the sweet
sorghum productivity traits like plant height, stem girth, total soluble solids, millable
sweet-stalk yield, and extractable juice yield indicates the importance of heterosis
breeding for genetic enhancement of sweet sorghum. The wide variability in germ-
plasm and hybrid parents offers bright scope for the development of high stalk
yielding sugar-rich varieties and hybrids. The introduction of the bmr trait in sweet
sorghums would result in a dual-purpose bioenergy crop that address both first- and
second-generation biofuel production issues. In sweet sorghum, a good effort has
been made to release many varieties; however, one hybrid is developed already, and
many are in pipeline (Table 7.5).

7.16 Need for Critical Analysis and Characterization

of Germplasm Collection

Because of their evolution and adaptation to poorer soils and unfavorable

agroclimatic conditions/environments, sorghum has developed unique attributes
such as tolerance to drought and heat, adaptation to poorer soils and unfavorable
conditions, nutritional and therapeutic values, processes of starch and vitamin
bio-synthetics, etc. Some of these attributes have been discussed earlier. The germ-
plasm collections of sorghum have been characterized for their morphological and
physical attributes. In the present context, the germplasm collections should be
analyzed for such specific physiological, nutritional, and therapeutic attributes and
identify the genes controlling them and their bio-synthesis and gene markers
characterizing such unique traits and processes. Such databases will be of immense
value to the improvement of millet crops by traditional as well as biotechnological
methods and marker-aided selection.
7 Sorghum Breeding 415

7.16.1 Public-Private Partnerships (PPP)

Public-private partnerships are described as collaborative efforts between public and

private sectors in which each sector contributes to the planning, resources, knowl-
edge, and capabilities needed to accomplish mutual objectives. Diversified use of
sorghum for demand generation and improvement of income is market driven. They
warrant collaborative research between agricultural research agencies, the concerned
industry, or even industrial research laboratories. Some opportunities to be explored
are in the areas as below.

Feed grains Poultry feed and dairy feed manufacturing

organizations with the private and cooperative sectors
like NDDB
Ethanol Sugar mills and ethanol manufacturing plants
Alcohol/beer Breweries association
Starch and starch-based Starch industry
production
Exports Export organizations
Straw Straw board manufacturers

7.16.2 Other Important Issues

Government policy is bound to be in favor of support for promotion of sorghum due

to increasing population growth rate and unmet demand for food consumption by
rice and wheat. Thus, it is expected that government policies are going to be
strengthened for millet promotion during different plan periods. Further, it is
expected that creation of awareness is being given more importance so as to generate
consumption demand owing to nutritional merits of sorghum. The increasing inci-
dence of lifestyle diseases which are linked with relatively poor nutritive composi-
tion of fine cereals especially rice and the promotion of nutri-cereals such as
sorghum will be more pronounced owing to their superior composition of nutrients
and minerals. It is also expected that sorghum as a healthy food is being included in
PDS which may gain some area under sorghum.
Overall, at least 88% increase in millet acreage over the current levels is expected
to be attained by 2050 AD, if policy push and demand creation trend is going to be
continued, even otherwise with current acreage, if continued with more productivity
enhancement through R & D in place, and the increase in production will be
doubled. Accordingly, the estimated production in sorghum with policy push and
R & D enhancement will be 35.0 million tons, of which rabi production contribution
alone will be 68% of total production.
Different genotypes suited to different growing conditions may be essential to
bring in all-round increase in productivity. The economic gains that may be aug-
mented by addressing envisaged benchmarks will result in significant improvement
416 Prabhakar et al.

in productivity, profitability, and even export earnings. All these are expected to
translate sorghum farming into a healthy and prosperous proposition, justifying the
public support for sorghum research in the country.

7.17 Breeding Progress/Varietal Development

7.17.1 Conventional Breeding

Sorghum improvement till the 1960s focused on selections from local landraces,
which were tall with low harvest index, photosensitive, late maturing after seize of
monsoon, and with localized adaptation. Notable varieties of this period are Saonar,
Ramkel, Aispuri, PJ, Maldandi, and Dagdi selections from Maharashtra; Bilichigan,
Fulgar white, Fulgar yellow, Kanvi, Nandhyal, Hagari, and Yanigar varieties from
Karnataka; Nandyal (N), Guntur (G), and Anakapalle series from Andhra Pradesh;
Co series from Tamil Nadu; BudhPerio (BP 53), Sundhia, and Chasation from
Gujarat; Gwalior and Indore selections from Madhya Pradesh; and RS selections
from Rajasthan. With the launching of the Accelerated Hybrid Sorghum Project
through the Rockefeller Foundation, a wide range of germplasm was made available
in India. This led to significant improvement principally through manipulation of
plant height and maturity.

7.17.2 Kharif Varietal Improvement

Hybrid sorghum breeding and variety development programs continue simulta-

neously in India. First outcome of focused sorghum breeding in India was the release
of early maturing variety, CSV 1, in 1968. The next decade witnessed the release of
five varieties, viz., CSV 2 to CSV 6. Out of these, CSV 2 and CSV 3 were of early
type, while CSV 4 and CSV 5 were dwarf, and CSV 6 was a relatively tall variety.
Zera-zera landrace from Ethiopia was brought into use to incorporate resistance
against biotic stresses. Further tan plant pigment got incorporated in all kharif
nurseries to confer resistance against leaf diseases. During the 1980s, five varieties,
like SPV 462 and CSV 9 to CSV 13 (K and R), were released. Further using SPV
462 and CSV 13 in crossing program, a high yielding dual-purpose variety, CSV
15, was released in 1996. Two new varieties were developed from the derivatives of
crosses involving this variety, viz., early maturing CSV 17 for light soils and
drought-prone areas and improved dual-purpose variety CSV 20. This was followed
by the release of two more improved dual-purpose varieties, viz., CSV 23 and CSV
27. Besides these central releases, there are several varieties released for specific
agro-ecologies of different states. These include Swati, PVK 801 (Parbhani Sweta),
SPV 297, PKV 809, Pratap Jowar 1403, JJ 938, JJ 1041, GJ 36, GJ 37, GJ 38, GJ
40, DSV 1, PSV 1, NTJ 2, etc. (Prabhakar et al. 2015) (Tables 7.6 and 7.7).
 7

Table 7.6 Nationally released kharif sorghum varieties

Year of Centre which
S. No. Variety release Pedigree of the hybrid/variety developed Area for which recommended
1 CSV 1 1968 Sel. from IS3924 NRCS (DSR) All sorghum-growing areas in the country
(currently
IIMR)
2 CSV 2 1974 IS 3922  Karad local NRCS (DSR) – do –
Sorghum Breeding

3 CSV 3 1974 IS 2954  BP 53 NRCS (DSR) – do –

4 CSV 4 1974 IS 3675  IS 3541 NRCS (DSR) – do –
5 CSV 5 1974 IS 3687  Aispuri NRCS (DSR) – do –
6 CSV 6 1974 IS 3922  Aispuri NRCS (DSR) – do –
7 CSV 7 1982 CS 3541 (Tall mutant) NRCS (DSR) – do –
8 CSV 10 (SPV 346) 1983 SB 1066  CS 3541 Udaipur Maharashtra, Karnataka, AP, MP, UP, Gujarat,
(SU 53) Rajasthan
9 CSV 11 (SPV 351) 1985 (SC 108-3  CS 3541)-11-1 ICRISAT Maharashtra, Karnataka, AP, MP, UP
10 CO 26 (USV 24) 1985 (IS2947  SPV232)  1022 Coimbatore Karnataka, Tamil Nadu, AP
11 CSV 13 (SPV 475) 1988 (IS12622  555)  IS ICRISAT Maharashtra, Karnataka, AP, MP, UP, Gujarat,
3612  E 35-1-52 Rajasthan, Tamil Nadu
12 CSV 15 (SPV 946) 1996 SPV 475  SPV 462 NRCS (DSR) Maharashtra, Karnataka, AP, MP, UP, Gujarat,
Rajasthan, Tamil Nadu
13 CSV 17 (SPV 1489) 2002 SPV 946  SPV 772 Udaipur Low rainfall and drought-prone sorghum-growing
regions of the country
14 CSV 20 (SPV 1616) 2006 SPV 946  Kh 89-246 DSR, All sorghum-growing areas of India
Hyderabad
15 CSV 23 (SPV 1714) 2007 SPV 861  SU 248 Udaipur All sorghum-growing areas of India
16 CSV 27 (SPV 1870) 2012 (GJ 38  Indore 12)-2-1-2-1; DSR, All sorghum-growing areas of India
GJ 38 ¼ GJ 35  E 35-1 Hyderabad
17 CSV 28 (SPV 1822) 2012 IRAT 204  SPV 1134 MPUA & T, All sorghum-growing areas of India
Udaipur
417

(continued)
Table 7.6 (continued)
418

Year of Centre which

S. No. Variety release Pedigree of the hybrid/variety developed Area for which recommended
18 CSV 31 (SPV 2122) 2014 SPV 462  SPV 1329 Palem Andhra Pradesh, Tamil Nadu, Rajasthan and
Gujarat
19 CSV 34 (SPV 2307) 2016 Sel from (AKMS PDKV, Akola Maharashtra, Karnataka, Madhya Pradesh and
37 B  AKMS 60B)—3 Gujarat
20 CSV 36 (JAICAR 2017 SPV 1231  NSV 13 IIMR- Tamil Nadu, Telangana, Andhra Pradesh,
HEERA; SPV 2301) Hyderabad Rajasthan, and Gujarat
21 CSV 39 (JAICAR SONA; 2017 SPV 772  SPV 1754 IIMR- Maharashtra, Karnataka, Madhya Pradesh,
SPV 2358) Hyderabad Rajasthan, Gujarat, Tamil Nadu, and Telangana
22 CSV 43 BMR (JAICAR 2019 SPV 2018 ¼ (SPV 462  IS IIMR Andhra Pradesh, Telangana, Karnataka,
Nutrigraze; SPV 2018) 21891)-3-1-1-1 Hyderabad Maharashtra, Tamil Nadu, Gujarat, M.P, Rajasthan,
UP, Uttarakhand, Haryana, and Jharkhand
Prabhakar et al.
7 Sorghum Breeding 419

Table 7.7 Nationally released dual-purpose sorghum varieties

Year Centre
of Pedigree of the which Area for which
S. No. Variety release hybrid/variety developed recommended
1 CSV 1996 SPV 475  SPV NRCS Maharashtra, Karnataka,
15 462 (DSR) AP, MP, UP, Gujarat,
Rajasthan, Tamil Nadu
2 CSV 2006 SPV 946  KH NRCS Maharashtra, Karnataka,
20 89-246 (DSR) AP, MP, UP, Gujarat,
Rajasthan, Tamil Nadu
3 CSV 2007 SPV 861  SU 248 Udaipur Maharashtra, Karnataka,
23 AP, MP, UP, Gujarat,
Rajasthan, Tamil Nadu
4 CSV 2012 (GJ 38  Indore DSR- All sorghum-growing
27 12)-2-1-2-1; GJ Hyderabad areas of India
38 ¼ GJ 35  E
35-1
Pedigree and origin of nationally released dual-purpose sorghum hybrids/varieties

7.17.3 Varietal Improvement in Rabi Sorghum

Focused rabi sorghum breeding was initiated in the early 1970s. The most popular
rabi variety, M35-1, was released in 1969 from Mohol, Maharashtra. It has remained
popular among farmers over the past five decades for its stable performance under
rainfed situations with above average yield and bold lustrous grains. Most of the
present-day improved varieties are the result of pureline selection practiced among
the local/popular varieties and their crosses. The popular varieties have lustrous,
bold, and globular grains. At the national level, the first rabi variety CSV 7R was
released in 1974. Subsequent releases are CSV 8R, Swati, CSV 14R, Sel 3, Phule
Yashoda (CSV 216R), CSV 18R, CSV 22R, CSV 26R, and CSV 29R. Out of these,
the last five are released in this millennium. Besides these, there are several state
varieties like for the state of Maharashtra are Phule Maulee, Phule Anuradha, Phule
Revati, Phule Vasudha, Phule Chitra, and Phule Suchitra from Rahuri center, Mukti,
Parbhani Moti (SPV 1411) from Parbhani center, and PKV Kranti from Akola.
Similarly, popular varieties released for Karnataka state are DSV 4 and DSV 5. NTJ
2 and NTJ 3 were released from the Nandyal station for Andhra Pradesh state. Many
of these varieties have yielding ability better than five-decade-old local variety
M35-1, with roti making quality at par or even better. Soil depths play an important
role in rabi sorghum-growing ecologies. In recent past, efforts have been made to
develop varieties adapted to specific soil situations (shallow, medium, and deep).
The variety Phule Maulee is released for shallow to medium soils, Phule Chitra and
Phule Suchitra for medium soils, Phule Vasudha for deep soils, Phule Revati for
medium to deep soils, and Phule Anuradha for shallow (Prabhakar et al. 2015)
(Table 7.8).
 420

Table 7.8 Nationally released rabi sorghum varieties

Year Centre
of which
S. No. Variety release Pedigree of the hybrid/variety developed Area for which recommended
1 CSV 7R 1974 IS 2950  M35-1 NRCS Maharashtra, Karnataka, Tamil Nadu, Gujarat, AP
(DSR)IIMR
2 CSV 8R 1979 R24  R16 NRCS – do –
(DSR)
3 CSV 14R (SPV 1992 (M35-1  (CS -2947  CS 2644)  M35-1 NRCS – do –
839) (DSR)
4 CSV 216R (SPV 2000 Land race selection from rabi germplasm Rahuri – do –
1359) (RSV 56) Dhulia
5 M35-1 1969 Land race selection from local Maldandi Mohal Maharashtra
bulk
6 Swati (SPV 504) 1984 SPV86  M 35-1 Rahuri Maharashtra
7 Sel.3 1995 Sel. from Bidar rabi local Rahuri Maharashtra
8 CSV 18 (Parbhani 2005 A selection from cross (CR 4  IS 18370) Parbhani For zone II
Jyothi) (SPV 1595) Maharashtra, Karnataka, AP under irrigation
9 CSV 22 (SPV 2007 SPV 1359  RSV 2 Rahuri Maharashtra, Karnataka, Tamil Nadu, Gujarat, AP
1626)
10 CSV 26 R (SPV 2011 Selection from the cross SPV-655  SPV- DSR Rabi season. Under shallow soils conditions of
1829) 1538 (IIMR) rabi sorghum-growing areas of India.
11 CSV 29R (SPV 2012 (CSV216R  DSV5)  CSV216R Bijapur Rabi sorghum-growing areas of Maharashtra,
2033) Karnataka and Andhra Pradesh under deep black
soils
Prabhakar et al.
7 Sorghum Breeding 421

7.17.4 Forage Sorghum Improvement

Forage sorghum is cultivated in about 3.0 million ha area in India each year. Forage
sorghums are principally cultivated in Punjab, Haryana, Delhi, western and central
Uttar Pradesh, and adjoining areas of Madhya Pradesh. In these states, it is grown
during kharif and summer seasons, either as single-cut (mostly in kharif, as rainfed)
or as a multi-cut (summer and kharif) forage crop. The major objectives in forage
sorghum breeding are to develop varieties both for single cut and multi-cut with high
tonnage, better quality, good seed yield, and resistance to insect pests and diseases.
The cultivar improvement before the 1970s was mostly through the straight selection
on available varieties and landraces. During this period, T-8B, 5-Tall, No. 9, 30-C,
and T-4 were released in Uttar Pradesh for grain as well as fodder production. JS
20, JS 29/1, and JS 263 were released exclusively for fodder purposes in the state of
Punjab. Out of these, JS 263 was sweet and juicier. These varieties were early in
flowering and possessed early vigor and high growth rate but were highly suscepti-
ble to foliar diseases and single tillered with poor seed potential.
Concerted breeding efforts for the improvement of forage sorghum were initiated
in 1970 under AICSIP. During the 1970s, single-cut varieties, viz., Pusa Chari
1, Haryana Chari 73/53, and SL44, were bred at IARI, Hisar, and Ludhiana,
respectively. In 1977, multi-cut forage sorghum variety SSG 59-3 developed at
Haryana Agricultural University. Barring the problem of poor seed yield, it is now
one of the most popular multi-cut varieties. Subsequently, in the 1980s, another
multi-cut variety, Pusa Chari23, was released, but it was highly susceptible to foliar
diseases. During this period, three single-cut forage sorghum varieties, PC 6 (from
IARI), HC136 (from Hisar), and UP Chari1 (from Pantnagar), were released for
general cultivation across India. Other single-cut varieties, PC 9, RC 1 and 2, and UP
Chari 2, were also released in that decade. Later from Hisar, two more single-cut
varieties, viz., HC171 and HC 260, were released for the whole country. Some of the
recent single-cut forage sorghum varieties are CSV 30F and CSV 32F. The latest
forage cultivars possess improvement in terms of resistance to leaf spot diseases,
stem borer, and seed yield. Beside these, several private sector hybrids are also
popular for multi-cut forage (Prabhakar et al. 2015) (Table 7.9).

7.17.5 Sweet Sorghum Improvement

Sweet sorghum, similar to grain sorghum except for its juice-rich sweet stalk, is
considered to be a potential bioethanol feedstock and is expected to meet food, feed,
fodder, fuel, and fiber demands. Some sweet sorghum lines contain 15–23% soluble
fermentable sugar (by comparison, sugarcane has 14–16%). Most of the sugars are
distributed in the stalk, making the crop particularly amenable to direct fermentable
sugar extraction. Further, the silage from sweet sorghum after extraction of juice has
higher biological value. Besides these, the whole plant biomass can also be used as a
substrate for production of lignocellulosic ethanol, known as second-generation
biofuel. Early efforts toward sweet sorghum improvement were made at Nimbkar
422 Prabhakar et al.

Table 7.9 Forage sorghum varieties

Year
of Pedigree of the Centre which Area for which
S. No. Variety release hybrid/variety developed recommended
1 HaryanaChari 1976 Sel. from local HAU, Hisar All India
(JS73/53) germplasm cultivation
2 PC 1 1976 Sel. from IS IARI, New All India
609 (bicolor) Delhi cultivation
3 MP Chari 1978 Jabalpur All India
cultivation
4 PC 6 1980 Sel. from IS IARI, New All India
5977 (Durra) Delhi cultivation
5 HC 136 1982 IS 3214 HAU, Hisar All India
(bicolor)  PC cultivation
7R
6 UP Chari-I 1982 Sel. from IS Pantnagar All India
4870 (Durra) cultivation
7 UP Chari-II 1985 Vidisha Pantnagar All India
60-1  IS 6953 cultivation
(Guinea-
caudatum)
8 PC 9 1985 Sel. from IS IARI, New All India
4870 (Durra) Delhi cultivation
9 Rajasthan 1985 CSV 6  NCL 3 Udaipur All India
Chari—1 cultivation
10 Rajasthan 1985 Sel. from local of Udaipur All India
Chari—2 Udaipur cultivation
11 HC 171 1987 SPV 8  IS 4776 HAU, Hisar All India
(Durra) cultivation
12 HC 260 1987 SPV 103  PC 9 HAU, Hisar All India
cultivation
13 HC 308 1996 SPV 8  IS 4776 HAU, Hisar All India
(Durra) cultivation
14 Pant Chari—5 1999 – Pantnagar All India
cultivation
15 CSV 21F 2006 GSSV 148  SR NAU, Surat All India
897 cultivation
15 SSG 59-3 1977 (Non-sweet HAU, Hisar All India
sudan grass  JS cultivation
263)
16 Pusa Chari—23 1985 Exotic hybrid IARI, New All India
Martin  99070 Delhi cultivation
10 sudan grass
17 Jadu Chari 1991 1) (PFF x PFB 2) Pioneer Seed All India
x PFM 1 Company cultivation
18 Hara Sona 1995 (PFS 5A  PFS Proagro Seed All India
5C)  PFS 5R) Company cultivation
(continued)
7 Sorghum Breeding 423

Table 7.9 (continued)

Year
of Pedigree of the Centre which Area for which
S. No. Variety release hybrid/variety developed recommended
19 Safed Moti PSA Proagro Seed All India
93016  FSR Company cultivation
93025
20 CSV 30 F 2014 NSS Rahuri All India
223  NARI 111 cultivation
21 CSV 32 F (SPV 2014 (HC 260  B DSR, Maharashtra,
2128) 35)-5-3-1-1 Hyderabad Karnataka,
Tamil Nadu,
Madhya
Pradesh, South
Gujarat
Telangana,
Andhra Pradesh,
and Tamil Nadu
22 CSV 33MF (SPV 2016 EMS Mutant of TNAU, Tamil Haryana,
2242) CO FS 29 Nadu Punjab,
Uttarakhand,
Uttar Pradesh,
Gujarat,
Rajasthan,
Tamil Nadu,
Karnataka,
Maharashtra
23 CSV 35F 2017 Pant Chari G.B. Pant Delhi, Gujarat,
(SPV2317); 5 (female)  IS University of Rajasthan,
(UTFSH 2) 7002 (male) Agric. and Uttarakhand,
Tech., Haryana, Uttar
Pantnagar Pradesh, and
Punjab
Maharashtra,
Tamil Nadu,
Karnataka and
Madhya Pradesh
for cultivation
during rainfed
kharif season.
Optimum
temperature for
good crop
growth
28–350  C.
24 CSV 38F—(SPV 2018 (CSV 20  Pant ICAR-Indian Rainfed kharif
2316 Chari 5)  (CSV Institute of areas of
JAICARHariyali) 20  PVK 809)- Millets Maharashtra,
11-1-1-2-1-1 Research, Tamil Nadu and
Hyderabad Karnataka
(continued)
424 Prabhakar et al.

Table 7.9 (continued)

Year
of Pedigree of the Centre which Area for which
S. No. Variety release hybrid/variety developed recommended
25 CSV 40 F (SPV 2019 PVK Vasantrao Rainfed, timely
2387) 809  1037 R Naik sown conditions
Marathwada of kharif season
Krishi in Maharashtra,
Vidyapeeth— Tamil Nadu, and
Parbhani Karnataka
26 CSV 44 F (SPV 2020 Selection from CCSHAU, Zone II of India
2445) cross HC Hisar comprising
308  S 437-1-2 states
Maharashtra,
Tamil Nadu,
Karnataka

Table 7.10 Sweet sorghum varieties released at national level

Year Centre
of Pedigree of the which Area for which
S. No. Variety release hybrid/variety developed recommended
1 CSV 19SS 2004 RSSV 2  SPV MPKV, Maharashtra,
(RSSV 9) 462 Rahuri Karnataka, AP, MP,
and Gujarat
2 CSV 24 SS 2010 NSS NRCS All India cultivation
(SPSSV 6) 1005A  (SSV (DSR)
84  401B)

Agricultural Research Institute (NARI), Phaltan, Maharashtra. At the International

Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, major
attempts were made to evaluate and identify useful sweet sorghum high biomass
germplasm from world collections. Sweet sorghum research under AICSIP started in
1989. Concerted research efforts during the last two decades have resulted in
excellent sweet sorghum varieties and hybrids for use in ethanol production and
for use as green/dry fodder. Promising nationally released varieties/hybrids are SSV
84 (high brix), CSV 19SS (High stalk yield, shoot fly tolerance), CSV 24SS (High
stalk and sugar yields), and hybrid CSH 22 SS (High stalk and sugar yields)
(Table 7.10). The productivity ranged between 40 and 50 tons/ha. Stalk yields
obtained during rabi are 30–35% less with reduced sugar content than kharif and
summer-grown crops (Prabhakar et al. 2015).
7 Sorghum Breeding 425

7.18 Genomics-Assisted Breeding

The genetic diversity in sorghum provides an opportunity to search for new genes
and alleles that are responsible for conferring desirable phenotypes. Genome
profiling using molecular markers would provide a large number of DNA markers.
Association mapping methods, joint linkage and linkage disequilibrium mapping,
genetic fingerprinting and diversity analyses, and genomic selection programs would
pave way for effective utilization of sorghum germplasm for crop improvement. The
development of large mutant population as a reverse genetic tool is envisaged to
unravel the expression of battery of genes and the mechanisms of their regulation.
State-of-the-art technologies would be utilized to select for traits that are other-
wise difficult to measure or that requires particular conditions for their expression.
Further, they provide genetic fingerprints that measure relationships between differ-
ent lines of sorghum and can be used to protect IPRs. Also, development of gene
variant specific markers for major genes controlling adaptive traits would help in
accomplishing requisite level of trait expression. It may be expected that genome-
wide selection methods that incorporate marker technology into practical breeding
processes would be routine in the future.
Another dimension of accomplishing traits of interest including novel ones in
sorghum cultivars is the deployment of transformation technology to transfer the
genes of interest or regulate the expression of host genes. The Bt transgenic sorghum
already developed in the system not only holds promise as an important source of
resistance to stem borer but exemplifies the possibilities of incorporating new genes
into sorghum for innumerable end uses. A similar approach would be a major option
for improving resistance to shoot fly, grain mold, aphids, etc. if suitable candidate
genes are identified. Research in functional genomics of sorghum would pave way
for identifying the sorghum candidate genes for such manipulations.
New avenues in understanding the genomics, evolution, and biology of sorghum
crop were opened with the availability of whole genome sequence (Paterson et al.
2009). In addition, gene-level comparative analysis was also made possible with the
sequencing of genomes of landraces, crop progenitors, and wild species. With the
availability of the sorghum genomic sequence, development of molecular markers
progressed steadily from development of genome-wide DNA markers such as
simple sequence repeats (SSRs), intron length polymorphism (ILP), insertion
deletions (indels), and single nucleotide polymorphisms (SNPs). Many high-density
SNPs are being generated for sorghum due to the advances in high-throughput
sequencing technologies, and these SNPs are valuable genomic resources for design-
ing SNP chips/arrays and GWAS leading to the identification of key genomic
regions associated with important target traits. This further helped in the identifica-
tion of genomic regions/QTL associated with economically important target traits,
which are the current targets for marker-assisted breeding in sorghum. Several
studies on transcriptomes have identified differentially expressed genes (DEGs)
related to abiotic stress tolerance paving way for better understanding of cellular
and molecular responses of the plants to stress factors. The data/information on
whole genome sequence, SNPs, gene expression, gene families, gene networks, and
426 Prabhakar et al.

annotation are available in the databases such as Phytozome (https://phytozome.jgi.

doe.gov/pz/portal.html), SorGSD (http://sorgsd.big.ac.cn), MOROKOSHI (http://
matsui-lab.riken.jp/morokoshi/Home.html), Sorghum Transcription Factor Data-
base (http://planttfdb.gao-lab.org/index.php?sp¼Sbi), and SorghumFDB (http://
structuralbiology.cau.edu.cn/sorghum/index.html).
Development and use of climate-resilient crops and genotypes therein are critical
to safeguard against global food scarcity and malnutrition (Mickelbart et al. 2015).
Sorghum is well-known for its ability to thrive under harsh growing conditions
across major global agricultural production regions. Understanding genetic variation
and underlying adaptive traits that are responsible for sorghum’s ability to tolerate
challenging growing environments would have implications for additional improve-
ment in sorghum as well as other agronomically important crops (Boyles et al.
2019). Several traits that are critical for broadening adaptation and enhancing
production have been the targets of genetic dissection and marker-assisted breeding
approaches in sorghum. Application of DNA markers is gaining importance in the
genetic improvement of sorghum crop. Several marker systems have been developed
and used for tagging and mapping of major effect genes and quantitative traits (QTL)
of economic importance like grain yield and its component traits; resistance to insect
pests, diseases, and Striga; drought; salinity; cold and nutritional quality; etc.
Genetic improvement of grain yield is a challenging task as it involves accumu-
lation of positive alleles involved in the expression of component traits like panicle
length, panicle weight, number of primary branches per panicle, grains per primary
branch, grain weight, etc. Several studies have identified QTL for grain yield and its
component traits (Brown et al. 2006; Hart et al. 2001; Murray et al. 2008; Mace and
Jordan 2011; Reddy et al. 2013; Ritter et al. 2008; Srinivas et al. 2009; Boyles et al.
2016; Zhang et al. 2015; Sukumaran et al. 2016; Bernardino et al. 2019). Sorghum
gene Sobic.001G341700 (like grain length and weight protein), an orthologous of
rice (GS3) and maize gene (ZmGS3) for grain size, has been reported in sorghum
(Tao et al. 2017).
Plant height and grain yield usually have a positive relationship under favorable
environment. Plant height in sorghum is a complex trait consisting of number and
length of internodes and the peduncle length. Four major effect genes (Dw1, Dw2,
Dw3, and Dw4) inherited independently have been described in sorghum (Karper
and Quinby 1947). QTL with major effects for plant height have been consistently
identified in different genetic backgrounds and were related to qualitative loci, Dw1
on SBI-09, Dw2 on SBI-06, and Dw3 on SBI-07 (Brown et al. 2008; Reddy et al.
2013; Higgins et al. 2014; Morris et al. 2013; Zhao et al. 2016; Lin et al. 1995; Zou
et al. 2012). Of these major loci, Dw1 was proposed to encode a putative membrane
protein of unknown function (Sobic.009g229800) that is highly conserved in plants
(Hilley et al. 2016; Yamaguchi et al. 2016). Morris et al. (2013) proposed that Dw2
phenotype is a result of loss of function in a sorghum histone deacetylase gene
(Sobic.006G067600) analogous to its function in controlling plant height in other
crops like maize, rice, and Arabidopsis. Dw3 has been fine-mapped, and the gene
(Sobic.007G163800) was cloned (Multani et al. 2003) coding for P-glycoprotein that
regulates polar auxin transport and is orthologous to br2 in maize.
7 Sorghum Breeding 427

Another adaptive trait which determines the extent of distribution of a crop in

diverse climatic conditions is flowering time (Bhosale et al. 2012; Craufurd et al.
1999). Though grain sorghum is a short-day plant and mostly photoperiod sensitive,
there are genotypes which exhibit differential sensitivity to varying photoperiods and
temperature regimes (Doggett 1988). For maturity, four major genes (Ma1, Ma2,
Ma3, and Ma4) with qualitative effect have been described, with multiple alleles at
each locus (Quinby 1967, 1974). Both Ma1 and Ma3 have been cloned. Ma3 encodes
a phytochrome B (Childs et al. 1997). The gene encoding pseudo-response regulator
protein 37 (PRR37) was identified as a likely gene candidate for Ma1 based on the
known roles of PRR genes in flowering of Arabidopsis (Murphy et al. 2011).
Sorghum Ma6, a strong repressor of flowering in long days, was identified as the
CONSTANS, CO-like, and TOC1 (CCT)-domain protein encoded by SbGhd7
(Murphy et al. 2014). Sorghum Ghd7 increases photoperiod sensitivity and delays
flowering by inhibiting expression of the floral activator SbEhd1 and genes encoding
FT. Sorghum germplasm, both photoperiod sensitive and photoperiod insensitive,
remain important sources of new genes for the continued development of cultivars
and hybrids in terms of improvement in yield and resistance to biotic and abiotic
stresses.
Disease and insect pest management through host plant resistance has been an
effective means of reducing economic losses in sorghum. Availability of DNA
markers for biotic stress resistance would do away with the need for phenotypic
screening, and undesirable plants can be removed before flowering by marker
analysis even at the seedling stage. Satish et al. (2009) and Aruna et al.
(2011a, b, c) reported QTL for leaf glossiness and seedling vigor, oviposition,
deadhearts, adaxial trichome density, and abaxial trichome density. Leaf glossiness
QTL on SBI-05 and SBI-03 was syntenic to maize LG 4 and LG3, respectively, and
carries genes glossy3 and glossy9 for leaf glossiness and harbors long-chain Acyl-
CoA synthetase and wax synthase genes involved in wax biosynthesis. Seedling
vigor QTL on SBI-03 hosts a gene for indole-3 acetic acid-amino synthase GH3.5
that promotes plant growth and light and stress adaptation. Similarly, the QTL on
SBI-10 where QTL for oviposition, deadhearts, and trichome density are co-located,
genes viz., Cysteine protease Mir1, Homogentisate phytyl transferase vte2,
Hydroxyproline-rich glycoprotein, NAC1, glossy15 and mh11 responsible for biotic
and abiotic stress resistance have been identified.
For midge, two QTL on SBI-03 and SBI-09 were associated with antixenosis
explaining 12% and 15% of variation in egg number per spikelet (Tao et al. 2003).
One region on SBI-07 was significantly associated with antibiosis and explained
34.5% of the variation of the difference of egg and pupal counts. For green bug
resistance, Punnuri et al. (2013) reported four major QTL regions on SBI-09
between Starssbnm 78 and Starssbnm 102 SSR markers collectively accounting
for 34–82% variation. A genic marker for Xa21-binding protein 3 was tightly linked
to greenbug resistance traits. Transcriptomic studies have shown the involvement of
signalling compounds and defence-activated R genes in defence response to green-
bug attack.
428 Prabhakar et al.

Grain mold is a major disease complex of sorghum that severely affects grain
production and grain quality. A complex of fungal pathogens, mostly Fusarium and
Curvularia are parasitic that can infect sorghum spikelet at anthesis itself. In a recent
association-mapping study, two SNP loci linked to grain mold resistance have been
identified (Upadhyaya et al. 2013). Among these, one contained a NB-ARCLRR
class of R gene (Sb02g004900) that shares 37% identity and 57% similarity to the
non-host resistance gene of maize, Rxo1. Recent genome-wide association mapping
using Ethiopian sorghum landraces identified a major grain mold resistance QTL
containing tightly linked transcription factors, YELLOW SEED1 (Y1), and a second
R2R3 MYB gene, YELLOWSEED3 (Y3), defining a narrow genomic region that
could be used for grain mold resistance selection.
A major QTL on SBI-06 between SSR markers Xtxp95 and Xtxp57 (Klein et al.
2001; Mohan et al. 2010) influencing resistance against various unrelated pathogens
causing foliar diseases was consistently detected with the phenotypic variation
ranging from 32% (bacterial leaf blight, zonate leaf spot) to 55% (anthracnose)
indicating involvement of a key gene for disease resistance. Genes known to be
involved in plant defense mechanisms like NB-ARC class of R genes, HR-related
genes, a transcription factor that functions in the R gene pathway, a gene that
functions in the non-specific host resistance, and a gene for antimicrobial compound
production were identified as putative genes for anthracnose disease resistance in
sorghum (Cuevas et al. 2014; Upadhyaya et al. 2013).
Charcoal rot disease is a root and stem disease caused by the soil-borne fungus
Macrophomina phaseolina (Tassi) Goid. QTL for charcoal rot resistance were
identified (Patil et al. 2012; Reddy et al. 2008a, b; Adeyanju et al. 2015). Ergot
(sugary disease) is an endemic fungal disease and causes significant losses in seed
production plots. It was also observed that the major QTL for percent ergot infection
on SBI-06 was co-located with QTL for a number of diseases including grain mold,
anthracnose, zonate leaf spot, and bacterial leaf spot (Klein et al. 2001; Mohan et al.
2010). Three other regions on SBI-07, SBI-10, and SBI-08 that are known to contain
QTL for grain mold and rust resistance (Klein et al. 2001; Tao et al. 1998) also
appear to contain a QTL for ergot resistance (Parh et al. 2008).
A single recessive gene controls low Striga germination stimulant (lgs) activity, a
well-known resistance mechanism in sorghum (Hess and Ejeta 1992; Vogler et al.
1996). Satish et al. (2012) precisely mapped and tagged the lgs gene on SBI-05
between two tightly linked SSR markers SB3344 and SB3352. The use of molecular
markers to breed for Striga resistance in sorghum has been shown to be possible
(Mohamed et al. 2014).
Stay-green is the best-characterized component of drought tolerance and
enhances the yield of sorghum grain under drought, by modifying canopy develop-
ment, root growth, and crop-water usage. Several QTL associated with stay-green
trait have been detected across genetic backgrounds.
Comparison of stay-green QTL (Xu et al. 2000; Subudhi et al. 2000; Tao et al.
2000; Tuinstra et al. 1997; Haussmann et al. 2002) introgressed lines (Kassahun
et al. 2010) and near-isogenic lines (Harris et al. 2007) involving B35 consistently
identified four major QTL, namely, Stg1 (SBI-03), Stg2 (SBI-03), Stg3 (SBI-02),
7 Sorghum Breeding 429

and Stg4 (SBI-05), which together accounted up to 53.5% phenotype variance. The
potential use of stay-green QTL in improving transpiration efficiency and water
extraction capacity in sorghum for terminal drought tolerance and grain yield
particularly under low yield environments has been demonstrated. Co-location of
stay-green and nodal root angle QTL in sorghum highlights the probable role of
roots in retaining leaves green through higher water uptake. Transcriptomic analysis
comparing stay-green and senescent lines identified a role for proline biosynthesis in
the stay-green trait. Current studies at IIMR, Hyderabad, on marker-assisted intro-
gression of stay-green QTL, Stg3a and Stg3b from B35 to Indian post-rainy sorghum
lines, CRS4, and RSLG262 have shown some promise in imparting terminal drought
tolerance. Some of the partial introgression lines (BC1F3 generations) of CRS4 and
RSLG262 had higher green leaf area retention at maturity, grain yield, and stover
yield under both stress and no-stress conditions. The introgression lines also showed
significantly better drought tolerance in terms of their low drought susceptibility
index compared to respective recurrent parents (R Madhusudhana
Unpublished data).

7.18.1 Cold Tolerance

Genetic mapping of cold tolerance detected two QTL for germination-one on SBI-03
contributing 12–15% of variation under both cold and optimal temperatures, while
the second QTL on SBI-07 showed greater significance only under cold temperature
accounting to 10% trait variation (Knoll et al. 2008). A major QTL with 8–27% trait
contribution was identified on SBI-01, which showed strong associations with
seedling emergence and seedling vigor under early as well as late field plantings.
Similarly, one QTL for both early and late seedling emergence was identified on
SBI-02, explaining 8–10% of trait variation. A new source of cold tolerance,
PI610727, was used to tag the genomic regions exhibiting significant contributions
to traits for early-season cold tolerance.
Some of the important QTL regions reported in sorghum are given here
(Table 7.11).

7.18.2 Modernization of Crop Improvement Program

The current genetic gains in several important crops are inadequate to meet future
food demand. This slow improvement rate is attributed partly to the long generation
times of crop plants. Recently, “speed breeding,” a method to greatly shorten
generation time and accelerate breeding and research programs, is introduced
(Watson et al. 2018). This method uses regulated environmental conditions and
prolonged photoperiods to achieve between four and six generations per year of long
duration crops (i.e., wheat, barley, and canola). The method has great potential for
integrating speed breeding with other modern crop breeding technologies, including
high-throughput genotyping, genome editing, and genomic selection, accelerating
430 Prabhakar et al.

Table 7.11 Important QTL in sorghum with their associated markers

Trait/genes/QTL LG LOD R2 Linked markers Reference
I. Agronomic traits
Plant height (Dw1) 9 6 20 isu140/PIO100016 Pereira and Lee
(1995)
Plant height (Dw2) 6 16 27 AG/CTG9 Ritter et al.
(2008)
Plant height (Dw3) 7 8 29 isu123/isu116 Pereira and Lee
(1995)
Maturity 6 91 86 pSB189/pSB580 Lin et al. (1995)
Maturity 1 6 15 txp58/Dsenhsbm63 Srinivas et al.
(2009)
Maturity 6 11 36 psb521/psb708 Kebede et al.
(2001)
Grain yield 2 4 18 AAG/CAA1 Ritter et al.
(2008)
Grain yield 6 5 15 GlumeT/Xtxp145 Srinivas et al.
(2009)
Grain yield 10 3 14 AAG/CTT2 Ritter et al.
(2008)
Grain yield 10 5 11 Xcup67/txa3777 Murray et al.
(2008)
Seed mass 1 13 20 TS138/rio72 Murray et al.
(2008)
Seed mass 1 – 11 bnl6.25/umc84 Rami et al.
(1998)
Seed mass 1 5 15 Dsenhsbm64/Xcup24 Srinivas et al.
(2009)
Seed mass 1 3 11 isu027/npi209 Pereira and Lee
(1995)
Seed mass 2 – 19 umc122/bnl16.06 Rami et al.
(1998)
Seed mass 3 6 10 psB443a/pSB614 Feltus et al.
(2006)
Seed mass 3 – 12 umc152/umc10 Rami et al.
(1998)
Seed mass 4 4 10 Xtxp12/Dsenhsbm39 Srinivas et al.
(2009)
Seed mass 4 4 16 txs604/cdo516.1 Feltus et al.
(2006)
Seed mass 4 5 16 Xtxp51/txa6257 Brown et al.
(2006)
Seed mass 6 7 10 pSB521a/pSB428a Feltus et al.
(2006)
Seed mass 6 8 15 txa2873/txa2067 Murray et al.
(2008)
Seed mass 7 – 31 umc23/sscir88 Rami et al.
(1998)
(continued)
7 Sorghum Breeding 431

Table 7.11 (continued)

Trait/genes/QTL LG LOD R2 Linked markers Reference
Seed mass 8 6 11 rio65/rio37 Murray et al.
(2008)
Seed mass 8 5 12 isu145.2/txa558 Brown et al.
(2006)
Seed mass 9 6 18 txs1703/cdo580 Brown et al.
(2006)
Seed mass 10 4 14 txs1106/bnl5.04 Feltus et al.
(2006)
Seed mass 10 5 16 isu156/isu034 Pereira and Lee
(1995)
II. Insect resistance
Shoot fly (glossiness) 5 3 17 Xtxp65/ Satish et al.
XnhsbmSFC61 (2012)
Shoot fly (deadhearts) 10 7 23 XnhsbmSFC34/ Satish et al.
Xnhsbm1039 (2012)
Shoot fly (trichome density) 10 9 20 XnhsbmSFC34/ Satish et al.
Xnhsbm1039 (2012)
Shoot fly (trichome density) 10 10 24 Xgap1/Xnhsbm1011 Satish et al.
(2012)
Midge 3 3 12 rz543/st698 Tao et al. (2003)
Midge 7 11 34 txs1931/sg37 Tao et al. (2003)
Midge 9 5 15 ST1017/SG14 Tao et al. (2003)
Green bug (biotype I) 1 2 15 Xtxp43/Xtxp85 Nagaraj et al.
(2005)
Biotype I 4 4 20 Sb1-10 Nagaraj et al.
(2005)
Biotype I 7 – 10 bdc098/csu61 Katsar et al.
(2002)
Biotype K 1 2 16 Xtxp335/Xtxp204 Nagaraj et al.
(2005)
Biotype K 4 3 13 Xtxp12/Xcup20 Nagaraj et al.
(2005)
Biotype K 10 – 15 psb0106/rz144 Katsar et al.
(2002)
III. Disease resistance
Anthracnose 6 13 40 Xtxp95-Plcor Mohan et al.
(2010)
Zonate leaf spot 6 5 14 Xtxp95-Plcor Mohan et al.
(2010)
Zonate leaf spot 6 5 17 Fdnhsbm107- Mohan et al.
Fdnhsbm24 (2010)
Zonate leaf spot 3 4 13 Xtxp228- Mohan et al.
Drenhsbm103 (2010)
Target leaf spot 6 20 50 Xtxp95-Plcor Mohan et al.
(2010)
Rust 1 3 26 bnl5.09/txs1625 Tao et al. (1998)
(continued)
432 Prabhakar et al.

Table 7.11 (continued)

Trait/genes/QTL LG LOD R2 Linked markers Reference
Rust 2 3 17 sscir51/txs2042 Tao et al. (1998)
Rust 3 4 24 rz323/isu102 Tao et al. (1998)
Rust 8 9 43 psb47/txs422 Tao et al. (1998)
Rust 6 8 24 Xtxp95-Plcor Mohan et al.
(2010)
Ergot (% infection) 1 5 12 sPb-8261 Parh et al. (2008)
Ergot (% infection) 6 6 14 sPb-1543 Parh et al. (2008)
Ergot (% infection) 7 4 10 Xtxp168 Parh et al. (2008)
Ergot (% infection) 8 4 11 AGG + CAG6 Parh et al. (2008)
Ergot (% infection) 9 3 20 Sb4-32 Parh et al. (2008)
Ergot (pollen viability) 7 3 13 sPb-5594 Parh et al. (2008)
Ergot (pollen viability) 8 3 10 Xtxp273 Parh et al. (2008)
Ergot (pollen viability) 6 7 20 AAG + CTT6 Parh et al. (2008)
Charcoal rot (internodes 2 4 19 Xtxp297 Reddy et al.
crossed) (2008a, b)
Charcoal rot (% lodging) 4 4 15 Xtxp343 Reddy et al.
(2008a, b)
IV. Weed
Striga (lgs) 5 SB3344, SB3343, Satish et al.
SB3346 (2012)
V. Abiotic resistance
Drought-stay-green (Stg1) 3 5 20 Xtxp442/Xtxp38 Xu et al. (2000)
Stg2 3 6 30 Xtxp2/Xtxp503 Xu et al. (2000)
Stg3 2 3 16 Xtxp430/Xtxp1 Xu et al. (2000)
Stg4 5 2 11 Xtxp225/Xtxp15 Xu et al. (2000)
Cold tolerance (late 1 – 21 PeriCol/OPK18 Knoll et al.
emergence %) (2008)
Cold tolerance (late 2 – 11 Xtxp201/Sb110 Knoll et al.
emergence %) (2008)
Cold tolerance (early vigor) 1 – 20 PeriCol/OPK18 Knoll et al.
(2008)
Cold tolerance (early vigor) 4 – 12 Xtxp51/Xtxp21 Knoll et al.
(2008)
Cold tolerance (late vigor) 1 – 28 PeriCol/OPK18 Knoll et al.
(2008)
Cold tolerance (cold 3 – 13 ubc171/SbAGE01 Knoll et al.
germination) (2008)
Cold tolerance (optimal 3 – 15 umc60/ubc171 Knoll et al.
germination) (2008)
VI. Agronomic traits
Plant height (Dw1) 9 6 20 isu140/PIO100016 Pereira and Lee
(1995)
Plant height (Dw2) 6 16 27 AG/CTG9 Ritter et al.
(2008)
(continued)
7 Sorghum Breeding 433

Table 7.11 (continued)

Trait/genes/QTL LG LOD R2 Linked markers Reference
Plant height (Dw3) 7 8 29 isu123/isu116 Pereira and Lee
(1995)
Maturity 6 91 86 pSB189/pSB580 Lin et al. (1995)
Maturity 1 6 15 txp58/Dsenhsbm63 Srinivas et al.
(2009)
Maturity 6 11 36 psb521/psb708 Kebede et al.
(2001)
Grain yield 2 4 18 AAG/CAA1 Ritter et al.
(2008)
Grain yield 6 5 15 GlumeT/Xtxp145 Srinivas et al.
(2009)
Grain yield 10 3 14 AAG/CTT2 Ritter et al.
(2008)
Grain yield 10 5 11 Xcup67/txa3777 Murray et al.
(2008)
Seed mass 1 13 20 TS138/rio72 Murray et al.
(2008)
Seed mass 1 – 11 bnl6.25/umc84 Rami et al.
(1998)
Seed mass 1 5 15 Dsenhsbm64/Xcup24 Srinivas et al.
(2009)
Seed mass 1 3 11 isu027/npi209 Pereira and Lee
(1995)
Seed mass 2 – 19 umc122/bnl16.06 Rami et al.
(1998)
Seed mass 3 6 10 psB443a/pSB614 Feltus et al.
(2006)
Seed mass 3 – 12 umc152/umc10 Rami et al.
(1998)
Seed mass 4 4 10 Xtxp12/Dsenhsbm39 Srinivas et al.
(2009)
Seed mass 4 4 16 txs604/cdo516.1 Feltus et al.
(2006)
Seed mass 4 5 16 Xtxp51/txa6257 Brown et al.
(2006)
Seed mass 6 7 10 pSB521a/pSB428a Feltus et al.
(2006)
Seed mass 6 8 15 txa2873/txa2067 Murray et al.
(2008)
Seed mass 7 – 31 umc23/sscir88 Rami et al.
(1998)
Seed mass 8 6 11 rio65/rio37 Murray et al.
(2008)
Seed mass 8 5 12 isu145.2/txa558 Brown et al.
(2006)
(continued)
434 Prabhakar et al.

Table 7.11 (continued)

Trait/genes/QTL LG LOD R2 Linked markers Reference
Seed mass 9 6 18 txs1703/cdo580 Brown et al.
(2006)
Seed mass 10 4 14 txs1106/bnl5.04 Feltus et al.
(2006)
Seed mass 10 5 16 isu156/isu034 Pereira and Lee
(1995)
VII. Insect resistance
Shoot fly (glossiness) 5 3 17 Xtxp65/ Satish et al.
XnhsbmSFC61 (2012)
Shoot fly (deadhearts) 10 7 23 XnhsbmSFC34/ Satish et al.
Xnhsbm1039 (2012)
Shoot fly (trichome density) 10 9 20 XnhsbmSFC34/ Satish et al.
Xnhsbm1039 (2012)
Shoot fly (trichome density) 10 10 24 Xgap1/Xnhsbm1011 Satish et al.
(2012)
Midge 3 3 12 rz543/st698 Tao et al. (2003)
Midge 7 11 34 txs1931/sg37 Tao et al. (2003)
Midge 9 5 15 ST1017/SG14 Tao et al. (2003)
Green bug (biotype I) 1 2 15 Xtxp43/Xtxp85 Nagaraj et al.
(2005)
Biotype I 4 4 20 Sb1-10 Nagaraj et al.
(2005)
Biotype I 7 – 10 bdc098/csu61 Katsar et al.
(2002)
Biotype K 1 2 16 Xtxp335/Xtxp204 Nagaraj et al.
(2005)
Biotype K 4 3 13 Xtxp12/Xcup20 Nagaraj et al.
(2005)
Biotype K 10 – 15 psb0106/rz144 Katsar et al.
(2002)
VIII. Disease resistance
Anthracnose 6 13 40 Xtxp95-Plcor Mohan et al.
(2010)
Zonate leaf spot 6 5 14 Xtxp95-Plcor Mohan et al.
(2010)
Zonate leaf spot 6 5 17 Fdnhsbm107- Mohan et al.
Fdnhsbm24 (2010)
Zonate leaf spot 3 4 13 Xtxp228- Mohan et al.
Drenhsbm103 (2010)
Target leaf spot 6 20 50 Xtxp95-Plcor Mohan et al.
(2010)
Rust 1 3 26 bnl5.09/txs1625 Tao et al. (1998)
Rust 2 3 17 sscir51/txs2042 Tao et al. (1998)
Rust 3 4 24 rz323/isu102 Tao et al. (1998)
Rust 8 9 43 psb47/txs422 Tao et al. (1998)
(continued)
7 Sorghum Breeding 435

Table 7.11 (continued)

Trait/genes/QTL LG LOD R2 Linked markers Reference
Rust 6 8 24 Xtxp95-Plcor Mohan et al.
(2010)
Ergot (% infection) 1 5 12 sPb-8261 Parh et al. (2008)
Ergot (% infection) 6 6 14 sPb-1543 Parh et al. (2008)
Ergot (% infection) 7 4 10 Xtxp168 Parh et al. (2008)
Ergot (% infection) 8 4 11 AGG + CAG6 Parh et al. (2008)
Ergot (% infection) 9 3 20 Sb4-32 Parh et al. (2008)
Ergot (pollen viability) 7 3 13 sPb-5594 Parh et al. (2008)
Ergot (pollen viability) 8 3 10 Xtxp273 Parh et al. (2008)
Ergot (pollen viability) 6 7 20 AAG + CTT6 Parh et al. (2008)
Charcoal rot (internodes 2 4 19 Xtxp297 Reddy et al.
crossed) (2008a, b)
Charcoal rot (% lodging) 4 4 15 Xtxp343 Reddy et al.
(2008a, b)
IX. Weed
Striga (lgs) 5 SB3344, SB3343, Satish et al.
SB3346 (2012)
X. Abiotic resistance
Drought-stay-green (Stg1) 3 5 20 Xtxp442/Xtxp38 Xu et al. (2000)
Stg2 3 6 30 Xtxp2/Xtxp503 Xu et al. (2000)
Stg3 2 3 16 Xtxp430/Xtxp1 Xu et al. (2000)
Stg4 5 2 11 Xtxp225/Xtxp15 Xu et al. (2000)
Cold tolerance (late 1 – 21 PeriCol/OPK18 Knoll et al.
emergence %) (2008)
Cold tolerance (late 2 – 11 Xtxp201/Sb110 Knoll et al.
emergence %) (2008)
Cold tolerance (early vigor) 1 – 20 PeriCol/OPK18 Knoll et al.
(2008)
Cold tolerance (early vigor) 4 – 12 Xtxp51/Xtxp21 Knoll et al.
(2008)
Cold tolerance (late vigor) 1 – 28 PeriCol/OPK18 Knoll et al.
(2008)
Cold tolerance (cold 3 – 13 ubc171/SbAGE01 Knoll et al.
germination) (2008)
Cold tolerance (optimal 3 – 15 umc60/ubc171 Knoll et al.
germination) (2008)

the rate of crop improvement. A method to shorten breeding cycle from the regular
17–11 week by embryo rescue was demonstrated in sorghum (Rizal et al. 2014).
Modern trends in digital agriculture have seen a shift toward artificial intelligence
for crop quality assessment and yield estimation (Mosley et al. 2020). Reliable,
automatic, multifunctional, and high-throughput phenotypic technologies are
increasingly considered important tools for rapid advancement of genetic gain in
breeding programs (Zhao et al. 2019). Phenomics platforms have allowed scientists
436 Prabhakar et al.

to use fast and simple quantitative and qualitative methods to assess plant growth
and development. This facilitates the detailed observation and measurement of the
different traits resulting from the expression of genetic characteristics of plants, both
physical and environmental factors. Several approaches to field-based plant
phenomics have been proposed of which aerial drones are promising. Aerial drones,
by contrast, can cover large areas quickly, allowing all genotypes in a study to be
measured simultaneously, and are not impeded by plant height, which allows them
to capture data throughout the entire growth season (Liebisch et al. 2015).

7.19 Status of Varietal Development and Maintenance

Breeding

Developing improved cultivars of sorghum requires considerable expenditure of

time and effort to put together the specific combinations of traits needed to achieve
high and stable production of grain and/or stover in a particular environment. These
traits include the correct phenology for the environment, the necessary resistances to
the biotic and abiotic constraints prevalent there, and the quality traits preferred by
farmers.
If improved cultivars are not maintained systematically, they are likely to deteri-
orate in yield and quality due to outcrossing with the unadapted cultivars lacking one
or more of the component traits. Deliberate and systematic maintenance of cultivars
and multiplication of their seed is, therefore, required to ensure that the genetic
package assembled by the plant breeder is kept together and delivered to farmers.
Similarly, attention should be given to the crop health of seed production plots to
ensure that the seed delivered to farmers is in good condition to germinate and
establish the intended crop.
A detailed information on varieties released in kharif, rabi, forage, and sweet
sorghum has already earlier appeared in the chapter, and only maintenance aspects
are given here.

7.20 Maintenance of Genetic Purity in Sorghum Varieties

7.20.1 Land Requirement

Land should be free from volunteer plants, Johnson grass, Sudan grass, and other
forage types. The same crop should not be grown on the same piece of land in the
previous one season unless it is the same variety and certified by certification agency
for its purity.
7 Sorghum Breeding 437

7.20.2 Isolation Requirement

Sorghum is a self-pollinated crop, but cross-pollination up to 8–10% may occur. In

some of the varieties with loose or lax panicle types, the extent of natural cross-
pollination may go up to 50%. Hence, the seed fields must be isolated from other
varieties of grain and dual-purpose sorghum and same variety not confirming to
varietal purity by 200 m for foundation seed class and 100 m for certified seed class.
An isolation of 400 m is required from Johnson grass (Sorghum halepense) and other
forage sorghums with high tillering and grassy panicles. Differential blooming for
modifying isolation distance is not permitted (i.e., time isolation is not permitted).

7.20.3 Brief Cultural Practices

Obtain appropriate class of the seed from the source approved by seed certification
agency. The seed rate required is 12–15 kg/ha, and the spacing adopted is 45 cm
between the rows and 15 cm between the plants. Other cultural practices are similar
to raising a commercial crop. Necessary prophylactic measures should be taken so as
to raise a good crop.

7.20.4 Rouging

Remove all the offtypes and volunteer plants before they start shedding pollen. The
rouged plants must be cut from the bottom or uprooted to prevent re-growth.
Offtypes can be identified based on morphological characters like plant height,
leaf shape, leaf color, stem pigmentation, days to flowering, etc. Rogue out other
related plants like Johnson grass, Sudan grass, forage plants, and plants affected by
kernel smut and head smut from time to time.

7.20.5 Number of Field Inspections

A minimum of three field inspection should be done. First inspection should be done
during vegetative stage to determine isolation, volunteer plants and designated
diseases, etc. Second inspection shall be made during flowering to check isolation,
offtypes, and other relevant factors. Third inspection shall be made at maturity prior
to harvest to verify designated diseases true nature of plants, head, and seed.

7.20.6 Harvesting and Threshing

The seed crop must be harvested when it is fully ripe. The harvested heads should be
sorted out to remove the diseased or otherwise undesirable. The heads should be
dried on the threshing floor or tarpaulin for a couple of days before threshing.
438 Prabhakar et al.

Threshing can be done by threshers or manually. The seed should be thoroughly

cleaned and dried to 10% moisture before storage.

7.20.7 Seed Yield

Depending up on the potentiality of the variety and the management practices

adopted, seed yield may be in the range of 35–40 q/ha.

7.21 Maintenance of Genetic Purity in Sorghum Hybrids

In sorghum hybrid seed is produced by utilizing cytoplasmic genetic male sterile

system. The source of male sterile cytoplasm used is combined kafir. Hybrid seed
production involves two steps:

• Maintenance of parental lines (A-line, B-line, and R-line)

• Commercial hybrid seed production (A  R)

Maintenance of parental lines is generally referred to as foundation seed produc-

tion and hybrid seed production as certified seed class. The A-line can be maintained
by crossing with B-line in an isolated plot, while in hybrid seed production, A-line
crosses with R-line or fertility restorer line. The B-line and R-line can be maintained
just like normal varieties by following the required isolation and field standards.

7.21.1 Seed Production of B-line and R-line

The seed is produced in an isolated plot, and it is similar to seed production of open
pollinated varieties. However, the isolation distance required and the fields’
standards are similar to that of maintenance of A-line.

7.21.2 Maintenance of A-line or Hybrid Seed Production (A 3 R)

7.21.2.1 Land Requirement

Land should be free from volunteer plants, Johnson grass, Sudan grass, and other
forage types. The same crop should not be grown on the same piece of land in the
previous one season unless it is the same variety and certified by certification agency
for its purity.

7.21.2.2 Isolation Requirement

The isolation distance for maintenance of A-line (A  B) is 300 m from fields of
other varieties of grain and dual-purpose sorghum and same variety not confirming
to varietal purity and 400 m from Johnson grass, Sudan grass, and other forage types.
7 Sorghum Breeding 439

For commercial hybrid seed production of (A  R), the isolation distance required is
200 m from fields of other varieties of grain and dual-purpose sorghum, and same
hybrid not confirming to varietal purity requirements of certification, 5 m from other
hybrid seed production plot having the same male parent and 400 m from Johnson
grass, Sudan grass, and other forage types. Differential blooming dates for modifi-
cation of isolation distance are not permitted.

7.21.2.3 Planting Ratio

The planting ratio of female to male plants is 4:2 with two rows of male parent all
around the field.

7.21.2.4 Brief Cultural Practices

The success in hybrid seed production depends on synchronization of flowering
between the male and female parent. For maintenance of A-line, synchronization of
flowering will not be a problem as both A- and B-lines are isogenic lines and come to
flowering at the same time, while in hybrid seed production, synchronization will be
a problem as A-line and R-line have different genetic constitutions. If there is any
difference between the male and female parent for days to flowering, the sowing
dates should be adjusted for proper synchronization of flowering. The seed rate
required is 8.0 kg/ha of A-line and 4.0 kg/ha of B or R-line. Other cultural practices
similar to commercial crop production should be adopted for raising a good crop.

7.21.2.5 Cultural Manipulation for Nicking

Proper synchronization of flowering between Aline and R-line is a common prob-
lem. In spite of taking the precautions like adjusting the sowing dates, sometimes,
synchronization may be a problem. If the difference between the male and female
parent is less than a week, it can be manipulated by cultural practices. The parent
which is lagging should be sprayed with 1% urea solution 2–3 times at an interval of
2–3 days, or additional irrigation should be given to the lagging parent. Blowing air
by operating empty duster with the mouth directed horizontally to the male ears will
help disseminate pollen.

7.21.2.6 Rouging
Before flowering, remove all offtypes from both seed parent and pollen rows based
on morphological characters. Some of the precautions to be taken while rouging are:

• Start rouging before offtypes, volunteers, and pollen shedders in female rows start
shedding pollen.
• Outcrosses can be easily identified because of their greater height and more
vigorous growth and should be removed.
• At flowering, rouging should be done every day to remove pollen shedders from
female parent rows. The sterile types have only stigma or pale aborted anthers
without pollen, while the fertile ones have yellow colored plumpy anthers which
shed large amount of residual pollen. Remove all plants out of their place (i.e.,
plants in between the lines) and male plants in female rows and vice versa. Special
440 Prabhakar et al.

attention should be given at the ends where there is a chance of male seed falling
in female rows.
• Remove other sorghum-related plants like Johnson grass, Sudan grass, and other
forage types from the seed plot and from within the isolation distance.
• Remove the plants affected by kernel bunt and head smut.
• Pre-harvest rouging may be done based on grain and ear characters.

7.21.2.7 Number of Field Inspections

A minimum of four field inspections should be conducted. The first field inspection
should be conducted before flowering stage, second and third during flowering stage,
and fourth before harvesting. During the first field inspection, verification should be
done for volunteer plants, isolation requirement, errors in planting, and the actual
acreage sown. During the second and third field inspection, verification should be
done for isolation requirement, offtypes, diseased plants, pollen shedders, and
objectionable weed plants. Actual counts should be taken during second or third
field inspection. Fourth or final field inspection should be done to verify for all the
above factors, and the offtypes can be identified based on panicle or seed characters.

7.21.2.8 Harvesting and Threshing

Harvest the male rows first, and keep their heads separate to avoid mixture male and
female seed. Then harvest the female parental line and thresh it separately.
Precautions may be taken while harvesting and threshing to avoid mechanical
mixtures.

7.21.2.9 Seed Yield

The seed yield may be in the range of 4–6 q/ha depending on the parent line and the
cultural practices adopted.

7.22 Coordinated System of Testing

Focused sorghum research in India started with the establishment of the Project for
Intensification of Regional Research on Cotton, Oilseeds and Millets (PIRRCOM) in
1958. Under the PIRRCOM sorghum research was led from the Indian Agricultural
Research Institute (IARI), New Delhi. In 1966, sorghum research was shifted from
New Delhi to Hyderabad as a part of IARI Regional Research. Realizing the success
of hybrid sorghum in the United States in 1962, the Indian Council of Agricultural
Research (ICAR) launched the Accelerated Hybrid Sorghum Project. In December
1969, All India Coordinated Sorghum Improvement Project (AICSIP) was launched
from the existing IARI RRS in Hyderabad. Subsequently, in 1987, a full-fledged
“National Research Centre for Sorghum (NRCS)” was established which has
evolved into the Indian Institute of Millets in 2015. Currently, AICSIP functions
with a total of 24 centers spread across nine states. Sorghum improvement efforts
since the 1960s were focused on improving grain and fodder yields. However, with
7 Sorghum Breeding 441

demands of sorghum as forage crop and in recent past as sweet sorghum, an alternate
source of bioethanol, intensive efforts toward these ends have also been initiated.
Detailed information on varieties and hybrids released in kharif, rabi, forage, and
sweet sorghum in the coordinated has already earlier appeared in the chapter.

7.23 Future Thrust Area

Sorghum improvement efforts have succeeded in increasing productivity of kharif

sorghum but could not impact much in rabi sorghum. Productivity of kharif sor-
ghum may further be improved through diversification of genetic base not only
through use of caudatum races but other races like guinea and kafir. In rabi sorghum
efforts need to improve parental lines with better combining ability, desired levels of
resistance to biotic and abiotic stresses, and acceptable grain qualities. Though
hybrids have not gained much popularity in rabi sorghum, to enhance productivity
of rabi sorghum, concerted efforts need to be focused on development of hybrids
with acceptable grain quality. Alternate use is another area of focus needed in rabi
sorghum breeding program particularly to breed cultivars suitable to specific end
uses. In forage sorghum, attention needs to be given toward improvement of
digestibility and resistance against foliar diseases. Use of bmr mutants has opened
up a new area of opportunity. Seed production of forage cultivars is a major concern.
Production of second-generation biofuels using lignocellulose components opens up
the new area of research in sweet sorghums.
Sorghum as health food is another area which needs concerted efforts to diversify
sorghum uses. Sorghum production can only be enhanced with appropriate policy
support by the government. With inclusion of sorghum and other millets in national
food security mission, there is a ray of hope that sorghum will regain a new place in
the food basket of the country.
In addition to the biotic and abiotic challenges, climate change is expected to
influence the sorghum area and its importance globally. With the current level of
greenhouse gas emissions and the associated temperature rise, the areas suitable for
sorghum are likely to increase by 9% globally, but many areas currently suitable for
sorghum will be lost. Increased temperature makes sorghum crops mature early.
Considering all these points, crop improvement research in sorghum needs to be
oriented toward genetic and cytoplasmic diversification for high yield and large
grain, shoot fly and grain mold resistance, drought and salinity tolerance, post-rainy
season adaptation, sweet stalk traits, and grain micronutrient density. Grain and
stover quality needs special attention to enhance the market value.

7.24 Conclusions

Climate change is expected to influence the sorghum area and its importance
globally, in addition to the biotic and abiotic challenges. With the current level of
greenhouse gas emissions and the associated temperature rise, the areas suitable for
442 Prabhakar et al.

sorghum are likely to increase by 9% globally, but many areas currently suitable for
sorghum will be lost. Increased temperature makes sorghum crops mature early.
Considering all these points, crop improvement research in sorghum needs to be
oriented toward genetic and cytoplasmic diversification for high yield and large
grain, shoot fly and grain mold resistance, drought and salinity tolerance, post-rainy
season adaptation, sweet stalk traits, and grain micronutrient density. Grain and
stover quality needs special attention to enhance the market value.
Various factors leading to the decline of sorghum crop in Indian agriculture are a
matter of concern. Sorghum-based agricultural systems need to withstand biotic and
abiotic stresses because of their cultivation mostly in unfavorable soil and climatic
conditions. Further, they also need to adjust to changing economic (prices and
income) and policy-induced stresses as has been the case in India where subsidized
wheat and rice are supplied through the public distribution system. With this
background in view, there is a need to embark on future approaches for improve-
ment. Promotion of genetic diversity, cropping system stability, and economic
advantage or parity will become the major criteria. The genetic approaches should
promote genetic diversity and cropping system performance and stability.
Concerted efforts to diversify sorghum as health food are another area which
needs attention. Sorghum production can only be enhanced with appropriate policy
support by the government. In India, with inclusion of sorghum and other millets in
national food security mission, there is a ray of hope that sorghum will regain a new
place in the food basket of the country.

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Small Millets Breeding
8
Vilas A. Tonapi, K. N. Ganapathy, K. Hariprasanna, B. Venkatesh Bhat,
B. Amasiddha, S. Avinash, and C. Deepika

Abstract

Millets are small-grained ancient cereal crops and one of the earliest sources of
food known in the prehistoric period. It is believed that they were under cultiva-
tion since 8000 BC. These crops adapted well to the marginal and dryland
ecosystem due to their climate resilience, biotic stress tolerance and ability to
grow in the wild besides providing nutritious grains. Among the millets, small
millets form a distinct group and comprise of finger millet (Eleusine coracana),
little millet (Panicum sumatrense), foxtail millet (Setaria italica), proso millet
(Panicum miliaceum), kodo millet (Paspalum scrobiculatum), barnyard millet
(Echinochloa frumentacea) and brown top millet (Brachiaria ramosa (L.)) in
India along with a few more cereals like teff, fonio, job’s tears and guinea millet
in some other parts of the world. Except finger millet, other small millets received
very limited attention with respect to crop improvement and crop husbandry.
Early efforts in finger millet and other crops mainly concentrated on introduction
and domestication of indigenous accessions and selection among the available
variability. This led to release of some cultivars prior to independence which were
major staples before green revolution. Post 1960s, the area and importance of
these crops started declining with the emergence of fine cereals. Realizing the
importance of small millets and lack of organized research efforts, the Indian
Council of Agricultural Research established the All India Coordinated Small
Millets Improvement Project in 1986 with its headquarters in University of
Agricultural Sciences, Bangalore. Since then, concerted efforts in germplasm
collection, recombination breeding and crop production and protection have

V. A. Tonapi (*) · K. N. Ganapathy · K. Hariprasanna · B. V. Bhat · B. Amasiddha · S. Avinash ·

C. Deepika
ICAR-Indian Institute of Millets Research, Hyderabad, India
e-mail: director.millets@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 449
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_8
450 V. A. Tonapi et al.

resulted in development and release of many improved cultivars for commercial

cultivation by the dryland farmers along with improved package of practices.
Development of early maturing, high yielding and drought-resistant varieties with
emphasis on both grain and biomass continue as important breeding objectives in
all the small millets. Breeding methodologies aiming at recombination breeding
slowly started gaining momentum in all the small millets though the progress is
hampered by typical floral biology and anthesis behaviour. In the last three
decades, more than 200 improved cultivars have been released by adopting
different breeding approaches to suit the location-specific requirements of the
farmers. This chapter describes the breeding efforts made in different small
millets crops and progress so far in India in other countries.

Keywords

Little millet · Barnyard millet · Foxtail millet · Proso millet · Minor millets

8.1 Introduction

Millets and sorghum comprise of an important group of cereal crops known for their
nutritional values. Small millets, also known as minor millets, are a group of small-
seeded cereal crops of the grass family Poaceae. Small millets are hardy and climate
resilient suitable for range of soil, environmental conditions and are prone to drought
and high temperature. Small millets are adapted to a range of temperatures, moisture-
regimes and input conditions and are perhaps the only cereal crops that can grow in
arid lands with only 350–400 mm annual rainfall. Millets, with their ability to
tolerate and survive under conditions of continuous or intermittent drought periods,
are the major crops successfully cultivated in dry regions where fine cereals such as
rice and wheat cannot be grown. The area under millet production has been on the
decline since green revolution, more so in case of small millets (80% for small
millets other than finger millet, 53% for finger millet). The period between 1961 and
2015 saw a dramatic decrease in cultivated area under millets. The area under all
small millets other than finger millet has declined drastically in all states, and the
total production of small millets has declined by more than 75% (Table 8.1). Low
productivity under marginally grown conditions, declining support has significantly
contributed to the fall of millets in Indian agriculture, which is gradually reversing.
However, the production has increased over time through productivity improvement
by crop breeding efforts (Ganapathy et al. 2021a, b).
Small millets are important crops of rainfed areas in semi-arid regions. Presently,
they are cultivated on a limited area globally mainly due to the shift from traditional
crops to more remunerative crops. Small millets serve as major food components in
various traditional foods and are generally eaten as rice apart from its use in various
value-added products and also for beverages and are ingredients in a variety of
multigrain and gluten-free cereal products. Due to sedentary lifestyle conditions and
its associated health concerns, there is a growing awareness among the consumers
 8

Table 8.1 All India area, production and productivity of small millets
Small Millets Breeding

1951– 1961– 1971– 1981– 1991– 2001– 2011– 2015– 2016– 2017– 2018–
Year/crop Element 1952 1962 1972 1982 1992 2002 2012 2016 2017 2018 2019a
Ragi Area 2.19 2.51 2.43 2.61 2.13 1.65 1.18 1.14 1.03 1.19 0.92
Prodn. 1.31 2.03 2.21 2.96 2.58 2.37 1.93 1.82 1.39 1.99 1.22
Yield 599 808 911 1134 1212 1442 1641 1601 1363 1662 1332
Other small Area 4.76 4.87 4.48 3.79 2.09 1.31 0.80 0.65 0.62 0.55 0.50
millets Prodn. 1.92 2.05 1.67 1.64 0.88 0.58 0.45 0.39 0.44 0.44 0.37
Yield 402 421 373 433 423 440 565 601 714 804 747
Total millets Area 32.41 36.91 35.44 34.78 26.61 22.28 17.01 15.01 14.26 14.24 12.25
Prodn. 11.64 15.76 16.92 22.20 16.23 18.80 18.64 14.52 16.2 16.44 13.97
Yield 359 427 491 638 610 844 1096 968 1136 1154 1140
Area, million ha; Prodn, million tonnes; Yield, kg/ha
Source: DMD, GoI and Agricultural Statistics at a glance 2018; https://eands.dacnet.nic.in/Advance_Estimates.htm
a
Fourth Advance Estimates
451
452 V. A. Tonapi et al.

and are seeking more diversified diets that are both tasty and healthy (Ganapathy et al.
2021a, b). Small millet fit in the diversified food system as a healthy food choice
because they provide high energy, high dietary fibre, quality protein and balanced
amino acid, essential minerals, vitamins and antioxidants, and many of them have low
glycaemic index (GI). Due to these inherent features of small millets, they are
popularly known as nutri-cereals. The nutrient content of grains varies among
different small millets. Finger millet grains contain high calcium (~350 mg/100 g).
Nutrient contents like grain iron, zinc, calcium, protein and crude fibre among small
millets are presented in Table 8.2. Small millets play a strategic role as a staple food
for the poor and, lately, as a healthy food for those in urban areas. It underlines the
necessity of directing more research and development towards these crops.

8.2 Genetic Improvement in Small Millets

Diversity in crop cultivars is very important for sustaining global food production.
Germplasm provides the required variability for genetic improvement of crops.
Small millets germplasm possess larger genetic variation for morpho-agronomic
traits, grain quality and stress tolerance traits, and promising germplasm sources
have been reported and are being utilized in the improvement programmes. Various
breeding methods such as pureline selection, pedigree selection, mass selection and
mutation breeding, which are applicable to self-pollinating crops, are followed in
small millets as well. Reports on small millets cultivars released over a period of time
shown that a majority of them were released following selection from local
landraces/cultivars, followed by pedigree selection in the early phase of crop
improvement. Recombination breeding has not been exploited to its fullest extent
as in other crops like sorghum, pearl millets and other fine cereals. The major reasons
are difficulty in hybridization due to small sized florets and irregular flowering
behaviour. Mutation breeding is one of the viable approach in different breeding
crops and has been successfully demonstrated in finger millet (Ganapathy et al.
2021a, b). Hybridization to create variability followed by selection in segregating
population has been an important breeding method in finger millet and compara-
tively less in other small millets like little millet, barnyard millet, foxtail millet and
proso millet. The diversity in small millets in the form of genetic resources, floral
biology, breeding methods, constraints and strategies for small improvement in each
of the seven small millets are discussed hereunder.

8.3 Finger Millet

Finger millet (Eleusine coracana (L.) Gaertn.) is an important food staple of Africa
and Southern Asia. Finger millet cropping area globally is estimated to be around
4.0–4.5 million ha. In India, the crop is estimated to be cultivated on an area of
1.2 million ha with an estimated production of 2.0 million tonnes. The major finger
millet-growing countries in Africa are the sub-humid regions of Ethiopia, Malawi,
 8

Table 8.2 Nutritive composition of millets vis-a-vis fine cereals (values per 100 g)
Small Millets Breeding

Crop Protein (g) Carbohydrate (g) Fat (g) Crude fibre (g) Mineral Matter (g) Calcium (mg) Phosphorous (mg)
Sorghum 10.4 72.6 1.9 1.6 1.6 25 222
Pearl millet 11.6 67.5 5.0 1.2 2.3 42 296
Finger millet 7.3 72.0 1.3 3.6 2.7 344 283
Proso millet 12.5 70.4 1.1 2.2 1.9 14 206
Foxtail millet 12.3 60.9 4.3 8.0 3.3 31 290
Kodo millet 8.3 65.9 1.4 9.0 2.6 27 188
Little millet 8.7 75.7 5.3 8.6 1.7 17 220
Barnyard millet 11.6 74.3 5.8 14.7 4.7 14 121
Barley 11.5 69.6 1.3 3.9 1.2 26 215
Maize 11.5 66.2 3.6 2.7 1.5 20 348
Wheat 11.8 71.2 1.5 1.2 1.5 41 306
Rice 6.8 78.2 0.5 0.2 0.6 10 160
Source: National Institute of Nutrition (NIN), Hyderabad
453
454 V. A. Tonapi et al.

Tanzania, Kenya, Uganda, Zambia, Zaire and Zimbabwe. Similarly, in South Asia,
the crop is mainly grown in Southern India followed by Nepal and to a certain extent
reported in Bhutan and Sri Lanka. In India, the crop is mostly grown in Karnataka
followed by other states like Tamil Nadu, Uttarakhand, Orissa, Maharashtra and
Andhra Pradesh. Cultivation of this crop extends from mean sea level to hilly regions
of Himalayas and is adapted to wide range of soil and environmental conditions but
performs well under well-drained, loamy or clay loamy soils. The grains of finger
millet are known for its highest amount of calcium and also with contents of iron,
zinc, dietary fibre and essential amino acids (Shobana et al. 2013). The grains are
resistant to storage infestation by pests, and with minimum attention, the grain can be
stored for up to 50 years (Iyengar et al. 1945). The stover after harvest of grains is a
source of nutritive fodder to animals and is highly preferred due to sweet-smelled
stalks. Comparing other small millets, genetic gain in yield is much pronounced in
finger millet but not exploited to the extent observed in other major cereals. The
reason is mainly due to irregular flowering behaviour, small-sized florets owing to
difficulties in hybridization. However, the diversity existing for grain yield,
nutritional superiority and its ability to tolerate range of environmental conditions
makes it a promising crop for the future. Research efforts aims at using a combina-
tion of approaches for genetic improvement of grain and forage yield, nutritional
parameters, biotic and abiotic stresses, identification of end-use specific genotypes
and exploring possibilities of exploitation of heterosis.

8.3.1 Gene Pool of Eleusine coracana

The cultivated Eleusine coracana is highly variable in their centres of origin both in
Africa and the Indian subcontinent. The species E. coracana is classified into
subspecies africana and coracana. The subspecies africana is a wild type and
consists of race africana and spontanea. The subspecies coracana is a cultivated
type and are classified into four different races based on inflorescence morphology,
viz. elongata, plana, compacta and vulgaris (Prasada Rao et al. 1993). Both wild
(subspecies africana) and cultivated finger millet (subspecies coracana) are being
collected conserved in various gene banks. africana subspecies occasionally crosses
with the subspecies coracana to produce fertile hybrids. Derivatives of such crosses
are aggressive colonizers and are grouped under the race spontanea (De Wet et al.
1984). Wild finger millet is native to Africa and believed to have been migrated to
warmer parts of Asia and America. The diploid wild species E. indica, E. floccifolia
and E. tristachya are believed to form the secondary gene pool, while the species
E. intermedia, E. jaegeri, E. kigeziensis, E. multiflora and E. semisterlis
(E. compressa) form the tertiary gene pool (Guarino 2012).

8.3.2 Floral Biology and Breeding Behaviour of Finger Millet

The floral biology has been described by Rachie and Peters (1977) and recently by
Gupta et al. (2011). Finger millet is predominantly self-pollinated, and extent of
outcrossing is reported to be less than 1%. The inflorescence consists of terminal
8 Small Millets Breeding 455

digitate spikelets, borne on a long peduncle from the end of 4–5 spikes which radiate
in a whorl called fingers with one finger a little lower the whorl referred to as thumb.
Rachis of the spikes is flat. Spikelets are sessile arranged in two rows alternatively
attached to one side of the rachis. Each spikelet consists of 3–7 flowers averaging to
5 florets and enclosed by common glumes. Androecium consists of three stamens
with long filaments and short oblong anthers. Ovary has two styles with plumose
stigma. The terminal floret is sterile. Anthesis proceeds from top spikelets and
progresses downwards. The maximum number of flowers opens on the third to
fourth day. Flower opening also depends on the earhead shape; the compact types
open during 2–3 am, fisty 3–5 am and open types during 1–2 am. Flower opening
varies from place to place depending upon the temperature and humidity. Flowering
takes place simultaneously in all fingers. Pollen viability is short, 10–15 min.
Complete opening of the inflorescence requires 7–8 days. Anthers require about
45 min for dehiscence after emergence. The stigma is receptive for about 5 min after
emergence from the glumes. Self-pollination is the general rule because the period of
anthesis is very short. Cross fertilization by wind and insects is not a rarity, but less
than 1%.

8.3.3 Germplasm Conservation and Utilization of Finger Millet

Gene bank assumes greater role and serves as reservoirs of diversity and source of
alleles for genetic enhancement of crop plants. In India, the National Active Germ-
plasm Collection Site (NAGS) located at All India Coordinated Small Millets
Improvement Project (AICSMIP), Bangalore, made efforts to assemble large
collections of germplasm at the global level with a total collection of 7070 germ-
plasm. Similarly, the National Bureau of Plant Genetic Resources based in New
Delhi, India, maintains 11,170 accessions of finger millet under long-term conser-
vation. Most of these collections are indigenous with about 117 accessions of exotic
origin. These Indian collections include six wild relatives, 154 advanced improved
varieties and 64 breeding/research materials. ICRISAT, Patancheru, India, maintain
a total of 7519 accessions. The Agricultural Research Station, USDA, Griffin,
Georgia, maintains about 766 accessions of which 17 are wild relatives belonging
to E. floccifolia, E. indica, E. jaegeri, E. multiflora and E. tristachya. The major
germplasm conservation centres in small millets are given in Table 8.3.
The Indian and African germplasm are highly diverse, and a very few systematic
studies have been conducted to compare the diversity among the accessions avail-
able in the gene banks. In general, the Indian germplasm are reported to be diverse
for grain and dry stover yield. Early maturing varieties combining high grain yield,
quality and stover yield are ideally preferred by farmers. The African germplasm
exhibited larger variation for plant height, stout plant stature, long narrow finger,
higher number of spikelets, poor threshability, late maturing and poor harvest index.
456 V. A. Tonapi et al.

Table 8.3 Major germplasm conservation centres in small millets

Number of
Crop Gene bank germplasm (Approx)
Finger National Active Germplasm Collection Site (NAGS), 7070
millet Bangalore. India
ICAR-National Bureau of Plant Genetic Resources, New 11,170
Delhi
International Crops Research Institute for Semi-Arid 7519
Tropics, Hyderabad
Proso Russian Federation 8778
millet Chinese Academy of Agricultural Sciences 8451
ICAR-National Bureau of Plant Genetic Resources, New 1005
Delhi
National Active Germplasm Collection Site (NAGS), 920
Bangalore, India
International Crops Research Institute for Semi-Arid 842
Tropics, Hyderabad, India
Foxtail Chinese National Gene Bank 26,670
millet ICAR-National Bureau of Plant Genetic Resources, New 4667
Delhi
National Active Germplasm Collection Site (NAGS), 2821
Bangalore, India
ORSTOM-MONTP, France 3500
Svalbard Global Seed Vault, Norway 2505
International Crops Research Institute for the Semi-Arid 1542
Tropics (ICRISAT), Patancheru
Little National Active Germplasm Collection Site (NAGS), 2000
millet Bangalore, India
International Crops Research Institute for Semi-Arid 1000
Tropics, Hyderabad, India
ICAR-National Bureau of Plant Genetic Resources, New 1799
Delhi
Barnyard National Institute of Agro-Biological Sciences, Tsukuba, 3671
millet Japan
ICAR-National Bureau of Plant Genetic Resources, New 1953
Delhi
National Active Germplasm Collection Site (NAGS), 2000
Bangalore, India
Kodo ICAR-National Bureau of Plant Genetic Resources, New 2362
millet Delhi
National Active Germplasm Collection Site (NAGS), 1537
Bangalore, India

The African germplasm are said to possess higher level of resistance to blast, the
most devastating disease in finger millet (Kiran Babu et al. 2013).
For effective utilization of the germplasm for genetic improvement programme,
Upadhyaya et al. (2006) established core collection of 622 genotypes representing
8 Small Millets Breeding 457

geographical regions and biological races from the entire collection. The African
(58.7%) and Asian (35.8%) collections were predominant, while those from Amer-
ica and Europe were represented by 0.8–1.1%, respectively. The cultivated subspe-
cies coracana occupied 97.4% of the core, while African accessions represented
only 2.6%. Among the coracana subspecies, race vulgaris were predominant
(62.5%) followed by plana (16.8%) compacta (12.4%) and elongata (8.3%). The
core collections were evaluated for 15 quantitative and five qualitative traits, and a
mini-core collection of 80 accessions was constituted. Wide variability was reported
among the mini-core collections for economically important traits like days to
flowering (51.24–93.73), plant height (72.66–113.31 cm), length of longest finger
(49.79–139.73 mm), finger per ear (6.13–9.41) and grain yield (691–2430 kg/ha).
Upadhyaya et al. (2007) reported diversity in 909 accessions introduced from
southern and eastern African region from ICRISAT gene bank and observed large
variability for plant pigmentation, growth characters, flowering, plant height and
inflorescence length and width and grain colour. Their study also characterized the
variability among different finger millet races. Daba and Keneni (2010) reported
little or low effect of geographical origin on the pattern of diversity studied from
native and exotic collections in Ethiopia. Their study revealed biomass, earweight
and grain weight contributing more towards the observed diversity.

8.3.4 Varietal Improvement of Finger Millet in India

Breeding methods such as pureline selection, recombination breeding and mutation

breeding are the widely used approaches for genetic improvement in finger millet.
Mass selection has been used for purification of the landraces and varieties devel-
oped by pureline or pedigree systems. Pureline selection has also been extensively
used in finger millet improvement. Single plants selections were made from
landraces (germplasm) and improved farmers’ varieties, and the promising lines
for earliness, pest and disease resistance and grain yield were evaluated under
multilocational trials and released as varieties (Ganapathy 2017a).
Hybridization was used extensively in finger millet compared to other small
millets. Until the 1950s, the improvement aimed at improving locally adapted
lines by centres. Subsequently millet improvement took place after establishment
of the Project for Intensification of Regional Research on Cotton, Oilseeds and
Millets (PIRRCOM) during the late 1950s and later formulation of the All India
Coordinated Millets Improvement Project during 1965. Genetic resources of finger
millet and small millets were assembled during the 1960s. The exotic lines from
Africa were introduced to India during the 1970s. The lines from Africa had greater
vigour, high finger length and good grain filling ability and thick robust stems with
broad dark green leaves (Seetharam 1982). Recombination breeding took place
between indigenous, exotic and indigenous with exotic lines. Selections were
458 V. A. Tonapi et al.

followed from crosses involving Indian and exotic lines in various combinations for
early, medium and late duration (more than 110 days).
Varieties developed from Indian
Indian crosses such as Udaya, K 7, Purna,
Annapurna, Cauvery, Shakti and HPB 7-6 had moderate productivity. Hybridization
among the Indian
exotic cross led to breakthrough in bringing greater variability
and improving productivity of finger millet. This led to 50–60% increased produc-
tivity in Karnataka and Tamil Nadu (Seetharam 1982; Nagarajan and Raveendran
1985).
The period of finger millet improvement during 1964–1986 witnessed a revolu-
tion due to the introduction of Indo-African crosses of finger millet by the late
Dr. CH Lakshmanaiah, who is known popularly as “Ragi Brahma” for his
pioneering work that resulted in the release of 16 varieties designated as “Indaf”
series. The yield levels of these varieties ranged from 3000 to 4000 kg/ha. In a
significant move, the All India Coordinated Small Millets Improvement Project
(AICSMIP) was launched in 1986 by the Indian Council of Agricultural Research
with its headquarters in GKVK, UAS, Bangalore. Following this, during the period
between 1986 and 2000, the yield potential has further improved ranging up to
4500 kg/ha with varieties which are resistant to blast disease. GPU 28 is one such
medium-duration variety maturing in 110–115 days released during 1996. The
variety is suited for delayed sowing under terminal drought conditions. It is also
resistant to neck and finger blast which is a major constraint to finger millet
production. The potential yield of the variety is 3500–4000 kg/ha. Presently the
variety is grown on a larger area (about 70% area) in Karnataka. Joint efforts were
made by the Department of Agriculture in each of the finger millet growing states,
state seed corporation, state agricultural universities and private seed sectors for
augmenting the availability of quality seed of GPU 28. During 2000–2012, upon
establishment of AICSMIP, efforts were laid on developing productive lines with
elite background through hybridization to improve high grain and straw yield
suitable for kharif and also rabi seasons. The yield levels further increased subse-
quently ranging up to 5000 kg/ha. Currently, research efforts are underway to
develop long-, medium- and short-duration varieties with high grain yield, resistant
to blast disease, and to address the challenges like drought, saline and alkaline soils,
cold season and hilly areas and mechanical harvesting. Some of the latest finger
millet varieties released for cultivation are given in Annexure.

8.3.5 Strategies for Enhancing Productivity and Utilization

of Finger Millet

8.3.5.1 Germplasm Evaluation

There is need for systematic evaluation of indigenous and exotic germplasm avail-
able with the national gene bank under multilocation germplasm for early maturity,
photo insensitivity, drought tolerance, blast and other disease and pest resistance,
8 Small Millets Breeding 459

nutritional (protein, calcium, iron, zinc and essential amino acids) and antioxidants
of therapeutic value.

8.3.5.2 Participatory Selection and Varietal Development

Farmers grow finger millet under marginal fertile soil conditions, and the perfor-
mance of these varieties largely depends upon edaphic and climatic conditions which
is least represented in research stations. This warrants participation of the farmers in
selection of desired genotypes/varieties. Appropriate selection and breeding efforts
involving farmers participatory approach is required to be taken up to develop high
yielding finger millet varieties for different production systems under varying
environmental conditions.

8.3.5.3 Breeding for Blast Resistance and Other Pests

Blast disease is major problem in finger millet affecting the crop at all stages of crop
growth, and number of varieties are susceptible. Understanding the pathogen diver-
sity in the geographical area, screening germplasm collections, identification of
resistant germplasm and development of blast resistant varieties based on knowledge
of the strains are desirable for development of durable resistance.

8.3.5.4 Interspecific Hybridization and Search for Novel Traits

There is need for search of novel traits in wild species especially from primary and
secondary gene pool for disease resistance, cytoplasmic genic male sterility and
other novel traits. The search and discovery of genetic or cytoplasmic male sterility
would be a substantial breakthrough in the improvement of this crop by opening up
the possibilities for effective population improvement.

8.3.5.5 Development of Early Maturing Varieties

Development of early maturing superior genotypes which can fit in different crop-
ping systems as well as provide substantial yield under water stress is one of the
important breeding objectives.

8.3.5.6 Genetic Improvement for Drought Tolerance

Systematic research to identify diverse drought tolerant genotypes, understand
mechanisms of drought tolerance from multilocational screening, as well as identify
key surrogate/adaptive traits needs to initiated. The identified lines should be used in
introgression breeding for development of improved drought tolerant finger millet
genotypes.

8.3.5.7 Stover Yield and Quality Improvement

Although finger millet crop is predominantly grown for grain/food purpose, the
stover after harvest of crop is an excellent source of nutritive fodder to cattle. There
is need to identify superior non-lodging tall types with superior grain and fodder
yield. The African types are known to possess more plant height, and there is need to
utilize these types for improvement of fodder yield and quality.
460 V. A. Tonapi et al.

8.3.5.8 High Yielding White Finger Millet Varieties

Few white grain types are rich in protein (~12%) compared to coloured types (~8%)
but are low yielding. Therefore, there is need to develop improved white grained
finger millet genotypes for malting purposes as well as other end uses such as
weaning foods, infant foods and malted milk foods, etc.

8.3.5.9 Nutritional Improvement

Finger millet is highly nutritious and thus calls for intensive evaluation of germplasm
to assess its nutritional qualities. Finger millet grains besides providing energy are
also a rich source of calcium and iron, and its proteins are a good source of essential
amino acids and can greatly contribute to micronutrient and protein malnutrition
affecting women and children in African and south-east Asian countries. The most
cost-effective approach for mitigating micronutrient and protein malnutrition is to
introduce varieties bred for iron, zinc and protein content in grains. Attempts to
breed finger millet for enhanced grain nutrients are still in its infancy. Evaluation of
finger millet core germplasm for grain nutrients and agronomic traits revealed a
substantial genetic variability for grain iron, zinc, calcium and protein contents.
Therefore, there is need to use the identified accessions in strategic research for
development of nutritionally rich cultivars of finger millet.

8.4 Foxtail Millet

Foxtail millet [Setaria italica (L.) Beauv.] is one of the oldest of the cultivated
millets in the world and is grown in about 23 countries in Asia, Africa and America.
It is a self-pollinating species (2n ¼ 2x ¼ 18), belonging to family Poaeceae and
subfamily Panicoideae. It is good as food, feed and fodder crop, which matures in a
short duration. It is cultivated mainly on poor or marginal soils in southern Europe
and in temperate, subtropical and tropical Asia (Marathee 1993). Its grain is used for
human consumption and as feed for poultry and cage birds. The total world area is
estimated to be about 10.5 lakh ha with a grain production of about 22.9 lakh tonnes.
The major growing countries are China, the USA and India, with a contribution of
only 2.4% to the total millets production in the world. In China, foxtail millet is next
to rice and wheat in importance. In India, because of the drought tolerance, it was
once an indispensable crop of vast rainfed areas in semi-arid regions, especially the
Deccan plateau. But the area under foxtail millet has come down drastically during
the 1990s mainly due to introduction of more remunerative crops like sunflower and
soybean in blacksoils (Hariprasanna 2017). At present, foxtail millet is cultivated on
a very limited area of about 70,000 ha mostly in Andhra Pradesh, Karnataka,
Telangana, Tamil Nadu, Maharashtra, Rajasthan, Madhya Pradesh and north-eastern
states.
Foxtail millet is adapted to a wide range of elevations, soils and temperatures and
can grow from mean sea level to up to 2000 m altitude. It is drought tolerant and has
a low water requirement, but does not recover well from drought conditions because
of shallow root system. It is mostly grown to meet the domestic needs of the rural
8 Small Millets Breeding 461

people and is widely used as an energy source for pregnant and lactating women and
also for sick people and children, and especially for diabetics (Sema and Sarita 2002;
Hariprasanna 2017). The grains are rich in protein (12.3%) and crude fibre (8%) and
gaining importance as a diabetic food due to relatively low-to-medium glycaemic
index (Janani et al. 2016; Dayakar Rao et al. 2017; Wahlang et al. 2018). It has been
suggested that foxtail millet protein be used as a food component to fight type
2 diabetes and cardiovascular diseases (Choi et al. 2005).

8.4.1 Origin and Taxonomy of Foxtail Millet

Foxtail millet has originated in China and has the longest history of cultivation
among the millets, having been grown in China since sixth millennium BC.
Carbonized foxtail millet has been identified in archaeological sites in China. The
cultivation has been mentioned in Chinese records as early as 2700 BC (Vinall 1924).
Its domestication and cultivation were the earliest identifiable manifestation of
neolithic culture, the beginning of which has been estimated at over 4000 years
ago (Chang 1968). The principal centre of diversity for foxtail millet is East Asia,
including China and Japan (Vavilov 1926). A multiple domestication hypothesis
(de Wet et al. 1979) is widely accepted though several hypotheses concerning the
origin and domestication of foxtail millet have been proposed. From Central Asia, it
spread to India and European countries (Oelke et al. 1990).
The genus Setaria consists of approximately 125 species (Dwivedi et al. 2012),
widely distributed in warm and temperate areas. The genus includes a large number
of valuable perennial forage grasses and grain crops (Chennaveeraiah and Hiremath
1991). Foxtail millet is the most economically valuable of the genus (Baltensperger
1996). Malm and Rachie (1971) thoroughly reviewed the domestication of foxtail
millets and the taxonomy. The geographical origin of foxtail millet based on
cytological studies indicated that wild ancestor of foxtail millet is S. viridis
(Li et al. 1945). Three main groups of cultivated foxtail millet gene pool were
suggested, namely, Chinese (from China, Japan and Korea), tropical (from Taiwan,
India and Kenya) and European group, on the basis of isozyme studies in accessions
of S. italica and S. viridis, respectively (Jusuf and Pernes 1985; Panaud 2006).
On the basis of inflorescence morphology, foxtail millet is classified into two
species, S. pumila and S. italica. The species S. italica is divided into two subspecies
viridis and italica. The subspecies italica is classified into three races and ten
sub-races (Prasada Rao et al. 1987). The race moharia (common in Europe, south-
east Russia, Afghanistan and Pakistan) is divided into sub-races aristata, fusiformis
and glabra; race maxima (common in eastern China, Georgia, Japan, Korea, Nepal
and northern India) is divided into sub-races compacta, spongiosa and assamense;
and race indica (remaining parts of India and Sri Lanka) is divided into sub-races
erecta, glabra, nana and profusa. Race maxima has also been introduced in
the USA.
462 V. A. Tonapi et al.

8.4.2 Germplasm Resources and Utilization of Foxtail Millet

Wide genetic diversity is available in foxtail millet, and more than 44,000 germ-
plasm have been conserved in different gene banks all over the world (Vetriventhan
et al. 2020). Major collections include Chinese National Gene Bank (CNGB, 26,670
accessions); ICAR-National Bureau of Plant Genetic Resources, New Delhi (4667);
ORSTOM-MONTP, France (3500); Svalbard Global Seed Vault, Norway (2505);
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT),
Patancheru (1542); National Institute of Agro-biological Sciences (NIAS), Japan
(1299); and North Central Regional Plant Introduction Station, USDA-ARS, USA
(1000).
The ICAR-Indian Institute of Millets Research, Hyderabad, holds about 4554
accessions in its medium-term storage module. The National Active Germplasm Site
(NAGS) for small millets was established at University of Agricultural Sciences,
Bengaluru, in 1992. It holds about 2559 accessions, most of which have been
characterized and catalogued. At Tamil Nadu Agricultural University, Coimbatore,
considerable diversity was observed among 741 accessions maintained for all the
agronomic characters (Nirmalakumari and Vetriventhan 2010). The Regional Agri-
cultural Research Station, Acharya NG Ranga Agricultural University, Nandyal,
Andhra Pradesh, also maintains an active collection of more than 1000 accessions,
which has been used in varietal development programmes. The ICRISAT has
constituted a core collection comprising 155 accessions using the taxonomic and
qualitative traits data (Upadhyaya et al. 2008). Multi-location evaluation of core
collection has resulted in identification of a number of diverse germplasm accessions
with agronomically and nutritionally (high seed protein, calcium, iron and zinc)
superior traits. Further, a mini core comprising of 35 accessions has been developed
(Upadhyaya et al. 2011), which is an ideal resource for studying population structure
and diversity and identifying new sources of variation for use in breeding and
genomics studies in foxtail millet.

8.4.3 Genetics and Cytogenetics of Foxtail Millet

The most common basic chromosome number in genus Setaria is x ¼ 9 (Singh and
Gupta 1977), although numbers like x ¼ 7, 8 and 10 are also found rarely. Cultivated
millet S. italica (L.) Beauv. and closely related species S. viridis L. are both diploids
with 2n ¼ 2x ¼ 18. Different levels of polyploidy (3x, 4x, 5x, 6x, 7x, 8x and 12x) are
also known in different species of Setaria. Intraspecific polyploidy has been reported
in many Setaria species like S. sphacelata showing 2x, 4x and 6x (Singh and Gupta
1977). Studies on chromosome structure revealed four pairs of metacentric, four
pairs of submetacentric and one pair of acrocentric chromosomes in foxtail millet
(Chandola 1959). Chikara and Gupta (1979) observed one pair of
SAT-chromosomes each in six varieties, which differed in the number of metacen-
tric, submetacentric and acrocentric chromosomes. These differences were attributed
to structural changes. However, meiosis was normal showing nine bivalents
8 Small Millets Breeding 463

(Chandola 1959; Singh and Gupta 1977). A complete set of nine primary trisomics
(2n + 1) (cv. Yugu No. 1) of foxtail millet was identified cytologically from
progenies derived from crosses between autotriploids (2n ¼ 2x ¼ 27) and their
diploid counterparts (Wang et al. 1999). In a S. italica
S. viridis cross regular nine
bivalent formation was noticed. Regular chromosome pairing in the hybrid and its
partial fertility suggests that genomes of foxtail millet (S. italica) and S. viridis are
similar and that foxtail millet originated from wild S. viridis through selection and
further cultivation (Li et al. 1945).
Genetic studies in foxtail millet have been conducted mostly on morphological
characters and disease response (Malm and Rachie 1971). Most of the previous
works have focused on estimating heritability and realized genetic gains, with little
attention directed to measuring levels of heterosis or to assessing the relative
importance of different types of gene action due to highly self-pollinated nature
(Athwal and Singh 1966; Gill and Randhawa 1975; Vishwanatha et al. 1981;
Gurunadha Rao et al. 1984; Prasada Rao et al. 1985; Nirmalakumari and
Vetriventhan 2010). Agronomic traits like days to 50% flowering, plant height,
total number of tillers, number of productive tillers, panicle length and days to
maturity exhibited highly significant positive correlations with grain yield.
Characters such as flag leaf area and 1000-grain weight were also observed to
influence yield. High heritability was observed for all the quantitative traits like
flowering duration, plant height, inflorescence length and test weight (Hariprasanna
et al. 2015, 2017, 2018, 2019). Negative association of protein content and calcium
content with grain yield has been reported along with negative association of
carotene with grain yield (Prasanna et al. 2013). So simultaneous improvement of
these traits along with grain yield may not be possible.

8.4.4 Reproductive Biology of Foxtail Millet

Foxtail millet matures in 60–90 days depending on genotype. It forms a slender,

erect, leafy stem varying in height from 40 to 150 cm. The stem produces an
inflorescence terminally. There is a very quick transition period from vegetative
growth to flower development (Baltensperger 1996). The inflorescence is a dense,
cylindrical terminal spike borne on a thin and very short pedicel (Sundararaj and
Thulasidas 1976) with short side branches bearing spikelets and bristles. The
shortened side branches are called secondary clusters or lobes. The compressed
hairy panicle 5–30 cm long resembles yellow foxtail, green foxtail or giant foxtail.
Each spikelet consists of a pair of glumes that embrace two minute flowers (about
1 mm in length), the lower one sterile and the upper one bisexual, with three stamens
and a long oval smooth ovary with two long styles, which terminate in a brush-like
stigma (Hector 1936). The spikelets are glabrous, elliptic to obovate and about 2 cm
long. One to three bristles develop at the base of each spikelet (Vinall 1924).
Anthesis in foxtail millet generally takes place near midnight and in the morning,
but varies significantly with the environment (Malm and Rachie 1971). The rate of
anthesis is generally favoured by low temperature and high humidity.
464 V. A. Tonapi et al.

The small seeds, around 2 mm in diameter, are encased in a thin, papery hull
which is easily removed after threshing. The seed coat and husk of foxtail are
generally of single entity with glossy appearance. The grains are very similar to
paddy rice in grain structure with outer husk, which needs to be removed in order to
be used. Seed colour varies greatly between genotypes and is usually yellowish,
cream to orange or yellow brown to black in colour (Seetharam et al. 2003). Seed
colour varies greatly between genotypes and is usually yellowish in colour. Mor-
phology and anthesis behaviour make foxtail millet one of the most difficult species
to cross pollinate.

8.4.5 Breeding Objectives of Foxtail Millet

The principal breeding objectives in foxtail millet include development of early

maturing, high yielding and drought-resistant varieties like any other small millets.
Maximization of biomass and the harvest index are also the target traits. Genotypes
have to be tailored for early, mid-late or late maturity, depending on the location-
specific requirements of soil, rainfall, temperature, humidity, day length and crop-
ping patterns (Harinarayana 1989). Dwarf plant stature to reduce lodging, water-use
efficiency and nitrogen-use efficiency, uniform maturity, etc. are other breeding
objectives.

8.4.6 Breeding Methods of Foxtail Millet

Pureline selection from the local germplasm remained the prime breeding method for
improving performance, particularly grain yield of foxtail millet. As foxtail millet is
largely self-pollinated and out-crossing is very much limited, and because of the
anthesis behaviour, hybridization followed by selection was a difficult breeding
procedure to adopt and could not gather much research efforts. Difficulties in
emasculation and pollination in small millets in general, identification of true
hybrids, limited heterosis in inter-varietal crosses (Srivastava and Yadava 1977)
and the non-availability of diverse germplasm resources to the breeders acted as
major constraints in varietal improvement in foxtail millet (Hariprasanna 2017).
Some of the latest foxtail millet varieties released for cultivation are given in
Annexure.

8.4.7 Production Constraints of Foxtail Millet

Though foxtail millet is not severely affected by any major biotic stress factors, blast
disease caused by pathogenic fungus, Magnaporthe grisea, is one of the major
diseases affecting the production, especially in northern China and India (Nakayama
et al. 2005). Blast affects both grain and forage production in foxtail millet.
Symptoms of the disease appear as circular spots with straw-coloured centres on
8 Small Millets Breeding 465

leafblades. Other frequently occurring diseases are sheath blight, downy mildew and
rust. Among the insect pests, shoot fly (Atherigona atripalpis Wiede) is one of the
important pests in foxtail millet. Shoot fly do not prefer the foxtail millet genotypes
possessing lower moisture, crude protein and total sugar content for its oviposition
and dead heart infestation (Sanjeev et al. 2011).
Drought stress and high temperature are important abiotic factors affecting grain
yield and biomass. Prolonged moisture stress severely affects crop establishment and
biomass yield. High temperature above 35  C coinciding with flowering affects seed
set. Lodging is another important yield and quality-reducing factor depending on the
environmental conditions. Thin stem, tall plant height and poor root anchoring due
to light soils often lead to lodging during maturity.

8.4.8 Future Prospects of Foxtail Millet

The foxtail millet genome has been sequenced, and the first assembled reference
genome of foxtail millet and green foxtail was released in the year 2012 by two
independent groups (Zhang et al. 2012; Bennetzen et al. 2012). The Joint Genome
Institute of the US Department of Energy and the Center for Integrative Genomics
had constructed a public domain database PHYTOZOME (http://phytozome.jgi.doe.
gov/pz/portal.html) to provide online resources for foxtail millet genomics with
unrestricted public access. The genome data generated by Beijing Genomics Insti-
tute (Zhang et al. 2012) are available in Foxtail millet Database (http://foxtailmillet.
genomics.org.cn/). A large volume of information on genomic, genic and ILP
marker resources are available in the Foxtail Millet Marker Database developed by
National Institute for Plant Genome Research, New Delhi (https://59.163.192.91/
foxtail/markers.html). Availability of genomic information and resources has now
provided numerous scientific leads to proceed further towards crop improvement of
millets, cereals and bioenergy grasses. The major research areas that need to be
further explored are structural genomics, genome-wide studies of gene families
involved in abiotic stress tolerance, epigenetics and gene expression regulation
and understanding the genetics and genomics of nutritional traits (Muthamilarasan
and Prasad 2015). More high yielding and nutritious varieties need to be developed
to popularize the crop and regain the lost area. Promotion of foxtail millet cultivation
through appropriate policy interventions can ensure food, nutrition, fodder and
livelihood security in the dryland agriculture.

8.5 Barnyard Millet

Barnyard millet (Echinochloa frumentacea (RoxB). Link), being a climate-resilient

crop, also produces multiple securities like food, nutrition, fodder, fibre, health,
livelihood and ecology. Globally, India is the largest producer of barnyard millet,
both in terms of area (0.146 million ha) and production (0.147 million tonnes) with
average productivity of 1034 kg/ha during the last 3 years (IIMR 2018). It is widely
466 V. A. Tonapi et al.

cultivated as minor cereal for food as well as fodder in India, China, Japan, Korea,
Pakistan, Nepal and Africa. Due to its remarkable ability to withstand erratic rainfall
and varying weather conditions, it has been classified as one of the drought stresses,
hardy crops which is largely cultivated in harsh and fragile environments. It is a
regular crop up to 2700 m above MSL during kharif season in Uttarakhand and
Tamil Nadu and forms a mainstay of agricultural diet and cultural system of hill
people. Diversity in this crop is eroded fast due to several reasons like cultivation on
poor, shallow and marginal soils under rainfed conditions, reduction in area under
cultivation and changing social, economic and cultural dimensions of farming
community in India (Maikhuri et al. 2001). Barnyard millet with rich nutritional
profile is one of the best choices for patients with dietary-based health defects like
diabetics, heart-related diseases and celiac diseases. Millets are free from gluten;
hence, gluten-allergic patients require these minor millets for health improvement.
Traditional foods prepared from barnyard millet such as roti, payasam, pongal,
pulav, idli, dosa and muruku are very popular in southern India. In addition to
human food, it has an important place in dairy due to high palatability of its fodder,
which can also be used for making hay or silage.

8.5.1 Origin and Taxonomy of Barnyard Millet

The barnyard millet belongs to the genus Echinochloa, the family Poaceae and
subfamily Panicoideae (Clayton and Renvoize 2006). The genus Echinochloa
comprises about 250 related species of annual or perennial grasses widely distributed
in temperate and warmer parts of the world (Bajwa et al. 2015). Xiaoyan et al. (2015)
conducted microfossil studies on both lithic implements and sediment samples from
previously studied levels of occupation, and they found evidence for the exploitation
of nuts, such as acorns (Lithocarpus/Quercus sensulato), and water chestnuts
(Trapa), as well as extensive evidence for the processing of another wetland grass,
barnyard grass (Echinochloa spp.), indicating that this wild millet was an important
resource harvested and processed alongside rice and only abandoned in favour of
rice at a later stage of the domestication process. The two species of barnyard millet
are grown as cereals. Echinochloa crus-galli is native to temperate Eurasia and was
domesticated in Japan some 4000 years ago. E. oryzoides, the most aggressive weed,
is recognized taxonomically as E. crus-galli var. oryzicola. It differs from E. crus-
galli in having 2n ¼ 36 rather than 2n ¼ 54 chromosomes (De Wet et al. 1983).
Echinochloa colona is widely distributed in the tropics and subtropics of the Old
World. It was domesticated in India. Echinochloa colona is morphologically allied
to E. crus-galli. Four morphological races are recognized, although these do not
have geographical, ecological or ethnological unity. Race laxa is confined to Sikkim,
while races robusta, intermedia and stolonifera are also grown in India (De Wet
et al. 1983). The two cultivated species under genus Echinochloa, E. frumentacea
(Indian barnyard millet) and E. esculenta (Japanese barnyard millet) are cultivated
for food and fodder by hilly and tribal communities in Asia particularly in India,
China, Africa and Japan.
8 Small Millets Breeding 467

8.5.2 Germplasm Resources and Utilization of Barnyard Millet

The most of the germplasm accessions of barnyard millet are housed in India and
Japan. ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan (VPKAS),
Almora, India; ICAR-National Bureau of Plant Genetic Resources, New Delhi;
ICAR-Indian Institute of Millets Research (IIMR), India; National Institute of
Agrobiological Sciences (NIAS), Japan; and International Crop Research Institute
for the Semi-Arid Tropics (ICRISAT), India, are actively involved in collection,
conservation and utilization of germplasm lines in barnyard millet. Germplasm
characterization for morphological traits is the preliminary step; this not only
provides information on heritability of the traits but also increases the germplasm
utilization. Gowda et al. (2008) evaluated 729 germplasm accessions of barnyard
millet for yield and related traits over the years. Correlation and path coefficient
analysis for morphological traits in barnyard millet showed significant direct effect
of heat units at maturity, photothermal units at 50% flowering, plant height, days to
50% flowering and weight of panicle on grain yield, and they could serve as a useful
criterion in the development of short high yielding cultivars (Mehta et al. 2007).
Wallace et al. (2015) have genotyped the core collection (89 accessions) follow-
ing genotyping-by-sequencing (GBS) approach and identified several thousand
SNPs and found four populations within E. colona and three in E. crus-galli,
which match with phylogenetic relationships. ISSR (Nozawa et al. 2004) and
RAPD (Deepti et al. 2012) markers were identified and used in the diversity analysis
in the germplasm accessions of Indian and Japanese barnyard millet accessions. Lal
and Maloo (2006) studied the path coefficient analysis in Indian barnyard millet and
found that main panicle weight, plant height and primaries had high effect on seed
yield. The 95 germplasm lines representing the global collection were evaluated for
qualitative and quantitative traits, and cluster analysis showed that Indian and origin
unknown accessions grouped in E. frumentacea group, Japanese accessions grouped
in E. esculenta group and third group contained the accessions from Russia, Japan,
Cameroon and Egypt (Sood et al. 2015). Gupta et al. (2009) evaluated 194 accessions
collected from different eco-geographical regions of India for 14 quantitative traits.
Five groups were formed based on location of collection; group C with unknown
origin exhibited maximum diversity with 17.67% coefficient of variation. The other
groups recorded mean coefficient of variation between 12% and 13%. Correlation
studies showed leaf width and number of racemes are useful to carry out selections in
segregating populations.

8.5.3 Reproductive Biology of Barnyard Millet

In barnyard millet, the inflorescence is seen in varying shapes (pyramidal, cylindri-

cal, globose and elliptic), colours (green, light green, light purple and dark purple)
and compactness (open, intermediate and compact) (Gupta et al. 2009; Sood et al.
2015). Raceme number varies from 22 to 64 per inflorescence (Renganathan et al.
2017) and varies in arrangement from one side, two sides or around the rachis. The
468 V. A. Tonapi et al.

position of florets varies from one side of raceme to around the rachis in which
spikelets will be arranged in 3–4 rows (florets positioned on one side of raceme) and
irregularly arranged (florets positioned around the raceme). Each spikelet contains
two florets; upper fertile floret contains two unequal glumes, lemma and palea, three
stamens (white, yellow and dark purple coloured) and plumose type of bifid stigma
(white, pink and purple coloured). Anthesis and pollination are basipetal in nature
where flower opening which starts at 5 am reaches maximum at 7–8 am and closes
by 10 am (Sundararaj and Thulasidas 1976: Jayaraman et al. 1997).

8.5.4 Breeding Objectives of Barnyard Millet

Barnyard millet is known for its high biomass production apart from grain yield;
hence, it is cultivated as a dual-purpose crop. The breeding goal is to improve its
biomass yielding ability (green fodder and dry fodder yield) along with grain yield.
The quality of the fodder for its easy digestibility and preference by the cattle is also
good in barnyard millet when compared to other millets. Breeding methodologies
focussing on the use of physiological traits-based phenotyping in millets will be one
of the potential areas to exploit for crop improvement. Development of cultivars with
dual-purpose types (early maturing quick growing and high biomass yielding lines)
is another breeding objective. The grain size in the developed cultivars is small, and
dehulling efficiency directly depends upon the grain size of the crop. Hence,
increasing the grain size in barnyard millet is another area of research to increase
the grain yield as well as dehulling percentage. The length of the panicle and number
of productive tillers are having high correlation with grain yield. Developing lines
with more spikes and long panicles is another targeted area. Grain smut is the major
biotic constraint causing yield loss up to 60%. Japanese barnyard millet and
E. colona are immune to the disease. Japanese type and Indian type are not easily
crossable because of hybrid sterility. However, E. colona, wild relative of Indian
barnyard millets, is crossable with cultivated type and may be used as a donor source
for resistant genes to grain smut. In barnyard millet, male sterile lines are not
available and hand emasculation and pollination are very difficult because of the
large number of tiny flowers in single inflorescence. Identification/development of
male sterile lines is of prime importance for recombination breeding. Barnyard millet
is rich in dietary fibre, iron and zinc minerals; targeting the nutritional traits and
developing varieties with high nutrient content are of great advantage in developing
naturally fortified cultivars.

8.5.5 Breeding Methods of Barnyard Millet

Barnyard millet is a self-pollinated crop with 5–10% of outcrossing. In kharif season

because of high relative humidity and less difference between day and night
temperatures, the flowers will open in less number, and pollination is mostly
cleistogamous. In rabi season because of low relative humidity, more difference
8 Small Millets Breeding 469

between day and night temperature (night cold temperature followed by early
morning exposure of florets to sunlight) leads to opening of a greater number of
florets and pollination after opening of the floret. Hence, in rabi season, the
outcrossing percentage is higher than in kharif season. The breeding objectives are
based upon the pollination type in the crop. Barnyard millet being a self-pollinated
crop uses breeding methods like selection, pedigree method, single seed descent
method and mutation breeding. Most of the varieties released in barnyard millet are
based on selection method from germplasm lines. In recent years, pedigree method is
in practice to combine the favourable traits of two parents with more understanding
of the traits and emasculation and pollination techniques.
Use of chemical hybridizing agents and mutation with physical and chemical
means are the other methods of creating variation for selection and also to identify
male sterile lines if any produced in the population. Improvement/modification over
the SSD method is single panicle descent method which is in practice in barnyard
millet for the development of improved cultivars. The information on molecular
marker development and use in breeding programs is lacking in this crop. Recently,
the Japanese barnyard millet E. crus-galli (STB08) genome is sequenced (Guo et al.
2017), and the draft genome sequence is available for use in development of markers
and identification of candidate genes for particular traits. Availability of the molecu-
lar markers (SSRs, SNPs) and the genome sequence information boosts the breeding
work through the application of advanced breeding tools like MABB and MARS for
the development of cultivars with specific defect correction or for multiple trait
improvement.

8.5.6 Production Constraints of Barnyard Millet

The developed cultivars in barnyard millet are based on selection from germplasm
collections without much intervention of advanced breeding methodologies. Lack of
clear information on physiological traits, biochemical traits and nutritional traits in
barnyard millet is hindering the progress in improving the crop for high yield other
end specific cultivar development. Negative correlation of earliness, high grain yield
and biomass yield is also limiting the development of superior varieties. Fodder yield
is one of the most important components nowadays along with grain yield; develop-
ment of high biomass lines hinders high grain production as photosynthates translo-
cate more to biomass production and less to reproductive parts hence lowering the
grain yield. Recombination breeding combines the favourable traits of two or more
parents and releases the variation in the segregating populations, but recombination
breeding is difficult in barnyard millet because of many tiny flowers arranged closely
in the inflorescence. Emasculation and hybridization are difficult in this millet like
other millets because of early hours of flower opening, non-abundance of pollen
grains, short viability of pollens, short opening time of flowers and tightly attached
lemma and palea around the stigma and anthers (Sood et al. 2015). Genomic
resources are helpful for the progress of any crop species, and they assist in effective
characterization of germplasm resources and subsequent use in the discovery of
470 V. A. Tonapi et al.

QTL/gene(s) for the crop improvement program. However, genome research in

barnyard millet is still in the early stage and far behind the other minor millets
(Renganathan et al. 2020). Very limited attempts have been made to discover the
genomic structure and associated downstream processes due to its genome complex-
ity and lack of research funding on this orphan crop. Some of the latest barnyard
millet varieties released for cultivation are given in Annexure.

8.5.7 Future Prospects of Barnyard Millet

Understanding the genetic base and inheritance pattern of traits governing the yield
and biomass is of prime importance in this crop. Usefulness of physiological trait-
based phenotyping to unravel the stress tolerance mechanisms and to identify the
suitable cultivars for stress-prone areas is urgently required to combat the changing
climatic conditions. The nutritional superiority available in barnyard millet germ-
plasm will help the breeders to develop suitable cultivarsnaturally enriched with
nutrients and minerals gives added advantage for popularization and also for
nutritional security. Widening the genetic base specifically for the traits like grain
size, panicle length, high biomass and number of productive tillers through recom-
bination breeding and mutational breeding is the way forward to bring improvement
in both pre-harvest and post-harvest processing aspects in barnyard millet. Use of
wild relatives and progenitor species for transferring the resistant genes for biotic
stresses may fetch rewards in the near future by avoiding the yield losses both in
grain and fodder.
The fertility barriers between Indian and Japanese types may be analysed, and
advanced biotechnological tools may be used to overcome the barriers. Overcoming
the barriers will help in many ways of combining the favourable traits of both types
in one background. Molecular sequence data generation and its use in breeding are
completely lacking in barnyard millet specifically in Indian barnyard millet when
compared to other millets like foxtail millet, proso millet, finger millet, pearl millet
and sorghum. Generation of genome sequence data, genome structure studies,
evolution pattern of the genome and relatedness of barnyard millet genome with
other millets, unraveling of nutrient accumulation pathways, identification of genes/
QTLs and tagging of genes with particular traits on particular linkage groups are the
niche areas of research in barnyard millet to bring suitable improvement in the
development of high yielding cultivars.

8.6 Little Millet

Little millet (Panicum sumatrense Roth. ex. Roem and Schultz) is indigenous to the
Indian subcontinent and also has wild ancestor Panicum psilopodium present
throughout India. It is widely cultivated as minor cereal across India and to a certain
extent in Nepal and western Burma. In India, the crop is majorly grown in Madhya
Pradesh, Chhattisgarh, Karnataka, Tamil Nadu, Orissa, Andhra Pradesh, Jharkhand
8 Small Millets Breeding 471

and Bihar. The crop is hardy and moisture stress tolerant and provides reasonable
harvest even in degraded soils and unfavourable weather conditions (Selvi et al.
2014). The crop is cultivated both in the tropics and subtropics even up to an altitude
of 2000 m above mean sea level. The crop is known for its drought tolerance and is
considered as one of the least water demanding crops. Other advantage is that the
grains can be stored for up to 10 years or more without much loss due to deterioration
(Selvi et al. 2014). Consequently, it has traditionally played an important role as a
reserve food crop. The crop is also grown in the eastern parts of India where it
formed part of tribal agriculture. Cultivated area under crop has drastically declined
from about 5 lakh ha during 2001–2002 to presently about 2–2.5 lakh ha and
production of about 1 lakh tonnes. However, exact figures on current area, produc-
tion and productivity are not available. Madhya Pradesh state occupies about
40–50% of the area under little millet followed by Chhattisgarh, Tamil Nadu,
Karnataka, Maharashtra, Orissa, Andhra Pradesh and Jharkhand. The average pro-
ductivity of the crop is around 500–600 kg/ha.
Nutritionally the grain of little millet is comparable or even superior to some of
the major cereals. In general, little millet is a disease-free crop, but occurrence of
grain smut (Macalpino mycessharmae) can lead to economic losses at times. Among
insect pests, incidence of shoot fly is widely reported and known to cause economic
losses. The crop is known for high content of crude fibre in its grains. It is also rich
source of protein (~7.7%) and fat (~4.8%), minerals and vitamins and requires
consideration as essential food for nutritional security. The crop matures in
80–120 days depending on the type of cultivar grown. Yield levels in this crop
may reach close to 3 tonnes/ha under favourable conditions.

8.6.1 Morphological Variation in Little Millet

Panicum sumatrense subsp. sumatrense is a morphological variable cereal largely

cultivated in India followed by Sri Lanka, Nepal and Burma. The species include
wild and cultivated forms. The species is divided into P. sumatrense subsp.
sumatrense to include cultivated one and subsp. psilopodium (Trin.) de Wet comb.
nov. to include the wild progenitor. These two subspecies cross where they are
sympatric to produce fertile hybrids, derivatives of which are often weedy in little
millet fields. Weedy types are derived between wild and cultivated types and escape
from cultivation due to the ability of efficient natural seed dispersal. P. sumatrense is
extensively variable with regard to growth habit and inflorescence morphology.
Based on the morphological variation and distribution, two races of cultivated little
millet are recognized, namely, nana and robusta (de Wet et al. 1983). Race nana
resemble wild subspecies of P. sumatrense with regard to inflorescence morphology.
Race nana includes plants with decumbent to almost prostrate culms that become
erect at time of flowering. Inflorescences are large and open with the upper branches
sometimes clumped and curved at time of maturity. Height of the plants ranges from
50 to 100 cm. Terminal inflorescences size range from 14 to 50 cm long and are
erect, open and strongly branched, and sometimes branches get clumped at time of
472 V. A. Tonapi et al.

maturity. Race robusta are erect plants with large strongly branched open or compact
inflorescence. Flowering culms grow tall and range between 120 and 190 cm and
robust. Terminal inflorescence is in range of 20–46 cm long, open or compact and
strongly branched. Open inflorescences are essentially erect, while compact
inflorescences are curved at maturity. This race is grown in northwestern Andhra
Pradesh and adjacent Orissa where it crosses with race nana (de Wet et al. 1983).

8.6.2 Genetic Improvement of Little Millet

Major work reported so far is on screening of the germplasm for improved genotypes
for yield and other important traits, germplasm diversity studies, identification of
resistant sources for smut resistance, testing association among different traits
influencing yield, proximate and mineral composition in grains, mutation studies
and creation of new variation and identification of surrogate/adaptive traits and
genotypes for drought tolerance (Ganapathy 2017b). The race nana matures faster
and generates less biomass than robusta (de Wet et al. 1983). In the tribal area of the
Indian Kolli Hills, diversity among locally grown landraces of little millet was found
to be high for all morphological traits measured both within and between landraces
(Arunachalam et al. 2005). High diversity and heritability and genetic advancement
was reported for yield and productive tillers in 109 landraces indicating selections
for varietal development (Nirmalakumari et al. 2010). Evaluation of about
460 collections of little millet held by ICRISAT revealed high genetic variation
for most of the quantitative traits tested (Upadhyaya et al. 2014). A core collection of
56 genotypes was constituted which represents seed bank collections. Increased
heritable lodging resistance has been introduced to a population of little millet
with γ-ray mutational breeding (Nirmalakumari et al. 2007). Channappagoudar
et al. (2007) identified traits influencing grain yield in the crop. Taller genotypes
were found to be high yielding, and shorter genotypes are medium to low yielding.
Other parameters are number of leaves and tillers per plant positively contributing
towards higher grain yield. Leaf area index and leaf area duration were also
important growth parameters for improving the yield and total dry matter as it
indicates the efficiency of the photosynthetic system. Overall, the study reported
TNAU 63 (20.2 q/ha) and DPI 1869 (18.3 q/ha) and TNAU 18 (16.9 q/ha) were high
yielding with high values for most morpho-physiological parameters. Gollagi et al.
(2013) analysed the biophysical basis of yield enhancement in little millet and
observed high transpiration rate in low yielding genotypes and low rate in high
yielding genotypes. They also observed that higher yielding types had higher
stomatal conductance (60 DAS) which could be because of higher stomatal fre-
quency on abaxial surface leading to enhanced canopy photosynthesis.
Nirmalakumari and Ulaganathan (2013) followed farmers’ participatory approach
to identify trait-specific genotypes. Twelve genotypes were evaluated by farmers on
community plots managed by them at several sites in agro-ecological areas. Farmers
evaluated for panicle type, yield traits, seed size and lodging resistance and rated the
varieties based on their preferences. Farmers showed more interests towards
8 Small Millets Breeding 473

compact panicles possessing bold seeds, pest and disease-free genotypes and
non-lodging characteristics.
Salini et al. (2014) evaluated 105 germplasm of little millet for various traits and
selected 12 promising lines as parents and reported several cross combinations. Gene
action was studied for 11 characters, and they reported non-additive gene action for
all the characters except plant height where additive and non-additive played equal
role. High coefficient of variation was observed for grain yield per plant and number
of basal tillers per plant. Heritability estimates were high for all the characters except
flag leaf sheath length. Inheritance of qualitative characters indicated monogenic
simple dominance inheritance for most traits except grain colour. Stability analysis
was carried out for 12 parents in four environments for eight characters and
identified IPmr 1046 and IPmr 889 as stable genotypes for grain yield.
Girish et al. (2013) evaluated six improved types, RLM 40, BL 4, RLM
186, DLM 14, GV-2-1 and RLM 141, to identify high yielding types with checks
JK 8 and OLM 203. They identified two lines, BL 4 (1141 kg/ha grain yield and
5 tonnes/ha fodder yield) and DLM 14 (grain yield of 1292 kg/ha and fodder yield of
5 tonnes/ha), as promising compared to check JK 8 which yielded 994 kg/ha with
6 tonnes/ha fodder yield. DLM 44 was reported to be early with height of about
100 cm and suited for intercrop with redgram. Sasamala et al. (2012) studied the
genetic diversity among 22 little millet lines evaluated over 12 environments. The
study identified KCM 42, KCM 102D, Sabar and Co 2 most divergent with KCM
594 and RCM 4 indicating that hybridization between these genotypes likely to give
better recombinants in segregating generations.
M.S. Swaminathan Research Foundation (MSSRF), Chennai, has taken
initiatives to collect, evaluate and conserve little millet in Tamil Nadu to improve
cultivation of the crop. In Kolli Hills of Tamil Nadu, little millets were preferred by
tribal farmers as they provided sustainable benefits. MSSRF attempted to bring back
cultivation of the small millets and also to revitalize their conservation of local
landraces and cultivars. The participatory rural appraisal conducted with farmers of
the regions revealed interest of the farmers in millets but are getting eroded due to
low productivity of landraces that are under traditional cultivation. Ideal approaches
are to introduce scientific steps to optimize their cultivation practices under site-
specific constraints. Arunachalam et al. (2005) from MSSRF studied the stability of
genetic diversity among landraces of little millet in south India at the ecological
level. Genetic divergence studies revealed high diversity among set of landraces
analysed at two locations for two seasons. Days to maturity and flowering
contributed most to the genetic differentiation. The study confirmed the sustained
availability of the divergence in little millet in Kolli Hills of Tamil Nadu. They
observed location specific expression of traits among the landraces and further
suggested that breeding and selection to be followed as per the needs of the region.
474 V. A. Tonapi et al.

8.6.3 Varietal Development of Little Millet

Varietal development has received less attention as the case in other small millets.
Most of the varieties released were developed through mass selection or pureline
selection methods. Breeding for new varieties using hybridization techniques is
limited owing to difficulties encountered in crossing due to tiny spikelets on brittle
pedicels (Nirmalakumari et al. 2007). Mutation breeding was used as complement to
conventional breeding methods for genetic improvement of little millet. A number of
high yielding varieties have been developed and released for cultivation in different
little millet-growing states. The improved varieties are able to meet the specific
requirements of different regions. Although yield has been the main criterion for
development of new varieties, the varieties OLM 20 possess drought tolerance,
OLM 36 for brown spot and sheath blight and OLM 203 blast and grain smut.
Birsa Gundli 1, selection from local developed from BAU, Ranchi, is very early and
matures in 55–60 days with reasonable grain yield. The latest varieties released in
different states and popular in different little millet growing states are given in
Annexure.

8.6.4 Future Prospects of Little Millet

For valuing the genetic diversity in the germplasm, systematic evaluation and
unlocking the genetic diversity in the germplasm should be the major objective for
genetic improvement. Grain yield has always been an important trait for genetic
improvement. Efforts towards improvement for yield have led to marginal improve-
ment. Selection for component traits such as compact panicle types and large seed
size should be done. Knowledge on floral biology and hybridization techniques
requires attention. Moreover, the small-sized florets in this crop have hindered in the
genetic improvement of this crop through hybridization techniques. Although
millets are grown on poor soils under dry conditions, genotypes/cultivars responsive
to high input conditions should also be identified. Little millet is well-known for its
drought tolerance and is considered as one of the least water-demanding crops. Few
isolated studies have indicated less loss in grain yield under water stress compared to
proso millet and foxtail millet.
Cultivars possessing drought tolerance and better regenerative capacity on rever-
sal of dry spell for harsh conditions should be focus of genetic improvement.
Farmers’ participatory approach should be followed for deriving improved varieties.
The dry fodder after harvest of the crop is source of nutritious fodder to animals. It is
possible that the variability in the quality stover could be exploited to develop
improved varieties with better nutritive value. Pests and diseases infecting little
millet are less. However, earlier studies have indicated shoot fly and grain smut
causing economic losses. Host plant resistance should be a major strategy for pest
and disease resistance. Lodging and grain shattering are the other important agro-
nomic traits which should receive due attention while improving for grain yield.
Breeding for specific end uses should receive priority as this attracts the private
8 Small Millets Breeding 475

sector industries to invest in millets. Little millet is known to mature in 60–80 days.
However, early maturing genotypes with substantial high yield and photo-
insensitive genotypes suiting different cropping systems should be developed.

8.7 Kodo Millet

Kodo millet (Paspalum scrobiculatum L.) is widely distributed in damp habitats in

the tropics and subtropics. It is grown in arid regions of Asia, New Zealand and the
USA as a pasture crop. It is an indigenous cereal of India largely grown in Madhya
Pradesh, Chhattisgarh, Uttar Pradesh, Tamil Nadu, Maharashtra, Karnataka and
some parts of Andhra Pradesh (Yadava and Jain 2006). It is popularly known as
kodo (Hindi), Varagu (Tamil), Arika (Telugu), Harka (Kannada), Kodra (Gujarati,
Marathi and Punjab) and Kodua (Oriya) in India (Ayyangar and Rao 1934;
Deshpande et al. 2015). It has several names in different parts of the world like
bastard millet, creeping paspalum, ditch millet, Indian paspalum, koda grass,
scrobic, water couch and Kodohirse (German) (Knees and Gupta 2013). In India,
kodo millet is widespread and grown in about 1.5–2.0 lakh ha with a productivity of
about 400–500 kg/ha depending on environmental conditions. Madhya Pradesh and
Chhattisgarh account for nearly 70–80% area under this crop, and other important
states are Tamil Nadu, Maharashtra, Uttar Pradesh and Gujarat.

8.7.1 Floral Biology of Kodo Millet

Kodo millet is a highly self-pollinated crop with cleistogamous flowers, but several
researchers observed opening of the flowers at varying time between 2:30 am and
11:30 am at various growing regions and also protogynous lines (Youngman and
Roy 1923; Ayyangar and Rao 1934; Verma 1989; Yadava 1997). Inflorescences are
composed of 3–5 racemes alternately arranged on a short to elongated primary axis.
Racemes are up to 13 cm long, with sub-sessile spikelets arranged in 2–3 rows along
one side of flattened rachis. Spikelets are glabrous, orbicular or broadly elliptic,
conspicuously plano-convex, 1.8–3.5 mm long. The lower glume is absent and
upper glume is as long as the spikelet. The lower lemma is flat more or less
membranaceous and without palea. The upper lemma is crustaceous, often brown
and shiny when grains are mature and embraces the crustaceous palea. The grain is
elliptic-orbicular in outline and 1.5–2.5 mm long (de Wet et al. 1983). Gynoecium is
monocarpellary, ovary is superior, one cell with one ovule, two stigmas, feathery
with distinct style. The grains are elliptic, convex in front and flat on back of palea;
scutellum is up to half the length of the grain. The grain is enclosed in hard,
corneous, persistent husks that are difficult to remove.
Three races of kodo millet were recognized based on arrangement of spikelets on
the raceme. They are regularis, where the spikelets arranged in the two rows on the
one side of flattened rachis; irregularis, where the spikelets are arranged in 2–4
irregular rows along the rachis; variabilis, where spikelets in the lower part are
476 V. A. Tonapi et al.

irregularly arranged and in the upper part the spikelets are in two regular rows on the
raceme. In all three types of racemes, spikelets are arranged on flattened rachis. The
grain may vary in colour from light red to dark grey (de Wet et al. 1983). The crop
matures in 3–4 months with average yield varying from 250 to 1000 kg/ha (Hulse
et al. 1980), and crop has a potential yield of 2000 kg/ha (Harinarayana 1989).

8.7.2 Germplasm and Core Collection Status

About 8000 accessions of kodo millet have been conserved in main ex situ gene
banks around the world. In Indian gene banks, around 3956 accessions have been
conserved at AICSMIP, Bangalore (1537); ICSRISAT, Hyderabad (665); and
NBPGR, New Delhi (2362) (Upadhyaya et al. 2014). National Active Germplasm
Site (NAGS), AICSMIP, published a catalogue on evaluation of 1038 accessions for
16 and 11 qualitative and quantitative descriptors, respectively, and at TNAU,
Coimbatore, 427 accessions have been maintained. ICRISAT established a core
collection comprising 75 accessions belonging to 53 distinct clusters of 656 kodo
millet germplasm collections (Upadhyaya et al. 2014). These genotypes could be
utilized in breeding programme aimed at development of new genetic variants and
recombinants.

8.7.3 Varietal Development of Kodo Millet

Kodo millet has received very less priority like other small millets in the agricultural
research though the genetic improvement work started before the independence in
the country. Some of the early efforts in crop improvement of kodo millet have
resulted in the release of improved varieties as early as the 1940s. The first improved
variety PLR 1 was released in 1942 for the rainfed areas of Tamil Nadu. Another
improved variety, T2, was released in 1949, and Co 1 was released from TNAU,
Coimbatore, during 1953. Post independence, the genetic improvement work was
initiated in Madhya Pradesh during 1964 with the financial assistance from the state
government. Niwas 1, another improved variety, was released in 1971 as the
outcome of this work for general cultivation in Madhya Pradesh (Yadava and Jain
2006). Since 1978, the centre of excellence for the improvement of small millets
established at Dindori (JNKVV) by ICAR with the assistance of International
Development Research Centre (IDRC), Canada, is devotedly working towards the
improvement of kodo millet.
With the establishment of AICSMIP in 1986, the IDRC centre became part of
AICSMIP, and varietal development gained momentum. The AICSMIP centres
located at Tribal Agricultural Research Station, JNKVV, Dindori, and Agricultural
College, JNKVV, Rewa, are exclusively working on kodo and little millets. Pres-
ently emphasis is being given to the development of high yielding varieties with
resistance to biotic and abiotic stresses; enrichment of germplasm; their critical
evaluation for morphological, physiological and biotic and abiotic resistance traits;
8 Small Millets Breeding 477

and enhancement in available genetic variability through hybridization/mutagenesis

for identification of ideotypes suitable for different farming situations (Yadava and
Jain 2006; Hariprasanna 2017).

8.7.3.1 Pureline Selection in Kodo Millet

The varieties released in kodo millet so far are mainly developed through selection
from landraces or germplasm. Some of the kodo millet varieties, namely, APK 1, GK
2 and KMV 20, were the product of selection from germplasm introduced in
different agro-ecosystem. The pureline selection remained the prime breeding
method for improving performance, particularly grain yield. Single plant selection
from landraces and cultivated varieties and their evaluation for economic characters
like earliness, resistance to biotic stresses and high yield have resulted in the
development and release of many varieties in kodo millet. During the period from
1942 to 2020, about 36 varieties have been released, of which 11 were released
before establishment of AICSMIP (1986) and rest after 1986. Among these, pureline
selection has resulted in the development and release of 22 varieties of kodo millet.

8.7.3.2 Recombination Breeding

The difficulties in emasculation and pollination due to small and delicate spikelets
combined with brittleness of flattened rachis have resulted in a slow progress in
recombination breeding in kodo millet. However, the methods of hybridization and
selection have been standardized and extensively used in the recent past for the
creation of variability and selection of transgressive segregants from advanced
generations. The hand emasculation technique developed by Verma (1989) and
modified by Yadava (1997) has been found effective in kodo millet. The controlled
pollination just after the emasculation helps in development of hybrids. The contact
method as suggested for finger millet is successfully used in kodo millet with slight
modifications. In this method, the panicles of selected plants are tied to other panicle
in which crossing is to be attempted before flowering to enhance the chances of
natural cross pollination. It resulted in low frequency of true hybrids which can be
identified with the help of marker characteristics of the parents.

8.7.3.3 Mutation Breeding

In kodo millet, Mishra et al. (1985) were first to introduce quantitative variation
through gamma irradiation. The sensitivity to gamma irradiation varied from geno-
type to genotype. Yadava (1997) found maximum mutation frequency and effec-
tiveness at 25 kR dose of gamma irradiation. The mutants having auricle
pigmentation, late maturity, complete panicle emergence and dark brown seed
have been developed (Yadava et al. 2003). A protogynous mutant having two
rows of spikelets on rachis was also identified from 5 kR dose of gamma irradiation
in JK 76. Among the mutants identified, KM 86 and KM 99 have high yield potential
coupled with early maturity. There is thus ample possibility for improvement
following physical and chemical mutagenesis in kodo millet (Yadava and Jain
478 V. A. Tonapi et al.

2006). Some of the latest kodo millet varieties released for cultivation are given in
Annexure.

8.8 Proso Millet

Proso millet (Panicum miliaceum) is an important minor millet belonging to the

family Gramineae. The crop is a short-duration millet variety and grown in India, the
USA and other countries. It is specially adapted to tropics and high altitudes, where
the growing season is short and the soil is marginal and poor in fertility. Among
grain crops, proso millet requires less soil moisture. The crop is well adapted to high
elevations and cultivated even in the Himalayan region up to an altitude of 2700 m.
The dehusked grain (about 70% of the whole grain) is nutritious and is generally
cooked like rice. Sometimes, it is ground to make roti and eaten. Green plants are
fodder for cattle and horses, also used as hay. The crop is ready for harvest in
70–80 days. The average grain yield in India varies between 500 and 700 kg/ha in
drylands and 1500 and 2000 kg/ha under irrigated/favourable conditions. The dry
stover is normally three times higher than grain yield and is used as cattle feed.

8.8.1 Morphology and Reproductive Biology

The plant grows to a height of 30–100 cm, and stem is hollow, hairy or glabrous with
swollen internodes and a shallow root system. It is a short-day, short-duration
(60–90 days) crop. The crop is harvested at its physiological maturity to avoid
shattering of grain. The flowering takes place usually between 10:00 am and 12:00
noon. However, flowering is influenced by environmental conditions especially
humidity and temperature. The inflorescence is a drooping panicle and looks like a
broom with basipetal opening of florets, i.e., from top to bottom. The spikelet
consists of two glumes and two lemmas. The lower lemma has a sterile floret, and
upper lemma has a fertile floret. The stamen possesses three anthers and two feathery
stigmas. The anther dehiscence coincides with stigma receptivity, and anthers appear
dry within a few minutes of flower opening. It usually takes 10–12 days for complete
flowering within an inflorescence. Though self-pollination is the rule, up to 10%
cross-pollination may occur (Popov 1970). Nelson (1984) reported crossing
techniques in proso millet using hand emasculation. Cold spray technique for
emasculation and crossing was reported by Nandini et al. in 2019. Seeds of proso
millet are oval and 3 mm long, and colour varies from white, golden yellow, orange,
red, brown to black (Baltensperger 2002).

8.8.2 Germplasm Resources of Proso Millet

The extensive collection of proso millet germplasm (8778) is maintained in Russia

followed by Chinese academy of agricultural sciences (8451). Other major gene
8 Small Millets Breeding 479

banks conserving the crop’s genetic variability are in Ukraine, India, and the USA
(Upadhyaya et al. 2014). In India, the AICSMIP, NBPGR and ICRISAT are
involved in plant genetic resource in collection, distribution and utilization.
AICSMIP is a national active germplasm site and maintains a collection of about
920 accessions of proso millet. NBPGR is maintaining about 1005 germplasm
accessions. ICRISAT with about 842 accessions is involved in germplasm charac-
terization and evaluation of proso millet. ICRISAT developed a core collection of
106 accessions from 842 proso millet accessions of 30 countries based on 20 quali-
tative and quantitative traits.

8.8.3 Genetic Improvement of Proso Millet

In India, AICSMIP centres located in different states are involved in screening the
germplasm lines since inception for grain yield and components. In proso millet,
crop improvement programmes are focused on improving traits like yield, lodging
resistance, non-shattering, early maturity, panicle type, waxiness, etc. Through
conventional methods like pureline selection and pedigree breeding, improved
varieties have been developed in proso millet in China, India, the USA, Russia
and Kenya. In India, K2 is a variety developed through pureline selection, which is
non-lodging and non-shattering (http://agritech.tnau.ac.in). The varieties TNAU
202 and ATL 1 are high yielding varieties developed by hybridization. Genetics
and inheritance of waxy traits have been carried out. Waxy trait is reported to be
controlled by duplicate recessive alleles. GBSSI gene (with two loci—S, L)
mutations are identified to result in waxiness, while the GBSSI-S locus mainly
contributes to the trait (Graybosch and Baltensperger 2009; Hunt et al. 2013; Rose
and Santra 2013; Santra et al. 2015). Rajput et al. (2014) used molecular breeding
tools to identify 18 quantitative trait loci (QTL) for phenotypic traits like heading
date, test weight, grains per panicle, lodging, plant height, peduncle length, grain
shattering and panicle length which may be validated and used for marker-assisted
selection. Waxy forms of grains are preferred in the food industry for glutinous
nature suited for beverage industry for their high fermentation efficiency.
Increasing proso millet production with declining area was the major challenge
and was overcome with the development of modern varieties with greater adaptabil-
ity to soil and environmental conditions and high yield potential of more than
4 tonnes/ha. Proso millet breeding programmes in Russia aimed at increasing
productivity, smut disease resistance and grain quality like uniform size and shape
and yellow endosperm with high carotenoid content. The major breeding method
employed in Russia is intra-specific hybridization. A number of varieties were
developed, and the notable cultivars are “Bistrove” and “Krupnoskoroe” (ssp.
subcoccineum), which recorded up to 5 tonnes/ha grain yield with very short
duration. Identification of genes for resistance, the improved varieties “Sputnik”
(ssp. coccineum) and “Slavjanskoe” (spp. subflavum) were developed during 2006.
The varieties were medium maturing and gave grain yield as high as 7 tonnes/ha.
Russian variety Alba is reported as non-shattering grain variety. During 2006–2010,
480 V. A. Tonapi et al.

the new selection technologies based on mutant forms, dihaploid plants production,
genotype identification with the use of storage proteins electrophoresis and DNA
markers were developed. As an outcome of this, a new variety “Regent” was
developed during 2011 using anther culture technique, and selection was done
keeping in mind the productivity and grain quality parameters. The variety had
high yield, medium maturity (95–105 days) and resistance to lodging and shattering.

8.8.4 Future Prospects of Proso Millet

The genetic and genomic resources development in proso millet lags behind most
cereals. There is a need for an extensive trait-specific germplasm evaluation or
donors for traits like biotic and abiotic stress tolerance, non-lodging, non-shattering,
yield, compact panicle, bold grains and genetic male sterility systems. Precision
phenotyping for major traits is a prerequisite. The identified germplasm can be used
for introgression of genes into popular cultivars using modern breeding methods like
genomics assisted breeding (marker assisted selection, marker assisted backcrossing,
haplotype breeding, speed breeding, etc.) and transgenic approaches. Functional
markers and gene introgression for traits like genetic male sterility, non-lodging,
etc. can also be attempted from the model grass species foxtail millet in which
genetic dissection of traits occurs at a faster pace.

8.9 Browntop Millet

Browntop millet (Brachiaria ramosa (L.) Stapf Nguyen) is an annual/perennial

warm-season grass originated in Southeast Asia, often used in forage/pasture man-
agement systems. It is a minor millet mostly confined to a few thousands of hectares
in South East Asia and parts of the USA. In India, it is grown mostly in southern
India (Bhat et al. 2018) where it is locally known as pedda sama or korle. Though
presently it is restricted to remote parts of Andhra Pradesh, Karnataka and Tamil
Nadu states in southern India, it appears to have been a major staple crop in the late
prehistory of the wider region of the Deccan. Domestic and wild/weedy forms of
browntop millet are found in agricultural systems, often within the same field.
Browntop millet grows in rocky, shallow soils from sea level up to 8000 ft above
MSL. It is adaptable to almost all upland soil (Mitchell and Tomlinson 1989), but
does not grow well in water-restricted, drought conditions. It will not survive in
temperature less than 52  F.
Browntop millet is used as both a human food crop and fodder. In some parts of
the USA, it is grown as a fodder crop and bird feed and was introduced from India
around 1915. Morphotypes or races are not known in browntop millet. Mulay and
Leelamma (1956) have reported 2n ¼ 36 chromosomes in this species from India.
The somatic chromosomes are small in size ranging in length between 1 and 2.5μ.
This species was found to show two cytological races, which are morphologically
indistinguishable. Diploid, tetraploid and hexaploid status has been reported in
8 Small Millets Breeding 481

browntop millet with basic chromosome number of 9 (2n ¼ 2x ¼ 18; 2n ¼ 4x ¼ 36,

72) (Vetriventhan et al. 2020).
Very limited genetic variability has been observed among the accessions assem-
bled at ICAR-Indian Institute of Millets Research, Hyderabad. Two different panicle
types have been found—open and bunchy. The florets are very minute, 1–2 mm in
size. There are few reports on floral characteristics and anthesis behaviour. Artificial
hybridization through hand emasculation and pollination has not been standardized
so far, and hence, recombination breeding has not taken up shape as a breeding
methodology. ICAR-Indian Institute of Millets Research maintains about 30 germ-
plasm of browntop millet which are used for assessing the variability and for its use
in further improvement programme. Pureline selection from the available germplasm
appears to be a feasible strategy for improvement and release of cultivars in this crop
as a short-term measure.

Annexure: Improved Varieties Developed and Released in Small

Millets in India (2005–2020)
 Year
482

Institute where of Maturity Avg. yield

S. No. Variety Pedigree developed release (days) (q/ha) Area of adaptation
Finger millet
1 GPU 48 GPU 26
L 5 PC Unit, Bengaluru 2005 95–100 28–30 Karnataka
2 PRM 1 Selection from Hill Campus, 2006 110–115 20–25 Hills of Uttarakhand
Ekeshwar of Pauri GBPUA&T,
Garhwal Region Ranichauri
3 Bharathi Pureline selection from ANGRAU, 2006 110–115 26–30 Andhra Pradesh
(VR 762) VMEC 134 Vizianagaram
4 GPU 66 PR 202
GPU 28 PC Unit, Bengaluru 2009 112–115 35–40 Karnataka
5 GPU 67 Selection from PC Unit, Bengaluru 2009 114–118 30–35 National
germplasm accession
GE 5331
6 Srichaitanya GPU 26
L 5 ANGRAU, 2009 110–115 26–28 Andhra Pradesh
(VR 847) Vizianagaram
7 KMR 301 MR 1
GE 1409 VC Farm, Mandya, 2009 120–125 35–40 Southern Dry zone of
UAS, Bengaluru Karnataka
8 KOPN 235 Selection from local MPKVV, Rahuri 2011 115–120 25–26 Sub-mountain and Ghat
germplasm zone of Maharashtra
9 OEB 526 SDFM 30
PE 244 OAUT, Bhubaneswar 2011 110–115 25–26 Odisha, Bihar,
Chhattisgarh,
Karnataka, Tamil Nadu
10 OEB 532 GPU-26
L-5 OAUT, Bhubaneswar 2012 110–115 22–25 Odisha, Bihar,
Chhattisgarh,
Karnataka, Tamil Nadu
11 KMR 204 GPU 26
GE-1409 VC Farm, Mandya, 2012 95–100 30–35 Karnataka
UAS, Bengaluru
12 VR 936 IE 2695
PR 202 ANGRAU, 2012 115–120 28–30 Andhra Pradesh
Vizianagaram
V. A. Tonapi et al.
 8

13 PPR 2700 KM 55
U22/B ARS Perumallapalle, 2012 105–110 25–30 Andhra Pradesh
(Vakula) A.P.
14 Indira Ragi 1 HR 911
GE 669 Jagdalpur, IGKVV 2012 120–125 25–26 Chhattisgarh
15 VL 352 VR 708
VL-149 ICAR-VPKAS, 2012 95–100 33–35 All Ragi growing areas
Almora of country
16 Chhattisgarh PR 202
GE 669 Jagdalpur, IGKVV 2012 115–118 32–35 Chhattisgarh
Ragi-2
Small Millets Breeding

17 VL 376 GE 4172
VL Ragi 149 ICAR-VPKAS, 2016 103–109 29–31 All Ragi growing areas
Almora of country
18 GNN-6 Selection from local Navsari Agricultural 2016 120–130 28–30 Gujarat
germplasm WN-259 University, Navsari
19 GN-5 Selection from local Navsari Agricultural 2016 120–130 25–27 Gujarat
germplasm WWN-20 University, Navsari
20 VL Mandua- VL Ragi 146
VL Ragi ICAR-VPKAS, 2016 104–112 18–20 Uttarakhand
348 149 Almora
21 KMR 340 OUAT-2
WRT-4 VC Farm, Mandya, 2016 90–95 35–40 Karnataka
UAS, Bengaluru
22 Dapoli- Soma-clone of Dapoli-1 Dr. BSKKV, Dapoli 2017 118–120 25–27 Konkan region of
2 (SCN-6) Maharashtra
23 CO 15 CO 11
PR 202 Centre on Excellence 2017 115–120 29.0 under Tamil Nadu
of Millets, TNAU, rainfed and
Athiyandal, Tamil 34.0 under
Nadu irrigated
24 GNN-7 Pureline selection from NavsariAgril. Univ., 2017 123–128 25.0 q/ha Gujarat
white type landrace of Gujarat
Nagli collected from
Ahwa-Dang District,
State: Gujarat
(continued)
483
 484

Year
Institute where of Maturity Avg. yield
S. No. Variety Pedigree developed release (days) (q/ha) Area of adaptation
25 VL-379 GE-440
VL-149 ICAR-VPKAS, 2017 105–107 30–32 Recommended for
Almora Uttarakhand, Bihar,
Jharkhand, Madhya
Pradesh and North
eastern states
26 Chhattisgarh PR-202
GE-669 ZARS, Jagdalpur, 2018 115–118 34–36 Chhattisgarh
Ragi- IGKVV
2 (BR-36)
27 DHFM-78-3 GE 1219
Indaf 8 ARS, Hanumanamatti, 2018 114–116 Recommended for
UAS, Dharwad cultivation in agro-
climatic Zone—3 and
8 of Karnataka state
28 VL Mandua- GEC 440
VL 149 ICAR-VPKAS, 2019 115–116 18–19 Uttarakhand
380 Almora
29 Vegavathi GE-3076
VR-854 ARS, ANGRAU, 2019 115–120 Grain yield is National
(VR 929) Vizianagaram 36.1 q/ha and
fodder yield is
7.2 tonnes/ha
30 Tirumala AE 3077
Ratnagiri ARS, Perumallapalle, 2019 115–120 Grain 35–37 q/ Andhra Pradesh
(PPR 1012) ANGRAU, Guntur ha fodder yield
7–8 tonnes/ha
31 GN 8 Pureline selection from Navsari Agricultural 2019 105–110 31–32 Gujarat
local collection of University, Navsari
Waghai Tal. Dist. Dang.
32 FMV-1102 VR-708
GPU-48 ZARS, Jagdalpur, 2019 110–115 30–32 q/ha Assam, Bihar,
IGKVV (grain) and Chhattisgarh,
11–12 tonnes/ Jharkhand,
ha (fodder)
V. A. Tonapi et al.
 8

Uttarakhand, Madhya
Pradesh
33 KMR-630 PR-202X GE1409 VC Farm, Mandya, 2020 95–100 28–30 Karnataka
UAS, Bangalore
34 VR-988 GE 3076
VR 855 ARS, ANGRAU, 2020 110–115 28–30 Andhra Pradesh
Vizianagaram
35 PR-10-45 GPU 28
GE 4931 ARS, ANGRAU, 2020 122–125 35–37 Andhra Pradesh
Small Millets Breeding

(Gowthami) Peddapuram
36 CFMV-1 VL 330
GE 532 ARS, ANGRAU, 2020 110–115 30–32 Andhra Pradesh,
(Indravathi) Vizianagaram Karnataka, Tamil Nadu,
Puducherry, and Odisha
37 CFMV-2 Pureline selection from Navsari Agricultural 2020 119–121 29–31 Andhra Pradesh,
local collections made University, Navsari Chhattisgarh, Gujarat,
under Dang District of Maharashtra and Odisha
Gujarat
38 VL-378 GEC 440
VL 149 ICAR-VPKAS, 2020 110–114 22–24 Rainfed organic
Almora conditions of
Uttarakhand hills
39 VL-382 WR 2
VL 201 ICAR-VPKAS, 2020 106–108 11–13 Rainfed organic
Almora conditions of
Uttarakhand hills
Foxtail millet
1 Co 7 (TNAU Co 6
ISe 247 TNAU, Coimbatore 2005 85–90 18–19 Tamil Nadu
196)
2 HMT 100-1 RS 118
PS 3 ARS, Hanumanamatti, 2008 90–95 20–25 Karnataka
UAS, Dharwad
3 SiA 3085 Pure line from SiA 2644 RARS, Nandyal, 2011 80–85 20–30 All foxtail millet
ANRAU growing areas of the
country
485

(continued)
 Year
486

Institute where of Maturity Avg. yield

S. No. Variety Pedigree developed release (days) (q/ha) Area of adaptation
4 Surya Nandi Pure line from SiA 1244 RARS, Nandyal, 2012 70–75 20–25 All foxtail millet
(SiA 3088) ANRAU growing areas of the
country
5 SiA 3156 Pure line from 2871 RARS, Nandyal, 2012 85–90 20–25 Andhra Pradesh, Bihar,
ANRAU Gujarat, Karnataka,
Madhya Pradesh, Tamil
Nadu and Uttarakhand
6 RAU Selection from Local Rajendra Agricultural 2017 80–83 23–25 Irrigated and rainfed
(Rajendra germplasm of Laukaria, University, Bihar, upland of Bihar
Kauni 1-2) Raxaul, East Champaran Pusa, Samastipur
7 DHFt-109-3 Co-5
GPUS-30 ARS, Hanumanamatti, 2018 86–88 Grain yield Recommended for
UAS, Dharwad 29 q/ha cultivation in agro-
Fodder yield climatic Zone 3 and 8 of
5.23 tonnes/ha Karnataka state
8 Hagari Sia 2644
PS-4 Agricultural Research 2019 85–90 16–20 q/ha Zones 1, 2 and 3 of
Navane-46 Station, Hagari, Ballari, (rainfed) Karnataka
University of 20–25 q/ha
Agricultural Sciences, (irrigated)
Raichur
9 SiA 3222 SiA 3075
SiA 326 Agricultural Research 2020 60 19–20 Andhra Pradesh
(Garuda) Station, ANGRAU,
Nandyal, AP
10 SiA 3223 Developed from GS Agricultural Research 2020 86–90 34–35 Andhra Pradesh
(Renadu) 96 population through Station, ANGRAU,
MDPLS breeding Nandyal, AP
11 ATL-1 (TNSi- PS 4
Ise 198 Centre for Excellence 2020 80–85 20–22 Tamil Nadu
331) in Millets, Athiyandal,
Tiruvannamalai,
V. A. Tonapi et al.

TNAU
 8

Kodo millet
1 JK 13 Selection from mutant Rewa, JNKVV, 2007 95–100 22–23 National
JK 76 Jabalpur
2 JK 106 Selection from Sidhi Rewa, JNKVV, 2009 100–105 19–20 M.P. State
dist. germplasm Jabalpur
3 JK 65 Selection from Sidhi Rewa, JNKVV, 2009 105–110 23–25 National
dist. germplasm Jabalpur
Small Millets Breeding

4 JK 98 Selection from GPLM Rewa, JNKVV, 2010 100–105 25–30 National

317 Jabalpur
5 DPS 9-1 Selection from local land Dindori, JNKVV, 2011 105–110 27–30 National
race Jabalpur
6 Indira Kodo 1 Pureline selection Jagdalpur IGKVV 2012 100–105 22–25 Chhattisgarh
7 Chhattisgarh Mutant Line of CO 3 Jagdalpur IGKVV 2014 95–100 days 25–26 Chhattisgarh
kodo-2
8 TNAU-86 Pureline selection from TNAU Coimbatore 2012 95–110 27–30 National
IPS 85
9 RK 390-25 Mutant of RK-390 Rewa, JNKVV 2012 100–105 25–28 National
10 Jawahar Kodo Mutant of RK-390 Rewa, JNKVV 2016 100–105 26–29 Rainfed areas of
137 Madhya Pradesh
11 KMV-543 Mutant of CO-3 ZARS, Jagdalpur, 2019 105–110 25–27 Andhra Pradesh,
IGKVV Chhattisgarh, Gujarat,
Jharkhand, Karnataka,
Madhya Pradesh and
Tamil Nadu
12 Kodo millet Pureline selection from Centre for Excellence 2020 105–110 28–30 Andhra Pradesh,
variety KMV DPS 63/58 in Millets, Athiyandal, Chhattisgarh, Gujarat,
545 (TNPsc Tiruvannamalai, Jharkhand, Karnataka,
262) TNAU Madhya Pradesh, Tamil
Nadu and Telangana
487

(continued)
 488

Year
Institute where of Maturity Avg. yield
S. No. Variety Pedigree developed release (days) (q/ha) Area of adaptation
14 GAK-3 Pureline selection from Hill Millet Research 2020 105–110 23–25 Dry lands, hilly and
locally collected Station Anand tribal region of Dahod
germplasm of Hilly Agricultural University and Panchmahal
regions of Rewa district Dahod 389 151 districts of Gujarat
of Madhya Pradesh
Barnyard millet
1 CO(KV) 2 Pureline selection from TNAU, Coimbatore 2008 95–100 21–22 Tamil Nadu state
EF 79
2 DHBM 93-3 VL-13XIEC-566 ARS, Hanumanamatti, 2016 90–95 22–24 National
UAS, Dharwad
3 DHB-93-2 EF-8
IEC-566 ARS, Hanumanamatti, 2018 86–88 Grain yield Recommended for
UAS, Dharwad 27.6 q/ha and cultivation in agro-
fodder yield climatic Zone—3 and
6.19 tonnes/ha 8 of Karnataka state
4 MDU-1 Pureline selection from Agricultural 2018 95–100 Grain yield of Suitable for southern
Aruppukottai local Engineering College 15–17 q/ha districts of Tamil Nadu
and Research Institute, (rainfed) and
TNAU, Madurai 22–25 q/ha
(irrigated)
Fodder yield of
30–33 q/ha
5 DHBM-23-3 VL-13
IEC-566 ARS, Hanumanamatti, 2019 88–100 20–21 Andhra Pradesh,
UAS, Dharwad Karnataka, Madhya
Pradesh and Tamil
Nadu
V. A. Tonapi et al.
 8

Little millet
1 OLM 208 Selection from Lajigada OUAT, Berhampur 2009 100–105 12–15 National
local
2 OLM 217 Selection from OUAT, Berhampur 2009 105–110 15–16 National
Udayagiri local
3 Co 4 Co 2
MS 1684 TNAU, Coimbatore 2005 75–80 16–20 Tamil Nadu
4 JK 36 Selection from local Rewa, JNKVV, 2009 75–80 10–12 M.P. state
Small Millets Breeding

Shahdol germplasm Jabalpur

5 BL 6 Paiyur 1
OLM 29 Jagdalpur, IGKVV, 2016 90–95 12–14 National
Raipur
6 DHLM 36-3 Co-4
Paiyur—2 ARS, Hanumanamatti, 2018 95–100 14–16 Karnataka
UAS, Dharwad
7 Chhattisgarh CO-2
TNAU 97 Jagdalpur, IGKVV, 2016 90–95 10–12 Chhattisgarh
Kutki- Raipur
2 (BL-4)
8 GV-2 Derivative from mutant Waghai, NAU, Navsari 2016 115–125 26–28 Gujarat
of released variety
‘Gujarat Vari-1’
9 Phule Selection from local ZARS, Kolhapur, 2016 120–130 12–14 Sub-montane and Ghat
Ekadashi germplasm MPKV Rahuri zone of Maharashtra
(KOPLM 83)
10 Jawahar Kutki DLM 42
Kutki1 Rewa JNKVV Jabalpur 2016 75–80 13–15 Rainfed areas of
4 (JK 4) Madhya Pradesh
11 DHLM-14-1 CO-2
TNAU-110 ARS, Hanumanamatti, 2018 97–99 Grain yield Recommended for
UAS, Dharwad 16.0 q/ha and Tamil Nadu, Karnataka,
fodder yield Gujarat, Maharashtra
6.10 tonnes/ha and Orissa
(continued)
489
 490

Year
Institute where of Maturity Avg. yield
S. No. Variety Pedigree developed release (days) (q/ha) Area of adaptation
12 GNV-3 Pureline selection from Waghai, NAU, Navsari 2018 110–115 28–29 Gujarat agro-climatic
local land races collected Zone I, II and III (dry
from the Dang district of lands/hilly/tribal region
Gujarat of Dang, Valsad,
Navsari and
Panchmahal districts of
Gujarat)
13 ATL-1 CO (Samai) 4
TNAU Agriculture Research 2019 85–90 Tamil Nadu
(TNPsu 177) 141 Station, Tamil Nadu
Agricultural University
14 LMV513 CO-2
TNAU-26 ARS, Hanumanamatti, 2019 93–96 17–19 Andhra Pradesh,
UAS, Dharwad Karnataka, Madhya
Pradesh, Maharashtra,
Chhattisgarh, Odisha
and Jharkhand.
15 BL-41-3 Paiyur 2
TNAU 97. ZARS, Jagdalpur, 2019 95–100 16–19 Chhattisgarh
IGKVV
16 Jaicar Sama Pureline selection from Indian Institute of 2020 98–102 15–17 Maharashtra, Andhra
1 (LMV-518) indigenous germplasm Millets Research, Pradesh, Telangana,
collection GPmr-1153 Hyderabad Tamil Nadu,
Puducherry
Proso millet
1 TNAU 145 PV 1454
TNAU 96 TNAU, Coimbatore 2007 70–72 18–20 Tamil Nadu
2 CO(PV) 5 PV 1403
GPUP 21 TNAU, Coimbatore 2007 70–75 23–25 National
(TNAU 143)
3 TNAU 151 TNAU 96
PV 1673 TNAU, Coimbatore 2008 72–75 18–20 National
V. A. Tonapi et al.
 8

4 TNAU 164 TNAU 137
CO 4 TNAU, Coimbatore 2009 70–75 18–20 National
5 PratapCheena- Pure line selection MPUA&T, Udaipur 2006 65–70 15–17 National
1 (PR-18)
6 PRC 1 Selection from GPMS Ranichauri, 2008 70–75 10–12 Uttarakhand hills
519 GBPUA&T, Pantnagar
7 TNAU 202 PV 1453
GPUP 16 TNAU, Coimbatore 2011 70–75 18–20 National
8 TNPm-230 TNAU-164
IPM-19 TNAU, Coimbatore 2017 70–75 21–23 National
Small Millets Breeding

9 DHPM-2769 Selection from ARS, Hanumanamatti, 2018 70–72 Grain yield Recommended for
IPM-2769 UAS, Dharwad 24.6 q/ha and cultivation in agro-
fodder yield climatic Zone—3 and
4.16 tonnes/ha 8 of Karnataka state
10 PMV-442 GPMS 109
GPMS Project Coordinating 2019 70–75 14–16 Andhra Pradesh,
908 Unit, UAS, Bengaluru Karnataka, Madhya
Pradesh and Tamil
Nadu, Bihar, Telangana,
Puducherry
491
492 V. A. Tonapi et al.

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Sugarcane Breeding
9
Bakshi Ram, R. Karuppaiyan, and G. Hemaprabha

Abstract

Sugarcane breeding in India started at the ICAR-Sugarcane Breeding Institute

(SBI), Coimbatore, in 1912. A major breakthrough in sugarcane breeding was the
use of wild species, viz. S. spontaneum, which led to the development of the first
sugarcane interspecific hybrid variety Co 205. About 78% of the total sugarcane
area is covered by ‘Co’ varieties alone, whereas Co and Co-allied varieties
covered about 99% of the total sugarcane area in the country during the season
2020–2021. Co 0238 (53.42%), Co 86032 (17.06%), CoM 0265 (6.90%), Co
0118 (2.45%) and CoLk 94184 (2.33%) were the top five sugarcane varieties in
cultivation during the season 2020–2021. There have been about 50 tonnes/ha
and 2.69% improvement in cane yield and sugar recovery, respectively, from
1930 to 2020 due to cultivation of varieties released by the ICAR-SBI. With new
challenges on sugarcane cultivation, it is essential that all future breeding
programmes focused on ecologically viable, environment-friendly and resource
matching technologies. Bioethanol and electricity production from sugarcane will
be the major focus in the coming years to meet the energy demands of India.
Research on true seed as sugarcane propagule is being pursued to develop
homozygous lines to bring in a paradigm shift to sugarcane agriculture. Recent
advancements in genome sequencing have provided opportunities to better apply
genomic selection (GS) to improve major traits and for more precise breeding of
this complex crop. Harnessing genetic diversity of the ‘Saccharum Complex’ is
progressing with the support of molecular cytogenetics and molecular markers.
Emerging tools like genome editing to improve an otherwise promising sugar-
cane variety is challenging but potentially very rewarding. India will continue to

B. Ram (*) · R. Karuppaiyan · G. Hemaprabha

ICAR-Sugarcane Breeding Institute, Coimbatore, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 499
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_9
500 B. Ram et al.

develop improved varieties to achieve profitable and sustainable sugarcane pro-

duction for food, fuel, fibre, fodder and high-value products.
This chapter is intended to provide basic and applied aspects of sugarcane
breeding useful to agriculture/botany students, plant breeders, sugarcane
researchers, cane development officials and sugar industry personnel. The origin
and movement of sugarcane; floral biology; species of Saccharum and allied
genera; hybridization techniques; progress made on varietal development in India
and other major sugarcane-growing countries such as Brazil, Australia, the USA,
West Indies, Java, South Africa, Thailand, etc. since time immemorial to present
day; and advances made on molecular breeding are covered in this book.

Keywords

Sugarcane · Saccharum · Wild species · Gene pool · Varietal development ·

Breeding strategies · Germplasm · Hybridization

9.1 Introduction

Sugarcane (Saccharum officinarum L.) is an important crop worldwide used for

producing sugar, jaggery (gur or panela) and ethanol as primary products and
molasses, bagasse and pressmud as co-products. Green leaves and tops of sugarcane
are used as cattle fodder. Sugarcane is grown over 26.47 million ha spread across
103 countries, situated mostly in the tropical region (FAOSTAT 2020). Sugarcane
contributes 78% of the world’s crystal sugar production, while sugar beet contributes
22%. Brazil is the largest sugarcane-growing country in the world with 9.90 mil-
lion ha of cane area followed by India with 4.85 million ha (2020–2021). Six
countries, namely, Brazil, India, China, Thailand, Pakistan and Mexico, together
accounted for three-fourths (76.41%) of the world’s sugarcane acreage in
2019–2020. Brazil, India, China, Thailand, the USA, Pakistan, Mexico, Australia,
the Philippines, Indonesia, South Africa, Colombia and Argentina are the major
sugarcane-producing countries in the world. These countries accounted for three-
fourths of the world sugar production.
India was the largest sugar producer in the world during 2018–2019 (33.07 mil-
lion tonnes) which accounts for nearly 17.57% of the total production (Anonymous
2019). In spite of poor rainfall in some of the tropical sugarcane-growing states of
India, the country had managed to produce surplus sugar from 2015 to 2020 except
2016–2017 and also exported sugar to more than 80 countries during 2011–2019.
The country emerged as the third largest sugar exporter (9.1%) in the world during
2019 by exporting worth 1.8 billion US dollars (Anonymous 2020a). It ranked
seventh among India’s Export of Principal Agricultural and Allied Commodities
(Anonymous 2020b). India by contributing 18.10% in area and 19.81% in produc-
tion ranks second among sugarcane-growing countries of the world for both area and
production of sugarcane during 2018 (FAOSTAT 2020). The turnover of sugar and
other related economic activities (which includes sugarcane, gur and others) was
9 Sugarcane Breeding 501

approximately Rs. 123,372 thousand crores per annum during 2018–2019 at the
current price, out of which, nearly Rs. 86,277 thousand crores were paid to the
sugarcane farmers by the sugar mill as prices for its supply during 2018–2019.
It is estimated that about 5.568 million sugarcane farmers and 6.769 million
sugarcane labourers (total of about 12.337 million sugarcane workers) are engaged
in the cultivation of sugarcane in India, which accounts for 1.427% of the total rural
population of India (Kumar et al. 2016). Out of the 6.26 million sugarcane
landholdings of the country, 82.82% are marginal and small (<2.0 ha) which occupy
nearly 54.44% sugarcane area. Five lakhs skilled and unskilled workers including
highly qualified and trained technologists are engaged in the manufacturing of sugar.
Sugarcane is more important than other crops as it is more remunerative. It
contributed nearly 0.616% in GDP of the country in the year 2018–2019 at current
prices with an area of nearly 5 million ha, and the same trend is expected to follow in
the coming years also. During 2020–2021, India produced 397.65 million tonnes of
sugarcane from 4.857 million ha area and produced 31.10 million tonnes of sugar
and 12.00 million tonnes of molasses (Anonymous 2021).
Sugarcane is a tropical plant in the grass family. It has C4 photosynthetic
apparatus (Kranz leaf anatomy) and is highly efficient in converting solar energy
into chemical energy. The photosynthetic rate is estimated up to 100 mg CO2 fixed
per dm2 leaf area per hour (Santos and Diola 2015). The theoretical maximum yield
of sugarcane estimated based on photosynthetic rate, energy content and energy
storage in sugarcane plant is 381 tonnes/ha/year equivalent to dry matter (biomass)
yield of 48.5 g/square metre/day (Waclawovsky et al. 2010). The maximum stalk
yield achieved in research stations is 212 tonnes/ha/year, and world average yield in
farmer’s field is 70.6 tonnes/ha (FAOSTAT 2020) with sucrose levels in the
commercial varieties ranging from 15% to 22%. Sugarcane distributes one-third of
their carbon into sucrose and two-thirds into tops and stems. The crop can accumu-
late large amounts of sucrose in the stem parenchyma cells, up to ~650 mM in the
vacuoles (Welbaum and Meinzer 1990).
More than 30 products are produced from crushing sugarcane at sugar mills. It
includes raw sugar, refined sugar, molasses, alcohol, rum, bagasse, syrups, dextran,
confectionary, crude wax, glucose, etc. (Perez 1997). Hundred tonnes of sugarcane
is estimated to produce 14.3 tonnes of raw sugar, 27.2 tonnes of bagasse, 5.2 tonnes
of filter cake, 2.6 tonnes of molasses and 50.7 tonnes of waste water (Allen et al.
1997). The annual production of white sugar in 2019–2020 sugar season (October–
September) globally is 171.57 million metric tonnes (ISO Quarterly, November
2020). Brazil is the largest sugar-producing country in the world (29.43 mil-
lion tonnes or 17% of world sugar output in 2019–2020 sugar season). India is the
second largest sugar producer (27.38 million tonnes or 16% of world sugar output in
2019–2020 sugar season). Other countries with largest sugar production (from
sugarcane and sugar beet) are the European Union (10.6% of the world sugar
production), China (6.0%), Thailand (4.8%), Russia (4.6%), the USA (4.3%),
Pakistan (3.2%), Mexico (3.0%) and Australia (2.5%). About 55–65 million tonnes
of sugar is traded annually in the international markets; the rest are consumed
domestically in the cane-growing countries.
502 B. Ram et al.

9.2 Progress Made in the Last 25 Years in Sugarcane

Agriculture

During the colonial period, sugar was considered as an expensive commodity,

consumed by rich and royals. The British called sugar as ‘white gold’. Now sugar
is an essential commodity for billions of common persons. Scientific advances made
in Australia, Brazil, India, Indonesia, the USA and elsewhere have fuelled progress
in sugarcane agriculture and the sugar sector. Hybridization with wild species has
given faster and desired genetic improvement in sugarcane; hence, interspecific
hybridization or ‘nobilization’ in sugarcane in the early 1990s has been heralded
as the top five achievement in the annals of plant breeding. Improved cane varieties,
crop production technologies and sugar-processing technologies have increased
sugarcane and sugar production in Brazil, India, Australia, Thailand, etc. The
conventional and molecular breeding tools have helped in evolving superior sugar-
cane varieties. In India, through conventional breeding varieties combining early
maturity, high sugar and high yield (they are negatively correlated traits) such as Co
0238 and Co 86032 evolved which in the 2019–2020 season occupied 54% and 13%
sugarcane area in the country. ‘Double-high’ (high in sugar content and yield)
varieties were bred in China (Zhang and Govindaraju 2018).
Another milestone in the conventional breeding is the development of short-
duration sugarcane varieties such as Co 11015 in India which attain sucrose maturity
at 8 months (with >20% brix, >18% sucrose and >85% purity with acceptable yield
level at 8 months) compared to 10–18 months in normal varieties. Short-duration
varieties enable farmers to take three crops in a span of 2 years (one plant + two
ratoon) instead of two crops in 2 years. Development of energy canes is yet another
progress in sugarcane research. In Coimbatore, Louisiana, Barbados, Mauritius,
Vignis (Brazil) and Puerto Rico, breeding programmes on Type I and Type II energy
canes (Tew and Cobil 2008) were developed. Type I energy canes are the genotypes
with relatively low sucrose (>15% brix) but moderate-to-high fibre content (>20%).
They are the dual-purpose canes, the juice can be used in distilleries for direct
fermentation and fibre for cogeneration. Type II energy canes are specifically bred
for high biomass yield with high fibre (>25%) and low brix (<15%) and are
exclusively used for energy generation and lingo-cellulosic-based second-generation
ethanol production (Alexander 1985; Matsuoka et al. 2014; https://sugarcane.icar.
gov.in).
Sugarcane varieties cultivated in the world are unusual among the Poaceae crops
in that they are polyploid interspecific hybrids (with approximately 80%
chromosomes from S. officinarum, 10–15% chromosomes from the wild spe-
cies S. spontaneum and 5–10% recombinant chromosomes), with singularly com-
plex genomes. And because of its huge complexity, it was the last among the major
cultivated plants to have its genome sequenced. Genetic maps of sugarcane have
been produced mainly based on single-dose markers that are the most informative
markers in this high polyploidy crop (Zhang et al. 2014). The genome size of
polyploidy sugarcane cultivar was determined to be about 10 Gb, while the mono-
ploid genome size is about 800–900 Mb, close to that of sorghum (750 Mb) (D’Hont
9 Sugarcane Breeding 503

and Glaszmann 2001). A reference genome sequence is a representative example of

the set of genes in one idealized individual of a species. It is a good approximation of
the DNA sequence of any single individual hence viewed as key platform for genetic
analysis and molecular breeding. The development of mosaic monoploid reference
genome sequence for the sugarcane commercial variety R570 (382 Mb single tiling
path) (Garsmeur et al. 2018), assembly of the 373k genes and their putative regu-
latory region in the variety SP80-3280 (Souza et al. 2019) and haploid assembly of
S. spontaneum clone AP85-441 (3.13 Gb) (Zhang et al. 2018) etc. are the large steps
toward a whole-genome assembly of a highly complex genome of sugarcane
cultivars.
Transgenic sugarcane varieties were evolved in Indonesia, Brazil, India and
Australia. In 2013, three drought-resistant transgenic events (NXI-1T, 4T, 6T)
were approved for field trial in Indonesia, but commercial cultivation has not yet
taken place (www.isaaa.org). In 2017, the CTNBio (National Biosafety Technical
Commission), Brazil, has given approval for cultivation of CTC175-A event, the
first GM sugarcane variety (CTC20 Bt) developed by the the Brazilian company
Centro de Tecnologia Canavieira (CTC) for the management of sugarcane borer
Diatraea saccharalis. In 2018, another transgenic variety (transgenic event
CTC91087-6) carrying the Cry1Ac gene which confers resistance to Diatraea was
approved for cultivation in Brazil (Cheavegatti-Gianottoa et al. 2019; CTNBio
2019). Transgenic sugarcane (in the cultivars Co 86032, Co 0238), carrying
drought-tolerant genes EaDREB2, EaHSP70 and PDH45 were developed at
ICAR-SBI, Coimbatore, India.
In the conventional method, sugarcane planting requires 7–9 tonnes of seed cane
per hectare, and this is the main reason for the slow rate of seed and varietal
replacement. Sugarcane being a long-duration crop and heavy biomass producer
requires more water, i.e. about 1200–1800 mm in subtropical region and
1600–2700 mm in tropical region. The availability of water is declining at a faster
rate. The problem is further aggravated by the variability of rainfall influenced by
climate change. So, unless sugarcane farmers are provided with technologi-
cal options of obtaining high yields using much less water, India will find it difficult
to meet its growing demand of sugar. Hence, there is a need to adopt water-saving
technologies for sustainable sugarcane production. The ICAR-SBI has developed a
sugarcane cultivation model comprising of integrated approach, keeping in mind the
likely problem to be faced in the future, for sugarcane agriculture (ICAR-SBI 2019).
Components of the model are (1) high yielding and better-quality varieties, (2) rais-
ing and transplanting of settlings raised from single-budded setts/bud chips, (3) sub-
surface drip irrigation and fertigation, (4) wider row planting, (5) intercropping,
(6) trash mulching, (7) multiple ratooning and (8) mechanization. The objective is to
increase the productivity of sugarcane and sugar, reduction in preparatory tillage and
seed costs (multiple ratooning), reduction in input costs (settling transplanting and
drip irrigation/fertigation, trash mulching), increased water and nutrient use
efficiencies (drip irrigation with fertigation and trash mulching), reduction in labour
requirement (wider row planting and mechanization of cultural operations from
planting to harvesting) and intermittent and additional income to farmers
(intercropping).
504 B. Ram et al.

Table 9.1 Decade-wise average area, sugarcane production, sugarcane productivity, sugar
production and sugar recovery in India
Area Sugarcane Sugarcane Sugar Sugar
(000’ production productivity recovery production
Years ha) (000’ tonnes) (tonnes/ha) (%) (000’ tonnes)
1989–1990 to 3814 258,074 67.59 9.92 12,928
1998–1999
1999–1920 to 4389 292,073 66.41 10.27 19,015
2008–2009
2009–2010 to 4837 348,297 71.98 10.41 25,834
2018–2019

In India, importance is given to produce disease-free planting materials. The

standardization of aerated steam therapy (AST) and moist heat aerated steam therapy
(MHAT) for elimination of sugarcane sett borne pathogens of sugarcane has been a
success story of ICAR-Sugarcane Breeding Institute and adopted worldwide to
generate pathogen-free sugarcane crop. The ICAR-Sugarcane Breeding Institute,
Coimbatore, India, was the first to develop sugarcane tissue culture (TC) and micro-
propagation protocols in India. Use of disease-free and vigorous tissue culture-
derived sugarcane plantlets is becoming popular in India. Besides healthy seeds,
the yields are improved by using TC plants. Significant progress has been made on
the mechanization front. Machineries and implements for planting sugarcane setts,
settlings at closure and wider spacing, for intercultural operation including earthing
up, combine harvester have been developed in the last 25 years and put into use in
grower’s field.
The decade-wise average area, sugarcane production, sugarcane productivity,
sugar production and sugar recovery in India is given in Table 9.1. Between the
decade 1989–1999 to 2009–2019, sugarcane productivity has increased by
4.39 tonnes/ha, whereas increase in sugar recovery is 0.49 unit. This improvement
could be due to research efforts, in terms of improved varieties and agronomic
practices. The increase in sugarcane productivity (5.57 tonnes/ha) and sugar recov-
ery (0.14%) during the decade 2009–2010 to 2018–2019 over the decade 1999–2020
to 2008–2009 has been mainly due to released and adoption of sugarcane variety Co
0238 in subtropical India. Increasing area, cane yield and sugar recovery led to
increase in sugarcane and sugar production over the decades.

9.3 Origin, Evolution and Distribution of Species of Sugarcane

9.3.1 Species of Sugarcane

The genus Saccharum belongs to the grass family Poaceae, tribe Andropogoneae.
Six species of sugarcane (Saccharum spp.) are recognized by classical taxonomist. A
detailed description can be found in Jeswiet (1925), Grassl (1946), Mukherjee
9 Sugarcane Breeding 505

(1954), Brandes (1958), Rao (1989), Heinze (1987) and Amalaraj and
Balasundaram (2014).

9.3.2 Wild Saccharum Species

9.3.2.1 Saccharum spontaneum L. (2n = 40–128)

This is the most primitive species which has its centre of origin and diversity in India
(Mukherjee 1957). This wild species has no sucrose but produces numerous thin
shoots. It has wider adaptability ranging from severe drought and prolonged water-
logged environments, so it was used in sugarcane breeding programmes in the early
years. It is speculated that the primitive form of cultivated sugarcane might have
evolved from S. spontaneum in the foothills of Himalaya in North India (Stevenson
1965). Natural occurrence of 31 cytotypes with somatic chromosome number
ranging from 2n¼40 to 2n¼128, i.e. 2n¼40, 48, 50, 52, 54, 56, 58, 60, 61, 62, 64,
66, 68, 70, 72, 74, 76, 78, 80, 82, 90, 93, 96, 100, 104, 112, 116, 120, 124, 126 and
128 was reported (Panje and Babu 1960).

9.3.2.2 Saccharum robustum Brandes and Jeswiet ex Grassl (2n = 60, 80)
This is another wild species discovered on mud flats on the banks of the Laloki River
near Port Moresby in the 1928 Sugarcane Expedition to Papua New Guinea. This
species has hardy, thin-to-thick exposed stalk without rhizome (like S. officinarum)
but has no sweet juice (like S. spontaneum). Saccharum robustum probably evolved
in New Guinea by natural hybridization between S. spontaneum  Erianthus,
Sclerostachya and Miscanthus species (Roach and Daniels 1987).

9.3.2.3 Saccharum edule (2n = 60–80)

This is a wild (or semi-wild) species which closely resembles S. robustum except
that the inflorescence is compacted and remains unopened and enclosed inside the
leaf sheaths. The species is cultivated as vegetable in small pockets in the islands of
the Pacific, Papua New Guinea and Fiji for its edible aborted inflorescence (hence
the name ‘edule’). It is known as ‘navisco’ in Vanuatu, ‘pitpit’ in Papua New Guinea
and ‘duruka’ in Fiji and Java (Grivet et al. 2004; Mudhaliar 2007). This species
possibly originated in the Polynesia islands by mutation of S. robustum (Brandes
et al. 1939) or by natural crossing between S. robustum and Miscanthus (New
Guinea form of S. edule) or S. officinarum and Miscanthus (Fiji form of S. edule)
(Grassl 1967; Roach and Daniels 1987). Some taxonomists do not recognize S. edule
as separate species and treat it under S. robustum.

9.3.3 Cultivated Saccharum Species

Three species of sugarcane were cultivated and used for chewing and production of
jaggery (gur) and crystal sugar from ancient time. They may be grouped into two
categories viz., (1) thick-stalked, soft rind, juicy, low-fibre, high-sugar-type
506 B. Ram et al.

sugarcane belong to S. officinarum L. (Dutch scientists in Java named this species as

‘noble cane’ on account of its majestic appearance and quality), and (2) thin-stalked,
hardy, high-fibre, low-juice and low-sugar-type sugarcane belongs to the species
S. barberi Jeswiet and S. sinense Roxb.

9.3.3.1 Saccharum officinarum L. (2n = 80)

It is the cultivated sugarcane of the world. Dutch scientists in Java named this species
as ‘noble cane’ because of its majestic appearance and quality. Its accepted centre of
origin is Papua New Guinea (Polynesia), but there are two centres of diversity,
namely, (1) Papua New Guinea and (2) the Indonesian (Java) archipelago. There
were two views regarding the origin of S. officinarum: (a) that it originated from
S. robustum due to natural and human selection in New Guinea/Polynesia (Grassl
1977) and (b) that it evolved from the complex introgression between
S. spontaneum, Miscanthus sinensis and Erianthus arundinaceus (Roach and
Daniels 1987) probably in India but could not survive in India because of red rot
disease and established well in New Guinea where the disease was not a problem
(Parthasarathy 1946; Rao et al. 1957). But, the widely accepted hypothesis is that the
noble cane evolved from S. robustum in New Guinea and then dispersed to the
Pacific Islands during 4500 BC and mainland Asia along human migrations. In
mainland Asia, it hybridized with local S. spontaneum giving rise to North Indian
and Chinese canes (Brandes 1958).

9.3.3.2 Saccharum barberi Jeswiet (2n = 111–120)

This species is called as North Indian cane. The canes are shorter, cylindrical
internodes, hard rind, high fibre but with low-to-medium juice and sucrose content,
and leaves are dark green. Together with S. sinense (the Chinese cane), these
indigenous canes were in cultivation in North India from prehistoric time. Barber
(1922) classified the indigenous canes that were in cultivation in North India into
five groups, namely, Mungo, Nargori, Saretha, Sunnabile and Pansahi. Later,
Jeswiet classified these clones as separate species. Clones in the first four groups
were treated as S. barberi (named in memory of Dr. C. A Barber and then the
Director of SBI Coimbatore), and clones in the Pansahi group were treated as
S. sinense. Both species may have originated from natural hybridization, undoubtly
in North-East India (erstwhile Assam-Bengal-Orissa region) about 1000 years BC.
These species exhibited better adaptability to cold weather (winter) climate of North
India and China. According to Parthasarathy (1946), in ancient India, thick noble
cane (S. officinarum) had existed, and S. barberi may have evolved from natural
hybridization between S. spontaneum and S. officinarum, but Grassl (1977) disputed
this view and suggested that Erianthus procerus, Sclerostachya and S. spontaneum
could have contributed to the origin of North India canes.

9.3.3.3 Saccharum sinense Roxb. (2n = 81–124)

This species is called as Chinese cane. It is morphologically similar to S. barberi
(hard rind, high fibre but its with low-to-medium juice and sucrose content), but the
internode shape is mostly bobbin, and leaves are light green or yellowish and taller
9 Sugarcane Breeding 507

than S. barberi. It was in cultivation in South of China, Indo-Burma region (along

with S. barberi) from ancient time. Consequently, these species are thought to be
ancient intergeneric hybrids (Roach and Daniels 1987). For the origin of Chinese
cane, Grassl (1977) suggested that Miscanthus sacchariflorus initially introgressed
with S. officinarum, and later introgression was with S. spontaneum.

9.3.4 Allied Genera and Saccharum Complex

The genus Saccharum is amenable to hybridization with eight genera such as

Eccoilopus, Erianthus, Miscanthidium, Miscanthus, Narenga, Ripidium,
Sclerostachya and Sorghum (Grassl 1963, 1977). Mukherjee (1954) reported that
the four genera Saccharum L., Erianthus Michx., Sclerostachya (Andersson ex
Hack) A. Camus and Narenga Bor. constituted a closely inter-breeding group and
concerned with the origin of Saccharum hence termed these large breeding pool as
‘Saccharum Complex’. Later, Daniels et al. (1975) included Miscanthus section
Diandra to ‘Saccharum complex’ as it was thought to be involved in the origin of
Saccharum. Detailed description on the allied genera of Saccharum may be found in
Heinze (1987) and Amalaraj and Balasundaram (2014).

9.4 Spread of Sugarcane Across the World

Two centres of origin for sugarcane were recognized, namely, (1) Polynesia Islands
of the South Pacific particularly Papua New Guinea as the home for the species
S. officinarum (proposed by Deerr 1911) and (2) India as the home for S. barberi
(proposed by Ritter 1841). The indigenous people of Papua New Guinea knew
sugarcane since 8000–6000 BC (Brandes and Sartoris 1936; Ming et al. 2006).
Over 1060 clones of S. officinarum and intermediate wild forms like S. robustum
collected from these Islands in different expeditions supported the origin of sugar-
cane in Papua New Guinea (Deerr 1949; Berding and Koike 1980). The natives in
these Islands did not prepare sugar from the cane, but doubtlessly they chewed the
stalks perhaps as source of food and for the sweet taste. From the South Pacific,
sugarcane might have first spread westward to Solomon, Hebrides and New
Caledonia Islands during 8000 BC and then eastward to Java, the Philippines and
India during 6000 BC. Irian Jaya, Kalimantan, Java and Sumatra (Indonesian
Islands) exhibited considerable diversity of S. officinarum; hence, Artschwager
and Brandes (1958) described Java as shifting or satellite centre of diversity for
sugarcane.
In India, S. officinarum might be naturally hybridized with indigenous canes
grown here (Saccharum barberi or S. sinense), and the hybrids spread further into
Western Eurasia and the Mediterranean (Daniels et al. 1974). According to Geerligs
(1912), Deerr (1949), Parthasarathy (1946) and Chaturvedi (1951) sugarcane and
sugar (gur in Sanskrit) were known to India from the prehistoric period. From India,
508 B. Ram et al.

the commercially grown sugarcane along with the art and skill of growing sugarcane
and making of ‘gur’ or jaggery from it gradually spread to other countries.
All the evidences now show that it was the Indian variety of sugarcane that was
taken from India to Persia after the Persian invasion into India (Alexander the Great
invaded India in 325 BC). After the return of Alexander the Great from India
(325–324 BC), the Indian cane and Sarkara were known to the Greeks, Persians,
Egyptians and Arabs (Deerr 1949). The region extending from the undivided Punjab
in the West to greater Assam in the East was the cradle of sugarcane cultivation
and gur manufacturing using indigenous technical know-how. Perhaps during
fourth century BC, the indigenous clones of S. barberi and later during fourteenth
century AD the ‘Puri cane’ or ‘Creole cane’, i.e., a naturally introgressed form of
S. officinarum  S. barberi, were taken from India to Babylon (Iraq) and Persia
(Iran) through Arab/Persian traders and travellers (Geerligs 1912; Deerr 1949;
Galloway 1989). Arabs played a great role in the cultivation and spread of sugarcane
in and around Iran, Iraq, Egypt and West Africa. From the Mediterranean region,
sugarcane spread to Africa through the Arabs and to Mauritius, Reunion (Bourbon)
and Europe through Portuguese and Spanish navigators.
When the Arabs conquered Persia, in the Middle East, they spread sugarcane to
their newly conquered territories: Syria and islands in the Mediterranean sea,
namely, Cyprus, Crete and Egypt (introduced in 641 AD). In 703 AD, the Arabs
introduced sugarcane to Sicily (island in Mediterranean sea, now under Italy; it was
an important sugar trade centre during the 1570s) and then to North Africa
(in 900 AD), Morocco and Spain (introduced in 714 AD especially on the south
coast of Andalusia). During that period (or around 400 AD), two important events
have happened: (1) the Arab innovations in irrigation (particularly the qanat system)
played a large part in making the arid Mediterranean region suitable for sugarcane
cultivation, and (2) probably, the Egyptian chemists perfected processing sugarcane
juice and began to make refined or white sugar or crystal sugar. The Indian cultivar
Creole cane (a soft yellow natural interspecific hybrid) was an important variety for
more than two centuries both in the Old World and in the New World before the
introduction of noble cane.
In the fifteenth century (1420 AD), the Portuguese brought sugarcane to Madeira
(an archipelago off the northwest coast of Africa in the North Atlantic Ocean) where
it grew up luxuriantly and spread fast. The Island soon produced unheard of
quantities of sugar. In 1444, the Azores (an archipelago in the North Atlantic
Ocean) and between 1456 and 1462 the Cape Verde Isles (small islands off the
northwest coast of Africa in the North Atlantic) were captured and colonized by the
Portuguese. In 1496, the Spanish colonized the Canary Islands (off the northwest
coast of Africa in the North Atlantic). Columbus during his second voyage (in 1493)
took sugarcane from Canary Islands and introduced into the New World/Caribbean
Islands particularly in Hispaniola (Haiti and Dominican Republic). Hispaniola acted
as a distribution centre from where sugarcane was taken to Cuba, Puerto Rico and
the other islands in the West Indies. From Hispaniola, sugarcane was introduced into
Mexico in 1520. In the year 1500, Brazil was discovered by Portuguese Navigator
Pedro Álvares Cabral. The Portuguese imported sugarcane from Madeira and Cape
9 Sugarcane Breeding 509

Verde and introduced it into the northeast coast of Brazil in 1532 (Geerligs 1912;
Edel 1969). The early production system in Brazil was like those techniques and
system developed in Madeira, where the owner (engenho) leased his land to a
number of smaller planters in return for a portion of the sugar produced (Edel 1969).
Historians mentioned that up to the first half of the fifteenth century, hardly any
slavery existed in Christian countries; it only occurred in Mohammedan lands
(Geerligs 1912). The Portuguese and Spanish followed Arabian examples and
introduced sugarcane in the islands captured by them and used African slaves for
cultivation. Sugarcane grew luxuriantly in the New World Islands (West Indies or
Caribbean Islands) due to mild and moist climate. Attempts to use convicted
labourers and African Negro slaves and the coercion of colonized natives to work
in sugar plantations encouraged expansion of sugarcane cultivation in the colonized
lands. In 1481 the Portuguese built three fortresses in Africa, namely, on the Gold
Coast, on an island in the Gulf of Guinea and at Loango, and from these sent slaves
to the New World colonies. Spanish, French, British, Dutch and Danes also imported
slaves from the Gulf of Guinea and Africa to their colonized American and West
Indies lands. In the New World, North Atlantic slave trade flourished, and African
Negro slaves were engaged in sugarcane cultivation and sugar manufacturing. After
Brazil, sugarcane spread to the new European colonies in Africa and in the Pacific
(Fiji). In the 1560s, Mauritius, Natal and Queensland in Australia started growing
sugarcane. Today, sugarcane is cultivated in all continents, except the Antarctic. The
Indian variety Puri/Creole which was in cultivation for more than 250 years was the
basis for development of sugar industries in Iberia (Portuguese and Spanish
colonies). It was the only variety in the Americas when the sugar industry was set
up (Heinze et al. 1994). Although the true name of Indian sugarcane variety was not
known (Watt 1893), it may be a natural interspecific hybrid between S. officinarum
and S. barberi and was called differently as Puri (India), Cana del pais (in Port Rico),
Country cane (in Jamaica) and Yellow Egyptian (in Java germplasm collection),
more popularly as Creole (in French), Criola (in Spanish) or Crioula (in Portuguese)
(Earle 1928).

9.5 Sugarcane Genetic Resources

The gene pool of sugarcane consists of three cultivated species (Saccharum

officinarum, S. barberi and S. sinense), one semi-wild species (S. edule), two wild
Saccharum species (S. spontaneum, S. robustum), allied genera (Erianthus,
Miscanthus, Narenga and Sclerostachya) and commercial cultivars (which are
mostly interspecific hybrids). Based on the genetic relatedness among the species/
clones, easy with which the hybrids are produced and the fertility/sterility of the
hybrid, and number of generations required to evolve superior clones, the cultivars
of sugarcane and species of ‘Saccharum complex’ may be grouped into the four
categories of gene pool.
510 B. Ram et al.

9.5.1 Gene Pool-1

It includes commercial cultivars and near-commercial clones/genetic stocks. They

are the products of the biparental crosses or the products of the cross/backcross
(S. officinarum/S. barberi/S. sinense)  S. spontaneum. In this group, the gene(s) are
fixed in the first sexual generation itself.

9.5.2 Gene Pool-2

It includes the clones of the basic (cultivated) species such as S. officinarum,

S. barberi and S. sinense. Utilization of these species in varietal improvement
programmes may necessitate few generations of crossing or backcrossing.

9.5.3 Gene Pool-3

It includes wild species S. spontaneum and S. robustum and the semi-wild S. edule. If
these species are utilized in the varietal development programmes, several
generations of breeding are required to eliminate the undesirable effects of these
wild species.

9.5.4 Gene Pool-4

It includes allied genera Erianthus, Miscanthus, Narenga and Sclerostachya.

Species like Sorghum, Zea and Bambusa may be included in the category, as
successful intergeneric hybrids were reported (Janaki-Ammal 1941; Sreenivasan
and Sreenivasan 2000; Nair et al. 2016; Karuppaiyan et al. 2021a).

9.6 Germplasm Collection

Collection, conservation, evaluation, characterization and utilization of the

‘Saccharum complex’ germplasm formed part of sugarcane improvement
programmes in the major sugarcane-growing countries. Germplasm expeditions to
the centres of origin (south of the Pacific islands) were mainly focused and promoted
by colonial governments, sugar industries and of late the International Society of
Sugar Cane Technologists (ISSCT) and the International Board for Plant Genetic
Resources (IBPGR). Expeditions were made to collect primarily S. officinarum,
S. robustum, S. edule plus related wild species from Polynesian-Melanesian islands
where greater diversity for these species exists and S. barberi, S. sinense,
S. spontaneum, Erianthus, Miscanthus and other species from Indo-Burma-South
China and adjoining region where these species exhibited greater diversity.
9 Sugarcane Breeding 511

9.6.1 World Collection of Sugarcane Germplasm

Saccharum and allied genera germplasm collections made by several institutions/

agency prior to 1956 from the centres of origin were held primarily in Florida (USA)
and Java (then the Dutch East Indies). These became known in the sugarcane world
as the ‘ISSCT World Collections’. Initially, the collection was maintained at the US
Department of Agriculture, Agricultural Research Service (USDA-ARS), Sugarcane
Field Station at Canal Point, Florida. Later it was shifted to Beltsville, Maryland,
and maintained in greenhouses. Since 1976, the ISSCT world collection (except
S. spontaneum) is maintained at the USDA-ARS, Subtropical Horticultural Research
Station, Miami, Florida. It is now known as World Germplasm Collection of
Sugarcane and Related Grasses. Saccharum spontaneum clones of the World
Collection were moved to the USDA-ARS Sugarcane Field Station, Canal Point,
Florida. In the USA, wild species S. spontaneum is classified as noxious weed and is
closely regulated. Therefore, individual clones are grown in containers to prevent
their spread by rhizomatous growth (Comstock et al. 1996).
The ISSCT World Collection at Java was lost in the 1940s during the World War
II. By the 1950s, plant breeders and research organizations across the globe showed
concern on the narrow genetic base of commercial sugarcane and the possible loss of
valuable wild germplasm. This issue was addressed at the eighth ISSCT Congress
held in 1953, and it was resolved to have another (duplicate) collection of sugarcane
germplasm of the world that lost in Java. As the Sugarcane Breeding Institute,
Coimbatore had undertaken the collection of S. barberi, S. sinense and
S. spontaneum and related genera from tropical Asia and Africa, the ninth ISSCT
Congress held in India in 1956 resolved that the Coimbatore (India) collection
should be recognized as the ‘Second world collection of sugarcane germplasm’
(Dutt 1956). One set of the world collection maintained at Canal Point was brought
to India during 1956–1958 to augment the Second World Collection of sugarcane
germplasm at Coimbatore. As mosaic disease was widespread in Coimbatore, only
clones of S. spontaneum and Erianthus spp. were retained at Coimbatore, while all
other clones were sent to the Agriculture Research Station, Taliparamba, Kannur
District (Kerala) in 1956 (Balasundaram et al. 1980). Then, the Research Centre of
the Sugarcane Breeding Institute was established at Cannanore (now known as
Kannur), Kerala, in 1962 exclusively for the maintenance of the World Collection.
Soon, the collection maintained at Taliparamba was shifted to Kannur.
In the 1992 hurricane (named ‘Andrew’), the World Collection at Miami was
severely affected. About 568 clones of S. officinarum and many clones of
S. spontaneum had lost, and identification tags of the germplasm were blown over
by the hurricane. Re-establishment of the S. officinarum from the collection already
shared to Copersucar, Brazil, and S. spontaneum clones from the breeding collection
maintained at Canal Point, Florida, and Houma, Louisiana, was carried out
(Comstock et al. 1996). As of 2014, 1427 accessions were maintained at Miami as
against 1787 accessions reported in 1987 (Heinze 1987; Todd et al. 2014; Fickett
et al. 2020). The Kannur Centre of SBI holds (as of January 2021), 1813 accessions
of ISSCT World Collection and 1550 accessions of Indian Collection, which is the
largest now (Table 9.2). The ISSCT World Collections of Sugarcane and Related
512 B. Ram et al.

Table 9.2 World collection of sugarcane germplasm and related grasses maintained at the USDA-
ARS-Subtropical Horticulture Research Station, Miami, and ICAR-Sugarcane Breeding Institute,
Research Station, Kannur
Miami, Florida, USA Kannur, Kerala, India
S. No. Species/genera (2014) (2020)
1 S. officinarum 254 (546a) 757
2 S. robustum 51 (97) 129
3 S. edule 6 (18) 16
4 S. barberi 38 (6) 42
5 S. sinense 33 (84) 30
6 S. spontaneum 316 (266) 384
7 S. brevibarbe 1 –
8 Erianthus arundinaceus 8 121
9 E. bengalensis 5 19
10 E. elephantinus – 1
11 E. longisetosis – 7
12 E. ravennae 3 –
13 S. kanashiroi (Syn: E. kanashiroi) 2 3
14 S. rufipilum (Syn: E. rufipilus) 2 –
15 S. procerum (Syn: E. procerus) 1 35
16 Erianthus spp 20 (172) –
17 Miscanthus floridulus 1 –
18 M. sinensis 4 –
19 Miscanthus hybrid 6 –
20 Miscanthus spp. 5 (8) 2
21 Miscanthidium 0 (8)
22 Narenga porphyrocoma 1 (11) 6
23 Sclerostachya fusca – 5
24 Imperata sp. 1 –
25 Eccoilopus 0 (2) –
26 Coix gigantea 1 –
27 Pennisetum spp. – 4
28 Sorghum plumosum 1 –
29 Sorghum arundinaceum 1 (5)
30 Vettiveria 11
31 Others + new collections 238 + 250 (381) 9
32 Indian hybrids/commercial cultivars 1031
33 Indo-American clones 130
34 Man-made/historical/natural 176 (174) 621
Saccharum hybrids
Total 1427 (1787) 3363
Source: Todd et al. 2014; ICAR-SBI (2020)
a
Number within bracket indicates maintenance at Miami in 1987 (Heinze 1987)
9 Sugarcane Breeding 513

Grasses maintained in Miami and Kannur includes accessions representing different

species of Saccharum, allied genera and man-made historical and commercial
hybrids, collected from over 45 countries (Todd et al. 2017; Balasundaram et al.
1980).
The IBPGR Working Group on the Genetic Resources of Sugarcane (1982) has
recognized the existing ISSCT world collections at Miami and Kannur as primary
collections as well as global field gene bank of sugarcane. In addition, 11 ‘secondary
collections’ in different countries having unique materials have been recognized
(Anonymous 1982). Besides the world collections, some countries are maintaining
working collection of Saccharum and related species for utilization in their breeding
programmes. The National Plant Germplasm System, USDA and the National
Institute of Agrobiological Resources (NIAR, now NIAS), Tsukuba, Japan were
designated as base seed collections for sugarcane by the IBPGR (Croft et al. 1996)

9.7 Floral Biology

Sugarcane inflorescence is known as ‘Arrow’ by virtue of its shape, but botanically it

is an open branched panicle or tassel (25–50 cm long) with 5000–8000 small florets.
The apical meristem, which is surrounded by a leaf sheath, ceases to form leaves and
develops into an inflorescence primordia about 3 months before the actual flower
emerges (Van Dillewijn 1952). The first sign of flowering is when the distance
between leaf triangle becomes greater as the successive leaf sheaths and internodes
become longer and leaf blades become shorter. This stage is called the ‘symptom
stage’. Then the distinctive flag leaf appears. The last leaf sheath is about 3 ft longer
fully enclosing the young panicle, while its leaf blade is only about ½ ft long and
shaped like a pennant. This stage is called ‘booting stage’ or ‘short blade stage’.
Then, the stalk elongates, and the panicle emerges out from the enclosed leaf sheath
(‘tip emergence stage’). The main inflorescence axis or rachis arises from the
terminal internode of 10–12-month-old crop. The primary branches (rachilla) arise
from main rachis. The secondary branches arise in two rows, alternatively along the
primary branches. The secondary branches may often bear tertiary branches, and the
ultimate branches bear a pair of spikelets; one is sessile, and the other is pedicellate.
Both spikelets have two florets: one is sterile and is represented by a delicate
pointed small lemma (shorter than glumes). The upper floret of each spikelet is larger
and hermaphrodite but do not have lemma (except S. spontaneum which bears scaly
lemma). Therefore, only one floret in each spikelet is visible to the naked eye. The
parts of florets from the outermost portion to inward are numbered as G1 (outer or
lower glumes or prophylletum), G2 (inner or upper glumes), G3 (a sterile lemma or
third glume) and in few species G4 (a fertile lemma or fourth glume) (Kruger 1899;
Rumke 1934; Grassl 1956). The whorl G4 is not present in S. officinarum but present
in S. spontaneum and its hybrids. The upper florets of each spikelet as mentioned
earlier are fertile and contain one palea, three stamens, one ovary and two long styles
514 B. Ram et al.

with brush-like feathery stigma. Lemma is absent. Anthers are bi-lobed. The inde-
hiscent anthers are usually yellow or pale yellow, while dehiscent anthers are brown
or purple. Ovary is round with single anatropous ovule. Two short wedge-shaped
lodicules are present inside the palea near the base of the ovary. They absorb water to
swell and force apart the glumes for the exertion of anthers and stigma during
anthesis. At the base of each spikelet in the pair, there are longer (than spikelet)
silken or callus or pappus hairs in whorl known as ‘fuzz’ or ‘fluff’ which gives the
arrow its characteristic silky appearance and helps disperse the seeds. The arrow is
longer in S. officinarum but shorter in S. spontaneum and S. barberi and intermediate
in S. sinense (Artschwager et al. 1929).

9.7.1 Flowering

Sugarcane is a short day plant and flowers when the day length is gradually reduced
during its grand growth phase. In the northern hemisphere, sugarcane flowers during
October to early December, whereas in the southern hemisphere, flowering occurs
from April to early June. The duration of flowering is generally longer as the equator
is approached (in equator flowering is throughout the year because of adequate day
length and temperature). If a clone is shifted from one latitude to another, there will
be a shift in flowering date by 2.4 days for each degree of latitude. Generally, ratoon
crop flowers earlier than the plant crop. The wild species Saccharum spontaneum
and S. robustum flower profusely in their original habitats and other established
locations (Ethirajan 1987), whereas S. officinarum is a shy flowering species. Many
clones of S. officinarum do not flower at Coimbatore condition. Flowering in
S. barberi and S. sinense is generally sparse and late at Coimbatore condition due
to their subtropical origin.

9.7.2 Anthesis and Pollination

Opening of florets or anthesis takes place in the early morning between 5:00 and
9:00 AM, and stigma emerges out from the florets little ahead of the anther
dehiscence (around 6:30–8:30 AM). Protogyny leads to cross pollination in sugar-
cane. The opening of flowers commences from the top and proceeds downward. An
arrow takes about 7–10 days to complete anthesis.
Pollen fertility may vary from 0% to 100% depending on the clone and environ-
ment. The percentage of pollen fertility in a clone is the deciding factor for its use as
a male or female parent in the crossing programme. Fresh pollen of suspected clone
is collected in the early morning, stained with 1% acetocarmine solution and
observed under the microscope for pollen fertility. Fertile pollen will be deep red
in colour. Those clones with low pollen fertility are used as the female parent. Heinz
9 Sugarcane Breeding 515

and Tew (1987) suggested clone with <8% pollen fertility as safe female parent, but
at Coimbatore, the following categorization is adopted:

Pollen fertility % Classification of parental clone

1–30 Safe female
31–70 Both male and female
71–100 Strong males

Pollen grains are viable for a short time after anthesis, but stigmas are receptive
for longer hours and persistent. After pollination, it takes 21–25 days for the seed to
fill and mature. Sugarcane has poor seed set and seed viability. The seed set under
Coimbatore condition ranged from 3.1% to 22.7% (Rao 1980). The matured seed is a
one-seeded fruit or caryopsis, yellowish brown, very small (1 mm long), ovate with
withered stigma persists at the tip, and at the base are whorls of silky hairs for wind
dispersal. The seeds along with its appendages are collectively called ‘fuzz’ (due to
fuzzy appearance) or ‘fluff’ or ‘true seeds’. The weight of a defuzzed seeds is
0.4–0.5 mg. The viability of the fuzz is low (30–35 viable seeds per gram fluff),
falls rapidly; therefore, it is stored in a freeze dryer. A gram of fuzz may contain 2013
seeds, and about 450–550 seedlings may be obtained from it. Good seed set and fuzz
germination is observed at Coimbatore condition. Therefore, in India, the National
Sugarcane Hybridization Garden (NHG) was set up at ICAR-Sugarcane Breeding
Institute, Coimbatore.

9.8 Hybridization Techniques

The miniature nature of spikelets creates problem for emasculation and is not
adopted in crosses meant for commercial breeding. The general practice is to use
the entire inflorescence as a unit, and clones with low pollen fertility are designated
as female parents in the crossing programmes. Heat treatments of inflorescence at
50  C for 5 min (Heinz and Tew 1987), hot water dipping at 50  C for 10 min
(Krishnamoorthy 1977) and dipping of tassel in 63–70% alcohol for 9 min have been
reported to provide complete male sterility, but these practices are not widely
adopted in commercial cane breeding. Breeders across the world take the advantage
of protogyny in making crosses. The hybridization techniques followed by breeders
may be grouped under two categories: (1) hybridization done with both parents kept
in situ and (2) hybridization done with the arrows of one or both the parents isolated.

9.8.1 Hybridization Techniques Where Both Parents Are Grown

In Situ

9.8.1.1 Open Field Crosses

When the female arrows are not covered to exclude contamination from foreign
pollen, the crossing method is designated as open crossing. Sugarcane is naturally a
516 B. Ram et al.

cross-pollinated crop. Moreover, due to its small floret size, controlled hybridization
was not performed in the past. In the early period of sugarcane improvement,
i.e. 1900s, fluffs of open pollinated arrows were collected and sown. This seeds
were called GC (General Crosses). Even today, GC collection is practised in many
countries including India and Brazil. In this method, there is no control on pollina-
tion or choice of male parent. In India, Venkatraman (1925, 1927) planted parents
for hybridization separately in isolation and called it as ‘arrowing plot’. In the
arrowing plot, a row of female parent was flanked on both sides by rows of male
parent. At the time of flowering, the arrows of adjacent rows were brought together,
covered with cloth bags, and in situ crossing was allowed to take place. The bags
with arrow are secured in position by erecting a bamboo pole in the field. This kind
of field crosses with minor modifications is used in Java, Barbados, Mauritius and
Taiwan (Stevenson 1965). Polycross employed at ICAR-SBI, Coimbatore, India, is
a modification of general crosses and is different from the Hawaii method. Polycross
is defined as a cross between a female parent surrounded by more than one male
parent. In polycross nursery, selected female parents with low pollen fertility are
planted in one row, and flanked on both sides are a large number of selected male
parents. The arrows of female rows are not covered. Natural (wind or insect)
pollination is allowed to take place. Fluff from the female row alone is harvested
and is designated as PC of that particular female parent. In polycross, the source of
specific male parent is not known, but the group of male parent is known.

9.8.2 Hybridization Techniques Where One or Both Parents Are

Isolated

9.8.2.1 Covered Field Crosses

Covered crossing was once widely used in Java, India, Hawaii, Formosa, Barbados,
Australia and Mauritius. But due to poor seed set of tassel enclosed in lanterns than
those allowed in the open, this method has been discontinued in Java and Hawaii but
continued in India and other countries.

9.8.2.2 Lantern Method

Controlled field crosses followed in India are described below. In the National
Hybridization Garden of ICAR-SBI, Coimbatore, about 500–600 diverse parental
clones, which originated from different geographical regions in the world, are
planted every year in the month of December. Flowering symptoms in early
flowering clones are seen during the second week of September and short blade
during the last week of September. Sugarcane breeders from different parts of the
country arrive at Coimbatore, and crossing programme generally begins in the
second fortnight of October. A day prior to crossing, selected female parent is
covered with cloth bag supported by aluminium cages. The cages are hung from
the bamboo poles erected close to the canes; hence, this method is called the lantern
method of crossing. A portion of inflorescence from the male parent that is likely to
open on the same day is identified with the aid of torch light and clipped off by
9 Sugarcane Breeding 517

pressing between thumb and forefinger at 5:00 AM. The excess moisture on the
clipped florets is removed by blotting paper and then kept under warm light (500 W
electric bulbs) for half-an hour to force dehiscence of anthers artificially in a
specially devised room called ‘pollen chamber’. After an hour, i.e. around 6:
30 AM, the dehisced pollen together with inflorescence is placed in a butter paper,
wrapped and gently dusted onto the female florets/inflorescent of female parent (after
lifting the enclosed cloth bag) before its own pollen dehisce and self-fertilize.
Dusting of pollen is continued for 6–7 days until all the florets are pollinated. The
hybridized arrows are severed from the mother stalk after a minimum maturity
period of 21 days, shade dried and sown immediately or stored in 20  C for
long-term storage.

9.8.2.3 Scaffolding: An Improved Platform for Easy Field Crossing

In the lantern method of field crossing, difficulties are encountered such as reaching
the female arrows positioned at 3–6 m from the ground level. Pollination is possible
difficult and possible only by using ladders. Ladders have to be shifted by two
labourers after every pollination, and several ladders have to be used simultaneously
to complete the targeted crosses within crossing time of 1–2 h (6:30–8:30 AM) under
Coimbatore condition. To overcome these difficulties and to simplify the pollen
collection and dusting operations, a robust structure called ‘Elevated Hybridization
Runways (EHR) or Scafolding’ was developed at ICAR-SBI Coimbatore (Nair et al.
2013). The EHR structure consists of two tiers of GI platforms. These platforms are
supported by H-shaped 48  2.65 mm G.I. pipe frames braced with 27  2.65 mm
GI pipes. The H-shaped GI pipe frames are assembled on top of each other with
interlocking arrangement to make the height to 4.5 m. Each unit has 42 H-shaped GI
pipe poles interconnected by cross bracing at an interval of 2.2 m. The width of the
structure is 1.0 m. The structure is positioned between two rows of female parents
with the row spacing of 1.2 m. Since the parental clones are planted in field on either
side of the platform, arrows are accessed easily for crossing. The height at which the
flowers are positioned on the sugarcane varies with genotypes; the unit is fabricated
in two different heights, i.e. the platforms are placed at 2.85 and 4.5 m height above
the ground to facilitate crossing of the flowers situated at different heights. The unit
is divided into two equal subunits each running a length of 13.2 m (span on either
side of the central platform), thus covering a total width of 26.4 m. If parental clones
are planted at 1.2 m row spacing, 11 main units are needed to cover an area of 700
m2. A ladder made of M.S. pipe enables the breeders to reach the platforms for
making crosses. The researcher can move freely from one platform to the other,
effect dusting on the female arrows while standing on the platform and collect
matured fluff.

9.8.2.4 Free Crossings

This is an open crossing, used mostly in Java and Hawaii before the development of
the Hawaiian crossing method. In this method, the female arrows remain attached to
the plant grown in field, while the male arrows are cut, placed in vases of water and
518 B. Ram et al.

fastened in position around the female arrows. The male arrows are replaced daily.
Pollination is aided by wind.

9.8.3 Hybridization Techniques Where Both Parents Are Isolated

9.8.3.1 Marcotting or Rooted Stalk Technique

A marcot is an air-layered rooted stalk. Way back in 1926, Venkataraman and
Thomas of SBI Coimbatore standardized a technique for inducing rooting and
then isolating flowering stalk from a standing cane for effecting crosses in shed
instead of in the field. This method was known as ‘tile pot technique’. In this
technique, during advanced symptom stage, roots are induced on standing sugarcane
stalk in the field by covering two to three internodes in the middle of the stalk
(or leaving top 7–8 internodes) with soil which is held around the stalk tightly by
placing two halves of a tile pot along the length of stalk and then tied by jute rope.
Water is poured from the top portion of tile pot daily to induce roots. After the root
formation, which takes place about 15–20 days, they are severed from mother cane
by cutting at bottom (just below the rooted node) and brought to the crossing shed. In
the hybridization shed, the arrow of male marcotted canes is kept slightly above the
arrow of female marcotted cane, and both are enclosed in an aluminium cage
covered outer with cotton cloth bags.
Everyday morning arrow pairs are tapped gently to ensure the pollen fall vis-à-vis
fertilization. The rooted marcots are watered periodically to prevent it from desicca-
tion. The fluffs from female arrows are collected 21 days after pollination. Later Dutt
and Hussainy (1956) improved upon the method using alkathene or plastic sheets in
place of the tile pot. A polythene tube is inserted from the cane top and is
positionedat at middle of the stalk. The tube is filled with soil mixtures, bottom
portion of the polythene tube is tied around the stalk tightly to prevent leakage of soil
and water. The tube is watered from the top daily to induce roots. Premature drying
of marcots is often encountered which affects seed set and viability of hybridized
fuzz. Providing an environment with high humidity of >80% and root temperature at
22  C for the isolated marcots was reported to prevent premature spikelet abscission
(Narasimhan et al. 1963). Nagarajan et al. (1996) suggested marcotting at the top of
the internodes so as to reduce the height for easy crossing. As of today, in India, this
method is not practised for commercial breeding, but countries like Brazil, the USA,
South Africa, Mauritius, Taiwan and Puerto Rico are following this technique.

9.8.3.2 Hawaiian Solution Technique

A solution for keeping the severed flowering stalks of sugarcane afresh for crossing
purpose was developed in Hawaii, which initially consisted of a diluted solution of
sulphurous acid. A small portion of stalk with arrows kept in the solution continued
to flower normally and produce viable seeds so long as the solution is kept fresh.
Later, phosphoric acid was added to improve the efficiency and seed set. The
standard Hawaiian solution contained 0.03% sulphurous acid and 0.01% phosphoric
acid. This solution was improved further by Mangelsdorf, with a composition of
9 Sugarcane Breeding 519

150–180 ppm sulphurous acid (SO2), 75 ppm phosphoric acid (H3PO4), 37.5 ppm
nitric acid (HNO3) and 37.5 ppm sulphuric acid (H2SO4) (Machado et al. 1987). In
this solution, arrows maintain viability for a period of 8 weeks, but the solution
requires renewal once in 3 days (Heinz and Tew 1987). The pH of the fresh solution
is 2.3, and it should be measured daily. If the pH has reached to 3.0, the solution is
changed. If not changed, then SO2 is replenished daily through the addition of
measured quantity of sulphurous acid. The hybridization procedure followed in
Hawaii and Brazil using solution technique is described below.
Arrowed stalks intended for the biparental or polycrosses are identified. Generally
tassel with light coloured or yellow anthers are used as females, and those with
brown anthers are classified as male parent. Arrows to be used in the crossing are cut
from field at 8 AM with 1.5 m stalk attached to it, and the bases of the stalk cut
diagonally. Male tassels are marked with black label and female arrow with red
label. The leaves of stalk are stripped off, the tassel is sprayed with fungicide and the
arrows in upright position are transported to crossing house. Arrows indented for
biparental crosses are bundled in such a way that six to eight female arrows from one
parent are surrounded by eight male arrows of another clone, and the height of male
arrows is kept 1 ft above the female arrows. In case of polycross, five to six male
arrows from different clones are kept along with one or two female arrows in one
bucket. Every morning, the arrows are slightly shaked to facilitate pollen dispersal
and pollination. After 3 days, the arrows are removed, the stalk bases are recut, the
solution is changed and the arrows are kept in the new solution. Success of Hawaiian
solution technique is dependent on the use of mineral free water. In India, the
solution rapidly turned toxic and panicle gets dried and falls off. Therefore, this
technique is not used in India’s commercial cane breeding programmes.
Solution technique is also used in combination with field crosses. The classical
‘Barbados lantern’ first used for field crosses in that country was big (30  30  30 ),
made of timber glazed on top and three sides and with a cloth shield on the fourth
side. A smaller version of the same was in use in Mauritius. Subsequently when
practice of using cut cane in crossing became popular, lanterns were modified
suitably. Finally, in Barbados, tail lantern batteries made of iron angles and fitted
with cross ties and horizontal bars were fixed permanently in the glass house itself.
They were provided with lantern skirts made of light, closely woven, pollen proof
cloth which when fully extended reached 2 ft from the floor. Just before the spikelet
opening, arrows of female parents are cut with a large portion of stalk, placed in
preservative solution and set up in lantern with minimum loss of time. The male
arrows are introduced in similar way and placed slightly above the female arrows.
The acid solution is changed twice a week. The canes are properly labelled and
tapped lightly every day to ensure proper shedding of pollen. After crossing is
completed, the arrows whose seeds are to be collected are transferred to seed
ripening shed, keeping them in solution. Paper cones are placed around and below
the arrows to collect the dried panicle branches and fuzz as they fall (Stevenson
1965). In South Africa, crosses are made both in field and glass house. In field, a
glass lantern is suspended over the female arrows on long bamboo poles. The male
arrows are then inserted into the lantern, and the cut stalks are placed in preservative
520 B. Ram et al.

solution. The lantern is closed at the bottom with linen cloth tied to stalks. Male
flowers are changed daily or alternate days. After crossing is over, male arrows are
removed. A muslin bag is then put on the female arrows till seed is matured.

9.8.3.3 Melting Pot Technique or Modified Polycross

The dictionary meaning of melting pot is a place where many different people and
ideas exist together, often mixing and producing something new. During World War
II, the Hawaiian Sugar Planters’ Association (HSPA) Experiment Station faced
labour shortage. They employed a modified polycross technique known as melting
pot (MP) technique (Mangelsdorf 1953). A large number of seedlings are produced
at minimal cost, but a disadvantage of this method is the loss of pedigree information
hence inability to repeat the crosses giving higher selection rate. Establishing MP
crosses is a 1-day operation per crossing date in contrast to 2 days for biparental
crosses. Stalks with arrows in early anthesis are cut and tagged in the field and then
brought to the MP crossing shelters where a female arrow is interspersed (kept in
Hawaiian solution) with large number of male arrows collected from diverse clones.
The arrows (both male and female) in the MP shelter are moved around periodically
to achieve wide distribution of pollen from each tassel. In many sugarcane breeding
stations where the Hawaiian method is used, the male arrows are thrown away after
pollination. Fluffs from female arrows alone are harvested; hence, the female parent
of the seedling produced in the melting pot alone is known (Warner 1953). A
modification of the melting pot is the ‘area crosses’ (Warner 1953) in which tassels
from a single male parent were used to pollinate a number of female varieties. In this
case, both the parents of the progeny are known, and this method enables screening a
large number of genetic stocks for general combining ability.

9.9 Molecular Cytogenetics and Breeding

Cytogenetic manipulations of the chromosome complements are one of the most

important methods available for introducing new variations into the crop plants.
Classical cytological studies such as changes in chromosome number, morphology
and chromosome behaviour in mitosis and meiosis played a pivotal role in
establishing a classification of the Saccharum genus and, to some extent, revealed
the process of ‘nobilization’ in varietal development. Molecular cytogenetic analysis
is an advanced technology in cytogenetics by incorporating applications of molecu-
lar biology to understand crop evolution, genetics, genetic recombination and
karyotype stability. Advent of these technologies has widened the scope of
applications of classical karyotype analysis for exploring the location of a gene in
the chromosome. The use of molecular cytogenetic studies in sugarcane research
provides a precise karyotype analysis to introgression of alien genome in interspe-
cific and intergeneric hybrids.
Recent molecular cytogenetic techniques such as fluorescence in situ
hybridization (FISH) and genomic in situ hybridization (GISH) together have
extensive use in identification of specific genomes, individual chromosomes or
9 Sugarcane Breeding 521

chromosomal segments. The basic chromosome numbers of 10 for S. officinarum

and S. robustum and 8 for S. spontaneum were established through FISH by physical
mapping of ribosomal RNA genes (D’Hont et al. 1996, 1998). In addition, in situ
hybridization studies using genomic DNA as probe have shown that the genomes of
modern hybrids are composed of 70–80% S. officinarum chromosomes, 10–20%
S. spontaneum chromosomes and 5–17% recombinant chromosomes containing part
of S. officinarum and part of S. spontaneum chromosomes (Piperidis and D’Hont
2001; D’Hont 2005). A major drawback in sugarcane cytogentics is the lack of
information on genome and chromosomal morphology which hampers clear identi-
fication of individual chromosomes from each genome.
The genome complexity in sugarcane has encouraged researchers to elucidate the
aspects of genome constitution and architecture through molecular studies. Critical
information on the behaviour of chromosomes during meiosis in modern cultivars is
lacking. Vieira et al. (2018) explored the meiotic process and chromosome associa-
tion at diakinesis using FISH. The use of centromeric probes confirmed the predom-
inance of bivalent associations, avoiding possible errors due to the small size and
high number of sugarcane chromosomes, and provided a model for analysing
meiotic behaviour in other canes with possible implications for sugarcane breeding
programmes.
GISH is a powerful technique with enormous potential for the identification of
parental genomes in interspecific and intergeneric hybridization by using the geno-
mic DNA from one species as the labelled probe. GISH allows monitoring the
introgression of alien chromosomes in the wide hybrids. GISH was first
demonstrated in synthetic Hordeum chilense  Secale africanum (Schwarzacher
et al. 1989) and Triticum aestivum (wheat)  S. cereale (rye) (Le et al. 1989). Since
then, many researchers could efficiently monitor chromosome transmission in inter-
specific and intergeneric crosses. Another huge advantage of the GISH is the ability
to visualize the sites of recombination on the physical chromosome (Khrustaleva
et al. 2005). For the first time, D’Hont et al. (1996) demonstrated that GISH can be
used to differentiate chromosomes in interspecific hybrids between BNS 3066
(S. officinarum) and SES 14 (S. spontaneum). In addition, they identified n + n
transmission of parental chromosomes in the interspecific F1 hybrid between
S. officinarum and S. spontaneum.
Using GISH, the typical S. officinarum with 80 chromosomes and atypical with
more than 80 were distinguished (Yu et al. 2018), and the results could be very well
used in selection of pure S. officinarum for sugarcane improvement. Of late, GISH
technique has been effectively used in elucidation of inheritance pattern of alien
chromosomes in intergeneric hybrids involving Erianthus. Pachakkil et al. (2019)
analysed the intergeneric hybrids of Erianthus and showed that 54–56 chromosomes
were transmitted from sugarcane cultivar, while 18–29 chromosomes were from
E. arundinaceus. These results could show that ‘n + n’ parental chromosome
transmission occurred during hybridization, with elimination of E. arundinaceus
chromosomes in varying degrees. In another study, GISH analysis showed unex-
pected number of E. arundinaceus chromosomes in the BC1 progeny which was
more than in their F1 female parents. This is the first cytogenetic evidence for an
522 B. Ram et al.

unexpected inheritance pattern of E. arundinaceus chromosomes in sugarcane

(Wu et al. 2014). The chromosome composition of E. procerus  S. officinarum
hybrids at F1, BC1 and BC2 stages via GISH was demonstrated, and the F1 resulted
from 2n + n chromosome transmission, while BC1 and BC2 from n + n transmission
(Sobhakumari et al. 2020).
For the first time, the chromosome composition and condensation behaviour of
sorghum chromosomes in hybrids involving Saccharum and sorghum were
demonstrated in two intergeneric hybrids of sugarcane, Co 86032 (2n ¼ 112)  Sor-
ghum (2n ¼ 20) and Sorghum (2n ¼ 20)  S. officinarum (2n ¼ 112), through
molecular cytological analysis. GISH using Sorghum genomic DNA as the labelled
probe revealed n + n chromosome segregation and introgression of ten Sorghum
chromosomes in both hybrids (Sobhakumari et al. 2018). These molecular cyto-
genetic tools provide a wider opportunity to analyse the genomic structure and
function, chromosome constituents, alien chromosome transfer, recombination,
genome evolution, aneuploidy and polyploidy in sugarcane.

9.10 Genetic Studies on Qualitative and Quantitative Traits

Quantitative genetic studies are very important and of great use if they can indicate
the relative importance of additive and non-additive genetic variance and of genetic
and environmental variances for a particular character. Many designs proposed for
studying the inheritance of quantitative traits are not suitable for sugarcane because
of high polyploidy, irregular meiosis, cross fertilization, heterozygosity, self-sterility
and incompatibility (of some varieties) and male sterility or low pollen viability of
many varieties. However, the effect of the violation of these assumptions did not
have serious effects on estimates of genetic parameters (Hogarth 1977).
Maternal effect has also been reported in sugarcane (Loh and Tseng 1950).
Natarajan et al. (1967) reported maternal effects for stalk number, stalk length and
hand refractometer brix. Rai et al. (1991) reported higher contribution of females
than that of female  male to the total variance for number of millable stalk (NMS)
and stool weight, which might be due to some self-pollination (unless the maternal
parent is pollen sterile) as the maternal parent of a cross is not emasculated (Hogarth
1973). Bhagyalakshmi et al. (1986) observed higher contribution of female  male
for NMS, stalk diameter, stalk length, Brix % and stalk yield. High contribution of
females to the total genetic variance for commercial cane sugar percent (CCS%),
Brix %, NMS, stalk diameter and stalk length indicates high gca (general combining
ability) variance, whereas contribution of variances due to sca were higher for sugar
yield, stalk yield, sucrose %, juice extraction % and single stalk weight (SSW).
Contrarily, Ram et al. (2005) reported the highest contribution (41.83%) of males
followed by that of female  male (34.26%) and females (23.93%) for red rot
disease index.
The mid-parent offspring covariance, which allows estimation of additive genetic
variance, requires fewer genetic assumptions than most other estimates and has the
additional attraction of being a meaningful statistical parameter as well as genetic
9 Sugarcane Breeding 523

parameter. Offspring-parent regression has been reported by Hogarth (1977),

Hogarth et al. (1981) and Ram and Hemaprabha (1998a). The additive and domi-
nance genetic variances were higher in commercial hybrids  first nobilized
progenies (N1) for sugar yield and stalk yield. The dominance variance was higher
in progenies of noble  N1 for stalk diameter and sucrose content (Ram and
Hemaprabha 1998a). They also reported higher additive genetic variance for
NMS, sucrose % and stalk diameter and negligible additive genetic variance for
stalk and sugar yields, sucrose %, juice extraction % and SSW. On the basis of
combining ability analysis, Ram and Hemaprabha (2000) found the importance of
non-additive effects for both sugar content and stalk yield. They also reported above
1.5 ratio of additive genetic variance to dominance variance for NMS and near unity
for stalk diameter and stalk length. Dominance variance was important for sugar
yield, stalk yield, CCS %, sucrose %, Brix %, juice extraction % and SSW.
Earlier, Hogarth (1980) reported that most genetic variance for Brix was additive,
but non-additive genetic variance was important for stalk yield and its components.
Hogarth (1977) reported that additive genetic variance was more important for Brix
and number of NMS per stool in the Australian population, whereas in the Hawaiian
population, dominance variance was more important for stalk number, and both
additive and dominance variances were important for Brix (Hogarth et al. 1981).
Based on combining ability studies, Yang and Chu (1962), Miller (1977) and Rao
and Ethirajan (1983) found that specific combining ability (sca) was more important
than general combining ability (gca) for stalk yield and Brix. Rai et al. (1991)
reported a predominant role of non-additive gene action in the inheritance of
NMS, stalk length, stalk diameter and stalk density and additive gene action for
SSW and stalk yield. They also reported that the degree of dominance was in the
range of over-dominance for NMS, stalk length, stalk diameter and stalk density.
Narrow-sense heritabilities for stalk and sugar yields were low, whereas it was
moderate to high for component traits. Data on additive dominance variance and
heritability suggest that yield component breeding may be an effective way to
indirectly increase sugar yield and stalk yield (Ram and Hemaprabha 1998b). In
another study, Ram and Hemaprabha (2000) reported negligible heritability in
narrow sense for cane yield. Cane yield and sucrose content are negatively
associated in sugarcane. The degree of negative correlation increases with improve-
ment in any of these two components above the present commercial status. However,
this negative association is not absolute. Even a high negative correlation of 0.8
between cane yield and sucrose % meant 36% (1  r2) independent variability,
which indicated the scope for simultaneous improvement in sugarcane yield and
sucrose content (Ram and Hemaprabha 1992). Based on experiments conducted
under water stress, waterlogging, salinity and non-stressed conditions, Ram et al.
(2001a) concluded that number of millable stalks (NMS) had the highest genotypic
coefficient of variation, heritability, expected genetic advance, higher correlations
and direct effects with sugar yield, higher inter-environmental correlations and near
unity relative response values. Hence, NMS was the most effective selection crite-
rion for selecting better ratooning and high sugar yielding clones in sugarcane under
different abiotic stresses.
524 B. Ram et al.

The best way to manage the disease is to develop resistant varieties, and all new
releases must be resistant to red rot. Study of large numbers of progenies involving
resistant and susceptible parents established Mendelian segregation for red rot
resistance (conferring vertical resistance) in many of the crosses (Ram et al.
2001b). Both additive and dominance variances were equally important, and herita-
bility (in narrow sense) was 0.51 for red rot resistance in sugarcane. A high (0.97)
broad sense heritability for red rot resistance indicates a high level of repeatability
across different environments for red rot disease development in sugarcane (Ram
et al. 2005). A detailed investigation involving interspecific and intervarietal genetic
stocks revealed the presence of both vertical (race specific) and horizontal (race
nonspecific) components for red rot resistance. It was also established that the level
of horizontal resistance decreased with a decrease in the S. spontaneum chromosome
complement present in the material (Natarajan et al. 2001).

9.11 Breeding Objectives

The objectives of sugarcane breeding are more or less the same throughout the
world: the production of high sugared and high yielding disease-resistant varieties
giving the maximum returns under the conditions for which they are intended
although different means are used in different places to attain the same end. With
the extension of sugarcane cultivation in non-conventional areas, the need was felt
for breeding for tolerance to adverse climatic conditions such as drought, frost,
waterlogging and salinity and emerging diseases such as red rot, smut, borer pests,
etc. The recent awareness on the advantages of using green fuel for generation of
electricity and use of bioethanol in automobiles to reduce greenhouse gas emission
have resulted in setting up of a number of cogeneration plants and distilleries in
various sugar mills. To achieve this dual goal of increased alcohol and cogeneration,
sugar industries need special varieties to meet their specific requirement of raw
materials. Sugarcane improvement, is therefore should be a continuous and dynamic
programmes and by taking into the need of end users, more and more specific
traits/gene(s) are to be introgressed now and then in the commercial cultivars. The
most important objectives of cane breeding across the world are highlighted here.

9.11.1 High Cane Yield and Sugar Content

Initially the breeding work was concentrated on the two important economic
characters: the yield of cane and sucrose content in juice. The theoretical possible
yield of sugarcane is 374–381 tonnes/ha/year (Moore 2009; Waclawovsky et al.
2010). The maximum stalk yield achieved in research stations in Brazil, Australia
and Columbia were in the range of 236–280 tonnes/ha (Duke 1983), and world
average cane yield in farmer’s field is 70.64 tonnes/ha (FAOSTAT 2020). The most
productive nations in the world with respect to sugarcane yield (>100 tonnes/ha) are
Peru (123 tonnes/ha), Senegal (114 tonnes/ha), Guatemala (112 tonnes/ha), Egypt
9 Sugarcane Breeding 525

and Nicaragua (109 tonnes/ha), Malawi (108 tonnes/ha), Zambia (103 tonnes/ha)
and Burkina Faso (102 tonnes/ha) (FAOSTAT 2020). Sugarcane productivity in
India and Brazil has been at 80.50 tonnes/ha and 76.13 tonnes/ha in 2019–2020,
respectively. There is tremendous increase in cane yield of improved modern-day bi-
and tri-specific hybrids in comparison to the yield of natural hybrids/species clones
cultivated during the 1890s.
During 1900s, the average cane yield of Badilla, a natural clone of S. officinarum,
was 40 tonnes/ha in Queensland and yield of varieties evolved in 1904–1908 such as
HQ 409 and Q 813 was 40–60 tonnes/ha (Roach and Daniels 1987). The average
cane yield of modern hybrids presently cultivated in Australia was 80–90 tonnes/ha.
Breaux (1984) reported 25% increase in sugar content in all CP varieties which
evolved during 1970–1971 in comparison to varieties grown in Louisiana in 1958. In
India prior to 1912, i.e. before the development of improved Co varieties, indigenous
sugarcane varieties such as Agauli, Chin, Dhaul, Dickchan, Hemja, Katha, Lalri,
Mungo, Matna, Nargori, Pathri, Rakhra, Kuswar, Saretha and Pansahi were in
cultivation. Their cane yields were in the range of 18–35 tonnes/ha, and sucrose
yield was 10–15.0%. However, with recent varieties such as Co 0238 and Co 86032,
few farmers in India are harvesting 252 tonnes/ha under subtropical condition and
300 tonnes/ha in ring pit planting in tropical region (The Hindu, 13 Feb 2012,
Business line, dt 14 Nov 2016). The mean cane yield and sucrose% of India’s
leading cane varieties Co 86032 is 105.33 t/ha and 19.28%, respectively and of Co
0238 is 81.08 t/ha and 17.99%, respectively. An analysis of cane yield of improved
sugarcane clones tested under the All India Coordianted Research Project (AICRP)
on Sugarcane was made zone-wise in comparison with the standards over a period of
6 years, from 2010–2011 to 2015–2016 (Ram and Karuppaiyan 2017). It showed
that the mean cane yield of improved clones across the zones in India was 82.93
tonnes/ha which was 4.6% improvement over the yield of standards (79.28 tonnes/
ha).
The data shows improved varieties are better in terms of cane yield and sugar
yield and contributing to the livelihood security of farmers. There are many success-
ful cases in India, Australia, Brazil and other countries on the improvement of
sucrose content in sugarcane through selecting right parental combinations
(Legendre 1995; Lo and Chen 1995). In 2012, the Federal University of Alagoas,
Brazil, released the RB99395 variety with 15.88% pol % in cane (Barbosa et al.
2015) which was 1.1 unit higher than the standard variety SP79-1011 (14.77%). The
sugarcane variety GT35, with very highest sucrose content (top, 19% or higher), was
recently bred by the Sugarcane Research Institute, Guangxi Academy of Agricul-
tural Sciences, Nanning, China (Huang et al. 2016). In West Indies Central Sugar-
cane Breeding Station, Barbados, a high sugar variety B 4362 with 24.1% sucrose
was reported. In Louisiana, where the growing condition is limited to 9 months as
opposed to 12 month elsewhere, clones with 14.9% sucrose were achieved through
recurrent selection cycle (Breaux 1984).
526 B. Ram et al.

9.11.2 Earliness

Sugarcane crop is said to be matured if the juice brix% is 18% and above, Pol% in
juice is 16% and above and purity of juice >85% (Sahi and Sundara 1986). Varieties
attaining such level of juice quality at 10 months after planting are called early
varieties, and those attaining sucrose maturity at 11–12 months are called mid-late
varieties. At the start of crushing season, if late maturing or low sugar varieties are
harvested, it will affect the sugar recovery (crush-to-kill period). Therefore, early
maturing high sugared varieties are preferred for crushing in the initial phase of
crushing season. For higher sugar recovery, it is always desirable to have one-third
of cane area in each sugar mill zone with early maturing varieties. Breeding for high
sugar early maturing varieties has been a major objective in India, Mauritius, the
USA, etc. (Cuenya and Mariotti 1986; Domaingue et al. 1990; Cox et al. 1990; Das
et al. 1997). Early varieties elongate earlier, but that final stalk height at harvest was
lesser than that of late varieties. The partitioning of photosynthates into sucrose was
higher and earlier in early varieties.
In Mauritius, the ratio of reducing sugars to sucrose is being used as a screening
criteria at the preliminary phase (stage 2) of selection in the plant cane crop of
6–8 months of age with a view to detecting early/high sucrose varieties at this stage
of selection (Mamet et al. 1996). Until the 1980s, relatively few early ripening
varieties were available for commercial cultivation in many countries, and earliness
appeared to be a difficult characteristic to attain in the breeding and selection
programmes due to negative correlation between earliness and high sucrose. CoJ
64, Co 89003 and CoS 8436 were the well-known early varieties in the subtropical
region of India, whereas CoC 671, Co 6806 and Co 997 were the known early
maturing variety in the tropical states of India. The negative relationship between
high sugar or high cane yield and red rot resistance is a bottleneck in sugarcane
improvement. Despite of it, Dr. BakshiRam, sugarcane breeder in India succeeded in
evolving high sugar high yield and red rot-resistant varieties such as Co 98014, Co
0118, Co 0237, Co 0238, Co 0239 and Co 05009 by suitably changing the selection
criteria in the ground nursery. Early selection during October in seedling ratoon
nursery is more efficient in identifying better quality clones for crushing during early
in the season (Ram et al. 1997).

9.11.3 Short-Duration Varieties

Short-duration varieties (SDV) are those that attain >18% brix, >16% sucrose and
>85% juice purity with acceptable cane yield at eighth month after planting (Sahi
and Sundara 1986). The age of sugarcane crop is 10–12 months, but the objective of
SDV is to harvest three crops (one plant and two ratoon crops, at 8 month interval) in
2 years instead of two crops in 2 years with conventional varieties. Short-duration
varieties are capable of bringing marked improvement in recovery and ultimately in
sugar production. The cropping intensity can be increased, as SDV can be profitably
fitted in a multiple cropping system. Development of short-duration sugarcane
9 Sugarcane Breeding 527

varieties has been a breeding objective at the ICAR-Sugarcane Breeding

Institute, Coimbatore. To reduce the crop duration of sugarcane from 12 to 8 months,
Dr. T.S. Venkatraman made crosses between sugarcane and sorghum, and hybrids
were produced.
The recent sugarcane  sorghum hybrids evolved at the institute showed HR brix
(hand refractometer Brix) up to 19.90% at 6 months as against 15.6% brix in the
popular cultivar (Nair 2012). Parental clones with high sucrose (>16%) such as Co
0237, Co 09004, Co 13001, Co 13006, Co 0237, Co 16001, Co 11015, CP 96-1662
and CoC 671 were identified (Karuppaiyan et al. 2021b). In India, two varieties, viz.
Co 8338 and Co 11015, were released as SDV. Co 11015 evolved from the cross
CoC 671  Co 86011 and was released in 2020 for commercial cultivation in Tamil
Nadu (Hemaprabha et al. 2019). The average sucrose % in Co 11015 at 240 DAP
was 17.2 which was 13.96% higher than that of the standard Co 86032 (15.09%
sucrose at 240 days after planting). Within a span of 2 years from its release, this
variety spread over 9500 ha in Tamil Nadu in the 2020–2021 crop season.

9.11.4 High Biomass, Bioethanol and Bioenergy

With the growing need for alternative sources of energy other than the currently
predominant petroleum matrix, there has been resurgence in interest in biomass
crops as a renewable energy source. Sugarcane is being viewed as an important
bioenergy crop and source of low cost raw material for the production of bioethanol
and bagasse-based electricity. The survival and profitability of sugar industry in the
future would rely on how far and fast they switch to diversification from the
monotonous sugar manufacturing. Sugar industries in Brazil, Columbia, Thailand
and India have already built cogeneration plants to generate electricity from bagasse
and distilleries to distill ethanol from molasses and/or raw sugarcane juice.
Redefining breeding objectives and utilization of new genetic stocks with high
biomass, total sugars and fibre content in breeding programmes in Brazil and India
are discernible but in slow phase. A few clones in Saccharum, Erianthus and
Miscanthus germplasm collections and in the prebreeding materials with high
biomass yield have been reported in India, Brazil, Puerto Rico, Texas and Japan
(Matsuoka et al. 2014). The recently made sugarcane  S. spontaneum and sugar-
cane  Erianthus arundinaceus crosses in India are focused to evolve Type I and II
energy canes. Energy cane is distinct from normal sugarcane in that it is selected for
total biomass and fibre production rather than for sucrose.
Type I energy canes are the sugarcane hybrids with relatively low sucrose (>15%
brix) but moderate-to-high fibre content (<25%). They are the dual-purpose
canes, its juice can be used in distilleries for direct fermentation and fibre for
cogeneration. Type II energy canes are specifically bred for high biomass yield
with high fibre (>25%) and low brix (<15%) and are exclusively used for energy
generation and lignocellulosic-based second-generation ethanol production
(Alexander 1985; Matsuoka et al. 2014; https://sugarcane.icar.gov.in). In the breed-
ing programmes at Coimbatore, Louisiana, Barbados, Mauritius, Vignis (Brazil) and
528 B. Ram et al.

Puerto Rico, identification of Type I and Type II energy canes were reported (Tew
and Cobil 2008). Govindaraj (2017, 2020) developed fibre-rich, high biomass
yielding dual-purpose energy canes (<20% fibre and 15% juice brix) such as
SBIEC 11001, SBIEC 11002, etc. from the cross between commercial sugarcane
varieties  S. spontaneum/Erianthus. SBIEC 11002 (Co 1148  S. spontaneum SES
404) was registered with ICAR-NBPGR for high harvestable biomass yield
(247.53 tonnes/ha/year), dry matter production (85.23 tonnes/ha) and fibre content
(22.58%) (Govindraj and Suganya 2012).
Molasses is the main source for ethanol production. Ethanol yielding ability of
sugarcane varieties depends on stalk yield and juice sugar content. To understand the
genetic variability for ethanol production, a study was undertaken in a set of
commercial varieties at ICAR-SBI, Coimbatore, during 1992. Wide variation was
observed for total sugars, fermentable sugars and alcohol yield. Total sugars ranged
from 16.4% (Co 1158 and Co 1305) to 22.2% (Co 8153). In general, varieties with
high total sugars also recorded high fermentable sugars with a significant positive
correlation (r ¼ 0.974). The highest alcohol yield of 13,619 L/ha was recorded in Co
8145, and the lowest alcohol yield of 5579 L/ha was recorded in Co 1305. A high
positive correlation between cane yield and alcohol yield was also observed
(r ¼ 0.890). Hence, a variety meant for ethanol production should have high total
sugars, cane yield and extraction percent (Rakkiyappan and Pandiyan 1992). Under
the subtropical condition of India, the estimated alcohol yield (L/tonne of cane)
ranged between 59.08 and 71.66 in plant crop and between 63.49 and 70.44 in ratoon
crop. The variety CoJ 88 recorded the highest alcohol yield 4791 L/ha in comparison
to 3071 L/ha in Co 1148 (Uppal et al. 2006).
The species Erianthus arundinaceus (Rez.) Jeswiet shows considerable potential
as breeding material due to its high biomass yield, high tillering, high fibre, better
ratooning ability, multiple pest resistance, drought and waterlogging resistance and
low nutrient requirement (Jackson and Henry 2011). In India, clones of Erianthus
arundinaceus were evaluated with view to using them as raw materials in paper and
cogeneration industries (Amalraj et al. 2008). Since 1928, hybrids between sugar-
cane  Erianthus spp. were reported (Rumke 1934; Janaki-Ammal 1941; Rao et al.
1963; Sreenivasan and Sreenivasan 2000; Aitken et al. 2006; Piperidis et al. 2000;
Nair et al. 2017; Babil et al. 2019). Shanmughasundaram et al. (2010) reported high
stalk yield in Saccharum  E. arundinaceus hybrids over the parents. The juice brix
in the hybrids was in the range of 14.00–16.30%, which is relatively high for hybrids
involving the wild species.
Miscanthus is a C4 perennial grass with strong, thick, long stem and high biomass
yield hence viewed as potential source of high cellulosic biomass and high degree
of chilling tolerance in temperate environment (Beale et al. 1996; Long and
Spence 2013). Two species, i.e. M. sacchariflorus and M. sinensis, are considered
superior source to S. spontaneum for improving chilling tolerance of commercial
sugarcane varieties and energy canes. The intergeneric hybrids between sugar-
cane  Miscanthus are often termed ‘Miscanes’ (Kar et al. 2019). Miscanes have
been studied since the late 1940s for their biomass production and adaptive traits
9 Sugarcane Breeding 529

especially under subtropical and temperate regions (Burner et al. 2015). Natural
hybrids between Saccharum and Mischanthus were reported by Price (1965).
Each tonne of sugarcane processed by a sugar mill generates approximately
270–280 kg of bagasse which has a net calorific value of 7300 kJ/kg. Bagasse has
been used as fuel in boilers to generate electricity (called cogen unit) that inturn is
used to run sugar industries. The excess electricity produced in sugar mills is sold to
the electricity grid. In 2016, Brazil produced 666 million tonnes of sugarcane and in
the same year produced 35,236 GWh of electricity from bagasse. In India, the
installed cogeneration capacity is estimated to be around 34 TWh, i.e. about
5575 MW in terms of the plant capacity (Mane 2016). The lignocellulosic biomass
yield (dry matter including bagasse) of sugarcane is 22.9 tonnes/ha/year (Van Der
Weijde et al. 2013). The bioethanol yield from bagasse is estimated at about 3000 L/
ha in a total yield of 9950 L/ha from sugar and bagasse (Somerville et al. 2010). The
ethanol output to input ratio is high from sugarcane bagasse (8–10) compared with
maize (1.6) (Lam et al. 2009; Waclawovsky et al. 2010; Loureiro et al. 2011). The
available lignocellulosic biomass from sugarcane worldwide is estimated at 584 mil-
lion dry tonnes/year. Bagasse has huge potential to yield bioethanol (Hoang et al.
2015) hence, it has been increasingly exploited as raw material for production
second-generation biofuel (ethanol). Future breeding programmes in leading
sugar-producing countries would focus on evolving high bioenergy and high biofuel
yielding sugarcane varieties.

9.11.5 Biotic and Abiotic Stresses

Biotic and abiotic factors have been the main limiting factors of crop productivity. In
the recent years, increasing concentration of greenhouse gases and increase in global
surface air temperatures caused through climate change create new environmental
conditions which may result in increased crop failure and frequent incidences of
abiotic and biotic stresses. Long growth cycle of sugarcane crop, for 10–12 months
and more, exposes it to several abiotic and biotic stresses, which get prolonged and
intensified under changing climatic conditions (Table 9.3). These factors necessitate
incorporation of new and diverse genetic resources into future sugarcane varieties.

9.11.5.1 Drought/Salinity/Waterlogging
Among the abiotic stresses, drought is the most serious threat throughout the world.
Drought coupled with waterlogging, i.e. early drought and subsequent waterlogging
in Bihar, Eastern Uttar Pradesh (UP) and Odisha, is a serious productivity constraint
affecting more than 50% of area under the crop. Waterlogging is experienced in
Tarai region in UP, Bihar and Kolhapur region in Maharashtra. Sugarcane is
basically a drought-tolerant species. However increasing intensities and duration
of water deficit stress not only cause yield reduction between the mean yield and the
potential yield but also cause yield instability. Recent occurrence of drought has
necessitated the need to evolve drought-tolerant varieties to sustain sugarcane
cultivation. In sugarcane, the formative phase (60–150 days after planting) was
530 B. Ram et al.

Table 9.3 Major biotic and abiotic factors to sugarcane productivity in different agroclimatic
zones of India
East North North North
Zone Peninsular coast central west east
A. Biotic factors
1. Diseases
(a) Red rot ✓ ✓ ✓ ✓ ✓
(b) Smut ✓ ✓ ✓ ✓ ✓
(c) Wilt
2. Pests
(a) Borers ✓ ✓ ✓ ✓ ✓
(b) Whit grub ✓ ✓ ✓ ✓
(c) SWWA ✓ ✓
B. Abiotic factors
1. Drought ✓ ✓ ✓ ✓ ✓
2. Waterlogging ✓ ✓ ✓ ✓
3. Salinity and Alkalinity ✓ ✓ ✓
4. High temperature with water ✓ ✓
stress
5. Cold ✓
✓, indicates presence of pest, diseases and environmental stress in the region

identified as the critical water demand period, and any amount of water stress at this
early growth phase had a direct influence on growth, dry matter accumulation, cane
yield and juice quality. Hence screening for drought tolerance is carried out by
withdrawing irrigation during the critical water demanding period. Number of
millable canes, cane height, juice extraction % and sucrose % in juice are the most
dominant parameters for yield build-up under stress, and these traits are used for
identifying resistant varieties. Development of stress-tolerant genotypes is the most
common approach in enhancing drought stress tolerance in sugarcane. A large
number of elite clones of commercial status having drought tolerance have been
identified through screening under natural drought conditions in addition to potential
parents for breeding for drought tolerance (Hemaprabha et al. 2006). Cane yield has
invariably remained the core selection index along with total sugar productivity
under drought conditions. The selection efficiency for development of drought
tolerant cultivars can be further improved by using a particular physiological
and/or morphological trait related to yield as selection criteria (Clarke and
Townley-Smith 1984). Almost all the clones of wild species S. spontaneum and
some clones of S. barberi such as Hemja, Khari, Katha and Ikhri provide drought
tolerance. Similarly, related genera such as Erianthus spp. (especially
E. arundinaceus) and Narenga spp. have inherent capability towards drought toler-
ance (Sreenivasan et al. 2001).
Efforts to introgress E. arundinaceus, which has wide distribution in India,
China, Myanmar, Thailand, the Philippines, Japan and Malaysia, into the sugarcane
varieties were challenging due to hybrid sterility, difficulty in identifying the
9 Sugarcane Breeding 531

true hybrids using the morphological traits, chromosome elimination during

the successive back crossing and lack of recombination between the chromosomes
of the two genera (D’Hont et al. 1996). In such cases, bridge crosses were found to
be effective. S. spontaneum was used as a bridge cross, and
S. spontaneum  E. arundinaceus hybrid when crossed with sugarcane resulted in
fertile hybrids which could be further backcrossed to sugarcane (Lalitha and
Premachandran 2007). Apart from sturdiness and yield improvement, hybridization
of Erianthus with sugarcane resulted in introgression of genes for cold tolerance and
red rot resistance (Ram et al. 2001c). Another major source is E. procerus (2n ¼ 40),
which is distributed mostly in India, Burma, Indochina, China, Indonesia and New
Guinea. Attempts were made to introgress desirable traits of E. procerus in sugar-
cane and diversify the genetic base. The BC1 hybrids showed substantial improve-
ment over F1 in terms of cane and juice quality traits (Nair et al. 2017). These
intergeneric hybrids could be the potential source for diversifying the genetic base of
sugarcane and combining resistance to drought and red rot. Characterization of
intergeneric hybrids of Erianthus rockii and Saccharum as well as estimation of
hybrid diversity were made possible with 400 amplified fragment length
polymorphisms (AFLP) markers (Aitken et al. 2006).
Lack cytoplasmic diversity can turn out to be a major limitation in the future
though we still are in the dark as to whether the cytoplasm from related wild species
may be able to provide more plasticity apart from higher yields and more stable
disease resistance (Mangelsdorf 1983). Premachandran et al. (2011) reported suc-
cessful development of new cytoplasm substitution lines in sugarcane with the
cytoplasm from S. spontaneum and E. arundinaceus. Apart from several genetically
diverse intergeneric hybrid derivatives both for nuclear and cytoplasmic genomes
under CYM series, two commercial varieties, Co 15015 and Co 16018, were
developed at ICAR-SBI with proven hybridity and novel cytoplasm. Co 15015,
which is a third-generation hybrid with 2n ¼ 106, revealed two E. arundinaceus
chromosomes through GISH (Lekshmi et al. 2017). Development of multiparent
advanced generation intercross (MAGIC) population in sugarcane is in progress at
ICAR SBI by using the best pre-bred clones which are highly diverse and derivatives
of different basic species of Saccharum and Erianthus (S. officinarum, S. robustum,
S. spontaneum, S. barberi/S. sinense and E. arundinaceus, E. bengalense,
E. procerus). Once developed, these hybrids with a mosaic of different genomes
would be the valuable novel and diverse genetic resources for genetic enhancement
for biotic and abiotic stresses apart from serving as a panel for mapping key traits
(Mohanraj et al. 2017).
Salinity and alkalinity stresses are experienced in India in about one-fourth of the
area under sugarcane. It is caused by the chlorides and sulphates of sodium, calcium,
magnesium and potassium. The electrical conductivity of these soils is more than
4 dS/m, while alkalinity is imparted mainly by sodium carbonate. High osmotic
pressure of the soil water restricts absorption of water and nutrients in adequate
quantities. Sugarcane is ranked moderately susceptible to salinity with a threshold
value of 1.4 dS/m (Maas 1986). The symptoms of salt damage are pale green or
yellow leaves, scorched tips and margins, reduced leaf area and stunted canopy. In
532 B. Ram et al.

addition to reduction in cane yield characters, sucrose content has also showed
reduction with increased accumulation of Na, K and Cl ions. Salt-resistant varieties
showed marginal accumulation of Na and hence lesser reduction. Though there is no
directed breeding for salinity tolerance programme at ICAR- Sugarcane Breeding
Institute, screening of elite selections at the AICRP(S) programmes has identified
several salinity-tolerant clones.
Waterlogging stress is caused by the deficiency of oxygen (required for root
respiration) following the replacement of air in the soil with water. Though sugar-
cane can tolerate long period of waterlogging, juice quality is drastically affected.
Reduced stalk elongation, formation of aerial roots, drying of lower leaves and
yellowing of younger leaves, shoot mortality and profuse flowering are the effects
associated with waterlogging stress. Cane yield loss occurs due to high tiller or stalk
mortality, reduced crop growth due to lack of nutrition and water uptake, lodging,
cane breakage, etc. Saccharum species clones and hybrids shows differential
response to waterlogging (Sreenivasan and Batcha 1963). About 15–20% yield
reduction, in certain cases up to 70%, was reported due to waterlogging (Gosal
et al. 2009; Singh et al. 2016; Swami et al. 2018).
Reduction in cane yield @ 0.5 t/ha for every day the water-table stagnating upto
50 cm of the soil surface was reported from Australia (Salter et al. 2018). Many
clones of S. spontaneum, S. robustum, E. arundinaceus and Narenga are flood
tolerant. Indian hybrids Co 513, Co 805, Co 815, Co 900, Co 958, Co 1290, Co
62100, Co 62136 and Co 62197 and foreign hybrids B 54-142, CB 40-13, CP 49-50,
CP 63-361, H 63-361, H 50-7209, H 52-3689, H 53-263 and Q 61 were reported to
be tolerant to waterlogging. The clones of S. spontaneum and E. arundinaceus and
Co 513, Co 785, Co 805, Co 62100, Co 62136, Co 8231, B 54142, CB 4013, Co
99006 and Q232A were suggested as better sources for waterlogging resistance.
Breeding for waterlogging is a continuous activity at the Kannur Centre of ICAR-
SBI, where waterlogging is a perennial problem. Anakapalle, Kolhapur, Pusa and
Thirvalla are other centres from where waterlogging-tolerant clones are emerging.

9.11.5.2 Cold/Frost/Winter Ratooning Ability

Sugarcane is a cold-sensitive plant (Tai and Lentini 1998). Sugarcane grown in
subtropical states of India, Northern China and Louisiana suffer from extreme cold,
and sprouting of stubbles is a major limiting factor. Chilling (low temperatures
above 0  C) and freezing (temperatures below 0  C inducing extracellular ice
formation) also limit the geographical distribution and growing season of sugarcane
and cause significant crop losses (Xin and Browse 2000). In 1932, the ICAR, New
Delhi has established a Regional Centre (of ICAR-SBI) at Karnal, Haryana, to
evolve sugarcane varieties suitable for the subtropical climate of North India (now
crop improvement work is restricted to the north-west zone of India). A good deal of
work was done at this institute. The breeding and selection programme at ICAR-SBI,
Regional Centre, Karnal, was modified to fit for selecting high sugared genotype
combined with better winter ratoonability. The seedlings raised from fluffs are
9 Sugarcane Breeding 533

ratooned during the last week of December to the first week of January, coinciding
with peak winter. Selection is made in seedling ratoon nursery instead of seedling
nursery. The time of selection in seedling ratoon is shifted from February to March to
October, and traits like NMC, stalk diameter, stalk height and HR Brix are used as
selection criteria (Ram and Sahi 2007). Varieties like Co 98014, Co 0118, Co 0237,
Co 0238, Co 05009, Co 05011, Co 06034, Co 09022, Co 12029, Co 13035 and Co
15023 are the outcome of modified breeding programme.
To assess winter ratooning potential of sugarcane clones, Ram et al. (2017)
proposed an index called ‘winter sprouting index’. Significant and positive correla-
tion between winter sprouting index (WSI) and tillers in plant crop (r ¼ 0.45) and
ratoon (r ¼ 0.41), WSI vs. number of millable canes in plant crop (r ¼ 0.37) and
ratoon (r ¼ 0.42), was reported. On the basis of WSI, sugarcane genotypes were
classified into four categories, namely, excellent winter sprouting (WSI > 3.0), good
sprouting (WSI ¼ 2.01–2.99), poor sprouting (0.10–2.00) and low-temperature-
sensitive (LTS) clones (WSI < 0.10). Ram et al. (2017) screened 632 genetically
diverse sugarcane germplasm during 2009 to 2015 for winter sprouting. Fourty
three clones were reported as excellent winter sprouters (winter sprouting index
>3.00). They were: Co canes such as Co 06035, Co 12026 and Co 12027; commer-
cial varieties such as CoP 9302, CoPant 96219, CoS 02264, CoS 109, CoS 797, CoS
94270, CoS 95222, CoS 97258, CoS 97264 and CoSe 95422; exotic genotypes such
as BO 348, BM 368, B 33-65, BM 555, BM 61/1, CP 11-61, F 133, L 62-37, LF
64-2815, LF 65-3661, Mali, PR 1013, SP 80-1816 and TUC 472; and ISH and IGH
clones derived from crosses involving S. spontaneum, S. barberi and Erianthus as
one of the parents such as 20-200, 97-12, 99-304, 99-316, 99-356, 99-488, CYM
06-935, CYM 06-1144, CYM 07-284, GU 07-1841, GU 07-3704, GU 07-3730, GU
07-3774, KGS 99-1109, KGS 2004-72 and KGS 2004-20. Utilization of these
clones in breeding programmes is suggested to concentrate genes for winter
ratoonabilty in sugarcane varieties suitable for growing in subtropical region.

9.11.6 Biotic Stresses

Sugarcane diseases are constraints to crop production all over the world, and more
than 125 diseases caused by fungi, bacteria, viruses, cytoplasma, etc. have been
reported (Rott et al. 2000). The major diseases of sugarcane in India are red rot, smut,
wilt, ratoon stunting disease, grassy shoot disease, mosaic, yellow leaf disease and
pineapple disease.

9.11.6.1 Red Rot

Red rot caused by Colletotrichum falcatum Went is one of the major biotic factors
limiting cane yield and quality (Chona 1980) both in the tropical and subtropical
region of India. Barber in 1901 made the first recorded report of red rot occurrence in
India. Since then a number of red rot epidemics have been reported, especially in
eastern Uttar Pradesh, northern Bihar and pockets of Punjab, Haryana and Coastal
Andhra Pradesh. The infected stalks become unfit for milling due to inversion of
534 B. Ram et al.

sugar to reducing sugars. The stem becomes red and forms hollow cavity, and the
canes perish completely causing heavy losses. The disease is primarily transmitted
through infected setts.
The best and the most effective way of managing red rot epidemic is through
growing resistant varieties. Resistance sources were identified in genotypes of
Saccharum officinarum, S. barberi, S. sinense, S. robustum and S. spontaneum as
well as related genera such as Erianthus, Sclerostachya, etc. Several clones of
S. spontaneum are highly resistant to red rot and constitute suitable donors of red
rot resistance. Biparental crossing, wherein one parent is red rot resistant, has been
generally adopted for development of clones with disease resistance. Two popular
methods of screening sugarcane clones to assess red rot resistance are plug and nodal
methods of inoculation. In the plug method, the clones are inoculated with the
pathogen culture when the crop is about 8 months old. The reaction of the clones
is classified into resistant (R), moderately resistant (MR), moderately susceptible
(MS), susceptible (S) and highly susceptible (HS) to red rot based on a 0–9 scale.
The resistance assessed by this method is referred to as protoplasmic resistance or
physiological resistance. In the nodal method of disease evaluation, the pathogen
inoculum is applied at the nodal region between the stalk and leaf sheath.
To overcome environment-induced variability in red rot disease reaction and to
rapidly screen a large number of sugarcane clones for red rot, a controlled condition
testing (CCT) was developed at ICAR-SBI. In this method, the pathogen is applied
by nodal swabbing in the cane tops of 6- to 8-month-old cane and kept in a
temperature- and humidity-controlled chamber. A new 0–9 scale was developed to
assess disease resistance as R, MR, MS, S and HS in the clones. The CCT method
has been aiding in screening a large number of selections emanating from breeding
experiments. Clones selected from the first and second clonal nurseries, pre-release
clones in Zonal Varietal Trials, are regularly screened against new isolates of
C. falcatum. As a policy matter, clones showing MR or R reaction to red rot alone
are approved for release in India.

9.11.6.2 Smut
This disease is of cosmopolitan distribution (particularly India, Pakistan, Brazil and
Australia) and is caused by the fungus Sporisorium scitamineum (Syd.), and the
fungus has no alternate host. Disease-affected clumps show profuse tillering with
occasional formation of whips. The disease is favoured by hot dry conditions.
Similar to red rot, smut disease severity also increases with increase in the levels
of sett-borne inoculum. Breeding for smut resistance yielded many disease-resistant
varieties. The resistance to smut appeared to be favoured by two dominant genes
(S1 and S2), whose action was greatly modified by inhibitor and anti-inhibitor genes.
Sources of resistance for sugarcane smut have been identified in S. spontaneum and
S. officinarum clones. To screen sugarcane clones for smut resistance, artificial
inoculation of the pathogen is being done in the field. The screening procedure
consists of dipping the seed setts in heavy spore suspension of smut fungus and
9 Sugarcane Breeding 535

planting in the field. Periodical observations of smut incidence is recorded, and on

the basis of cumulative final percentage of disease incidence, varieties are graded
as R, MR, MS, S and HS. A simple technique was developed to inoculate sugarcane
setts using dikaryotic cultures. Smut pathogen colonization was assessed by trypan
blue staining. This method ensures rapid screening for smut disease, and diseases
escapes can be minimized.

9.11.6.3 Wilt
Wilt is common in locations where conducive environment and susceptible hosts are
available (Viswanathan 2013). Fusarium sacchari (E.J. Butler) is the causative
fungus. Abiotic factors like drought predisposes the plant for wilt infection. Wilt
incidence is higher in ratoon crops and leads to reduction in yield and juice
extraction.

9.11.6.4 Sugarcane Pests

About a dozen of insect and non-insect pests are recorded in sugarcane crop in India.
Borers and sucking pests are the major aerial pests, whereas termites and white grubs
are subterranean in nature. Among borers, early shoot borer is the key pest through-
out the country. Internode borer is prevalent in southern states and stalk borer, top
borer and root borer in subtropical states. Sugarcane white woolly aphid (SWWA)
appeared in an epidemic form in Maharashtra and Karnataka in 2002. Scale insects,
mealy bugs, mites, rodents and wild boar are other pests of sugarcane. The first
potential source of resistance to be examined is the commonly grown and adapted
varieties in the area where the experiments are being conducted. If resistance can be
found among such varieties, the problem of breeding a satisfactory variety is greatly
simplified.

9.12 Other Objectives

During 1918, a sugarcane station was established at Canal Point, Florida, with the
objective of breeding for mosaic resistance varieties in Louisiana. One of the best
varieties released for Louisiana was CP44-101 which occupied the State for a long
period of time. Sereh disease was a major threat to sugarcane cultivation in Java and
Fiji during the early 1900s, and it was addressed through breeding. Rust in Brazil
and yellow leaf syndrome in Australia are considered important biotic stresses
limiting cane yield. They are the objectives of sugarcane improvement in those
countries. Nowadays, mechanization in sugarcane harvest is picking up fast, and to
make it suitable for machine harvest, sugarcane is to be planted at a minimum row
spacing of 4 ft. So far, selection of varieties in countries like India, Pakistan, China,
Thailand and Indonesia has been practised for 3-ft row spacing. In the future,
sugarcane breeders may have to include varieties suitable for mechanical harvest
536 B. Ram et al.

as one of the breeding objectives besides yield, quality and resistance to biotic and
abiotic stresses.

9.13 Exploitation of Heterosis and Hybrid Development

Sugarcane parental pool is highly polyploid (octaploid) and heterogeneous. Crosses

are made between two diverse parents with desired complementary traits. In general,
one parent is the cultivar, whereas the other one is a resistant source of major disease
of the zone. The progenies segregate in the first generation itself, and hence desired
clones are selected for further evaluation in subsequent clonal selection stages. Being
an asexually propagated crop, the variability is fixed in the first generation itself.
A number of quantitative inheritance studies have been conducted on sugarcane
using various statistical designs (Hogarth 1971, 1977; Hogarth et al. 1981; Miller
1977; Yang and Chu 1962). The higher yields in F1 may be partially due to additive
or non-additive gene actions, or both. Hogarth (1977) reported non-additive variance
for sugar content, which was equal to additive genetic variance for stalk yield. Miller
(1977) and Yang and Chu (1962) reported importance of non-additive effects for
both sugar content and stalk yield. Rai et al. (1991) reported that the degree of
dominance was in the range of over-dominance for NMS, stalk length, stalk diameter
and stalk density. The proportion of additive genetic variance in relation to domi-
nance variance was above 1.5 for NMS and near unity for stalk diameter and stalk
length, whereas dominance variance was predominant for sugar yield, stalk yield,
commercial cane sugar % (CCS%), sucrose %, Brix %, juice extraction % and single
stalk weight (SSW) (Ram and Hemaprabha 2000). Ram et al. (2005) reported equal
importance of additive and non-additive genetic variance for disease index of red rot.
A study on 15 crosses indicated variation in heterosis for different crosses as well as
for ten traits studied (Ram and Hemaprabha 2000). The authors reported positive
heterosis over midparent value and over nobilized first generation (N1) for stalk and
sugar yields in 12 mating groups, whereas for sucrose %, positive heterosis was
observed in (OB)H, (OR)H and (OS)O mating groups only (where O is
S. officinarum; B is S. barberi; H is commercial hybrids; R is S. robustum; S is
S. spontaneum).
In order to meet the future demands from the presently available area, there is
need to exploit the dominance variance/heterosis to the maximum possible level.
Research on developing hybrid varieties and propagation through true seed through
developing homozygous lines was initiated at ICAR-SBI during 2015. The success
of the programme will lead to paradigm shift to sugarcane agriculture. By adopting
the seedling transplanting method in combination with true seed hybrids, it would be
possible to change the mode of transportation of sugarcane-seed from truck to pocket
(ICAR-SBI 2050).
9 Sugarcane Breeding 537

9.14 Breeding Approaches

9.14.1 Conventional

The varietal development process in India, spanning over a century, has brought in
refinements to the entire process of hybridization and selection and improved
precision of sugarcane breeding. The major steps and significant findings which
facilitated accelerated varietal development are mentioned below.

9.14.2 Hybridization

In India, hybridization is carried out coinciding with flowering during the months of
October–December. The National Hybridization Garden accommodates about
600 parents and regularly adds new parents to maximize geographical and genetic
diversity and elimination of poor parents based on progeny performance. Similarly,
an arrowing plot with about 300 parents of broad genetic base is utilized by the
ICAR-SBI breeders for specific breeding programmes, such as resistance breeding,
quality improvement, development of short-duration clones and breeding for abiotic
stresses especially drought. On an average, about 1000 crosses are made in both
parental gardens.
The common hybridization methods adopted are biparental crossing (50–60%),
polycrosses (1–5%) and open pollination (30–50%). However, breeders concentrate
mostly on biparental crossing through careful choice of two parents guided by their
per se performance, complementarity of characters, specific combining ability and
genetic diversity measured based on pedigree, biometry or molecular methods. In
contrast, polycrosses and open pollination are based on general combining ability.
The merit of biparental crossing was evident from the pedigree analysis of Co canes
developed over a century (1918–2017). Out of 1454 Co canes produced during this
period, and maintained in the variety garden, 1241 (85.4%) were bred through
biparental mating, while 81 (5.6%) were from open pollination and 31 (2.1%)
from polycrosses, in addition to a few somaclones, mutants and selfs.
The large proportion of Co canes from biparental mating gives ample evidence of
the importance of specific combining ability as well as genetic diversity of the
parental combinations in choosing parents (Hemaprabha et al. 2019). Several bipa-
rental crosses with greater progeny performance index have been designated as
proven crosses for raising large populations over 1000 seedlings per cross. These
proven crosses facilitate adoption of family selection. Ethirajan in 1987 explained
the concept of zonal crosses as a rational approach in the selection of parents.
Accordingly, promising varieties identified from AICRP(S) trials of a zone are
chosen as parents and crossed with genotypes with established excellence for a
target trait. The fluffs from such crosses are distributed to all centres for further
selection under respective location-specific conditions in the zone.
538 B. Ram et al.

9.14.3 Selection

In total, over 200,000 seedlings are raised in ground nurseries in the country every
year. The selection starts with screening in the ground nursery. Though the practice
varies across the research centres, selection of seedlings in the ratoon crop has been
found to be beneficial for selecting the best progeny. However, wide disparity in the
performance of progeny at single stool seedling stage and subsequent clonal stages
has been noticed, as evidenced by non-uniformity of correlation estimates for
economic characters over locations and years. Ram et al. (1997) concluded that
selection in seedlings and seedling ratoon nurseries was not effective because of low
inter-stage correlations, non-significant regression coefficients and the number of
significantly superior clones common at selection and evaluation stages. Consider-
ing both the effectiveness of selection methods and the costs involved, visual
selection for superior seedlings based on the number of millable canes per plant,
thickness of stalks, stalk height and HR Brix seems to be the best over the methods of
selection through stalk yield and brix yield which are labour intensive, time-
consuming and hence costly (Ram et al. 1997). However, realizing the importance
of ratoonability trait in sugarcane, selection in seedling ratoon nursery has been
adopted since 1998 at ICAR-SBI, Regional Centre, Karnal (subtropical India) and
since 2016 at ICAR-SBI, Coimbatore (tropical India). Realizing the success of
varieties evolved at Regional Centre, Karnal, a few State Sugarcane Research
Stations also started following selection in seedling ratoon nursery stage.

9.14.3.1 Sample Size and Selection Criteria

Bhagyalakshmi and Ethirajan (1987) reported that a sample size of 40–50 seedlings
was minimum for estimating family means for stalk diameter, stalk length, internode
number, internode length and hand refractometer Brix (HR Brix), whereas samples
of more than 100 were needed for yield, stalk number and single cane weight.
Studies on time of selection in subtropical India indicated that HR Brix of
sugarcane clones recorded during August (7–8 months crop age) gives a good
indication of HR Brix during October (9–10 moths). However, pol % in juice during
January (12 months) was not correlated with HR Brix during August, but it was
associated with HR Brix during October. The rate of sugar accumulation varied
among sugarcane clones from August to January. The earliest possible period to
classify sugarcane clones on the basis of HR Brix, as low-, medium- and high-
quality types, is during October. However, if selection is delayed to beyond
12 months’ crop age (spring season), selection based on pol % was effective as
differences among clones for HR Brix narrowed down.
Genotypic and phenotypic coefficients of variation along with heritability and
genetic advance of all yield and quality characters have been studied extensively to
identify suitable selection criteria. Based on experiments conducted under water
stress, waterlogging, salinity and normal conditions, Ram et al. (2001a) identified
number of millable stalks (NMS) as the most effective selection criterion for
selecting better ratooning and high sugar yielding clones as this character recorded
the highest genotypic coefficient of variation (GCV), heritability, expected genetic
9 Sugarcane Breeding 539

advance, higher correlations and direct effects with sugar yield, higher inter-
environmental correlations and relative response values near unity. Ram (2007)
reported that selection for juice quality traits would be easier if selection was
practised at an early stage of crop age as higher GCV, heritability and genetic
advance values were observed at 8 months of crop age (October). Improvement in
sugar yield will also be faster if sugarcane clones are selected for stalk yield traits,
namely, NMS, single stalk weight and stalk diameter, in comparison to selection for
juice quality traits.
The maximum gains from selection may be achieved by selection based on
several traits simultaneously than selection based on single trait. The extent of
change in a character due to index based selection will depend upon the heritability,
the economic weightage assigned and the magnitude and nature of genetic correla-
tion with other traits. In practice, selection indices are not widely used in sugarcane,
although they provide the most effective selection method. Selection indices are
often inefficient when costs as well as results are considered. There are a few reports
on selection indices for selection at clonal stages in sugarcane. Miller (1977)
constructed various selection indices for each of the four populations of sugarcane.
They reported 89% genetic advance in stalk yield and 92.2% in metric tonnes per
hectare of sucrose. Another selection index based on internode length, Brix %, purity
%, CCS % and sucrose % gave 43.54% expected genetic gain in sucrose content.
Kang et al. (1983) calculated indices for tonnes per hectare of stalk and tonnes per
hectare of sugar from ratoon crop data and correlated with actual performance in the
final selection stage and reported low but significant correlation coefficients. Selec-
tion based on index can lead to selection efficiency in succeeding clonal stages.
When specific and general indices were applied in different open pollinated
populations, it was found that specific selection indices were most effective only
in their own source population (Ram et al. 1997). General selection index, when
used in different populations, was better in terms of mean of selected clones and
number of clones significantly superior to the best check, in comparison with
specific indices.

9.14.4 Recurrent Selection

Recurrent selection programmes for improving yield and quality separately or

simultaneously have been practised. Initial efforts substantially improved cane
yield through improving cane diameter and single cane weight (Balasundaram
2002). These were consistent with the results of Bressiani et al. (2006), who reported
gains through recurrent selection that were continuous and progressive with increase
in the frequency of desirable genes for the target trait. In order to generate genetic
stocks for high sucrose content, a simple recurrent selection scheme was employed
with a base population of 25 Co canes and 12 foreign hybrids with juice sucrose of
19.0% at 12 months. After two cycles of selection, the progress made for sucrose
content in comparison with the base population was significant with cycle II
progenies recording an average juice sucrose of 22.8% which was a 13.40%
540 B. Ram et al.

improvement over the base population (Shanthi and Alarmelu 2012). Another
recurrent selection programme for simultaneously improving both cane yield and
juice quality resulted in identifying several elite clones after three cycles of selection
while maintaining sufficient genetic variability in cycle 1 and cycle 2 for selection in
cycle 3 (Alarmelu et al. 2015).
Intraspecific improvement of major Saccharum species prior to interspecific
hybridization had been suggested to achieve faster gains in interspecific
hybridization (Walker 1987). Attempts were made during the 1980s at ICAR-SBI
to develop improved populations of S. officinarum and S. robustum through repeated
cycles of intraspecific hybridization and selection (Nair et al. 1998). In S. robustum,
significant improvement in brix% (20.53%) and sucrose% (26.24%) was achieved
after three cycles of selection and in S. officinarum, improvement in NMC/ha
(37.18%), single cane weight (16.67%) and cane yield (61.51%) was achieved in
two cycles of selection (Karuppaiyan et al. 2020a, b).

9.15 Specific Breeding and Research Programmes

In addition to the main mandate of developing high sugar high yielding disease
resistant varieties for the country, specific time-bound programmes are conducted to
develop short-duration varieties suitable for harvesting from 8 months onwards, use
of foreign commercial varieties in breeding, recurrent selection programmes, trait-
specific breeding programmes for high sucrose, red rot resistance, drought tolerance,
pests including top borer tolerance, varieties suited for ethanol, paper and biomass
production, deployment of advanced pre-bred material derived from diverse germ-
plasm with respect to nuclear and cytoplasmic genomes, molecular diversity-based
selection of parents in breeding programmes for sucrose, red rot, water stress and
salinity, improving selection efficiency, crossing techniques, stability analysis. Test-
ing of new statistical methods and experimental designs has contributed to improved
methods for breeding and selecting new varieties. Specific investigations in breeding
and biotechnology are in progress to develop homozygous lines (Annadurai and
Hemaprabha 2016) for true seed production in sugarcane that could revolutionize
sugarcane planting through substantial reduction in seed, which is about 6 tonnes of
canes to about 32 g for planting a hectare (ICAR-SBI 2015).

9.16 Breeding for Disease Resistance

Disease resistance breeding has been an integral part of sugarcane improvement. In

India, the most important diseases requiring varietal resistance are red rot caused by
Colletotrichum falcatum and smut caused by Sporisorium scitamineum. Red rot has
wiped off many popular varieties out of cultivation both in the subtropical and
tropical regions. The first report of red rot in India was by Barber in 1901 from
Godavari Delta in Andhra Pradesh and later in 1906 by Butler from West
Champaran in Bihar (Alexander 1989). The best way to manage the disease is to
9 Sugarcane Breeding 541

develop resistant varieties, and all new releases must be resistant to red rot. Study of
large numbers of progenies involving resistant and susceptible parents established
Mendelian segregation for red rot resistance (conferring vertical resistance) in many
of the crosses (Ram et al. 2001b). Ram et al. (2005) reported that both additive and
dominant variances were equally important and heritability (in narrow sense) was
0.51 for red rot resistance in sugarcane. A high (0.97) broad sense heritability for red
rot resistance indicates a high level of repeatability across different environments for
red rot disease development in sugarcane. The level of horizontal resistance
decreased with a decrease in the S. spontaneum chromosome complement present
in the material (Natarajan et al. 2001). In general, the proportion of resistant/
moderately resistant (R/MR) progeny is more when both parents are resistant in
comparison to one parent with R/MR reaction. However, a few resistant progenies
were also observed when both parents were susceptible to red rot.

9.17 Precise and High-Throughput Phenotyping Protocols

for Key Traits

Phenotyping is a challenging area of plant breeding and is labour intensive as it

requires manual harvesting and assessing plants for particular criteria or visual
ratings. Breeding programmes worldwide are exploring the possibility of
implementing high-throughput phenotyping as an integral component of variety
selection process. Rapid developments in phenomics technologies could be utilized
to improve early-stage selection in sugarcane breeding programmes. Sugarcane lags
behind in phenomics research. Sugarcane phenotyping for red rot and smut diseases
is carried out under controlled conditions testing facility and field screening, respec-
tively. Phenotyping for salinity is done using microplot facility, while screening for
drought is done at seedling stage using pots and at tillering phase under field
conditions.
An unmanned aerial vehicle (UAV)-based high-throughput phenotyping
approach was tested for capturing valuable phenotypes in early stages of sugarcane
breeding trials for improving clonal selection and assessing the potential new
varieties for different yield and stress-related parameters (Basanayage 2017). The
rapid and dense growing nature of sugarcane can be effectively captured from the air
using drones fitted with a range of cameras and sensors, and integrated software is
expected to enhance this process. The aerial platform required 15–17 min to survey
7 ha of sugarcane crop and to take measurements. This cutting-edge technology is
being used to assess how potential new sugarcane varieties perform through the
growing cycle, with the aim of delivering better varieties sooner for the Australian
sugarcane industry. To add further credit to this technology, two crucial parameters
such as canopy temperature (a proxy for canopy conductance) and crop vigour, if
measured at the right time, could be associated with yield. Based on a single-row
early-stage clonal assessment trial involving 2134 progeny derived from diverse
crosses, and a multi-row experiment with an unrelated population, screening was
done at several stages using visual, multispectral and thermal sensors mounted on a
542 B. Ram et al.

UAV for indirect traits, including canopy cover, canopy height, canopy temperature
and normalised difference vegetation index (NDVI). The results highlighted the
potential of high-throughput phenotyping of indirect traits and developed a selection
index based on indirect traits which are correlated with yield to improve clonal
assessment in early stages of sugarcane breeding (Natarajan et al. 2019).
The application of UAV was also demonstrated on predicting the leaf nitrogen
content and biomass following UAV optical imaging approaches, namely, LiDAR
and surface from motion (SfM) photogrammetry in precision agriculture (Shendryk
et al. 2020), and for monitoring growth response in sugarcane, measured in terms of
height. The study also examined the possible correlation between sugarcane bio-
physical parameters of stalk population, total fresh biomass and cane yield.

9.17.1 Non-conventional Breeding Approaches Including Use

of Genomic Tools

The non-conventional or advanced plant breeding is complementing the conven-

tional breeding in improving the potential of crop plant by inducing gene(s) of
interest in crop plants. Production of interspecific and intergeneric hybrids is useful
for transfer of desirable genes from wild species into cultivated species (Nair et al.
2006, 2017; Pachakkil et al. 2019; Meena et al. 2020). Some varieties developed
through mutagenic approach were also released for commercial cultivation (Jalaja
et al. 2006). In sugarcane suitable explants for in vitro culture and plant regeneration
have already been standardized (Lakshmanan 2006). The callus induction from leaf
whorl independent of genotype is well established in sugarcane. Compared to other
cereal crops, callus induction and plant regeneration are challenging.
Molecular marker technology has been evolving more than a quarter century to
address these issues, and notable among them are the advances in molecular
markers, structural and functional genomics and transgenics. Application of these
approaches in sugarcane improvement is largely in the area of assisting plant
breeding programmes for the evolution of better varieties through selection of
parents for crossing, use as an efficient selection tool in screening progenies and
for characterization of germplasm and introgression of wild germplasm, DNA
fingerprinting, varietal identification and characterizing genes of economic impor-
tance and their selective transfer to the desired genetic background. The comparative
analysis of molecular diversity and agronomic diversity in hybrid populations has
increased the chance of relating markers to agronomic traits. The molecular marker
techniques involving RAPD, AFLP, TRAP, ISSR, STMS, SSCP, SSR, ESTs are
being employed for genetic diversity studies, gene mapping and quantitative trait
loci (QTL) identification, DNA fingerprinting of varieties, functional genomics and
marker-assisted selection and development of transgenics for important agronomic
traits in sugarcane in India.
AFLP profiles of commercial cultivars with that of their progenitor species, viz.
S. officinarum and S. spontaneum, revealed the presence of 78.8% of S. officinarum-
specific DNA fragments and 28.85% of S. spontaneum-specific fragments (Selvi
9 Sugarcane Breeding 543

et al. 2006). Several studies have used different markers to discriminate elite hybrids,
commercial varieties, inbreds, induced mutants and somaclones in micropropagated
plants of sugarcane (Hemaprabha et al. 2006; Sindhu et al. 2011). Using sugarcane
and sorghum microsatellite markers, different combinations of Saccharum complex
hybrids were successfully identified (Selvi et al. 2010). The markers identified have
already been integrated in the breeding programmes as diagnostic tools to identify
intergeneric and interspecific hybrids.
A considerable and remarkable success in genetic transformation was for genetic
improvement for biotic and abiotic stresses (Lakshmanan et al. 2005; Babu et al.
2020). Sugarcane transgenics developed with different genes from various sources
have showed better phenotypic performance under water deficit stress conditions
(Augustine et al. 2015a, b, c; Mohanan et al. 2020; Narayan et al. 2021). Genetically
modified sugarcane has been approved for commercial cultivation in Indonesia and
Brazil, and in other countries, transgenic products are in different stages of field trials
and/or commercialization. These include transgenics with genes conferring resis-
tance to diseases and pests, salt and drought tolerance and high sucrose or herbicide
tolerance (Babu et al. 2020). Sugarcane is also considered as a ‘biofactory’ for the
production of high-value bioactive compounds due to high biomass production
potential (Palaniswamy et al. 2016). Molecular breeding could be used to make
improvement involving marker-assisted selection, genomic selection techniques and
genome engineering approach. Recent advances in biotechnology of sugarcane
highlight that the crop is on the threshold of genetic revolution as potential
applications and benefits of molecular technology are being realized. Precision
genome editing by homology directed repair has been reported in sugarcane for
genetic improvement (Zhao et al. 2021).

9.17.2 Other Supporting Research and Development

The national sugarcane improvement programme is supported by different

departments of research and development, viz. genetics and cytogenetics, tissue
culture, crop production, crop protection, healthy seed nursery and agriculture
extension. Mutation breeding was implemented in 1959 (Panje and Jagadesan
1959). Physical and chemical mutagens were used for improvement of many
sugarcane varieties. Different varieties, viz. Co 8152 of Co 527, Co 8153 of Co
775, Co 8517 and Co 85035 of Co 740 and CoLk 8901 of CoJ 64, were subjected to
mutagenesis, but none attained commercial status. Exploiting somaclonal variations,
Co 85001, Co 85003, Co 85006, Co 85007, Co 85008, Co 85011, Co 85015, Co
85033 (Parent variety (Pv) Co 7704), Co 85035 (Pv Co 740), Co 85032, 85038
(Pv Co 7707), CoPant 93227 (Pv CoS 8118), VSI 434 (Pv CoC 671) and Co 94012
(Pv CoC 671), were also tried by different sugarcane research stations in India with
focus on defect elimination in otherwise good commercial varieties. Presently, VSI
434 and Co 94012, two somaclones with high sugar content, are in cultivation in a
limited area of Maharashtra.
544 B. Ram et al.

9.18 Emerging Challenges at National and International Level

Sugarcane being a long-duration crop (12 plus months) faces many challenges. The
following challenges are foreseen with regard to sugarcane agriculture. Sugarcane
needs 1500–2000 mm water annually. Due to climate change, there is uneven
distribution of rains in different states/countries. Scarcity of water for sugarcane
agriculture is the biggest challenge. Water stress leads to lesser tillering and growth
and reduction in juice quality and cane yields. Most of the sugarcane area is irrigated.
Continuous exploitation of underground water coupled with lesser rainfall results in
salinity problem. Therefore, water stress and salinity are going to be the major
emerging abiotic stress challenges (Ram and Karuppaiyan 2018). Due to climate
change, the minor insect pests and diseases of the past are emerging as the major
ones, e.g. incidences of pokkah boeng and wilt are on the rise in North India.
Similarly, there are increased incidences of white fly and mealy bugs in South
India. For the new diseases and insect pests, screening techniques are not available.
In general, plateau in cane yield and sugar recovery is observed throughout the
world (Walker 1987). However, there is improvement in average cane productivity
and sugar recovery in India due to large-scale adoption of sugarcane variety Co 0238
in subtropical and central India. Due to increasing prices of inputs used in sugarcane
cultivation coupled with disproportionate increase in cane price, the cost of produc-
tion of sugarcane and hence sugar is increasing. This makes Indian sugar incompe-
tent in the international market. Further, with improvement in cane productivity and
sugar recovery due to increase in area of Co 0238, sugar is produced in excess in the
country. Many sugar factories are finding it difficult to store the excess sugar,
particularly in subtropical India.
Availability of labourers in sufficient number at the required time is another major
challenge in sugarcane agriculture. Most of the medium and large farmers are finding
it difficult to complete the different cultural practices in time. Complete mechaniza-
tion, from planting to harvesting, of sugarcane agriculture is the solution to this
problem. The varieties with erect habit, self-detrashing and lesser canopy are the
traits of importance for mechanization. Breeders need to incorporate these traits in
their selection criteria. Further, as For the evolution of a new sugarcane varieties it
takes about 12–14 years. This long perido is to be shortened. There is need to
identify the genetic stocks from the germplasm, genes for different traits and the
screening techniques for evaluating the progenies for desired traits. All these
emerging challenges need to be addressed in the near future.

9.19 Breeding Progress/Varietal Development

9.19.1 Conventional Breeding

Professionally directed sugarcane research in India was started in 1907 at Pratapgarh

(Uttar Pradesh) by George Clarke, who was the Agricultural Chemist of United
Provinces. This work gained impetus with the simultaneous establishment of
9 Sugarcane Breeding 545

Sugarcane Breeding Station at Coimbatore and Sugarcane Research Station at

Shahjahanpur in 1912 and the appointments of Dr. C. A. Barber as the Imperial
Sugarcane Expert at Coimbatore and George Clarke at Shahjahanpur. In order to
strengthen sugarcane improvement activities and production of cane and sugar in the
then British India, a network of research stations were created across the country.
Apart from the Imperial Council of Agricultural Research, Pusa (Bihar), other
stations established for sugarcne research were Peshawar, Raisalwala (Punjab-now
in Pakistan), Shahjahanpur (UP), Mushari (Bihar and Orissa), Dacca, Jorhat
(Assam), Padegaon (Maharashtra), Anakapalle (Andhra Pradesh) and Tarnab
(Kashmir).
Dr. Charles Alfred Barber initiated sugarcane varietal improvement based on the
principles of plant breeding and developed an interest in the systematic crop
improvement in all provinces in the country. The city of Coimbatore was endowed
with climatic conditions favourable for good flowering and seed setting in sugarcane
and thus chosen as suitable base for hybridization. It was also noticed that at
Coimbatore the canes not only produced flowers every year but also shed pollen
under natural conditions. Accordingly, Barber assembled a collection of sugarcane
varieties from all parts of India in Coimbatore and produced sugarcane seedlings
in 1912, a rare feat in those days. The first batch of seedlings was produced
from the fluffs harvested in 1912. From these seedlings 1912, Dr. Barber and
Dr. T.S. Venkatraman developed the first batch of 16 sugarcane varieties or Co
canes (Co 201 to Co 216) at Coimbatore from the breeding efforts from 1912 to 1918
(Table 9.4) which was sent to different sugarcane-growing states of North India such
as Punjab, Bihar, United Provinces, etc. for cultivation. Research stations at
Lyallpur, Gurdaspur, Shahjahanpur and Pusa did much of the evaluation,

Table 9.4 Details of first batch of Co Canes

Name Parentage Name Parentage
Co 201 Pansahi seedling Co 209 Khelia seedling
Co 202 Chittan seedling Co 210 POJ 213 seedling
Co 203 Saretha seedling Co 211 Green Sports of Stripped
Mauritius  Saretha
Co 204 Chittan seedling Co 212 POJ 213  M2 (Unbagged
Cross)
Co 205 S. officinarum (Vellai)  S. spontaneum Co 213 POJ 213  Kansar
(Coimbatore form) (Bagged Cross) (Unbagged Cross)
Co 206 Ashy Mauritius seedling Co 214 Stripped
Mauritius  (Saretha  S.
spontaneum)
Co 207 POJ 213  Saretha (Unbagged Cross) Co 215 Stripped
Mauritius  (Saretha  S.
spontaneum)
Co 208 POJ 213 seedling Co 216 Green Sports of Stripped
Mauritius  Saretha
Source: Agricultural Journal of India, 1922
546 B. Ram et al.

multiplication, distribution and cultivation of these clones. From this work, the
famous clone Co 205, suited to the harsh subtropical environment of India, was
identified. Co 205 emerged as the best variety, and cane yield improvement was
remarkably higher in Punjab, about 50% more than the indigenous varieties, mainly
Katha. The pedigree chart of Co 205 is given below.

Saccharum officinarum (Vellai) (2n=80) x S. spontaneum (Coimbatore) (2n=64)

Co 205 (2n=112) (2n+n chromosome transmission)

The development of Co 205 was an important milestone in the history of

sugarcane breeding because crossing the cultivated species S. officinarum with a
wild species of grassy nature directly produced a successful hybrid of commercial
value. Among the available thick-stalked canes (S. officinarum), Vellai was the first
to flower which made it easy to cross with S. spontaneum canes characterized by
early flowering. It may be noted that only 60 seedlings were obtained from which Co
205 was selected.
Along with Co 205, varieties such as Co 210, Co 213 and Co 214 were also
popular among growers of North India and led to significant increases in cane and
sugar production. Co 214 was the first early maturing variety bred at Coimbatore.
Facilitated by the improved methods of sugarcane cultivation developed by George
Clarke at Shahjahanpur Station, these varieties brought in a spectacular and revolu-
tionary surge in cane and sugar production within a couple of years. This transfor-
mational research of Indian scientists attracted global attention, and Coimbatore
received worldwide recognition for developing many world famous and highly
productive Co varieties starting with Co 205. The impact of this program was
enormous: the ancestry of almost all modern commercial sugarcane varieties in the
world traces to early Co varieties. Howard (1940) attributed three factors, viz.
sugarcane varieties bred at Coimbatore, sugarcane research work done at
Shahjahanpur and protection policies of the governments, which made India self-
sufficient in sugar production during 1940s.
Co 205 also spread to many countries including Cuba, the USA, Australia,
South Africa, Argentina and Brazil. In Natal, a field trial conducted with Co
205, Co 210, Cuban Selection CH 64/21, Uba, Agaul, Kavangire, Oshima, Merthi,
Townsend’s selection, POJ 213 and SC 12/4 demonstrated the advantage of two
Coimbatore varieties, viz. Co 205 and Co 210, which yielded 18% and 14%,
respectively, more sugar per acre than the standard (Uba) (Todd 1939).
The SBI continued to supply Co canes after preliminary evaluation at Coimbatore
to State Sugarcane Research Stations in the country for further evaluation under local
conditions. Fluff was also supplied to these State Sugarcane Research Stations.
Important commercial varieties identified were Co 285, Co 290, Co 312, Co
313, Co 419, Co 421, Co 449, Co 453, Co 467, Co 617, Co 1148, Co 1158 and
Co 7717. These varieties had nearly 35% more sucrose content than their
predecessors and also matured quickly, tolerated waterlogging and drought and
9 Sugarcane Breeding 547

were resistant to red rot and Sereh diseases. They were cultivated in poor soils and
were widely used as parents in breeding programmes of many countries (Roach
1989). Co 281 became a success in South Africa, while Co 419 was widely adopted
in the tropics worldwide. Realizing these major scientific contributions and services,
the Viceroy of British India Lord Irwin in 1930 praised Sugarcane Breeding Institute
(SBI) at Coimbatore as the Mecca of Sugarcane Research. Further details are
provided under coordinated system of testing.

9.19.2 Genomics-Assisted Breeding

Deploying genome-assisted breeding in sugarcane genetic improvement has always

been challenging on account of complex nature of chromosomal pairing and assort-
ment during meiosis, gametic sterility and hybrid inviability/sterility which hinder
allele segregation in a Mendelian pattern. The lack of detailed genome information
further reduces the quantitative trait loci (QTL) mapping resolution. A major break-
through in marker development was utilization of the high-throughput sequencing
methods that had already been developed for diploid crops. Bundock et al. (2012)
identified 280,000 SNPs from sorghum coding regions and the sugarcane EST
collections within a genotype, while Song et al. (2016) identified 1.1 m SNPs
from 12 accessions from the Saccharum complex. The two main genotyping
methods followed were array-based SNP genotyping and genotype by sequencing
(GBS). The first fixed array developed was an Affymetric Axiom array (Aitken et al.
2017) which was specifically developed for use within breeding germplasm, and
from the sequence information from Song et al. (2016), a second 100K Affymetric
Axiom array was developed. Relatively high cost of screening large numbers of
clones has been a drawback of the Affymetric Axiom array.
GBS method has been used to genotype many other crops (Scheben et al. 2017)
but has not been very successful in sugarcane to discover single-dose SNP variants
due to the complexity of sugarcane genome. However, encouraging progress is
being made to implement markers in breeding programmes. The two approaches
currently being adopted are marker-assisted selection making use of single genes or
QTLs with large effect and a genomic selection. Both these methods have been
developed in sugarcane. For marker-assisted selections, single candidate gene
markers are used. A typical example is the brown rust resistance gene, BruI,
which was first identified by Daugrois et al. (1996). However, P. melanocephala
race evolution has broken down the resistance conferred by Bru1 gene and
necessitates more sources of resistance to combine with Bru1 for use in MAS. At
ICAR Sugarcane Breeding Institute, already identified and validated candidate genes
for drought and red rot are being used to explore the possibility of MAS for these two
traits.
Genomic selection (GS) is a relatively new powerful breeding tool which is an
upgraded form of marker-assisted selection. Individuals are selected based on their
predicted breeding values that are estimated from genome-wide markers. Gouy et al.
(2013) first tested the genomic selection approach in sugarcane, and predictions of
548 B. Ram et al.

genetic values were carried out on two independent panels, each composed of
167 cultivars and breeding materials covering the worldwide diversity. Seven
predictive models were used, and the accuracies of predictions were assessed
through correlations between observed and predicted genetic values. Depending
on the trait considered, the average GS accuracy values related to within-panel
prediction ranged from 0.29 to 0.61 in the Reunion panel and from 0.13 to 0.5 in
the Guadeloupe panel. In another study, three different populations of clones in early
and advanced stage selection were evaluated for cane yield and sugar content in field
trials and genotyped using a SNP array. The levels of prediction accuracy obtained in
most datasets (0.25–0.45) are encouraging for developing applications of genomic
prediction to predict breeding values of yield and sugar content in sugarcane
breeding programmes (Deomano et al. 2020). A joint collaborative work between
ICAR Sugarcane Breeding Institute and Sugar Research, Australia, is into develop-
ing a suitable genomic selection approach for traits such as sugar content, drought,
red rot resistance and cane yield. Axiom array developed by Aitken et al. (2017) was
used to develop genomic predictions for sugar content and cane yield in sugarcane
clones in different stages of selection in a breeding programme (Deomano et al.
2020). The emerging results on red rot resistance are also encouraging to predict the
breeding value.

9.20 Modernization of Crop Improvement Programme

With new challenges on sugarcane cultivation, it is essential that all future breeding
programmes focused on ecologically viable, environment-friendly and resource
matching technologies aimed at enhancing the production and productivity of
sugarcane per unit time in the country. Sugarcane is now looked upon as a sugar
and energy crop. Bioethanol production from sugarcane is a major focus in the
coming years to meet the fuel demands of the country which warrants focus on
prebreeding activities of germaplasm resources. Sugarcane is also emerging as a
practical and viable platform in biopharming for high-value biomolecules.
The traditional varietal development programmes in most of the sugarcane
research stations are mainly based on phenotypic selection which is very tedious
and time-consuming. It takes around 12–14 years for development and release of
new cultivar. Along with long breeding cycles and large populations, synchrony of
flowering, insufficient planting materials for early generation trials, experimental
errors, competition between adjacent plots and GxE interaction effects were typi-
cally causing problems and affecting the selection process. Maximizing the rate
of genetic gain by reducing cycle length through rapid generation advancement,
effective utilization of data-driven information management systems, advanced
high-throughput phenotyping technologies and molecular tools would be a major
step forward in improving sugarcane breeding programmes in the future.
9 Sugarcane Breeding 549

9.20.1 Rapid Generation Advancement Through Speed Breeding

Rapid generation advancement in light-, temperature- and humidity-controlled

conditions can significantly reduce the breeding cycle, thereby resulting in reduction
of time and cost of crop varietal development. Recognizing the potential of speed
breeding for accelerating crop improvement, many countries have initiated to use
speed breeding platforms in crops such as wheat, barley, groundnut, chickpea, etc.
The ability to induce flowering faster in sugarcane would significantly reduce the
generation-to-generation cycle time and therefore speed up prebreeding activities
such as introgression breeding, production of inbreds and transfer of GM events
from a single cultivar into a range of backgrounds. Integration of speed breeding
with other modern technologies like gene editing and genomic selection would
maximize the genetic gain.

9.20.2 Advanced High-Throughput Phenotyping

One of the biggest bottlenecks in conventional sugarcane breeding is the ability to

rapidly phenotype larger populations throughout the growing season. Current
techniques are time and labour intensive and often introduce variation in collected
data. Field-based high-throughput plant phenotyping (FB-HTPP) when applied to
breeding programmes can contribute toward improving selection intensity with
larger field trials, increasing selection accuracy by reducing human error and
identifying novel genetic variation by capturing multiple phenotypes over time
(Thompson et al. 2020). High-throughput phenotyping using unmanned aerial
vehicles also provides an opportunity to improve the efficiency and effectiveness
of clonal selection in early stages of sugarcane improvement programme (Natarajan
et al. 2019). In sugarcane, the use of UAV-based high-throughput phenotyping
approaches has been demonstrated for capturing valuable phenotypes in early stages
of sugarcane breeding trials.

9.20.3 Molecular Tools for Effective Selection

The availability of a whole genome-sequencing (WGS) platform, genotyping by

sequencing and advanced genetic models, such as genome-wide association studies
(GWAS) and genomic prediction, presents opportunities to develop comprehensive
datasets in sugarcane to accelerate genetic gains in the sugarcane breeding
programmes. Genomic selection appears to be a promising approach in sugarcane
as large numbers of markers that cover the genome are simultaneously fitted in GS
models to predict the performance of new lines. With the anticipated publication of
the complete commercial sugarcane genome, opportunities for high-throughput
genotyping technologies for marker-trait associations and genomic selection would
improve precision and reduce the varietal generation time tremendously. Consider-
ing the achievements done in the crop so far, there is all possibility of having
550 B. Ram et al.

different cost-effective genotyping methods for varying breeding applications to

reform sugarcane breeding.

9.20.4 True Seed as Sugarcane Propagule

Transportation of sugarcane seed is a difficult task as a truckload of sugarcane

material (7–8 tonnes) is required as seed for planting 1-ha area. At the modest
estimate, approximately 14.42 million tonnes of sugarcane is used as seed to plant
2.22 million ha of area in the country. The Settling Transplanting Technology (STT)
will be advantageous to reduce the seed rate to 1/6th, 10–20% higher cane yield,
faster multiplication and replacement of desired varieties and development of small
entrepreneurs. In order to meet the future demands from the presently available area,
there is need to exploit the dominance variance/heterosis to the maximum possible
level. Research on developing hybrid varieties and propagation through true seed by
developing homozygous lines needs to be strengthened. The success of
the programme will lead to paradigm shift to sugarcane agriculture. By adopting
the STT method combined with true seed hybrids, it would be possible to change the
mode of transportation of sugarcane seed from truck to pocket (ICAR-SBI 2015).

9.20.5 Plant Breeding Data Management Platforms

Information management is essential for every plant breeding programme, and large
amount of data will be generated, and decision-making becomes difficult. Develop-
ment and utilization of advanced plant breeding data management platforms would
help sugarcane breeders decide better crosses and further selection. At Sugar
Research Australia, Brisbane Sugarcane Plant Improvement Database System
(SPIDS) is currently used for all sugarcane research and selection activities
(https://sugarresearch.com.au).

9.21 Status of Varietal Development and Maintenance

Breeding

The ICAR-SBI has been catering sugarcane varieties in India since the release of the
first interspecific variety Co 205. A list of popular sugarcane varieties in cultivation
in tropical (Table 9.5) and subtropical region of (Table 9.6) India during different
decades is given below. The five top varieties, in terms of area occupation, during
2020–2021, are given in Table 9.7. Co 0238 was occupying the maximum area,
i.e. 2.78 million ha, which was 53% of the total sugarcane area in the country
followed by Co 86032 (0.89 million ha, 17.1%). Other varieties were CoM 0265
(6.9%), Co 0118 (2.4%) and CoLk 94184 (2.3%). Co 0238, Co 0118 and CoLk
94184 are the subtropical varieties, whereas Co 86032 and CoM 0265 are the
tropical varieties.
9 Sugarcane Breeding 551

Table 9.5 Popular usgarcane varieties in cultivation in the tropical region of India
Decade Varieties
1920s Co 213
1930s Co 213, Co 243, Co 281, Co 290, Co 313
1940s Co 213, Co 419
1950s Co 419, Co 449, Co 527
1960s Co 419, Co 527, Co 658, Co 740, Co 853, Co 975, Co 997
1970s Co 419, Co 527, Co 658, Co 740, Co 975, Co 997, Co 853, Co 62175, Co 6304, Co
6806, Co 6415
1980s Co 419, Co 740, Co 975, Co 62175, Co 6304, Co 6907, Co 7219, CoC 671
1990s Co 62175, Co 6304, Co 7219, Co 7508, Co 7504, Co 8011, Co 8014, Co 8021, Co
8208, Co 8362, Co 8371, Co 8338, Co 85004, Co 86032, Co 86249, Co 97009, CoC
671
2000s Co 86032, Co 7219, Co 8371, Co 97009, CoM 0265, Co 94012, Co 91010, Co 8011,
Co 62175, Co 2001-15, Co 86002, Co 8338, Co 86249, CoV 09356, CoC 23, CoC
24, Si 6, PI 1110, CoV 92102, CoA 95081, CoA 96081, CoA 93081
2010s Co 86032, CoM 0265, Co 91010, CoV 09356, Co 11015

Table 9.6 Popular sugarcane varieties in cultivation in the subtropical region of India
Decade Varieties
1920s Co 205 Co 210 Co 213 Co 214 Co 223 Co 281 Co 290
1930s Co 205 Co 213 Co 223 Co 244 Co 281 Co 285 Co 290 Co 312 Co 313
1940s Co 213 Co 312 Co 313 Co 331 Co 356 Co 453
1950s Co 312 Co 313 Co 453 Co 951 CoS 245 CoS 510
1960s Co 312, Co 975, Co 1107, Co 1148, BO 17, CoS 510
1970s Co 312, Co 1148, Co 1158, BO 17, CoS 510
1980s Co 1148, Co 1158, Co 7717, BO 91, BO 99, CoJ 64, CoS 687, CoS 767, CoLk 8001
1990s Co 89003, Co 7717, Co 1148, CoS 767, BO 120, BO 128, Co 87263, Co 87268, CoH
92, CoPt 84211, CoLk 8102
2000s Co 89003, Co 98014, Co 1148, CoJ 64, CoS 767, CoS 97261, CoPant 97222, CoPant
90223, CoSe 92423
2010s Co 98014, Co 0238, Co 0118, CoS 8432, CoS 8436, CoS 97261, CoSe 96436, CoPant
97222, CoPant 90223, CoSe 92423, CoSe 96234, CoPant 99214, CoPant 03320, CoSe
01434, CoLk 94184, Co 05009, Co 05011, Co 06034, Co 09022, Co 12029, Co 13035,
Co 15023

Table 9.7 Top five varieties in cultivation in India during 2020–2021

Area
S. No. Varieties Region In million ha In percentage
1. Co 0238 Subtropical 2.794 53.42
2. Co 86032 Tropical 0.892 17.06
3. CoM 0265 Tropical 0.361 6.90
4. Co 0118 Subtropical 0.128 2.45
5. CoLk 94184 Subtropical 0.122 2.33
552 B. Ram et al.

9.22 Maintenance Breeding

Genetic purity of sugarcane varieties is being maintained through maintenance

breeding and micropropagation. Maintenance breeding is being done by following
cane-to-row method of planting. Individual canes are cut into single-budded setts to
plant in a 6 m length row. Rows are monitored regularly, and the rows, if any, with
mixture are excluded from the bulk nucleus seed. In vitro studies were initiated in the
late 1970s, and protocols were standardized for tissue and meristem culture of
sugarcane for the first time at ICAR-SBI (Sreenivasan and Jalaja 1979).
Micropropagation technology has been adopted by many seed-cane production
agencies and companies in the country. Micropropagation is also useful in the
rejuvenation of old and degenerated varieties, possibly through elimination of
endogenous pathogens, and the benefits have been demonstrated in farmers’ fields
(Neelamathi et al. 2017). About 500,000 micropropagated plants are produced
annually by different laboratories in India.

9.23 Coordinated System of Testing

The All India Coordinated Research Project on Sugarcane {AICRP(S)} came into
being during 1970. The Project Coordinator’s office was housed at the Indian
Institute of Sugarcane Research (IISR) to coordinate research efforts and to test
the technologies developed by the State Agricultural Universities (SAUs), State
Research Stations and Indian Council of Agricultural Research (ICAR) Institute,
but with a strong emphasis on the development of improved varieties. Under the
AICPR(S) network, presently, there are 24 regular centres and 14 voluntary centres
across the country in five agroclimatic zones, viz. Peninsular Zone, North West
Zone, East Coast Zone, North Central Zone and North Eastern Zone.
A National Hybridization Garden (NHG) facility was established at ICAR-SBI in
1972 for crossing and for country-wide sugarcane seed (fluff) supply. Out of
38 stations of AICRP(S), 24 stations are full-fledged sugarcane breeding stations
and participate in hybridization activities at the NHG. Sugarcane breeders from
different research stations in the country visit the NHG during flowering season,
chose the parents / crosses according to their local requirements, and the seeds are
germinated for selection programmes in the respective stations. On average 200,000
seedlings are raised in these stations. After initial evaluation of 5–6 years at
respective research stations, the selected best clones are pooled to conduct common
(multi-location) trials in the respective zones under AICRP(S). Once accepted for
evaluation under AICRP(S), these clones are multiplied for 2 years to generate
sufficient seed material for the subseuent Initial Varietal Trials (IVT-1-year) for
1 year in all centres within each zone. Clones performing better than the check
varieties in the IVT are promoted to Advanced Varietal Trials (AVTs), which consist
of two plant and one ratoon crop experiments. The test clones performing better than
the best check variety are identified by the Varietal Identification Committee of the
AICRP(S). Elite selections from AVTs are recommended for commercial release
9 Sugarcane Breeding 553

and official notification of sugarcane varieties for respective zones. This programme
(since 2000) has released 63 sugarcane varieties by 16 stations in four zones for
cultivation.
The flow chart of varietal development (Table 9.8) followed at ICAR-SBI is
generally followed throughout the country with minor variation based on the popu-
lation available and the seasonal variations which determine planting and harvesting.
Taking into consideration the breeding history of the sugarcane stations, the flow-
chart of sugarcane breeding generally followed in India is included.

Table 9.8 Flow chart of sugarcane breeding followed in India

Selection criteria and number of clones
Year Activity selected
I Choice of parents and hybridization Parents are selected based on pedigree,
(600–700 crosses) molecular diversity, combining ability,
registered genetic stocks
II Seedling raising and transplanting in Sowing in March to August, transplanting in
ground nursery (200,000–500,000 June to December
seedlings)
III Ratooning ground nursery Brix, no. canes/stool, flowering, cane
Selection and planting in I Clonal trial diameter, cane height, cane morphology
(30,000–40,000 clones) (~20% selection)
IV Selection in I Clonal trial Brix, no. canes/stool, flowering, cane yield
parameters (~25% selection)
V II Clonal trials One row trials in Aug RCBD/RBD (~25%
selection)
VI Pre-Zonal Varietal trials (PZVT)— ~250 clones—2 rows trial—Juice quality
Multiplication analysis at 240, 300 and 360 days post-
planting
Screening for red rot, crop stand, flowering
VII PZVT trials/final clonal trials (RBDa) 60–100 clones; Yield, quality evaluation, red
rot screening by plug and nodal inoculation,
smut screening, ethanol and fibre content, Pol
% cane
VIII Selection elite clones for multilocation 20–25 Co canes, 30–40 Co allied, 2–5 other
testing centre selections
IX, Multiplication and exchange of AICRP 60–75 to AICRPS trials (5–25 clones for the
X (S) entries five agroclimatic zones); multiplication for
2 years
XI Initial Varietal Trial 1 year in RBDa
XII, Advanced Varietal Trial Two plant crops and one ratoon crop to select
XIII the best clones (with >10% improvement in
cane yield and no reduction in quality or 5%
improvement in sucrose content and no
reduction in cane yield over the zonal
standard)
Varietal release (within 2 years of AICRP
multilocation testing)
a
RBD randomized block design; RCBD augmented randomized complete block design
554 B. Ram et al.

In addition to hybridization at NHG at Coimbatore, efforts have also been made

in some states to develop varieties utilizing their local hybridization gardens. These
include Bihar and Orissa (developing cultivars including BO 10, BO 54, BO 70, BO
72, BO 91, BO 108, BO 110, BO 137, BO 145, BO 147, BO 154), Uttar Pradesh
(UP 1, UP 3, UP 5, UP 15, UP 39, UP 0097, UP 9530, UP 05125), Maharashtra
(MS 68/47, MS 7110, MS 7455, MS 10001) and Karnataka (HM—Hebbel Mysore
320). Vasantdada Sugar Institute, Pune, has an in-house crossing facility to partially
meet the varietal development needs of their local region and has developed varieties
including VSI 12121, in cultivation in Maharashtra state. M/S EID Parry (India) Ltd.
the only private company in the country to breed sugarcane varieties, with its
hybridization facility in Bangalore, produces and releases varieties designated with
the prefix PI (Parry India). A few locally adapted PI varieties have been released. PI
1110 is one such clone with excellent performance under irrigated conditions.
Table 9.9 summarizes the details of the research stations engaged in sugarcane
improvement in India and names of prominent varieties produced from those
centres.

9.24 Future Thrust Areas

The sugarcane breeding efforts continues in India since the inception of ICAR-
Sugarcane Breeding Institute, Coimbatore (ICAR-SBI), in 1912. The first sugarcane
interspecific hybrid variety Co 205 (S. officinarum  S. spontaneum) was released in
1918, which replaced all existing north Indian canes (S. barberi) in the subtropical
region. Since then, and till 2021 about 3179 Co canes have been evolved by the
ICAR-Sugarcane Breeding Institute. The ICAR-SBI is keeping its National
Hybridization Garden dynamic with additions of new releases and phasing out of
old and unproductive parents for the larger gains of sugarcane research stations all
over the country under AICRP.
Sugarcane is coming up as an energy crop with options like co-generation and
second-generation ethanol production. Research on development of high biomass
clones with high fibre content might be strengthened, depending on demands, for
developing Type 1 and Type 2 energy canes which are characterized and found
promising as biofuel crops. Selection of the right clones starting from ground nursery
has to be scientific based on parameters that are visibly scorable and indirect
selection aided by statistical tools to add prediction.
With availability of ‘omics’ technologies in ‘genomics era’ of modern plant
breeding, sugarcane research has gone rapid transformation. To harness the benefits
of these technologies, linking modern techniques with the conventional breeding is
very essential in sugarcane. ICAR-SBI has integrated the biotechnological tools in
breeding programmes to improve precision and efficiency. Genomics has been the
key in unravelling the crop complexities and in developing and adopting several
molecular markers with wide applications including DNA fingerprinting, diversity
 9
Table 9.9 Organizations involved in sugarcane improvement in different crop production zones in India
Organization Affiliations/funding source Key activities Major varieties
Peninsular zone
ICAR-Sugarcane Breeding Institute, ICAR Germplasm collection evaluation, Co 205, Co 285, Co 312, Co
Coimbatore utilization, breeding, selection, varietal 313, Co 419, Co 740, Co
trials, tissue culture, genomics, transgenics 6304, Co 62175, Co 86032
Vasantdada Sugar Institute, Manjari Co-operative members of the Sugar Germplasm evaluation, utilization, breeding, Co VSI 9805, VSI 12121
Sugarcane Breeding

Block, Pune, Maharashtra factories in the state of Maharashtra selection, varietal trials, tissue culture,
genomics, transgenics
Central Sugarcane Research Station, Mahatma Phule Krishi Vidyapeeth Breeding, selection, varietal trials CoM 88121, CoM 0265
Padegaon, Maharashtra (MPKV), Rahuri
Zonal Agricultural Research Station, Jawaharlal Nehru Krishi Vishwa Breeding, selection, varietal trials CoJn 86141
Powarkheda (Madhya Pradesh) Vidayalaya, Jabalpur, MP
Regional Sugarcane and Rice Professor Jayashankar Telangana State Breeding, selection, varietal trials 98R 278, CoR 9301
Research Station, Rudrur, Agricultural University, Rajendranagar,
Telengana Hyderabad
Regional Sugarcane and Jaggery Mahatma Phule Krishi Vidyapeeth, Selection, varietal trials –
Research Station, Kolhapur, Rahuri, Ahmednagar, Maharashtra
Maharashtra
Sugarcane Research Centre, Akola, Dr. Panjabrao Deshmukh Krishi Selection, varietal trials –
Maharashtra Vidyapeeth, Krishinagar
Regional Sugarcane Research Gujarat Agrl. University Navasari Breeding, selection, varietal trials CoN 05071
Station, Navasari, Gujarat
Sugarcane Research Station. Kerala Agricultural University, Kerala Breeding, selection, varietal trials CoTl 88322
Kallunkal, Tiruvalla, Kerala
Agricuture Research Station, Acharya N.G. Ranga Agricultural Breeding, selection, varietal trials CoT 8201, CoT 10367
Perumalapalle University, Andhra Pradesh
Zonal Agricultural Research Station, University of Agricultural Sciences, Breeding, selection, tissue culture, varietal CoVc 14061
V. C. Farm Mandya (Karnataka) Bangalore (Karnataka) trials
Sugarcane Research Station, Tamil Nadu Agricultural University, Breeding, selection, varietal trials CoG 773, CoG (SC) 5
555

Melalathur, Tamil Nadu Coimbatore

(continued)
Table 9.9 (continued)
556

Organization Affiliations/funding source Key activities Major varieties

Sugarcane Research Station, Tamil Nadu Agricultural University, Breeding, selection, varietal trials CoSi 776, CoSi 96071, CoSi
Sirugamani, Tamil Nadu Coimbatore (SC) 6
M/s E I D Parry, Pugalur, Tamil M/s E I D Parry (India), Chennai Breeding, Selection, Tissue culture PI 00-1110
Nadu
K.J. Somaiya Institute of Applied Godavari Refineries Varietal trials –
Agricultural
North west zone
ICAR Indian Institute of Sugarcane ICAR Breeding, selection, germplasm utilization, CoLk 8102, CoLk 94184
Research, Lucknow tissue culture, varietal trials, genomics,
transgenics
U.P. Council of Sugarcane Research Government of Uttar Pradesh Breeding, selection, germplasm utilization, CoS 510, CoS 687, CoS
(UPCSR), Shahjahanpur, Uttar tissue culture, varietal trials, genomics 767, CoS 8432, CoS 8436,
Pradesh CoS 88230, CoS 95255,
CoS 96268, CoS 08279
Punjab Agricultural University, Punjab Agricultural University-Ludhiana, Breeding, selection, varietal trials –
Regional Research Station, Faridkot Punjab
(Punjab)
CCS HAU Regional Agrl. Research Chaudhary Charan Singh Haryana Breeding, selection, varietal trials CoH 56, CoH 119
Station, Uchani (Haryana) Agricultural University, Hisar (Haryana)
PAU, Regional Research Station, Punjab Agricultural University-Ludhiana, Breeding, selection, varietal trials CoJ 46, CoJ 64, CoJ 83, CoJ
Kapurthala (Punjab) Punjab 85, CoPb 91
G.B. Pant University of Agriculture G.B. Pant University of Agriculture and Breeding, selection, varietal trials CoPant 84212, CoPant
and Technology, Pantnagar, Technology, Pantnagar 97222
Uttarakhand
Agricultural Research Station, Kota, Agriculture University, Kota, Rajastan Selection, varietal trials CoPK 05191
Rajastan
Sugarcane Research Station, Swami Keshwanand Rajasthan selection, varietal trials –
Sriganganagar, Rajasthan Agricultural University, Bikaner
B. Ram et al.
 9
Regional Centre of Sugarcane ICAR SBI Coimbatore Breeding, selection, germplasm utilization, Co 285, Co 312, Co
Breeding Institute, Karnal varietal trials 1148, Co 1148, Co 1158, Co
62399, Co 7717, Co 89003,
Co 98014, Co 0118, Co
0238, Co 15023
North central zone
Sugarcane Research Institute, PUSA Rajendra Agricultural University, Pusa, Breeding, selection, varietal trials BO 17, BO 54, BO 70, BO
(Bihar) Bihar 91, CoP 9301
Sugarcane Breeding

Sugarcane Research Station, UPSCR, Shahjahanpur Selection, varietal trials

Gorakhpur (UP)
Genda Singh Sugarcane Breeding UPSCR, Shahjahanpur Breeding, selection, varietal trials CoSe 92423, CoSe 95422,
and Research Institute, Seorahi (UP) CoSe 98231, CoSe 01434
Sugarcane Research Station, Department of Agriculture, Govt. of West Breeding, selection, varietal trials CoB 94164
Bethuadahari (West Bengal) Bengal
Indian Institute of Sugarcane ICAR IISR, Lucknow Breeding, selection, varietal trials Co 89029, Co 0233
Research Centre, Motipur, Bihar
North eastern zone
Sugarcane Research Station, Assam Agricultural University, Jorhat, Breeding, selection, varietal trials CoBln 9101, CoBln 9105
Buralikson (Assam) Assam
East coast zone
Regional Agricultural Research Acharya N.G. Ranga Agricultural Breeding, selection, varietal trials CoA 7601, CoA 92081,
Station, Anakapalle, Andhra University, Guntur, Andhra Pradesh 2001A 63
Pradesh
Sugarcane Research Station, Acharya N.G. Ranga Agricultural Breeding, selection, varietal trials CoV 94102, CoV 09356
Vuyyuru, Andhra Pradesh University
Sugarcane Research Station, Orissa University of Agriculture and Breeding, selection, varietal trials CoOr 03151
Panipoila, Nayagarh Technology, Bhubaneshwar
Sugarcane Research Station Tamil Nadu Agricultural University, Breeding, selection, tissue culture, varietal CoC 671, CoC (SC) 25
Cuddalore, Tamil Nadu trials
M/s. E I D Parry (India) Ltd. M/s. E I D Parry (India) Ltd, Chennai Breeding, selection, tissue culture, varietal PI 00-1110
Nellikuppam, Cuddalore, trials
557

Tamil Nadu
558 B. Ram et al.

analysis, markers linked to traits, marker-assisted selection, etc. Transcriptomics,

metabolomics and proteomics approaches are employed for important traits such as
sugar accumulation, yield, resistance to diseases and tolerance to drought, salinity,
waterlogging, cold and pests. However, being a complex polyploid, no single
technique is found to be the best. Biotechnological approaches combined with
bioinformatics analysis will pave way for identification of new genes, regulatory
elements and promoters and expressed sequence tags (ESTs), etc. The Brazilian
initiative of SUCEST database with over 2 lakhs of sequence tags and the SUCEST-
FUN database created to manage sugarcane genome data and provide tools of
interest for sugarcane functional genomicists and molecular breeders (sucest-Fun.
org) owe a lot of applications for translation to the field level.
Success in genetic transformation in sugarcane has opened up newer avenues of
crop improvement and product diversification. In India, ever since the first sugarcane
transgenic was developed during 1999 (Subramonian et al. 1999a, b), several
transgenics with improved tolerance to drought and sugarcane borers are developed
and awaiting field trials (Sruthy et al. 2015) along with isolation of effective
promoters (Chakravarthi et al. 2016). Opportunities on viral and fungal resistance,
increased sugar content, lignin synthesis and sugar accumulation need to be
explored. Sugarcane is also considered as a biofactory to produce high-value
molecules and pharmaceuticals, and ICAR-SBI has perfected a vacuolar targeting
protocol for localizing the proteins in the cell vacuoles (Harunipriya et al. 2016),
which makes it easy to extract from the sugarcane juice.
At present, transportation of sugarcane seed is a difficult task as a truckload of
sugarcane material is required as seed for planting 1 ha of area. The settling
transplanting technique economizes planting cost with the requirement of just
5000–6000 plants for planting an acre. Guided by this success, the ICAR-SBI has
been working on a programme on sugarcane true seed development through devel-
oping homozygous parental lines by repeated selfing, creation of haploids through
various means and standardizing the seed defuzzing technique. It is expected that the
research in this direction based on conventional and biotechnological means would
deliver the right product in the form of a pocketfull of homogeneous seed in a packet
from the present level of a truckload of seed.
Sugarcane breeding, the continuous process of evolving better varieties, has been
evolving with newer and improved technologies and approaches. We can be proud
that the target for 2030 AD (32.5 million tonnes) has already been achieved with a
record production of over 33.2 million tonnes of sugar during 2018–2019. Now
sugarcane can be projected as the crop to cater to multiple needs of food, fuel, fibre
and fodder under normal and constraint situations. The research at ICAR-SBI has
been reoriented towards product diversification employing the technical know-how
from all the disciplines so that future sugarcane varieties would have specialized
roles to make the country self-reliant in sugar and energy apart from yielding value-
added products.
9 Sugarcane Breeding 559

9.25 Conclusions

A major breakthrough in sugarcane improvement was achieved through the use of

wild species, viz. S. spontaneum, which led to the development of the first sugarcane
interspecific hybrid variety Co 205. The variety became very popular and replaced
all existing north Indian canes (S. barberi) in the subtropical region. Since then,
about 3179 Co canes have been evolved by the ICAR-Sugarcane Breeding Institute.
In efforts to increase diversity in the progeny of commercial crosses, tropical parents
were crossed with subtropical parents to facilitate genetic recombination and to
break the linkage drag. Screening of large seedling populations under conditions
of winter and selection has been a success, which resulted in a new series of varieties
under Karan series from ICAR-SBI, Regional Centre, Karnal (Ram 2007). Notable
among these are Co 98014, Co 0118, Co 0238, Co 05011 and Co 15023. The
institute holds the unique distinction that its varieties cover over 78% of the area in
the country, and among these Co 86032, a tropical cane (about 0.89 million ha), and
Co 0238 (2.79 million ha) together cover over 3.6 millon ha (70% area under
sugarcane) in the country during 2020–2021.
AICRP trials provide opportunity to identify stable clones with high sugar yield.
As utilization of such clones from the four agroclimatic zones in breeding
programmes is expected to earn better genetic gains, the Institute is keeping its
National Hybridization Garden dynamic with additions of new releases and phasing
out of old and unproductive parents for the larger gains of sugarcane research
stations all over the country.
Sugarcane breeding has evolved into a systematic activity with the inputs in the
form of new and diverse genetic material, statistical and analytical approaches to
improve precision and to bring scientific touch in crop improvement. Achievements
made through breeding new varieties have been quantified, and a steady improve-
ment in juice quality has been noticed over decades. The yield plateauing
necessitated the use of new genetic resources. Evaluation of selected hybrids under
ISH (interspecific hybrids) series in multi-locations and for multiple stresses has
yielded valuable parents for sugarcane improvement.
The rate of replacement, variety as well as seed, is very slow in sugarcane due the
requirement of huge quantity of seed per unit area. The cost of the seed itself
contributes to 16–18% of cultivation cost. At present, transportation of sugarcane
seed is a difficult task. The success of single bud/bud chip settling raising and
transplanting has been demonstrated resulting in increased productivity and profit-
ability. It is expected that the research on development of true seeds initiated at
ICAR-SBI would change the transportation of sugarcane seed from truck to pocket.
Linking modern ‘omics’ technologies in ‘genomics era’ of modern plant breeding
with the conventional breeding is expected to achieve introgression of targeted trait
in the desired varieties of sugarcane. Success in genetic transformation in sugarcane
has opened up newer avenues of crop improvement and product diversification.
Sugarcane is also considered as a biofactory to produce high-value molecules and
pharmaceuticals, and ICAR-SBI has perfected a vacuolar targeting protocol for
560 B. Ram et al.

localizing the proteins in the cell vacuoles, which makes it easy to extract from the
sugarcane juice.
Sugarcane breeding, the continuous process of evolving better varieties, has been
evolving with newer and improved technologies, and it can be expected that the pace
of development can initially sustain sugarcane production and then accelerate crop
production for multiple needs as food, fuel, fibre and fodder under normal and
constraint situations.

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Jute Breeding
10
C. S. Kar, Pratik Satya, and Gouranga Kar

Abstract

Jute (Corchorus spp.; 2n ¼ 14) is an annual crop and ranks next only to cotton as
a source of natural bast fibre. Unlike other field crops, the economic product is
fibre from stem which is a vegetative part. Jute breeding is a challenge to plant
breeders as selection of better genotype is cumbersome as generation advance-
ment of selections requires two growing seasons compared to one season in other
field crops. Moreover, hybridization is also a tedious process. In spite of these
difficulties, a number of high-yielding varieties of both C. olitorius and
C. capsularis have been developed in India, Bangladesh and China using differ-
ent breeding methods. During the last 50 years, the improvement of fibre yield
potential has almost doubled. Advanced plant breeding methods along with
genomic tools are only way to bring next quantum jump by breaking yield
plateau. Draft genome sequencing of jute has been accomplished by India,
Bangladesh and China independently in recent years. But due to the narrow
genetic base of Corchorus species, lack of suitable transformation protocol
using tissue culture and lack of high-throughput phenotyping technology, the
pace of jute crop improvement is slow. The use of genomic tools and advanced
breeding methods like marker aided selection, speed breeding and transgenic
research and the use of genome editing tools may open a new avenue in future in
crop improvement in jute to establish it as a climate-smart crop by imparting
biotic and abiotic stress resistance along with better fibre quality.

C. S. Kar (*) · P. Satya · G. Kar

ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, West Bengal,
India
e-mail: chandan.kar@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 571
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_10
572 C. S. Kar et al.

Keywords

Germplasm · Molecular breeding · Breeding objectives · Coordinated system of

testing · Varietal development

10.1 Introduction

Jute is the second most important fibre crop next to cotton in terms of global
production and use. The term jute is used for fibre obtained from the bark of two
cultivated species (Corchorus olitorius and C. capsularis). Jute is grown in India and
in Bangladesh in the pre-monsoon (pre-kharif) season within a small growing
window of mid-March to mid-July (110–120 days) in the Eastern Gangetic Plain
(EGP). The north-western monsoon during April and the heavy monsoon shower
during June–July (80% of the total rainfall) in the EGP are not suitable for cultivation
of other crops during pre-monsoon. Competitive alternate crops of jute are boro rice,
wheat, sesame, maize and summer vegetables. Boro rice and wheat require longer
duration (November–May), and vegetables require protection from rain. However,
during the past 20 years, monsoon rainfall decreased significantly in the river basins
of EGP (Yaduvanshi and Ranade 2017). More interestingly, it was observed that
short-term fluctuations (<10 years) are the major cause for variability (77.6%) in
annual rainfall (Yaduvanshi and Ranade 2017). Such abrupt changes in rainfall
distribution and occurrence of frequent drought spells have increased vulnerability
of jute cultivation in the recent decades, which is reflected in the reduction of area of
jute cultivation during the past few decades (Fig. 10.1). Despite this, production of
jute has remained comparatively stable due to an increase in productivity. Progress
in breeding and management of jute crop has resulted in an increase of both average
yield and potential yield of jute crop. The jute-rice cropping system is prevalent in
90% of the jute growing area.
Learning objectives include (1) importance of jute crop as a source of natural
fibre; (2) origin and evolution of Corchorus species, distribution of wild relatives
and genetic resources; (3) morphological differences, floral biology and
hybridization technique of Corchorus species; (4) genetics of quantitative and
qualitative traits; (5) breeding for fibre yield improvement and associated traits
including heterosis, biotic and abiotic stress; (6) maintenance breeding and evalua-
tion system in jute; and (7) knowledge of advanced breeding methods including
genomic tools.

10.2 Origin, Evolution and Distribution of Species and Forms—

Wild Relatives

According to the Linnaean classification, jute was first classified in the family
Tiliaceae under the order Malvales, but was later placed under the family Malvaceae
(Table 10.1). The family distribution under the order Malvales has been debated
10 Jute Breeding 573

Fig. 10.1 Occurrence distribution of major Corchorus species (GBIF data; accessed on 23 June
2021)

Table 10.1 Taxonomic Kingdom Plantae

classification of jute
Phylum Magnoliophyta
Class Angiospermae
Category Malvids
Order Malvales
Family Malvaceae
Subfamily Grewioideae
Tribe Sparmannieae
Genus Corchorus
Species C. capsularis, C. olitorius

repeatedly in recent decades. According to the Angiosperm Phylogeny Group (APG)

classification system, Corchorus is classified under the subfamily Grewioideae.
However, Grewioideae has been divided into two tribes, Grewieae and
Sparmannieae. The tribe includes Corchorus (jute) and Oceano papaver.
C. olitorius has a pantropical distribution, with a higher concentration in African
countries around the equatorial line, such as Ethiopia, Kenya, Tanzania, South
Sudan, Nigeria, Ghana, Benin, Togo and Guinea. In addition, it is also distributed
in Australia, South China, India and Bangladesh and sporadically found in South
East Asia, Europe, North America and South America. Natural distribution of
C. capsularis is limited mostly in South China, India, South East Asia, Australia
and Zambia. Initial assessments on the origin of C. olitorius were based on
574 C. S. Kar et al.

geographical distribution, morphological features and species richness. Based on

these parameters, Kundu (1951) proposed Africa as the primary centre of origin of
C. olitorius and India or the Indo-Burma region as secondary centres. Molecular
studies confirmed an African origin of C. olitorius (Benor et al. 2012; Kundu et al.
2013; Satya et al. 2014; Yang et al. 2018). Further, Sarkar et al. (2019) reconfirmed
the African origin of C. olitorius using SNP markers and proposed peninsular India
as a secondary centre of origin. The origin of C. capsularis, however, is still debated.
Kundu (1951) suggested Indo-Burma as the origin of C. capsularis, while Vavilov
placed the species under China centre. Archaeological evidences of C. capsularis
jute fibre in Harappa around 2200–1900 BC (Wright et al. 2012) suggest an Indian
origin of C. capsularis.
Basu et al. (2016) noticed that while the nuclear genomes of C. capsularis and
wild Corchorus species distributed in India show high genetic distance, the organelle
genomes of the two species were quite close. They suggested that C. capsularis
evolved earlier than C. olitorius and a specific haplotype of C. capsularis might have
originated in the Indo-China region. Contrary to this, Benor et al. (2012) and Benor
(2018) suggested an African origin of C. capsularis based on the distribution of wild
Corchorus species and genome size variation. Since a natural distribution of
C. capsularis was not documented from Africa, it may be possible that
C. capsularis was originated from the wild Corchorus species in India. The closest
relative of C. capsularis was found to be C. pseudo-capsularis (Benor 2018). Most
of the studies identified C. aestuans as the closest wild relative of C. olitorius
(Kundu et al. 2013), although C. pseudo-olitorius (Kundu et al. 2013) or
C. orinocensis and C. pilosus (Benor 2018) might also be the progenitor of
C. olitorius.
The two cultivated species C. capsularis and C. olitorius have similar morphol-
ogy, growth duration and physiology. They can be distinguished by a number of
features, the most prominent of which are fruit shape and size. While pods of
C. capsularis are round, pods of C. olitorius are smooth cylindrical shaped. Besides,
they have differences in several other plant and fibre characteristics. The general
features of C. capsularis and C. olitorius, as noted by Kundu (1956) and Maiti
(1988), are described in Table 10.2.

10.2.1 Wild Relatives of Jute

There are several contradictory reports on the number, occurrence and distribution of
wild Corchorus species. Since these species have been reported in different
continents with partial information, there is a lot of ambiguity, particularly over
the species relationship in Corchorus. Possibly the number of distinct species is
only 60–100, while the rest might be duplications and sub-types. The Global
Biodiversity Information Facility (GBIF, www.gbif.org) enlists 81 Corchorus
species. The occurrence distribution of these species is in the order of
C.olitorius>C.tridens>C.aestuans>C.sidoides>C.hirtus>C.siliquosus>C.trilocu-
10 Jute Breeding 575

Table 10.2 Morphological features of the two cultivated species of jute

Characters C. capsularis C. olitorius
Seed Chocolate brown seed coat colour; 1 g Seed coat colour varies from bluish
contains about 300 seeds green to steel grey or even black; 1 g
contains about 500 seeds
Seedling Seed germinates uniformly by 24 h; Seed germinates in instalment by 48 h;
seedling growth faster; full-grown seedling growth slower; full-grown
cotyledon larger cotyledon smaller
Stem Stem tapers from the base to the apex; Stem tapers gradually from the base to
the rate of transverse growth is quicker the apex forming nearly a cylinder; the
at the base, resulting in higher basal rate of transverse growth is slower at
diameter; pigment on the stem varies the base, resulting in lower base
from full green to dark red with diameter; stem pigments are full green,
intermediate shades; periderm at the light red and deep red; periderm
base develops predominantly, the formation is almost absent; height at
extent of which varies with stage of flowering is comparatively taller; less
maturity; after 40–50 days of sowing, lodging resistant
stem grew slower; height at flowering is
comparatively shorter; more lodging
resistant
Branching Auxiliary buds may or may not be Axillary buds present but branches
habit present, resulting in branched or usually develops less vigorously
non-branched stem, respectively;
auxiliary buds if present may or may
not develop into full-grown branches
Leaf Leaf base contains two free lateral Leaf base contains two free lateral
stipule stipules; green or red pigmented; may stipules; green or red pigmented
be modified into foliaceous or even
full-grown leaf like but smaller in size
in comparison to normal leaf; in
exceptional cases, the number may
vary even up to 6 at each node (3 on
each side of the leaf base)
Petiole 4–8 cm length; varies in colour from 4–9 cm in length; may be green or red
green to dark red pigmented
Lamina Usually, ovate-lanceolate in shape with Usually, ellipsoidal lanceolate with
coarsely serrated margins; lower most smooth serrated margin, lower most
pair of serrations develop into filiform pair of serrations develop into filiform
appendages, in dark red types, red appendages more predominantly; in
pigmented develop uniformly on leaf deep red types, red pigment develops in
surface, particularly on veins; taste of patches on leaf surface; taste of leaves
leaf is bitter; rate of leaf fall is less non-bitter; rate of leaf fall is more
Root Tap root less deep, more lateral roots; Tap root deeper, less lateral roots; less
more tolerant to waterlogging; tolerant to waterlogging condition;
produces a greater number of produces a smaller number of
adventitious roots adventitious roots
576 C. S. Kar et al.

>C.tridens>C.aestuans>C.sidoides>C.hirtus>C.siliquosus>C.trilocularis>C.hi-
C.tridens>C.aestuans>C.sidoides>C.hirtus>C.siliquosus>C.trilocularis>C.hirsu-
C.tridens>C.aestuans>C.sidoides>C.hirtus>C.siliquosus>C.trilocularis>C.hirs-
>C.aestuans>C.sidoides>C.hirtus>C.siliquosus>C.trilocularis>C.hirsutus>C.f-
C.aestuans>C.sidoides>C.hirtus>C.siliquosus>C.trilocularis>C.hirsutus>C.fasc-
icularis > C. capsularis (Fig. 10.1). Most of the species, except C. aestuans, show
very little/nil crossability with C. olitorius and no crossability with C. capsularis,
limiting the primary gene pool within the respective species. C. aestuans has a
pantropical distribution with high occurrence in China, Australia, India, South
East Asia and West Africa. Surprisingly, report of natural distribution of
C. aestuans in East Africa, particularly in Kenya and Ethiopia, is very low (GBIF,
www.gbif.org).
The Flora of China (2007) enlists four species, C. olitorius, C. capsularis,
C. aestuans and C. trilocularis, to be present in China. Eight wild Corchorus species
(C. aestuans, C. depressus, C. fascicularis, C. pseudo-olitorius, C. tridens,
C. trilocularis, C. urticifolius and C. velutinus) and the two cultivated species are
found in natural habitats in different parts of India. Among these, C. aestuans has the
highest distribution, followed by C. olitorius, C. capsularis, C. tridens,
C. trilocularis and C. fascicularis, respectively. The wild jute species harbour
several important traits that can be useful in jute breeding. For example,
C. aestuans exhibits higher resistance to diseases, particularly to stem rot. A wild
accession of C. aestuans has been registered in India as a resistant genetic stock and
is being utilized in jute breeding programme. Another interspecific derivative of
C. olitorius and C. aestuans, RS-6, exhibits high resistance to stem rot disease, has
considerable resistance to early flower initiation and produces fibre comparable to
the popular cultivars (Mandal et al. 2021).

10.3 Plant Genetic Resources

Based on species richness of Corchorus, explorations were made by the Interna-

tional Jute Organization (IJO) in 1987 in Kenya and Tanzania, and a total of
374 seed samples representing 12 Corchorus species were collected. Explorations
were also made in different countries including China, Indonesia, Nepal, Thailand
and Pakistan to collect wild Corchorus germplasm from their natural habitats. A
total of 2300 accessions were collected by the IJO and distributed to different
countries for evaluation, conservation and utilization in Corchorus breeding
programmes. The Gene Bank of the Germplasm Division, Bangladesh Jute Research
Institute (BJRI) was designated as the IJO Centralized Germplasm Repository.
Presently, BJRI maintains about 6000 germplasm of jute and mesta, including
2380 accessions of C. capsularis and 1450 accessions of C. olitorius (Miah et al.
2020). A total of 655 accessions covering landraces and wild relatives of Corchorus
and allied fibre crop species from different agroclimatic regions were collected
during 1999–2004 under NATP (National Agricultural Technology Project) and
10 Jute Breeding 577

characterized. As of 2021, India has a working collection of 3500 Corchorus

accessions being conserved in the midterm gene bank of Central Research Institute
for Jute and Allied Fibres (ICAR-CRIJAF), Barrackpore. A base collection is
maintained in the National Gene Bank at the National Bureau of Plant Genetic
Resources, New Delhi. The Institute of Bast Fibre Crops, Changsha, and the Fujian
Agriculture and Forestry University, Fuzhou, in China hold 10,970 germplasm of
bast fibre crops including jute (Zhang et al. 2019).

10.4 Floral Biology, Emasculation and Pollination Techniques

10.4.1 Key to Cultivated Species

• Capsule globose, seed brown, without transverse septa between seeds

(C. capsularis).
• Capsule elongated, cylindrical, seed dark greyish to bluish with transverse septa
between seeds (C. olitorius).

10.4.2 Floral Biology

10.4.2.1 Corchorus olitorius

Inflorescence is cymose, opposite to leaves, 2–5 flowered, sometimes solitary,
peduncle about 1 cm long, pedicle 1–3 mm long, bract up to 3 mm long and all
glabrous. Sepals are usually 5–6, free green 5–7 cm long, tips prolonged into flower
bud, ciliate at the basal margin. Petals are usually 5 in number, rarely 6 or more, pale
yellow, oblanceolate, 4–7 mm long. Stamens are numerous, free, about 30–60
anthers, yellow. Ovary is superior, elongated, cylindrical, up to 3.5 mm long,
5 carpelled usually, rarely 6 or more, placentation axile, ovule linearly placed in
each locule, style 3–5 cm long, stigma globular, entire, pubescent. Fruit is cylindri-
cal, 10 ribbed, beaked capsule, 5–10  0.5–0.8 cm in size, dehiscing by 5 valves
with transverse septa between seeds. Seeds are small, pyramidal, angular, 1–2 mm
long, dark greyish, bluish in colour, about 500 in number per gram.

Floral formula:

10.4.2.2 Corchorus capsularis

Inflorescence is cymose or solitary, 2–5 flowered, opposite to leaves; sepals are
usually 5, free, narrow, 4–5 cm long. Petals are usually 5, yellow, 4–7 mm long,
oblanceolate. Stamens are 20–30, free, filament short, anthers small, bi-lobed; ovary
is superior, 5 carpelled, syncarpous with numerous ovules, placentation axile; styles
short, 2–4 mm, stigma flattened, 2–3 fid, pubescent. Fruit is globose capsule,
1.2–2 cm in diameter, wrinkled, 10 ridged, flattened at the top, dehiscing
578 C. S. Kar et al.

loculicidally into 5 valves, without transverse partition between seeds. Seeds are
small, 2–3 mm long, oval, pointed, conclave on one surface, copper brown in colour,
about 300 in number per gram.

Floral formula:

10.4.3 Emasculation

Emasculation is done 1 day ahead or at the time of opening of the flowers. In

C. capsularis, emasculation could be done in the very early morning before 5:
30 a.m. on the date of pollination, as anthesis in the species starts one after sunrise.
Emasculation at that time is sometimes preferred because of larger bud size. In
C. olitorius, emasculation in the morning is not advised because anthesis starts about
1 h prior to sunrise. The most advanced bud in the inflorescence can be identified
from its size and yellow colour of the petals and anthers. The buds selected are
opened and the stamens are removed with fine pointed forceps. The emasculated
flowers are covered with small butter paper bags to protect them from the dew
and rain.

10.4.4 Pollination Technique

Self-pollination is the rule in this crop in both Corchorus capsularis and Corchorus
olitorius. The natural crossing in C. capsularis is higher rate, and it is due to the wind
pollination and insect visitation. Anthesis starts 1–2 h after sunrise in C. capsularis
and about an hour before sunrise in C. olitorius. The stamens usually burst before
anthesis.

10.4.4.1 Selfing
To ensure self-fertilization, the flowers may be protected by covering them with fine
mesh muslin bags or a polyethylene lantern. This is necessary in the C. capsularis
species where cross-pollination is much higher. The supports by bamboo stakes are
given to bags which are covering the flowers, since the jute is a tall plant and
inflorescence is at the top.

10.4.4.2 Crossing
Cross-pollination between varieties within a species is readily made, but the inter-
specific crosses are rarely successful. This is due to endosperm abortion. The flowers
which will be used as pollen source are wrapped with cotton in the afternoon of the
day preceding pollination. This process precludes contamination. The stigma of the
emasculated flower is lightly touched with a ripe anther, and the pollen is dusted on
the stigma. Pollination should be started immediately after opening of the flower. In
C. olitorius, flowers open around 7:30 a.m., and in C. capsularis, that happens
10 Jute Breeding 579

around 8:30 a.m. It is desirable that pollination in both the species be completed
within half an hour before blooming. Rain immediately after pollination washes the
pollen and poses a hindrance to pod setting. For assured pod setting at least 2 h,
rain-free weather after pollination is essential in both species. After pollination, the
flowers are bagged for 24 h. Seed capsules matured in about 6 weeks.

10.5 Molecular Cytogenetics and Breeding

Studies on molecular cytogenetic in jute species C. olitorius and C. capsularis very

less as it is a neglected crop but a major cash crop of South East Asian countries. The
genomes and chromosomes of tossa jute and white jute (Corchorus species) are
poorly studied. Chromosome-specific physical localization of genes in jute was
investigated by studying association and localization of single copy expressed
sequence tag (EST) loci in the Corchorus olitorius genome (Joshi et al. 2014) in
mitotic interphase nuclei of specific trisomic(s) for fluorescence in situ hybridization
and validating using a cDNA fragment of the 26S rRNA gene (600 bp) as a
molecular probe. When same probe was hybridized, the pachytene chromosomes
of diploids confirmed that 26S rRNA occupies the terminal end of the short arm of
chromosome 5 in C. olitorius. Similarly, physical localization of 63 single copy EST
chromosome-specific association were determined on chromosomes 2, 4, 5 and
7. This will be useful in the construction of genome-wide physical maps of jute.
Begum et al. (2013) used a comparative analysis through FISH karyotyping of a
prominent satellite DNA family, identified in this study, to reveal its diversification
and emerging subfamily structure in both jute genomes with conserved heteroge-
neous distribution along chromosomes. A reference karyotype for both jute species
also generated using ribosomal genes and retrotransposon sequences for
chromosome-specific distribution of the satellite DNA for in situ hybridization.
This study will be useful for genetic mapping and analysis of hybridity.

10.6 Genetic Studies of Qualitative and Quantitative Traits

Genetic analysis in jute was initiated in India during the first decades of the twentieth
century. Finlow and Burkill (1912) first reported that red pigmentation in stem was
dominant over green pigmentation and exhibits monogenic inheritance. Later, more
genes were reported to control plant pigmentation (Basak et al. 1993). Although this
trait is controlled by few genes, its expression changes with age, exposure to sunlight
and stress. In India, jute farmers prefer green stem over red stem believing red
pigmentation might interfere with fibre colour. But the pigmentation is formed in the
outer epidermal layer, which is eaten away by microbes during retting; thus, there is
no valid reason to support this idea. However, most of the elite cultivars of
C. capsularis and C. olitorius bear green pigmentation considering the farmers’
preference.
580 C. S. Kar et al.

10.6.1 Genetics of Qualitative Characters

Among the various qualitative traits in jute, anthocyanin pigmentation of stem has
been studied more extensively, and it was found complex in nature. Other qualitative
characters studied are related to stem, leaf colour, leaf texture, leaf surface, shape,
serration, flower seed coat colour, leaf taste, pod shape, stipule, pod shattering and
fibre colour in both C. olitorius and C. capsularis. Almost all characters are found
to be controlled by monogenic recessive genes with exceptions of digenic leaf
characters (leaf glossiness, leaf rolling in C. olitorius and narrow leaf in
C. capsularis) and digenic duplicate for fuzzy seed coat colour (Table 10.3).
The three major plant characters that form the ideotype of present-day elite jute
cultivars are non-shattering property of pod, resistance to earliness in flowering and
non-branching plant type. Earliness in flowering (also referred to as premature
flowering) is a typical problem of jute cultivation. Being a short-day plant, jute
flowers bloom during September–October (white jute) and October–November
(tossa jute). For fibre cultivation, the recommended sowing period of jute is first
week of April. As it is a rainfed crop, sowing depends on the onset of monsoon, and
farmers often sow the crop in early or late March. C. capsularis is comparatively
more tolerant to premature flowering than C. olitorius. Resistance to earliness in

Table 10.3 Genetics of some important qualitative characters in jute

Character Inheritance pattern Reference
Undulated hypocotyl Duplicate dominance Satya and Sarkar (2018)
Dwarf stem Monogenic recessive Basak et al. (1993)
Stiff stem Monogenic recessive Basak et al. (1993)
Broad/narrow leaf Three interacting genes Basak et al. (1971)
each with two alleles
Chlorina leaf Monogenic recessive Thakare et al. (1973)
Yellow leaf Monogenic recessive Thakare et al. (1973)
Waxy leaf Monogenic recessive Basak et al. (1993)
Leathery leaf Monogenic recessive Basak et al. (1993)
Rolled leaf Digenic complementary Basak et al. (1973)
Drooping leaf Monogenic recessive Basak et al. (1993)
Crumpled leaf Monogenic recessive Basak et al. (1993)
Palmate leaf Monogenic recessive Ghosh and Sen (1971)
White flower Monogenic recessive Basak et al. (1993)
Round pod Monogenic recessive Basak et al. (1993)
Fruit dehiscence Monogenic recessive Joseph (1972)
Fuzzy seed coat Digenic duplicate Basak et al. (1971)
Green seed coat colour Monogenic recessive Basak et al. (1971)
Ribbon leaf Monogenic recessive Mitra (1977)
Bitter leaf test Monogenic recessive Ghosh et al. (1948)
10 Jute Breeding 581

flowering in C. olitorius was first identified in an African accession Sudan Green,

which was then transferred to the new cultivars.
Since flowering itself is a complex organized process at the cellular level, change
in the external environment such as onset of drought can cause drastic morphological
changes. With global warming and change in climatic conditions, the tolerant
cultivars are also showing sign of susceptibility during the past few years under
harsher climatic conditions. The inheritance of premature flowering is not well
understood. However, insensitivity to photoperiod in jute is controlled by a mono-
genic dominant gene. Branching is an undesirable character in jute, because it
reduces fibre quality. The branching habit in jute is controlled by a single gene,
branched type being dominant over non-branched type. The same genotype, when
sown for seed crop, exhibits branching under long day. Thus, branching is also
controlled by environmental conditions and crop management.
Transition to non-shattering pod type from shattering pod type is a common sign
of plant domestication of many crop species, such as rice, wheat, grain legumes, etc.
Certain genetic stocks of jute are shattering type, but the released cultivars are all
non-shattering type. This character exhibits monogenic inheritance, non-shattering
type being dominant over shattering type.

10.6.2 Genetics of Quantitative Characters

As jute is a bast fibre crop, the product fibre is obtained from the bark of the plant.
Also, commercially useful fibre and seed cannot be obtained from the same crop. A
variety of mating designs, including line  tester, diallel and triallel, have been used
to partition the genetic variance into additive and dominance components. Most of
these reports suggest that fibre yield is controlled predominantly by dominance gene
action, although additive gene actions are also important. As the fibre yield in jute is
polygenically inherited and is highly influenced by genotype and environment
interactions, selection of plant is based indirectly on two most important component
characters, i.e. plant height and base diameter of the stem. Other traits like fibre
percentage, green weight, top diameter and fibre wood ratio are also considered for
indirect selection criteria. Genetic association studies revealed that these two
characters along with other characters such as leaf biomass, internode length and
node number have good correlation with fibre yield. Both these characters are under
control of quantitative gene action. Contradictory reports have been published
regarding genetics of these two characters, although dominance gene action seems
to be more important than additive gene action. Most of the reproductive characters
are also controlled by quantitative gene action (Table 10.4).
582 C. S. Kar et al.

Table 10.4 Inheritance of major quantitative characters in jute

Inheritance
Character Mating design pattern Reference
Fibre yield Diallel (12-parent) VA ¼ VD Rahman (1968)
Diallel (5-parent) VD > VA Jana (1972)
Diallel (10-parent) VA > VD Jana (1972)
Diallel (7-parent) VD> > VA Singh (1975)
Generation mean h>d Paul et al. (1977)
analysis
Diallel (7-parent) VA > VD Kumar (1987)
Half-diallel (7-parent) VA ¼ VD Mandal and Choudhury
(1988)
Diallel (11-parent) VD > VA Kumar and Palve (1995)
Diallel (11-parent) VD > VA Mitra et al. (2005)
Half-diallel (7-parent) VD > VA Kumar et al. (2016)
Basal diameter Diallel (7-parent) VD only Singh (1975)
Diallel (11-parent) VD > VA Kumar and Palve (1995)
Diallel (10-parent) VA > VD Khatun et al. (2010)
Half-diallel (7-parent) VD > VA Kumar et al. (2016)
Plant height Diallel (5-parent) VA > VD Jana (1972)
Diallel (10-parent) VD > VA Jana (1972)
Generation mean Duplicate Basak and Dana (1971)
analysis epistasis
Diallel (11-parent) VA > VD Kumar and Palve (1995)
Diallel (11-parent) VD > VA Mitra et al. (2005)
Diallel (10-parent) VA > VD Khatun et al. (2010)
Half-diallel (7-parent) VD > VA Kumar et al. (2016)
Number of Generation mean Duplicate Basak and Dana (1971)
nodes analysis epistasis
Diallel (5-parent) VA > VD Jana (1972)
Diallel (10-parent) VD > VA Jana (1972)
Diallel (11-parent) VA > VD Mitra et al. (2005)
Fibre Diallel (11-parent) VA > VD Kumar and Palve (1995)
percentage Diallel (11-parent) VA > VD Mitra et al. (2005)
Days to Diallel (5-parent) VA > VD Jana (1972)
flowering Diallel (10-parent) VA > VD Jana (1972)
Diallel (11-parent) VA > VD Kumar and Palve (1995)
Internode length Diallel (8-parent) VD > VA Ghosh and Das (1980)
Root weight Diallel (8-parent) VD only Basak et al. (1973)
10 Jute Breeding 583

10.7 Breeding Objectives

Till the 1970s, jute was grown in the filed for a period of 150–160 days, and plants
were harvested at early pod setting stage. Tossa jute flowers at early vegetative stage
if sown during March as it is a short-day plant, so the usual sowing practice of tossa
jute was end of April to mid-May. As most farmers grew one crop in a year, jute and
rice were not grown in the same field in a year. However, with the introduction of
semi-dwarf photo-insensitive rice varieties, a new jute-rice cropping system emerged
in the Gangetic delta. To fit to this cultivation practice, jute was harvested by
120–130 days, and farmers started to be pre-pone sowing of tossa jute to
mid-March to mid-April. Thus, the ideotype of jute in India and Bangladesh was
changed to suit the growth duration. New cultivars developed in the later part of the
twentieth century (JRO-524) and the early twenty-first century (JRO-204, CO-58,
JRO-128) have been developed considering the growth period of 110–120 days and
sowing in mid-March to mid-April.

10.7.1 Fibre Yield and Yield Contributing Characters

The economic product of jute, the fibre strand, is a vegetative tissue, which lies
within the secondary phloem of the bark. The fibre strands are cells with thickened
lignocellulosic cell wall. The primary breeding objective is to increase the amount of
fibre strands, which can be achieved by increasing the number of fibre cells,
increasing the length of each fibre cell or increasing the thickness of individual
fibre cells. Since the length and thickness of each fibre cell do not vary much,
increasing the number of fibre cells through more biomass accumulation is the only
practical breeding target. Breeders have traditionally targeted to increase this by
selecting for more plant height and increased radius of the stem. Under favourable
condition, jute plant reaches a height of 3.5–4.5 ft within a period of 120 days. Since
the growth duration is the main limiting factor, selection should be made for faster-
growing genotypes. However, jute is not a deep-rooted crop, so increasing above-
ground biomass without giving attention to root architecture increases the chance of
lodging. This can be observed in the rainy season when jute is grown in highly fertile
loose soil. The plants tend to lodge also under wind pressure at higher dose of
nitrogenous fertilizer application. Thus, the development of lodging tolerant jute
varieties which can also utilize more nitrogen to increase fibre content is also
becoming a priority. The present-day tosha jute varieties are capable to produce
40–45 q/ha fibre under favourable conditions and 30–32 q/ha under moderately
fertile soil with proper crop management practices. There is not much scope for fibre
yield improvement for the present plant type, and farmers are more concerned with
quality and marketability of jute fibre.
584 C. S. Kar et al.

10.7.2 Quality Characters Including Biofortification

Farmers are more concerned with quality and marketability of jute fibre. Therefore,
the current focus on genetic improvement is to develop varieties for specific target
environments and diverse end uses. In addition to its traditional use as bags and
sacks, alternate use of jute fibre is becoming more popular day by day as people are
becoming more concerned with the ill fates of using synthetic fibres. Demand for
jute plant and jute fibre as geotextiles, fibre composites, upholsteries, value-
enhanced carrying case and textile blends is on the rise. In addition, industries are
being established for the production of biofuel, biochar, herbal products and vegeta-
ble jute, which have high market demand in both Eastern and Western countries.
Considering the present and future jute cultivation scenario, jute breeders are trying
to develop jute varieties for alternate use. For example, for the production of
diversified jute products, fibre fineness is an important parameter. On the other
hand, for geotextile, fibre strength and meshiness of the fibre are important so that
coal tar can better adhere to the fibre surface.

10.7.3 Biotic Stresses

Over 40 insect pest species infect jute. However, only a few of them are major insect
pests of jute, namely yellow mite (Polyphagotarsonemus latus), hairy caterpillar
(Spilosoma obliqua), stem weevil (Apion corchori), indigo caterpillar (Spodoptera
exigua) and jute semilooper (Anomis sabulifera). The jute cultivars, in general,
exhibit good field resistance to insect pests, except yellow mite. Only a few resis-
tance sources have been identified against these insect pests in jute. Most of the
resistance sources have come from the indigenous and exotic germplasm of jute. The
cultivar JRO-204 exhibits moderate resistance to yellow mite. The major diseases of
jute are stem rot (c.o. Macrophomina phaseolina), anthracnose (c.o. Colletotrichum
corchorum and C. gloeosporioides), black band (c.o. Botryodiplodia theobromae)
and soft rot (c.o. Sclerotium rolfsii). Stem rot is the most prevalent disease of jute
causing a crop loss of 15–20%. However, in specific zones, 100% crop loss can
occur. The causal organism Macrophomina phaseolina is a soil-borne/seed-borne/
air-borne pathogen and infects over 150 species. Despite many attempts, genetics of
resistance to stem rot is not well understood. One of the major reasons is
non-availability of suitable artificial screening techniques for screening and definite
disease scoring pattern. Of the cultivars grown in India, JRO-204 exhibits moderate
resistance to stem rot. Wild species are good sources of resistance to insect pests and
diseases. C. aestuans, a close relative of cultivated jute, exhibits good resistance
against hairy caterpillar. A C. aestuans genotype, WCIN-136-1 (INGR21036),
exhibits high resistance against stem rot. Interspecific hybridization between
C. olitorius and C. aestuans has resulted in the development of advanced breeding
lines showing resistance to stem rot (Mandal et al. 2021). Another wild species,
C. fascicularis, has resistance against indigo caterpillar. A list of jute genotypes that
exhibit resistance to major insect pests and diseases of jute is provided in Table 10.5.
10 Jute Breeding 585

Table 10.5 Important target traits in jute breeding

S. no. Trait Genotype Reference
1. High fibre yield C. olitorius: Chinsurah Green, JRO-524, Pandey et al. (2015)
JRO-204, JRO-8432, JRO-878, S-19,
Tarun, JRO-128, JROMU-1, JROB-2;
O-4, O-9897, OM-1, O-72, Yueyuan-
5hao, Cuigreen, Guangfengchangguo
C. capsularis: D 154, JRC-321,
JRC-212, JRC-517, JRC-532, JRCJ-11,
Huangma-971, Huangma-179, Xinyuan-
2, Minma-91, CVL-1, C-83
2. Resistance to C. capsularis: All varieties (early march)
earliness in C. olitorius: JRO-204 (mid-March);
flowering NJ-7010, JROBA-3 (early March), RS-6
(early March)
3. High fibre JRO-204, JRO-128
strength
4. Better fibre C. capsularis: JRC-212, JRCM-2 Pandey et al. (2015)
fineness C. olitorius: JROG-1, JROM-1, S-19,
JROB-2
5. High plant C. olitorius: JROB-2 AINPJAF Annual
biomass Report, 2018–2019
6. Vegetable jute C. olitorius (India): JRO 204, BJRI Deshi Islam (2019)
pat Shak-1 and BINA pat Shak-1
7. Climate resilient JROB-2 Sharma et al. (2019)
jute
8. High fertilizer JROB-2, JRO-204 AINPJAF Annual
use efficiency Report, 2018–2019
9. Insect pest Yellow mite: JRO-204, JROG-1 Dikshit et al. (1989)
resistance Stem weevil: C. capsularis—JRC-5145, and Roy et al. (2019)
Mogra, Maniksari, Capsularis Hard
Stem, BJRI Deshi Pat-7
C. olitorius—JRO-878, JRO-514
10. Disease Stem rot: C. olitorius—JRO-204, RS-6, Mandal et al. (2021)
resistance OIN-154
C. capsularis—CIM-036
11. High biomass JROB-2 Indian Gazette
notification
12. High cellulose JROB-2 Sharma et al. (2019)
content in
biomass
13. High β-carotene JRO-204, JRO-8432 Choudhary et al.
(2013)
14. High foliage JRO-204, JRO-8432 Choudhary et al.
yield (2013)
15. High potassium JRO-204, JRO-8432 Choudhary et al.
content (2013)
(continued)
586 C. S. Kar et al.

Table 10.5 (continued)

S. no. Trait Genotype Reference
16. Low lignin C. olitorius: Sengupta and Palit
C. capsularis: dlpf (7%) (2004) and Kundu
et al. (2013)
17. Phytoremediation Cu-phytoremediation— Nizam et al. (2016)
HongTieGuXuan (HT), C-3 and Saleem et al.
As tolerance—CVE-3 (2020)
18. High flavonoids C. olitorius—T-8, Kuangyechangguo, Biswas et al. (2020)
Funong-6
19. Anti-oxidation C. olitorius—T-8, Funong-6 Biswas et al. (2020)
capacity
20. Tolerance to D-154, CVL-1; C. capsularis more Prodhan et al. (2001)
waterlogging tolerant than C. olitorius
stress
21. Tolerance to JRO-204, O-4; C. olitorius more tolerant Yang et al. (2017)
drought stress than C. capsularis
22. Tolerance to JRC-517, CIN-536, CIN-538 Sharma et al. (2012)
salinity stress

10.7.4 Abiotic Stress Resistance Including Climate Change

Jute yields are seriously impacted by biotic factors (~30% loss from stem rot
diseases Macrophomina phaseolina) and by abiotic stresses (such as waterlogging,
drought and salinity). Among the two cultivated species, C. capsularis L. is a
drought-sensitive species, and C. olitorius L. is a drought-tolerant species. The
jute crop faces drought stress in early growth phase and waterlogging stress during
later growth stage. In competition with food crops and other remunerative crops, jute
cultivation is declining gradually. Genotype-environment interaction is more promi-
nent in crops like jute where economic produce is obtained from the vegetative part
of the plant. Commercially valued fibre should fulfil a certain criterion for proper
grade jute fibre, which is largely impacted by abiotic stress. One of the abiotic stress-
induced traits is early flowering of jute specifically in C. olitorius jute. Low night
temperature, cloudy sky and short daylength coupled with drought often induce
early flowering in jute, which is detrimental for fibre quality. Early flowering of jute
is always followed by stem bifurcation at top and branching which impact fibre
grade. India is successful in intro-gressing late flowering gene from African
genotypes to adapted Indian varieties of tossa jute. Therefore, it is necessary to
develop jute varieties that are tolerant to changing environmental conditions via
molecular breeding strategies. Gene and QTL mapping involved in jute drought
stress is not reported till date. Drought tolerance in jute plants is carried out mainly
on the evaluation of drought-resistance germplasm and morphological, physiologi-
cal and biochemical changes during drought response and transcriptome sequencing
(Kabir et al. 2021; Yang et al. 2017).
10 Jute Breeding 587

10.7.5 Exploitation of Heterosis and Hybrid Development

Several attempts were made to exploit heterosis in jute for the development of new
cultivars. Although dominant genetic variation contributes significantly to fibre yield
and its component characters like plant height and basal diameter, the extent of
heterosis was low in most of the cross combinations tested. Moreover, flowering in
jute is indeterminate that continues for a period of 64–72 days (Mukherjee and
Kumar 2002) on both primary and secondary branches. Moreover, C. olitorius
exhibits 10–12% cross-pollination. Under such condition, a mechanism for
controlled pollination is essential to develop an economic hybrid seed development
method. However, no such controlled pollination (male sterility/self-
incompatibility) is available in jute. A ‘ribbon’ mutant of C. capsularis cv. JRC
212 was reported to exhibit male sterility (Rakshit 1967), but was later lost.
Moreover, sterility in this mutant had pleiotropic relation with several undesirable
characters, such as delayed anthesis, small flower and weak growth, rendering it
unsuitable for hybrid breeding (Mitra 1977). A ribbon leaf mutant (bfs) of
C. olitorius (Kundu et al. 2012) exhibits high pollen fertility. A total of 1541
accessions of C. olitorius germplasm were screened by Mukherjee and Kumar
(2002), but no male sterile line could be identified. Sharma et al. (2017) used various
chemical agents to induce male sterility in jute and reported maleic hydrazide as a
promising chemical hybridizing agent. Induced male sterility, therefore, may be a
promising option for hybrid breeding in jute.

10.8 Breeding Approaches—Conventional

and Non-Conventional Including Use of Genomic Tools

10.8.1 Conventional Breeding

Jute breeding was initiated a century ago by R. S. Finlow and I. H. Burkill in India
using (1) selection of superior genotypes from the cultivated types and
(2) hybridization of promising genotypes (Roy 1968). The initial selection was
based on ‘single plant culture’ using characters like plant height, sparse branching
and freedom from chlorosis. Two mega-varieties of jute, ‘D-154’ of C. capsularis
and ‘Chinsurah Green’, were identified based on the principles of pure line selection,
for which R. S. Finlow must be given due credit. Later, R L. M. Ghosh and J. S. Patel
established high correlation of fibre yield with plant height (r ¼ +0.76) and thickness
of the plant (basal diameter) (r ¼ +0.91) and used replicated progeny row trials,
selecting the most promising families, resulting in selection of promising lines like C
39–212 and C 42Kj-321 in C. capsularis and 040–632, 040–753 and 039–620 in
C. olitorius (Roy 1968). Partitioning of India and Pakistan destabilized the breeding
programme, resulting in loss of most of the genetic material. Indian breeding
programmes were re-initiated at newly established Jute Agricultural Research Insti-
tute (JARI), Nilganj, Barrackpore (later renamed as ICAR-CRIJAF). Jute breeding
work continued at Pakistan under the Jute Agricultural Research Laboratory (JARL),
588 C. S. Kar et al.

Dhaka, which was renamed first as Jute Research Institute in 1951 and then as
Bangladesh Jute Research Institute in 1971 after the independence of Bangladesh.
Roy (1968) proposed an additional criterion, fibre/wood ratio for selection. Overall,
in a segregating progeny, characters like germination, pigmentation, plant height,
basal diameter, uniformity of the population and dry weight of fibre are considered.
Based on the breeding objectives, the following breeding methods have been
adopted in jute.

10.8.1.1 Direct Introduction of Cultivars from Other Countries

Often, successful cultivars developed in other countries are introduced for direct
cultivation. The most prominent example of direct introduction of jute is cultivation
of C. olitorius cultivar JRO-524 in Bangladesh which was developed in India
(Mukul and Akter 2021; USAID/EAT 2014). While the cultivar JRO-524 is not
notified in Bangladesh (USAID/Enabling Agricultural Trade (EAT) project report
2014), about 2500–4000 ton seed of JRO-524 is exported from India to Bangladesh
each year, which is 80–85% of the total jute seed requirement of Bangladesh (IMED
2016). D-154, developed in India, was introduced in China and is cultivated for a
long period (Yang et al. 2018). Tanganyika-1, an African landrace, was introduced
and domesticated in India as a fibre-type cultivar. Several tossa jute varieties were
introduced from India (Cuilv), Pakistan (Bana 72–1, Bana 72–1, Bana 72–1,
Bachang 4/O-4) and Mali (Maliyeshengchangguo) to China (Zhang et al. 2019).

10.8.1.2 Pure Line Selection

Pure line selection is performed either to select superior lines from landrace/germ-
plasm through selfing and progeny test or to purify old cultivars. Replicated trials are
performed in later generations to minimize environmental effects. A number of jute
cultivars have been developed through pure line selection (Table 10.6). It can be
observed from the table that cultivars like D-154, JRC-212 and Xinxuan-1 were
purified through this method for the development of new cultivars. For
re-purification of cultivars, Roy (1968) suggested to take 200 seeds of the initial
cultivar and grow single plant progenies to identify the original pure line.

10.8.1.3 Pedigree Breeding

Pedigree breeding involves hybridization between two or more homozygous
genotypes (pure line/inbred) and selection of improved genotypes from segregating
generation through single plant selection. Pedigree breeding and its modified
schemes are widely utilized to develop new improved genotypes in all the sexually
propagating crops including jute. For comparative evaluation, Roy (1968) suggested
growing of F3 nursery along with parents and selection of superior F3 lines using
modified mass selection method. For microplot trials of advanced generations,
simple lattice design should be followed. Several jute varieties have been developed
through this method in India, Bangladesh and China (Table 10.7).
 10

Table 10.6 Cultivars developed through pure line selection in jute

C. capsularis C. olitorius
Country Variety Source Variety Source
India D-154 Kakya Bombai Chinsurah Green Local Landrace
Jute Breeding

JRC-206 Liza Fanduk Local Landrace

JRC-212 Local Landrace JRO-632 Local Landrace
JRC-321 Hewti JRO-620 Local Landrace
KJC-7 Local Landrace Guangfong Local Landrace
KTC-1 IC-30730
BCCC-1 CIJ-123
BCCC-2 CIN-492
China Hongtiegu Local variety Zhema-1 Cuilv
Hepingzhuhaoma Local variety Yuanjiang-101 Cuilv
Hainanqiongshan Local variety Heganhuangma Local Landrace
Xinfeng Xinfengqingpi Guangfengchangguo Local Landrace
Yuanguo-564 Meifeng-4 Xianhuang-2 Guangfengchangguo
Xinyuan-1 D-154 Changguo-134 Yuanjiang-101
Xinyuan-2 JRC-212
Yueyuan-1 Taiwan local
Yueyuan-2 Xinxuan-1
Yueyuan-1 Xinxuan-1
Bangladesh D-154-2 D-154 OM-1 (BJRI Tossa Pat-3) –
CVL-1 – BJRI Tossa Pat-7 OM-1
CVE-3 – BJRI Tossa Pat-8 Mutant line
(Derived from: Sinha and Satya 2014; Zhang et al. 2019; Islam 2019; Mukul and Akter 2021)
589
590 C. S. Kar et al.

Table 10.7 Varieties developed through pedigree breeding method in different countries
Country C. capsularis C. olitorius
India JRC-4444, UPC-94, Padma, JRC-698, JRO-878, JRO-7835, JRO-524,
JRC-80, C-517, C-532, Monalisa, JRO-3690, JRO-66, JRO-8432,
NDC-2008, JBC-5, JRCM-2, KJC-7, JRO-128, S-19, JRO-204,
JRC-9057, AAU-CJ-2, JRCJ-11 AAU-OJ-1, JBO-2003-H, CO-58,
JBO-1, JRO-2407
Bangladesh BJRI Deshi Pat-5, BJRI Deshi Pat-6, O-9897, BJRI Tossa Pat-4, BJRI
BJRI Deshi Pat-7, BJRI Deshi Pat-8, Tossa Pat-5
BJRI Deshi Pat Shak-1, BJRI Deshi
Pat-9
China Huangma-971, Yueyuan-4, Yueyuan-5, Guangbaai, Kuanyechangguo,
Yueyuan-6, Meifeng-1, Meifeng-2, Xianghuangma-1, Xianghuangma-2,
Meifeng-4, Minma-5, Huangma-179, Y007–10, Funong-4
Fuma 1, Minma-273, Minma-407,
Minma-603, Qiongyueqing, Huangma-
71–10, Zhonghuangma-1, Fuhuangma-3
(Derived from: Sinha and Satya 2014; Zhang et al. 2019; Islam 2019; Mukul and Akter 2021)

Table 10.8 List of mutant cultivars developed in jute

Crop Country Mutant variety Source Mutagen
C. capsularis India JRC-7447 JRC-212 X-ray
Bidhan Pat-1 D-154 γ-ray
KC-1 (Jaydev) JRC-4444 γ-ray
China 912 Huangma 179 γ-ray
C2005–43 Zhonghuangma 1 γ-ray
C. olitorius India KOM-62 JRO 878 γ-ray
JROMU-1 JRO 204 γ-ray
JROB-2 JRO-204 γ-ray
China Changguo-751 Guangfengchangguo –
Funong-1 Taizi-4 γ-ray
Xianghuangma-3 Kuanyechangguo γ-ray
(Derived from: Sinha and Satya 2014; Zhang et al. 2019; Islam 2019; Mukul and Akter 2021)

10.8.1.4 Mutation Breeding

Mutation breeding, the process of induction of mutation through physical/chemical
mutagenesis and selection of superior lines from the mutant progenies, has been very
successful to develop new cultivars. The application of γ-ray, a physical mutagen,
has been most successful for the development of new jute varieties (Table 10.8).

10.8.2 Genomics-Assisted Breeding

The development of molecular markers and genomics technologies during the

twenty-first century has triggered augmentation of these technologies in traditional
plant breeding. Though a number of molecular markers, particularly SSRs, have
10 Jute Breeding 591

been developed in jute, the application of these technologies is limited due to several
bottlenecks, such as delayed developments in marker and genomics technologies,
low genetic diversity, incomplete genetic maps, low marker coverage in genetic
maps, difficulty in trait-marker linkage establishment, low power of QTL detection
and preponderance of dominance variation for the quantitative traits related to fibre
yield and component characters. Despite these biological and developmental
roadblocks, significant achievement has been made in marker discovery and genetic
map construction.
Genome size as determined by various authors for C. capsularis and C. olitorius
are 280 Mb and 324 Mb, respectively (Sarkar et al. 2011), C. capsularis ~ 274
mb (Akashi et al. 2012); C. capsularis and C. olitorius ~ 336 Mb and 361 Mb
(Zhang et al. 2021), respectively. In general, C. capsularis has a smaller genome
compared to C. olitorius.
A preliminary genetic map of C. olitorius was developed by Das et al. (2012) that
placed 36 SSR markers on six linkage groups (LGs) covering 784.3 cM. Another
genetic map was developed by Topdar et al. (2013) identifying 7 LGs carrying
82 SSR markers over 799.9 cM. The first genetic map of C. capsularis was
developed by Chen et al. (2014) that contained 18 RAPD, 57 ISSR and 44 SRAP
markers. But the map contained 8 LGs and was stretched to 2185.7 cM. The first
high-density genetic map of C. olitorius was developed by Kundu et al. (2015) that
contained 503 RAD markers in 7 LGs over a much smaller distance of 358.5 cM.
Following this, a high-density genetic map of C. capsularis was developed that
contained 913 specific locus amplified fragment (SLAF) markers on 11 LGs cover-
ing 1621.4 cM (Tao et al. 2017). Yang et al. (2019) developed a C. olitorius map
containing 4839 SNP markers over a length of 1375.41 cM. Both the maps, though
have many markers, are much longer than the map length reported by Kundu
et al. (2015).
A few QTLs for fibre yield and component characters have been mapped on these
maps, such as QTLs for plant height, stem diameter, node number, fibre yield, wood
yield, green biomass and root weight (Sarkar et al. 2016). Three fibre quality
associated traits, namely fibre strength, fibre fineness and histological fibre content,
were also mapped by Kundu et al. (2015). A total of 16 QTLs for salt tolerance were
identified in C. olitorius with LOD values ranging from 2 to 4 (Yang et al. 2019). In
addition, a number of mapping populations using multiple parents are being devel-
oped to reduce linkage drag. A multi-parent advanced generation intercross
(MAGIC) population involving 20 parental lines of diverse geographical origins
has been developed (Sarkar et al. 2016), which show significant variability for fibre
yield, plant height, base diameter and green biomass. While the genetic markers
developed in jute have shown good potential for population structure and diversity
analyses, jute breeding is yet to gain benefits of genomic selection approaches.
592 C. S. Kar et al.

10.9 Precise and High-Throughput Phenotyping Protocols

for Key Traits

Since the economic product of jute is fibre, a precise phenotyping system for the
estimation of physical and chemical properties of jute fibre is a priority. An
automated fibre quality testing system has been developed in India by ICAR-
NINFET, which can estimate fibre strength, fibre fineness, colour and lustre for
grading the quality of jute fibre. Till date, no high-throughput phenotyping system
for morphological characters has been developed.

10.10 Emerging Challenges at National and International Levels

• Narrow genetic base.

• Lack of a high-throughput phenotyping system.
• Lack of efficient transformation protocol through tissue culture or other method.
• Establishment of jute crop suitable for diversified uses like biomass, biofuel, etc.

10.11 Breeding Progress/Varietal Development

Since the inception of concerted crop improvement efforts in jute during the early
twentieth century, several varieties of jute have been developed worldwide. In
accordance with the contemporary cultivation practices and demand of farming
community, each of these varieties was targeted for certain specific traits. While
the primary goal of the jute breeders is to increase fibre yield, the plant type of jute
has changed considerably over this long time period, and a number of diversified
applications are upcoming.

10.11.1 Modernization of Crop Improvement Programme

As jute is a fibre crop of regional importance, the research thrust is also limited in
national and international levels. With the increase in awareness about the detrimen-
tal effect of synthetic fibres including plastics, more emphasis has been directed
towards research on environment-friendly jute crop. Modern crop improvement
programme includes genomic research in jute in different countries like India,
China and Bangladesh. The use of genomic tools and advanced breeding methods
like marker aided selection, speed breeding and transgenic research and the use of
genome editing tools may open a new avenue in future in crop improvement in jute.
10 Jute Breeding 593

10.11.2 Status of Varietal Development and Maintenance Breeding

The breeding history of jute is very short. In the fertile tracts of Eastern India, jute
has been fitted to a cropping season starting from March to April which favours
vegetative growth and delays initiation of reproductive phase. During earlier years,
i.e. up to the 1960s, jute was being cultivated for longer crop duration, starting from
March extending up to August.
Under high rainfall conditions, C. capsularis (white jute or guti pat) was much
preferred over C. olitorius (tossa jute or shuti pat). Capsularis jute had three major
advantages: tolerance to premature flowering during early growth phase, ability to
withstand waterlogging condition and production of fibre having better quality.
C. olitorius was less cultivated by farmers during that time, and the cultivation
was limited to certain pockets. However, the situation has reversed during the last
50 years. Tossa jute is now cultivated over 95% of the jute area, whereas the area
under white jute has reduced to 5% of the total area under cultivation.
The system of jute-based agriculture has also changed over the past 50–60 years
considerably, challenging breeders to change the ideotype for enhancement of
productivity and quality. Thus, the crop ideotype of jute has undergone considerable
changes, challenging of directed breeding efforts. Systematic crop improvement for
jute was started by R. S. Finlow in 1904 at Burdwan district of West Bengal,
followed by establishment of Jute Agricultural Research Laboratory (JARL) at
Dhaka in 1939 where some breeding works were carried out. Varietal development
in capsularis jute was initiated through selection during 1900–1920. The first white
jute variety Kakya Bombai was developed in 1916. Further improvement of Kakya
Bombai resulted in the development of D-154 in 1919, which was less susceptible to
chlorosis and more resistant to stem rot. The first tossa jute variety D-38, commonly
known as Chinsurah Green (CG), was developed in 1915 through selection. It was
the only tossa jute variety for general cultivation for a long period.

10.11.3 Varietal Development: Post-Independence of India

After India gained independence in 1947, the major jute area goes to Bangladesh,
whereas the Hooghly River based jute industries remained in India. The major
challenge for Indian jute breeders was to develop varieties suitable for new areas
having wider adaptation. After 1947, jute researches were carried out initially at Rice
Research Station, Chinsurah, Hooghly of West Bengal from 1948 to 1952. The Jute
Agricultural Research Institute came into existence at Barrackpore, West Bengal,
during 1953 and was renamed as Central Research Institute for Jute and Allied
Fibres in 1990. Two very popular varieties, JRC-212 and JRC-321, were developed
through selection and released in 1954. JRC-212 has same maturity as of D-154 but
with much higher yield than the latter. JRC-321, besides high yield and early
maturity, produces finer quality fibre and is suitable for growing in low-lying
areas. The development of varieties like JRC-321 enabled farmers to fit jute into
the jute-rice cropping system, harvesting two crops from same land in a year.
594 C. S. Kar et al.

However, other capsularis varieties developed during the 1970s and 1980s were of
longer duration (150–160 days), which gradually were replaced by higher-yielding
olitorius varieties.
Introduction of resistance to premature flowering was a path-breaking achieve-
ment in tossa jute. Although tossa jute had higher productivity, it did not fit well to
the cropping system as farmers had to sow the crop almost 1 month later than white
jute (Tables 10.9 and 10.10). Moreover, under the high rainfall situation, capsularis
jute was more advantageous. However, rainfall pattern gradually changed, particu-
larly in South Bengal where olitorius jute started to replace capsularis jute. Still,
during the 1970s, the area under jute cultivation was dominated by capsularis
varieties (capsularis: olitorius ¼ 75: 25). Sudan Green (SG), an exotic germplasm
from Sudan, Africa, having premature flowering resistance was identified and
hybridized with JRO-632 and JRO-620, followed by pedigree selection, which
resulted into varieties like JRO-524, JRO-7835 and JRO-878 during the 1970s at
CRIJAF, Barrackpore.
Among these three varieties, JRO-524 (Navin) began to supplant capsularis
varieties rapidly. Being released in 1977, it became popular among the farmers
during the early 1990s and still maintains dominance. It reaches harvestable maturity
within 120 days, has premature resistance to flowering derived from Sudan Green,
has moderate tolerance to pest and disease attack and can produce up to
34–36 q fibre/ha under high-input agriculture. The major concern of jute farmers
was the fluctuating price of produce, rather than its productivity. The new olitorius
variety JRO-524 satisfied the farmers’ need. Like Sudan Green, Tanganyika-1, an
exotic strain from Tanzania, was identified to possess resistance to premature
flowering character. Utilizing this strain in the hybridization programme
(IC-15901  Tanganyika-1), JRO-8432 (Shakti) was developed and released in
1999, which exhibits 8–12% higher productivity than JRO-524. Another variety,
JRO-204 (Suren), a promising variety, has been released in 2007, which
outperformed both JRO-524 and JRO-8432 with a yield potential of 35–40 q fibre/
ha. This variety has high strength and is becoming increasingly popular among the
farmers.

10.11.4 Need of Varieties for Diversified Applications and Climate

Resilience

The resurgence of jute-based products over rising concerns of environmentally

hazardous synthetic fibres in the past decade has opened up new avenues for jute
demanding new types of jute varieties. Jute cultivation is one of the major solutions
for reducing environmental pollution and increasing carbon credit. Besides, the
application of jute fibre has been extended over the past years from fibre composites
to textile blends and geotextiles, each of which needs tailor-made varieties suitable
for each application. Geotextile materials need durability and strength, for which
varieties with better fibre strength and low degradability are required. Both of these
are influenced heavily by the presence of lignin in fibre. On the other extreme, some
10 Jute Breeding 595

Table 10.9 Characteristic features of improved varieties of tossa jute (C. olitorius L.) in India
Developing
Variety institute and year Parentage Significant attributes
‘JRO-632’ CRIJAF, Selection from Suitable for late sowing; pods
(Baisakhi Barrackpore, indigenous type shattering type; fibre
Tossa) West Bengal fineness—3.06 tex
Yield: 3.0–3.2 ton/ha
‘JRO-878’ CRIJAF, ‘JRO-620’  ‘Sudan Premature flowering
(Chaitali Barrackpore, green’ resistance; suitable for early
Tossa) West Bengal sowing; pods non-shattering
(1974) type; very fine fibre (2.60 tex).
Yield: 3.0–3.2 ton/ha
‘JRO-7835’ CRIJAF, ‘JRO-632’  ‘Sudan Premature flowering
(Basudev) Barrackpore, Green’ resistance; pods
West Bengal non-shattering type; withstand
(1974) waterlogging to some extent at
later stage; coarse fibre (3.50
tex). Yield: 3.2–3.4 ton/ha
‘JRO-524’ CRIJAF, ‘Sudan Green’  ‘JRO- Premature flowering
(Navin) Barrackpore, 632’ resistance; suitable for early
West Bengal sowing; pods non-shattering
(1977) type; fairly tolerant to yellow
mite and root rot disease and
drought; coarse fibre (3.40
tex). Yield: 3.4–3.6 ton/ha
‘TJ-40’ BARC, Trombay, Selection from inter- Premature flowering
(Mahadev) Maharashtra mutant cross resistance; pods
(1981) non-shattering type. Yield:
3.0–3.5 ton/ha
‘JRO-3690’ CRIJAF, ‘Tobacco leaf’  ‘long Premature flowering
(Savitri) Barrackpore, inter-node’ resistance; pods
West Bengal non-shattering type; coarse
(1985) fibre. Yield: 3.0–3.3 ton/ha
‘KOM-62’ Jute Research Gamma-ray derivative Premature flowering
(Rebati) Station, of ‘JRO-878’ resistance; pods
Kendrapara, non-shattering; stem colour—
Orissa (1993) Purple red; coarse fibre (3.80
tex). Yield: 3.0–3.5 ton/ha
‘JRO-66’ CRIJAF, Multiple crosses Premature flowering
(Golden Barrackpore, involving six parents resistance; suitable for late
Jubilee West Bengal sowing; pods non-shattering;
Tossa) (1998) fibre fineness—3.10 tex;
strength—Good (25.60 tex).
Yield: 3.5–4.0 ton/ha
‘JRO-8432’ CRIJAF, ‘IC- Pods non-shattering type;
(Shakti) Barrackpore, 15901’  ‘Tanganyika resistant to premature
West Bengal 1’ flowering; fine fibre (2.80 tex).
(1999) Yield: 3.5–4.0 ton/ha
‘JRO-128’ CRIJAF, ‘TJ-6’  ‘Tanganyika Pods non-shattering type;
(Surya) Barrackpore, 1’ resistant to premature
West Bengal flowering; very fine fibre (2.57
(2002) tex). Yield: 3.2–3.8 ton/ha
(continued)
596 C. S. Kar et al.

Table 10.9 (continued)

Developing
Variety institute and year Parentage Significant attributes
‘S-19’ CRIJAF, (‘JRO-620’  ‘Sudan Pods non-shattering type;
(Subala) Barrackpore, green’)  ‘Tanganyika resistant to premature
West Bengal 1’ flowering; fine fibre (2.70 tex).
(2005) Yield: 3.5–4.0 ton/ha
‘JRO-204’ CRIJAF, ‘IDN/SU/ Pods non-shattering type;
(Suren) Barrackpore, 053’  ‘KEN/DS/060’ resistant to premature
West Bengal flowering; very fine fibre (2.38
(2007) tex). Yield: 3.6–4.0 ton/ha
‘AAU-OJ-1’ RARS (AAU), ‘Tanganyika 1’  ‘JRO Pods non-shattering type;
(Tarun) Nagaon, Assam 640’ resistant to premature
(2007) flowering; fine fibre (2.60 tex).
Yield: 2.8–3.0 ton/ha
‘JBO-2003— CRIJAF, (‘JRO-632’)  (‘Sudan Pods non-shattering type;
H’ (Ira) Barrackpore, green’)  ‘Tanganyika resistant to premature
West Bengal 1’ flowering; grade TD2;
(2008) strength 23.89 g/tex; fine fibre
(2.86 tex). Yield: 3.4–3.6 ton/
ha
‘CO-58’ CRIJAF, ‘TJ-40’  ‘Tanganyika Pods non-shattering type;
(Sourav) Barrackpore, 1’ resistant to premature
West Bengal flowering; tolerant to stem rot,
(2010) root rot, yellow mite,
semilooper; fibre strength
26.61 g/tex; very fine fibre
(2.49 tex). Yield: 3.0–3.4 ton/
ha
‘JBO-1’ CRIJAF, ‘JRO-632’  ‘Sudan Pods non-shattering type;
(Sudhangshu) Barrackpore, green’  ‘Sudan green’ resistant to premature
West Bengal flowering; low lignin; very
(2010) fine fibre (2.38 tex);
strength—Fairly good
(25.25 g/tex). Yield:
3.0–3.4 ton/ha
‘JROM-1’ CRIJAF, Selection from ‘JRO- Highly tolerant to stem rot,
(Pradip) Barrackpore, 524’  ‘TAN/NY/ root rot and anthracnose
West Bengal 018C’ disease of jute; tolerant to
(2013) yellow mite, semilooper and
stem weevil; very fine fibre
(2.57 tex). Yield: 3.0–3.1 ton/
ha
‘JROG-1’ CRIJAF, Selection from ‘JBO- Resistant to premature
(Rithika) Barrackpore, 1’  ‘JRO-524’ flowering; resistant to root rot,
West Bengal yellow mite, semilooper and
(2015) moderately resistant to stem
rot; fine fibre (2.87 tex). Yield:
2.7–2.8 ton/ha
(continued)
10 Jute Breeding 597

Table 10.9 (continued)

Developing
Variety institute and year Parentage Significant attributes
‘JRO-2407’ CRIJAF, Selection from ‘KEN/ Resistant to premature
(Samapti) Barrackpore, SM/024’  ‘JRO-524’ flowering; tolerant stem rot,
West Bengal root rot, yellow mite,
(2015) semilooper and stem weevil;
tolerant to drought at early
stage; very fine fibre (2.30
tex). Yield: 3.3–3.4 ton/ha
‘KRO-4’ ZARS, Selection from ‘OIM- Resistant to premature
(Gouranga) Krishnanagar 028’  ‘JBO-2003-H’ flowering; fine fibre (2.70 tex).
(Dept. of Ag.), Yield: 2.9–3.0 ton/ha
West Bengal
(2017)
‘BCCO-6’ BCKV, West Selection from ‘OEX- Resistant to premature
(Kisan Pat) Bengal (2017) 05’ flowering; fine fibre (2.81 tex).
Yield: 2.8–2.85 ton/ha
‘NJ-7010’ Nuziveedu Seeds Mutant selection (EMS Resistant to premature
(Rani) Pvt. Ltd. (2018) induced) from ‘JRO- flowering; fine fibre (2.66 tex).
524’ Yield: 3.0–3.1 ton/ha
‘JROMU-1’ CRIJAF, Mutant selection Resistant to premature
Barrackpore, (gamma-ray induced) flowering; tolerant stem rot,
West Bengal from ‘JRO-204’ yellow mite, semilooper and
(2020) apion; fine fibre (2.90 tex).
Yield: 3.2–3.3 ton/ha
‘JROB-2’ CRIJAF, Mutant of JRO-204 Stem colour green; suitable for
(Purnendu) Barrackpore, both fibre as well as biomass
West Bengal for paper pulp industries;
(2020) resistant to yellow mite, stem
weevil and hairy caterpillar.
Yield: 3.2 ton/ha. Biomass:
55–60 ton/ha

varieties need to have finer fibre with low strength and lower meshiness for blending
in textile material. During 2002, JRO-128 (Surya) was released for quality fibre
(fineness 2.7 tex) with a yield potential of 35–40 q/ha. S-19 (Subala) was released
during 2005 with high yield (35–40 q/ha) and better-quality fibre (fineness 2.7 tex,
strength 25.95 g/tex with less lignin content). It can be sown during middle of
March.
Newer varieties like JBO-1 (Sudhangshu), JRO-2407 (2.30 tex) and JROM-1
(2.57 tex) have better fibre fineness being more suitable for numerous textile and
non-textile diversified applications. In capsularis jute, JRCM-2 (1.25 tex), KJC-7
(1.30 tex) and JBC-5 (1.45 tex) are promising white jute varieties for textile
blending. The value of these new varieties lies in higher fibre fineness with appre-
ciable yield potential, which is expected to fetch higher income for jute farmers of
the country.
598 C. S. Kar et al.

Table 10.10 Characteristic features of improved varieties of white jute (C. capsularis L.) in India
Year
Developing of
Variety institute release Parentage Significant attributes
‘JRC-321’ ICAR- 1954 Selection from Premature flowering
(Sonali) CRIJAF, indigenous type ‘Hewti’ resistant; pods
Barrackpore, non-shattering type;
West Bengal very fine fibre (1.50
tex); suitable for jute-
cotton blended yarn
and fabric. Yield:
2.5–2.8 ton/ha
‘JRC-212’ ICAR- 1954 Selection from Premature flowering
(Sabuj CRIJAF, indigenous type (Dacca) resistant; pods
Sona) Barrackpore, non-shattering type;
West Bengal very fine fibre (1.61
tex). Yield:
2.0–2.1 ton/ha
‘JRC-7447’ ICAR- 1971 X-ray derivative of Premature flowering
(Shyamali) CRIJAF, ‘JRC-212’ resistant; pods
Barrackpore, non-shattering type;
West Bengal responds to higher N
dose; very fine fibre
(1.71 tex). Yield:
2.2–2.5 ton/ha
‘JRC-4444’ ICAR- 1980 Selection from ‘JRC- Premature flowering
(Baldev) CRIJAF, 212’  ‘D-154’ resistant; pods
Barrackpore, non-shattering type;
West Bengal very fine fibre (1.90
tex). Yield:
3.0–3.2 ton/ha
‘UPC-94’ JRStation 1983 Selection from ‘JRC- Premature flowering
(Reshma) Bahraich, 321’  ‘JRC-212’ resistant; pods
NDUAT, non-shattering type;
Uttar Pradesh very fine fibre (1.50
tex). Yield:
2.5–2.7 ton/ha
‘Hybrid-C’ ICAR- 1983 Selection from ‘JRC- Premature flowering
(Padma) CRIJAF, 6165’  ‘JRC-412’ resistant; pods
Barrackpore, non-shattering type;
West Bengal coarse fibre (2.50 tex).
Yield: 2.5–2.8 ton/ha
‘KC-1’ JRS 1992 Gamma-ray derivative of Premature flowering
(Jaydev) Kendrapara, ‘JRC-4444’ resistance; pods
OUAT, non-shattering type;
Odisha fine fibre (2.10 tex).
Yield: 2.6–2.7 ton/ha
‘KTC-1’ Jute Research 1994 Selection from ‘IC- Premature flowering
(Rajendra Station 30730’ collected from resistance; pods
pat 1) (BAU), Tripura non-shattering type;
Katihar, Bihar less infestation of pest
and diseases. Yield:
2.7–2.8 ton/ha
(continued)
10 Jute Breeding 599

Table 10.10 (continued)

Year
Developing of
Variety institute release Parentage Significant attributes
‘JRC-698’ ICAR- 1999 Directional disruptive Premature flowering
(Shrabanti CRIJAF, selection from multiple resistance; pods
white) Barrackpore, crosses of five non-shattering type;
West Bengal indigenous and eight very fine fibre (1.80
exotic parents tex). Yield:
2.0–2.5 ton/ha
‘Bidhan B.C.K.V., 2001 Gamma-ray derivatives Photoperiod
Pat-1’ Mohanpur, of ‘D-154’ insensitive; pods
West Bengal non-shattering type;
can be harvested in
60–65 days. Yield:
1.2–1.3 ton/ha
‘Bidhan B.C.K.V., 2001 Selection from ‘D- Photoperiod
Pat-2’ Mohanpur, 154’  ‘D-18’ (mutant) insensitive; pods
West Bengal non-shattering type;
can be harvested in
90–110 days. Yield:
2.0–2.2 ton/ha
‘Bidhan B.C.K.V., 2001 Selection from ‘D- Photo-insensitive; pods
Pat-3’ Mohanpur, 154’  ‘D-18’ (mutant) non-shattering type;
West Bengal suitable for paper pulp
industry; can be
harvested in 110 days;
very fine fibre (1.80
tex). Yield:
2.4–2.5 ton/ha
‘JRC-80’ ICAR- 2005 Selection from ‘CIN- Premature flowering
(Mitali) CRIJAF, 114’  ‘JRC-321’ resistant; pods non
Barrackpore, shattering type; very
West Bengal fine fibre (1.25 tex).
Yield: 2.2–2.3 ton/ha
‘JRC-517’ ICAR- 2009 Selection from ‘JRC- Premature flowering
(Siddhartha) CRIJAF, 212’  ‘JRC-4444’ resistant; pod
Barrackpore, non-shattering; very
West Bengal fine fibre (1.49 tex).
Yield: 2.2–2.5 ton/ha
‘JRC-532’ ICAR- 2009 Selection from ‘CHN’/ Premature flowering
(Sashi) CRIJAF, ‘FJ’/‘044C’  ‘JRC- resistant; pod
Barrackpore, 321’ non-shattering; very
West Bengal fine fibre (1.83 tex).
Yield: 2.5–2.6 ton/ha
‘RRPS ICAR- 2009 ‘JRC-321’  ‘NPL’/ Premature flowering
-27-C-3’ CRIJAF, ‘KUC’/‘094C’ resistant; pod
(Monalisa) Barrackpore, non-shattering; red
West Bengal stem; very fine fibre
(1.61 tex). Yield:
2.9–3.0 ton/ha
(continued)
600 C. S. Kar et al.

Table 10.10 (continued)

Year
Developing of
Variety institute release Parentage Significant attributes
‘NDC- Jute Research 2009 ‘7 I’/‘20’  ‘JRC-321’ Premature flowering
2008’ Station resistant; pod
(Ankit) (NDUAT), non-shattering; light
Faizabad, red stem. Yield:
Uttar Pradesh 2.5–2.6 ton/ha
JBC-5 ICAR- 2010 ‘JRC-321’  ‘THA/Y/ Premature flowering
(Arpita) CRIJAF, 086C’ resistant; pod
Barrackpore, non-shattering; stem
West Bengal green with light red
pigmentation; very fine
fibre (1.45 tex). Yield:
2.8–2.9 ton/ha
‘JRCM-2’ ICAR- 2013 ‘JRC-321’  ‘THA/Y/ Premature flowering
(Partha) CRIJAF, 086C’ resistant; pod
Barrackpore, non-shattering; stem
West Bengal green; tolerant to stem
rot; hairy caterpillar;
very fine fibre (1.25
tex). Yield:
2.7–2.8 ton/ha
‘KJC-7’ JRS 2016 ‘KC-1’  ‘JRC-212’ Premature flowering
(Shrestha) Kendrapara, resistant; pod
OUAT, non-shattering; stem
Odisha green; very fine fibre
(1.30 tex). Yield:
2.8–2.9 ton/ha
‘JRC 9057’ ICAR- 2016 ‘JRC-698’  ‘CIJ-121’ Premature flowering
(Ishani) CRIJAF, resistant; tolerant to
Barrackpore, stem rot and
West Bengal semilooper; very fine
fibre (1.31 tex). Yield:
2.5–2.8 ton/ha
‘AAU-CJ- RARS 2017 ‘CEX-045’  ‘CEX- Resistant to lodging
2’ (AAU), 050’ and pod shattering;
(Kkhyati) Nagaon, stem rot and root rot;
Assam tolerant to semilooper
and yellow mite; fine
fibre (1.93 tex). Yield:
2.7–2.8 ton/ha
‘BCCC-1’ B.C.K.V., 2018 Selection from ‘CIJ-123’ Tolerant to stem rot,
(Shweta) Mohanpur, semilooper and hairy
West Bengal caterpillar; very fine
fibre (1.65 tex). Yield:
2.7–2.8 ton/ha
(continued)
10 Jute Breeding 601

Table 10.10 (continued)

Year
Developing of
Variety institute release Parentage Significant attributes
‘BCCC-2’ B.C.K.V., 2019 Pure line selection from Tolerant to apion,
(Shweta) Mohanpur, ‘CIN-492’ semilooper and hairy
West Bengal caterpillar; very fine
fibre (1.68 tex). Yield:
2.7–2.8 ton/ha
‘JRCJ-11’ ICAR- 2021 Pedigree selection from a Premature flowering
(Shweta) CRIJAF, cross CIN-146  JRC- resistant; high
Barrackpore, 321 tolerance to Bihar hairy
West Bengal caterpillar and
moderate tolerance to
stem rot; fine fibre
(1.78 tex). Yield:
3.1–3.2 ton/ha

10.12 Maintenance Breeding

The production of nucleus seed is the starting point in maintenance breeding of jute
crop. When an entry enters advance varietal trial (AVT-II) stage in All India
Network Trial and its performance is promising, the concerned breeder initiates
the nucleus seed production and continues the process after the identification and
release till the variety enters seed production chain and the indent or demand for
breeder seed exists. Jute is a self-pollinated crop, although some percentage of cross-
pollination is observed in both species. The nucleus seed is produced by growing
plant to progeny rows. The various steps to be followed in the production of nucleus
seed are listed below.

Cycle I A given variety is grown (minimum 10,000 plants) under optimum

conditions with an isolation of 100 m and free from preceding jute crop. The
appearance of volunteer plants is avoided resulting from mechanical mixture.
About 500–600 true-to-type single uniform plants are selected to maintain the
genetic constitution and to avoid any genetic drift. The selected plants are harvested
and threshed separately. The seeds are examined for post-harvest characters like seed
colour, size, etc., and the seeds not conforming true to type are rejected.

Cycle II Finally selected plants (400–500) are grown in isolations of 100 m follow-
ing plant to progeny rows. Each block should contain single row plant progenies
along with two rows of parental variety for comparison. As jute seed is small in size,
3–7 g of seed may be collected from a single plant. Five border rows of the same
variety are grown around the seed plot to set a barrier. Varieties of the same species
are grown at a safe isolation distance of 100 m. Fast-growing barrier crops like
Sesbania are grown between two varieties of the same species. Interspecific cross
602 C. S. Kar et al.

incompatibility is also utilized by sowing varieties of two cultivated species of jute

adjacently. Full package of practices recommended for a variety is followed. A wide
space of 60 cm is kept after every five rows to facilitate roughing and other field
operations. The progeny rows are examined periodically throughout the growing
season, especially at early growth stage, flowering stage, capsule formation and at
maturity stage. The progeny rows which show off-type(s) or phenotypic variation
may be rejected and uprooted as and when the off-types are detected. The diseased
and agronomically poor progeny rows should also be rejected. The single plant
progenies selected are harvested separately, which are true to type of the original
variety. The single plant progenies, which meet all the standards mentioned in the
descriptor, are bulked to get the nucleus seed.
Selection of individual plants followed by progeny row evaluation is done in two
seasons, and this cycle of nucleus seed production is to be carried out every year
compulsorily. Grow-out test is carried out to ascertain the genetic purity of nucleus
seed and to test the fibre yield potential of the variety retaining the allelic frequencies
of the original population for the character. Prior to harvesting, another batch of true-
to-type single plants is selected for the next cycle.

10.13 Coordinated System of Testing

Various trials are conducted for the evaluation of a line for identification and release
as variety if it is found superior over the best-existing variety(ies) in fibre yield
and other traits like biotic or abiotic stresses and fibre quality parameters under
All India Network Project on Jute and Allied fibre crops (AINPJAF). In general,
there are six different types of trials/tests: (1) station trial; (2) multilocational trials
(IET, AVT-I, AVT-II); (3) disease and insect trials; (4) agronomic-fertilizer
responsiveness trial; (5) adaptive trial; (6) quality test.

10.13.1 Station Trial

This trial is conducted by Breeder developing the variety and may be conducted for
one or more years with the objective of identify superior to be included in AINPJAF
for multilocation trial. In station trials of jute, the plot size is generally 3 m  1.8 m
with a spacing of 30 cm between rows. Plant-to-plant spacing is maintained at
5–7 cm with a minimum replication of 3–4 and best-existing varieties as checks.
Disease and pest reaction of the new line are also evaluated. The data from station
trials are required for the inclusion of an entry in the multilocation trials.

10.13.2 Multilocation Trials

These trials are conducted under All India Network Project on Jute and Allied fibre
crops at different test locations across different agroclimatic zones. The objective of
10 Jute Breeding 603

these trials is to evaluate the performance of newly developed lines. The number of
zones for jute is four: (1) north-eastern plain zone (eastern UP and Bihar); (2) eastern
zone (West Bengal, Assam, Tripura, Meghalaya); (3) south-eastern zone (Odisha &
AP); and (4) southern or peninsular zone (Maharashtra and Tamil Nadu). The
various trials conducted under AINPJAF are IET, AVT-I, AVT-II and adaptive
trails. The IET trials are conducted in seven to eight locations across these zones
with larger plot size, and the best entries are promoted to AVT-I. The AVT-I trials
are conducted in seven to eight locations in larger size plots. The AVT-I is generally
repeated in next season and termed as AVT-II. Simultaneously, fibre quality tests of
all entries in IET and AVT-I are carried out. The best one to two entries are identified
every year based on yield and other characters like fibre quality parameters and
disease and pest resistance and recommended for adaptive trials in farmers’ field in
larger plots. Based on combined data over 4 years, a variety superior in yield and
other characters compared to check varieties is recommended for identification and
subsequent release by Central Sub-Committee on Crop Standards Notification &
Release of Varieties for Agricultural Crops and Horticultural Crops. For State release
of a variety in jute, in addition to 3-year state varietal trial’s data, 1-year evaluation at
AINPJAF trial is mandatory.

10.14 Future Thrust Area

Jute being a regional and orphan crop, there are opportunities for future research on
different emerging areas. The main objective of future research is to orient research
activities, particularly plant breeding activities, towards establishing it as a climate-
smart crop. The present monopolistic use jute as fibre (~3% fibre of total biomass)
should be transformed to a crop having diversified uses (~97% waste) with 100 prod-
uct conversion efficacy. In fibre aspect, the main challenge is to improve the fibre
quality aspect, particularly fibre fineness, which makes jute fibre for manufacturing
diversified products. The emerging areas are to develop varieties which will be
source of non-timber-based source of paper pulp with continuous round the year
supply, varieties suitable for biofuel, leafy vegetable (high antioxidant), etc. Thus,
environment-friendly jute crop may play an important role in future as an alternative
to plastic use which poses threat to the environment.

10.15 Conclusions

Jute is the second most important fibre crop next to cotton globally. Jute denotes
fibre obtained from the bark of two cultivated species (Corchorus olitorius and
C. capsularis). This crop is grown in India and in Bangladesh in the pre-monsoon
(pre-kharif) season within a small growing window of mid-March to mid-July
(110–120 days) in the Eastern Gangetic Plain. Unlike other crops, genotype-
environment interaction is comparatively high in jute. Progress in jute breeding
and management has resulted in an increase of both average yield and potential yield
604 C. S. Kar et al.

of this crop. Being environment friendly, this crop is drawing attention to

policymakers to combat the ill effect of synthetic fibre including plastics and to
increase the carbon credit related to the environment. After achieving yield improve-
ment through a series of high-yielding varieties, breeding objective has shifted
towards improved fibre quality suitable for diversified fibre uses. In addition,
diversified use of jute is anticipated through use as biomass, biofuel, paper pulp
and leafy vegetables in the near future. Plant breeding techniques, assisted by
advanced genomic tools and gene editing tools, have eminent scope for the improve-
ment of jute for yield, quality and resistance to diseases and pests.

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Cotton Breeding
11
Vijay N. Waghmare

Abstract

Cotton (Gossypium spp.) is an economically important cash crop grown in more

than 90 countries in tropical, sub-tropical and temperate climate for its fibre, oil
and protein. Cotton belongs to the genus Gossypium that contains 50 species, of
which 43 are diploids (2n ¼ 26) and seven tetraploids (2n ¼ 4x ¼ 52). The diploid
species are grouped in seven genomes designated as A–G and K. The tetraploid
species with AADD genome originated from natural crossing involving
cultivated diploid G. herbaceum (A1) and wild diploid species G. raimondii
(D5), followed by polyploidization. Cultivated cotton has a narrow genetic base
which is becoming a hindrance in sustaining cotton productivity worldwide.
Broadening the genetic base of cultivated cotton by mobilizing the useful genetic
variations from diverse exotic accessions, races of cultivated species and wild
accessions requires to be the top priority. The use of molecular markers and
advances in sequencing technology has resulted in the development of huge
genomic resources that includes molecular markers, several linkage maps and
more than 6497 quantitative trait loci (QTL) representing more than
30 agronomically important traits mapped on specific chromosomes. To facilitate
high-throughput genotyping of the breeding populations, SNP arrays have been
developed and extensively used for genetic mapping and marker-assisted breed-
ing programmes. The last decade witnessed complete genome sequencing and
resequencing of cultivated and more than a dozen wild species of cotton. Whole
cotton genome sequence data provides a major source of candidate genes with
potential for genetic improvement of cotton quality and productivity. Insect- and
herbicide-resistant transgenics are under cultivation across the cotton-growing

V. N. Waghmare (*)
ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, India
e-mail: Vijay.Waghmare@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 609
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_11
610 V. N. Waghmare

countries. Genotype-dependent genetic transformation is known in cotton. Ver-

satile and robust somatic regeneration protocol suiting to a diverse set of
genotypes would facilitate transgenic development for economic traits. Precision
genome editing tool CRISPR/Cas9 and further refinement in the technology has
demonstrated successful simultaneous multiple gene-targeted mutagenesis in
several crops including cotton. This technology holds promise to develop
transgene-free edited plants for economic, quality, resistance and adaptation traits
in cotton. This chapter dwells upon all broad aspects of conventional breeding
and molecular tools for cotton improvement, present status and perspectives for
cotton production sustainability.

Keywords

Cotton · Genetic resources · Breeding methods · DNA markers · Marker-assisted

selection (MAS) · Genome-wide association studies (GWAS) · Genotyping by
sequencing (GBS) · Transgenics, Genome editing

11.1 Introduction

Cotton (Gossypium spp.) is an economically important cash crop grown in more than
90 countries in tropical and sub-tropical climate for its fibre. Now, cotton is
extensively being cultivated in temperate climates. Globally, cotton is cultivated
on an area of 31.36 million ha which accounts for about 2.5% of the world’s arable
area and an estimated production of 24.612 million tonnes in 2020–2021. Among
the leading cotton-producing countries, India, China, the United States, Brazil and
Pakistan account for about more than 80% of the world’s cotton production. The
world’s cotton consumption for the year 2020–2021 stands at 25.658 million tonnes.
The total cotton trade (import and export) is about 9.9 million tonnes, and the ending
stock stands at 20.349 million tonnes by April 2021 (USDA 2021).
Cotton played a significant role in industrial revolution that began in the eigh-
teenth century. It also played an important role in evolution of the textile industry.
Cotton and its value-added products are among heavily traded agricultural commod-
ity across 150 countries. Asian countries dominate the global cotton production, but
most of the produce is domestically consumed. For several years, China and India
have been the core markets for cotton consumption. In India, the highly evolved
textile sector consumes most of the country’s cotton. In recent years, Bangladesh,
Vietnam and Uzbekistan have emerged as major consumers of cotton, next to China
and India, and consequently the core importers are China, Bangladesh and Vietnam.
Similarly, among considerable cotton exporters are the United States, Brazil and
India. The United States has been the largest exporter for many years, accounting to
37.8% of global cotton exports in 2019.
11 Cotton Breeding 611

11.2 Cotton Production and Consumption Situation in India

At the time of independence (1947–1948), India produced a meagre 0.39 mil-

lion tonnes of cotton from 4.4 million ha with a productivity of 88 kg lint/ha. The
production steadily increased with adoption of improved varieties, production and
protection technologies and reached an all-time high of 6.77 million tonnes in
2013–2014 from 11.96 million ha (Fig. 11.1). Currently, India has the largest area
under cotton, is the largest producer and the second largest consumer of cotton
(Figs. 11.1 and 11.2). The average productivity during the last decade was 512 kg
lint/ha. There was a 5.2-fold increase in domestic consumption in the last six
decades. From 2005 to 2006, India became the net exporter of cotton. It imports
extra-long-staple and long-staple cotton from the United States, Egypt, Sudan or
Australia. India exports its cotton mainly to Bangladesh, China and Pakistan and in
small quantity to other countries.

Fig. 11.1 Cotton area, production and productivity in India during 1950–2019

Fig. 11.2 India’s cotton consumption, import and export during 1950–2019
612 V. N. Waghmare

11.3 Origin, Evolution and Distribution of Species

India has a history of cotton cultivation of more than 3000 years. The latest
archaeological discovery in Mehrgarh (now in Pakistan) puts the dating of early
cotton cultivation and its use to 5000 BC (Menon and Uzramma 2017). The ancient
Indus Valley Civilization discovered through Mohen-jo-daro relics treats the time of
cotton cultivation and manufacture of cotton fabrics to about 5000 years ago.
A close study of these relics at Technological Laboratory of the Indian Central
Cotton Committee (now ICAR- Central Institute for Research on Cotton Technol-
ogy) indicates the coarse cotton from which fabrics were manufactured related to
G. arboreum types (Sethi 1960). Alexander the Great, during his sojourn in India,
described cotton ‘as a plant from which the natives plucked the vegetable wool
which they spun to admirable clothing’. Herodotus, an ancient Greek historian,
described Indian cotton in the fifth century BC as ‘tree, bearing as their fruit, fleeces
which surpass those of sheep in beauty and excellence’. Sufficient evidence has been
recorded by the Arabian travellers describing Indian fabrics and flourishing export
trade in cotton and cotton goods as early as 569–525 BC. The available evidence
proves that India was the original habitat of cotton and an exporter of fine fabrics
since the ancient times. Marco Polo, who travelled to India in the thirteenth century,
Chinese travellers to Buddhist pilgrim centres, Vasco Da Gama, who entered Calicut
in 1498, and Tavernier in the seventeenth century all have praised the superiority of
Indian fabrics.
Historically, cotton is domesticated for its fibre (lint), mainly used for clothing by
the textile industry. Besides, cotton provides cellulose from lint and fuzz (short
fibres) for several industries (foods, wood, paper, pharmaceutical and cosmetic
industries), oil for human consumption and seed as feed for animals. Practically,
every part of the cotton plant is used for one or other purpose, i.e. shoot (stem) for
manufacturing particle boards and fuel and acids are extracted from leaves.
Cotton is classified as a malvaceous plant in the genus Gossypium that belongs to
a small taxonomic tribe, the Gossypieae (Fryxell 1968, 1979). Gossypium appears to
have diverged from its closest relatives during the Miocene, perhaps 10–15 mya,
subsequently spreading around the world via trans-oceanic dispersal to acquire its
modern geographic range. With the recent addition of new tetraploid species,
Gossypium ekmanianum, the genus Gossypium contains approximately 50 species
(Fryxell 1992; Stewart et al. 2008; Wendel and Grover 2015), of which 43 are
diploids with chromosome number 2n ¼ 2x ¼ 26 and 7 tetraploids with chromosome
number 2n ¼ 4x ¼ 52. The diploid species are grouped in seven genomes designated
as A–G and K (Table 11.1). The species belonging to the genome A, B, E or F are of
African or Asian origin; the species of C, G or K genome are of Australian origin,
while species with D genome are of American origin. Although all diploid species
share the same chromosome number (n ¼ 13), there is two- to threefold variation in
DNA content per genome (Hendrix and Stewart 2005). The chromosomes of African
and Asian diploids are larger in size and have more DNA content than the American
diploid species. The DNA content of the African Asian diploids (2C ¼ 3.47 pg) is
1.92 times higher than the American diploids (2C ¼ 1.81 pg), while the K genome
11 Cotton Breeding 613

Table 11.1 Gossypium species with their designated genome and geographic origin
Species Genome Geographic origin/distribution
Diploid species (2n ¼ 13)
G. herbaceum A1 Africa
G. arboreum A2 Asia/India
G. anomalum B1 Africa
G. triphyllum B2 Africa
G. capitis-viridis B3 Cape Verde Islands
G. trifurcatum B* Somalia
G. sturtianum C1 Australia
G. robinsonii C2 Australia
G. thurberi D1 Mexico, Arizona
G. armourianum D2-1 Mexico
G. harknessii D2-2 Mexico
G. davidsonii D3-d Mexico
G. klotzschianum D3-k Galapagos Island
G. aridum D4 Mexico
G. raimondii D5 Peru
G. gossypioides D6 Mexico
G. lobatum D7 Mexico
G. trilobum D8 Mexico
G. laxum D9 Mexico
G. turneri D10 Mexico
G. schwendimanii D11 Mexico
G. stocksii E1 East Africa, Indo-Arabia
G. somalense E2 Africa
G. areysianum E3 Arabia
G. incanum E4 Arabia
G. trifurcatum E5 Arabia
G. benidirense E* Somalia, Ethiopia, Kenya
G. bricchettii E* Somalia
G. vollensenii E* Somalia
G. longicalyx F1 Africa
G. bickii G1 Australia
G. australe G2 North Trans Australia
G. nelsonii G3 Central Australia
G. costulatum K1 North Kimberley of W Australia
G. populifolium K2 Kimberley, Australia
G. cunninghamii K3 The northern tip of NT, Australia
G. pulchelium K4 Kimberley, Australia
G. anapoides K6 N Kimberley, Australia
G. enthyle K7 Australia
G. exiguum K8 Australia
G. londonderriense K9 Australia
G. marchantii K10 Australia
(continued)
614 V. N. Waghmare

Table 11.1 (continued)

Species Genome Geographic origin/distribution
G. nobile K11 Australia
G. rotundifolium K12 Australia
G. pilosum K* Australia
Tetraploid (2n ¼ 52)
G. hirsutum (AD)1 America
G. barbadense (AD)2 South America
G. tomentosum (AD)3 Hawaii Island
G. mustelinum (AD)4 Brazil
G. darwinii (AD)5 Galapagos Island
G. ekmanianum (AD)6 Dominican Republic
G. stephensii (AD)7 Wake Atoll
*Not yet recognized

(2n ¼ 5.26 pg) is 2.9 times higher than the D genome. The tetraploid species with
AADD genome (2n ¼ 4x ¼ 4.91 pg) originated from natural crossing involving
cultivated diploid species G. herbaceum (A1 genome) and wild diploid species
G. raimondii (D5 genome), followed by polyploidization (Phillips 1963).
The available evidence establishes that the New World tetraploid cottons are
allopolyploids containing an ‘A’ genome similar to the Old World cultivated
diploids and a ‘D’ genome similar to the New World diploid species (Endrizzi
et al. 1985; Wendel 1989). Molecular data and cytological analysis indicate that
all allopolyploids in Gossypium share a common ancestry, monophyletic origin,
i.e. polyploid formation occurred only once. In addition, all allopolyploids contain
an Old World (A genome) chloroplast genome, indicating that the seed parent
involving the initial hybridization event was an African or Asian A genome (Wendel
1989). Contrary to the views of varied polyploid formation, the molecular data
suggest a geologically recent (Pleistocene) origin of the allopolyploids, perhaps in
the last 1–2 million years, is consistent with cytogenetic analysis (Phillips 1963) and
ecological considerations (Fryxell 1979). Subsequent to polyploidization, the mor-
phological diversification and spread of allopolyploid must have occurred relatively
rapidly; however, the spread of wild forms remained restricted to small regions. At
present, there are seven allopolyploid species of Gossypium, of which two are
cultivated and five are wild. G. darwinii is native to the Galapagos Islands,
G. tomentosum to the Hawaiian Islands (DeJoode and Wendel 1992) and
G. mustelinum is restricted to a relatively small region of north-east Brazil (Wendel
et al. 1994). G. ekmanianum Wittm. was recently included in the cotton genus and
validated (Grover et al. 2015) by molecular sequence data. G. stephensii relatively
closely related to G. hirsutum from two islands (Wake, Peale) in the Wake Atoll in
the Pacific Ocean has also been included in the Gossypium genus (Gallagher et al.
2017).
Among the total Gossypium species, four species producing spinnable fibre (lint)
were extensively domesticated and are under cultivation. These include Gossypium
arboreum L. and Gossypium herbaceum L. commonly referred to as Asiatic or Old
11 Cotton Breeding 615

Table 11.2 Races of cultivated species

Cultivated species Races
Gossypium herbaceum Acerifolium, Kuljianum, Persicum, Wightianum
Gossypium arboreum Bengalense, Burmanicum, Cernuum, Indicum, Sinense, Soudanense
Gossypium hirsutum Punctatum, Palmeri, Marie-Galante, Mirilli, Latifolium, Richmondii,
Yukatenance
Gossypium barbadense Brasiliense

World cottons, native of India and Africa, respectively; Gossypium hirsutum L., an
American cotton, native of Central America; and Gossypium barbadense L., an
Egyptian or Sea Island cotton originated in Peru (South America). G. herbaceum is
considered to be earliest cultivated cotton, originated in the Middle East. It may have
been carried to India by travellers, which later differentiated to give rise to
G. arboreum. G. arboreum has wide adaptability and widely cultivated in India
covering all the states. G. hirsutum is the major cultivated cotton which accounts for
about more than 90% of the area and also the world’s cotton production.
G. barbadense is known for its superior fibre quality and extra-long staple, also
known as Sea Island, Egyptian or Pima cotton. It is now grown around the world,
including China, Egypt, Sudan, India, Australia, Peru, Israel, South Western United
States, Tajikistan, Turkmenistan and Uzbekistan, and accounts for about 5% of the
world’s cotton production. In the course of domestication, cultivated species in
different geographical areas over the extended period of time differentiated to give
rise to sub-species or races (Table 11.2). Races of cultivated species are important
sources of resistance to biotic and abiotic stresses besides traits of agronomic
importance.

11.4 Plant Genetic Resources

Plant genetic resources are the foundation and key drivers of any crop improvement
programme. Most of the major cotton-producing countries maintain its cotton
germplasm resources for utilization in cotton improvement programmes
(Table 11.3). Uzbekistan has, to its credit, the highest germplasm holding of
32,580 accessions, followed by India (12,335), the United States (10,311), China
(8868), Russia (4296) and France (3069). The germplasm maintained by different
countries include working collection, wild resources, interspecific derivatives, aneu-
ploid lines, mutants, varieties, mapping populations, RILs and trait-specific
resources.
In India, ICAR-Central Institute for Cotton Research (ICAR-CICR) has the
responsibility of maintaining a National Cotton Gene Bank at Nagpur since its
establishment in 1976. ICAR-CICR has the mandate of exploration, collection,
conservation, maintenance, characterization, documentation, utilization and distri-
bution of cotton germplasm among cotton researchers. National Cotton Gene Bank
was initially started by obtaining representative seed samples from the genetic
 616

Table 11.3 Germplasm resources maintained in major cotton-growing countries

Gossypium Gossypium Gossypium Gossypium Other
Country hirsutum barbadense herbaceum arboreum species Total Source
Uzbekistan 24,571 4190 1292 1623 937 32,580 Abdurakhmonov et al.
(2014a)
India 8851 536 565 2053 330 12,335 CICR Annual Report
(2019)
United 6302 1584 194 1729 502 10,311 Percy et al. (2014)
States
China 7752 633 18 433 32 8868 Jia et al. (2014)
Russia 4503 1057 336 365 15 6261 Campbell et al. (2010)
Brazil 1660 1509 19 219 889 4296 Campbell et al. (2010)
France 2173 483 50 69 294 3069 Campbell et al. (2010)
V. N. Waghmare
11 Cotton Breeding 617

resources scattered within the country. ICAR-CICR, in collaboration with ICAR-

National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, and State
Agricultural Universities, has collected cotton germplasm by launching germplasm
collection missions in areas of origin and diversity of the mandate crops. Further, the
cotton gene bank was enriched through donations from various domestic as well as
institutions around the world dealing with cotton. India’s National Cotton Gene
Bank is now maintaining over 12,335 accessions, consisting of geographically
diverse germplasm accessions of Gossypium hirsutum (8851), Gossypium
barbadense (523), Gossypium arboreum (2094) and Gossypium herbaceum (565),
wild species of Gossypium (24), perennials (254) and races, viz. G. hirsutum (4),
G. barbadense (1), G. arboreum (6), G. herbaceum (1), and synthetic derivatives
(40). A complete set of cotton germplasm is stored at ICAR-NBPGR, New Delhi,
under long-term storage (LTS), while the other set is conserved as an active
collection at ICAR-CICR, Nagpur, under medium-term storage (MTS, at 5  C and
below 30% relative humidity). Wild species are being maintained in situ in the
species garden.

11.4.1 Unique Germplasm

Genotypes unique for specific traits, viz. morphological, economic or quality traits,
are being regularly added to the existing germplasm. Fifty (50) genetic stocks
[Gossypium hirsutum (28), introgressed (6) and Gossypium arboreum (16)] have
been registered for their unique, novel and distinct characteristics. These would
serve as an important source for specific traits and unique morphological markers.

11.5 Floral Biology: Emasculation and Pollination Technique

Cotton flower is extra-axillary, terminal and solitary. It emerges as tiny triangular

bud surrounded by three triangular bracts generally referred to as squares. As the
square grows in size, the twitted corolla becomes prominent, and it is termed as bud
(unopened flower). The twisted corolla emerges from the bud taking shape of fully
open flower before anthesis. When the flower first opens, the corolla is either cream,
yellow or white in colour. In G. hirsutum, generally, corolla colour is cream at the
flower opening but turns pink or red after anthesis and later remains attached or falls
from the developing boll. Pistil consists of three to five carpels united to form a
cylinder. The number of carpels fairly corresponds to the number of locks or locules
in the boll. The stamens are united at the base forming a tube that encloses the styles
and is united at the base of the corolla. Anthesis occurs after the flower opens and the
pollen sheds directly on the stigma or carried to the stigma by insects.
618 V. N. Waghmare

11.5.1 Mode of Pollination

Cotton is normally considered to be a self-pollinated crop. Cotton pollen is heavy

and sticky, normally not transferred by wind. The extent of cross-pollination
depends on the abundance of vector population that primarily constitutes various
wild bees, bumble bees (Bombus spp.), honey bees (Apis mellifera) and other insects.
In normal circumstances, natural cross-pollination ranging from 0% to 10% is
considered as a self-pollinated crop. When natural cross-pollination exceeds 50%,
it may be treated as a cross-pollinated crop. Usually, in the presence of vector
population, cross-pollination varies from 5% to 30%; hence, cotton is grouped in
the category of often cross-pollinated crops. Cross-pollination in excess of 50% has
been reported in Tennessee, Georgia and North Carolina. However, the intensive use
of insecticides to control dozens of major harmful insect pests of cotton has reduced
the pollinating insects’ populations in the cotton ecosystem, thus reducing the
relative extent of cross-pollination in cotton. Cross-pollination also varies with
different varieties and their morphological attributes including flower opening,
pigmentation, position of stigma and anthers and presence and prominence of flower
nectaries.

11.5.2 Self-Pollination

Cotton flower is relatively bigger in size than the leguminous crops and thus easy for
selfing and hybridization. Cross-pollination in cotton is controlled by preventing the
flower bud to open until anthesis, pollination and early boll development. The flower
bud which would normally open the next day is selected and sealed using malleable
wire, thread string, paper clips, sticky mud and other similar materials to prevent
opening of the flower and entry of insects visiting flowers for nectar or responsible
for cross-pollination. Alternately, the flower bud may be covered with a small paper
bag to prevent cross-pollination. This simple technique ensures self-pollination and
to get pure selfed seeds of the genotypes in the breeding programme or for the
maintenance of genotypes/varieties.

11.5.3 Crossing Technique

Hybridization is relatively easy to perform in cotton. Emasculation is performed by

removing the corolla and the staminal column by hand, curved scalpel or small
scissors on the preceding day the flower would normally open. The emasculated bud
is covered with a paper bag to avoid cross-pollination and desiccation. On the
following day, the pollen from the male flower is collected and placed on the stigma
of the emasculated flower either by brush, directly rubbing the male flower dehisced
anthers on the stigma or by soda straw partially filled with anthers slipped over the
stigma. The pollinated flower bud is covered with paper bag and appropriately
labelled recording name of male and female parent and date of pollination. This
11 Cotton Breeding 619

method of hybridization is popularly known as Doak method (Doak 1934). Nor-

mally, emasculation is done in the afternoon and pollination on the following day
morning. However, pollination may be effected late on the same day of emasculation
if male flower buds of appropriate size are available. With good emasculation and
pollination technique by a skilled/trained person, success of artificial crossing in
terms of boll and seed setting would be as high as 75% of natural pollination.
Intensive research has been done on male sterility in cotton, and the genetic male
sterility is being widely used in hybrid seed production in India. With the availability
of male sterility, crossing in cotton has become easier. The female flower buds,
before opening, are covered with paper bags, and pollination is effected on the
following day. Use of male sterility eliminates the tedious process of emasculation
and saves about 50% labour in commercial hybrid seed production.

11.6 Molecular Cytogenetics and Breeding

Accurate chromosome count of diploid and tetraploid cottons was reported by

Nikolajeva (1923) and Denham (1924). Following these studies, cytological rela-
tionship between the species in the genus, their size and pairing behaviour were
established. Skovsted (1934) showed that the New World tetraploid cotton is allote-
traploid, containing 13 large and 13 small chromosomes; large chromosomes were
homologues to large chromosomes of Asiatic cotton, while 13 small chromosomes
were homologues to New World diploid species. It was concluded that the tetraploid
species were amphidiploids combining diploid Asiatic ‘A’ genome and American
wild diploid ‘D’ genome species (Skovsted 1934). Beasley (1940) and Harland
(1940) independently synthesized amphidiploids between G. arboreum
(A genome) and G. thurberi (D genome) and confirmed Skovsted hypothesis. The
genomes of G. herbaceum and G. arboreum were shown to differ from one recipro-
cal interchange, indicating that G. arboreum was derived from G. herbaceum like
genome. A sub-genome of allotetraploids in chromosome pairing in triploid F1
revealed two reciprocal translocations with ‘A’ genome of G. herbaceum and three
reciprocal translocations with ‘A’ genome of G. arboreum. The data clearly showed
that ‘A’ genome of G. herbaceum was structurally more close (G. herbaceum also
available in wild form i.e. G. herbaceum var. africanum while G. arboreum has no
wild forms) to ‘A’ sub-genome of allotetraploid and considered as progenitor of
present-day allotetraploids (Gerstel 1953; Menzel and Brown 1954). Similarly,
morphological characteristics of F1 hybrids involving allotetraploid and American
diploids and chromosome pairing of (AD)D and (AD)A hexaploids clearly revealed
that G. raimondii is the probable progenitor of D sub-genome of allotetraploid cotton
(Stephens 1944a, b; Hutchinson et al. 1945, 1947). Further, the chromosomes of the
‘A’ and ‘D’ genomes of two diploid progenitors and the allohexaploids exhibited
little or no evidence of divergence during evolutionary history (Phillips 1963). All
the recognized allotetraploid species were having the same chromosome end
arrangements including multivalent formation and segregation ratios in synthetic
hexaploids (Gerstel and Sarvella 1956; Endrizi 1966; Hasenkampf and Menzel
620 V. N. Waghmare

1980) favoured hypothesis of monophyletic origin of amphidiploids and subsequent

radiation and divergence.
In recent years, molecular cytogenetics is greatly adding to the understanding of
genome organization and evolutionary studies. Besides an increase in the speed,
sensitivity and specificity of conventional cytogenetic techniques, molecular cyto-
genetics offers opportunities to perform a variety of tasks which include analysis
and distribution of repeated sequences, assignment of repetitive and single copy
DNA sequences to positions on chromosomes, relationship between specific
chromosomes and linkage groups, relationships between physical and genetic
distances, differentiation of the genomes, detection of alien DNA in introgressed
lines and others (Konan et al. 2009). Over the decades, various kinds of tools have
been used (Wendel and Cronn 2003) collectively demonstrating that the best extant
models of the ancestral genome donors are G. arboreum or G. herbaceum
(A genome) and G. raimondii (D genome).
The repetitive DNA fraction accounts for most nuclear DNA in higher plants
and animals which can be remarkably different, even in closely related taxa. Zhao
et al. (1998) reported some A genome dispersed repeats spread to D genome
chromosomes through FISH analysis in tetraploid cotton. The spread of dispersed
repeats in the early stages of polyploid formation may provide an indication to
identify diploid progenitors of a polyploid. Analysis of (2n) nuclear DNA content of
all diploid species indicated two- to threefold variation in DNA content per genome,
although all diploid species (n ¼ 13) share the same chromosome number (Hendrix
and Stewart 2005). Phylogenetic and genomic in situ hybridization (GISH) analysis
of nine diploids (two A genome and seven D genome) and four tetraploids
(AD genome) supported the hypothesis of ‘A’ sub-genome donor as G. arboreum
or G. herbaceum and ‘D’ sub-genome donor as G. raimondii and provided direct
evidence for the monophyletic origin of the polyploidy Gossypium species (Wu et al.
2013).
The 2,4-D and kinetin induced relatively high somaclonal variation in tissue
culture regenerated plantlets via somatic embryogenesis which could be effectively
detected using RAPD and SSR markers. Chromosome number counting and flow
cytometry analysis revealed stability for the number of chromosomes and ploidy
levels in all regenerated plants except two regenerated plantlets (lost 4 and
5 chromosomes, respectively). The study also implicates that these cytological
changes were not correlated with the marker polymorphisms (Jin et al. 2008).
Price et al. (1990) using A biotin-labelled cloned fragment of 18S–28S ribosomal
DNA from soybean following in situ hybridization of metaphase I meiocytes from
two translocation heterozygotes and monosomics involving chromosome 9 mapped
cloned DNA sequences to chromosomes 9 arms of cotton. Cui et al. (2015) com-
pared the cytogenetic map with genetic linkage maps and showed that most of the
identified marker-tagged BAC clones appeared in same orders in different maps
except three markers showing different positions indicating chromosomal segmental
rearrangements.
Tafvizei et al. (2010) in cytogenetic and molecular studies of ten tetraploid cotton
cultivars (G. hirsutum) including four parental genotypes and their F1 progenies
11 Cotton Breeding 621

showed that the parental genotypes differed significantly in their chiasma frequency
and distribution as well as chromosome pairing indicating their genetic differences.
Adjacent and alternate quadrivalents were detected in the cultivars which might
facilitate new genetic recombination in the progenies. Variety-specific markers were
identified which will be useful for varietal identification. Morphological, molecular
and cytological analyses confirmed the hybridity of the hexaploid (involving
G. hirsutum and G. anomalum and with 0.15% colchicine obtained a putative fertile
hexaploid) with 78 chromosomes. Genome-wide molecular analysis with
683 EST-SSR markers revealed that a high polymorphism between species and A
genome-derived markers were found to be helpful in distinguishing the genomic
differences than the D genome-derived markers (Zhang et al. 2014).

11.7 Genetic Studies of Qualitative and Quantitative Traits

Cotton is one of the ideal crops for genetic studies of various morphological and
economic traits. Availability of distinct morphological variation, easy for
hybridization and differences in ploidy level in cultivated and wild species make
this crop ideal to study genetics and to unravel events of its evolution. Cotton was
one of the first crops to which rediscovered Mendelian principles were applied.
Qualitative inherited traits controlled by major genes consisting of distinct morpho-
logical variation and mutants provided the base for genetic studies in cotton. Balls
(1906) reported the inheritance of lint colour in G. barbadense. Subsequently,
inheritance of okra leaf (Shoemaker 1908), inheritance of red leaf (Mc Lendon
1912) and several other traits were reported in Asiatic diploid and tetraploid cottons.
Early genetic studies involving crosses between the cultivated species led to the
understanding of ploidy level differences as diploids (G. arboreum and
G. herbaceum) and allotetraploids (G. hirsutum and G. barbadense), the relationship
between the diploids and allotetraploids and probable progenitors of the allotetra-
ploid cotton.
Distinct mutant stocks in cotton helped to study the mechanism of inheritance,
metabolism, biochemical and developmental pathways of plant traits. Examples of
mutants that helped to get insight into the developmental pathways include the
virescent mutant for the study of chlorophyll development and photosynthesis
(Benedict and Kohel 1968) and fibre mutants for the development of lint fibre
(Kohel et al. 1974). Morphological mutants also play an important role in cotton
varietal improvement. Okra leaf, a leaf variant, has potential to reduce the incidence
of boll rot and enhance early maturity (Jones and Andries 1967). Frego bract was
found to affect boll weevil incidence (Clower et al. 1970). Leaf and stem hairiness or
hirsute types effectively control jassids (Knight 1952), while the absence of leaf
hairs, i.e. glabrousness, helps to reduce the incidence of whitefly. Nectariless trait
has a significant effect on bollworms and on insects those feed on nectarines. The
pigmented gossypol glands confer resistance to several pests while glandless mutant
produce cotton seeds free from gossypol (Mc Michael 1960). Endrizzi et al. (1984)
reviewed the inheritance of different morphological trait mutants and compiled
622 V. N. Waghmare

available mutants in Asiatic and tetraploid cotton with assigned gene symbols,
names and source. Recently, Percy et al. (2015) reviewed morphological markers,
comprehensively updated the mutants list and summarized integration of morpho-
logical markers with molecular marker maps and application of qualitative traits in
breeding.
Most economic traits are quantitative in nature controlled by several genes with
variable effect on the trait and highly influenced by the environment. Finding genetic
association among various traits contributing to an increase in yield and appropriate
procedure to be applied for combining several positively associated characteristics
had been the focus of conventional breeders. Various mathematical models to
analyse the genetic variability in the breeding material, genotype and environment
interaction with certain basic assumptions were developed to improve breeding
strategies for crop improvement. For quantitative inheritance, understanding of
gene action and its partitioning in additive, dominance, epistatic effects and their
interaction with the environment is most important. The additive effects refer to
average effects of genes, dominance as interaction of allelic genes and epistasis as
the interaction of non-allelic genes influencing specific traits. The diallel cross has
been the widely used method for the analysis of gene action in cotton (Hayman
1954). Generation mean analysis is often used to estimate additive, dominant and
epistatic effects. Different generations of material are used, and the standard errors
are relatively smaller than estimated by variance component analysis. When several
lines are used in crossing programme, reciprocal differences can also arise. The use
of full diallel design in cotton genetic studies effectively compares reciprocal
differences. In general, reciprocal differences are not observed in the segregation
of nuclear genes, except in cases where cytoplasmic differences exist and maternal
parent contribute to such differences. Contribution of maternal parent in cytoplasmic
male sterility and fertility restorer from G. harkensii (Meyer 1975) and oil content in
seeds of F1s has been reported (Kohel 1980).
The combining ability as proposed by Sprague and Tatum (1942) has great
significance for breeding programmes designed to explore heterosis through the
development of F1 hybrids. Combining ability studies also provide information on
gene action thereby help in selection of parents for generating segregating
populations. Matzinger (1963) indicated that the general combining ability (average
performance of the line in hybrid combination) consists of additive and addi-
tive  additive epistatic variances, while specific combining ability (refers to cases
where the performance of certain combinations is relatively better or least on the
basis of average performance of the line involved) consists of dominance and all
types of epistatic variances. Heterosis breeding makes use of dominance, domi-
nance  dominance and epistasis gene action. High specific combining ability for
yield and higher heterosis is generally preferred for hybrid development. In most of
the self-pollinated crops, the near homozygous lines developed that equal or surpass
the F1 (Matzinger 1963). El-Adl and Miller (1971) conducted cotton breeding
experiments and reinforced the same conclusion.
The phenotypic performance of a genotype is influenced by its environment,
and phenotypic responses may not be the same for all genotypes.
11 Cotton Breeding 623

Genotype  environment interactions and their statistical significance are important

in estimating various genetic and environmental parameters that help to decide the
most likely area of adaption of a cultivar. Large interaction components than the
genetic component limit adaptions of cultivar to a specific environment where as if
interaction component is small, the cultivar is considered to have general adaptabil-
ity and may be recommended for general cultivation in all environments, also
referred to as universally accepted cultivars. Miller and Rawlings (1967b)
demonstrated a method of computing phenotypic and genetic correlation from
covariance analysis in cotton. If genetic correlations among the traits are high,
selection for one trait facilitates simultaneous improvement of both the traits. But
if negatively correlated, selection for one may affect the performance of the other.
The correlated responses were caused normally by pleiotropy or linkage. It is
assumed that recombination and arrangements of linked genes can occur in hetero-
zygous condition and there would be little chance of new recombination to occur
after F2 generation. To overcome this situation, Hanson (1959) recommended
several generations of random inter-crossing to break undesirable linkages. Similar
results were obtained in independent studies of Miller and Rawlings (1967a),
Meredith and Bridge (1971), Singh et al. (1989) and Waghmare (unpublished).
Heritability of the trait under selection is one of the important parameters to
predict success of selection. Heritability in a broad sense includes the total genetic
variance but in a narrow sense includes only additive genetic variance. Narrow-sense
genetic heritability is of much significance for making steady progress during
selection for improving the desired traits. Heritability of yield is generally lower
than its yield components and fibre quality traits. That is the reason for slow gains in
yields, and it is imperative to base selection for major yield components and quality
traits concurrently to make steady gains for yield and quality during selection.
With recent advancements in molecular marker technology and adoption of
transgenic Bt cottons, there is a shift in application of techniques and methodology,
though the principles used in conventional cotton breeding remains the same.
Improvements in host plant resistance, selection for yield and fibre quality are
being facilitated by DNA markers. Improvement of lint yield still remains the
major selection criterion in the changed scenario; however, the pace and way of
collecting phenotypic data of plant attributes contributing to yield component traits
and host plant resistance is slowly changing. Availability of improved version of
machines for fibre quality measurements, new digital tools and platforms for
collecting phenological data in high throughput is making a difference slowly but
steadily on future cotton breeding.

11.8 Breeding Objectives

In general, the major breeding objectives in cotton are high lint yield, early maturity,
fibre quality, plant type to adapt higher population density and mechanical
harvesting, wide adaptability and resistance to biotic (insect pests and diseases)
and abiotic (drought, salinity and heat) stresses.
624 V. N. Waghmare

11.8.1 Breeding for Higher Yield

Cotton is cultivated mainly for its natural fibre which is the most economic produce.
Fibre yield can be enhanced through improvement of positively associated yield
components. Various studies indicate that yield is majorly influenced by boll number
per plant, size/weight of boll and proportion of lint (lint percent). These major
components of yield are highly interrelated affecting the final lint yield. Plants
with prolific boll bearing potential give higher yield. Higher the boll number, the
boll size (expressed as weight of the seed cotton per boll) may reduce; on the
contrary, plants with high boll weight may have less number of bolls. Lint is
produced on the surface of the seed, and the density of lint on the seed affects lint
production which is a varietal character. Thus, higher seed set per boll is desirable to
increase lint yield. Seed size is associated with size of boll. Bigger seed size normally
has low lint proportion or lint percent, while small boll varieties invariably have
smaller seeds and high lint percent. Varieties with high proportion of five locule
bolls would produce high yield than the variety with four lock bolls. Along with lint
yield, fibre quality is also most important. Cotton lint yield and fibre quality are
negatively associated. Selection for higher yield often results in reduction in fibre
quality. Thus, while improving lint yield, cautiously maintaining requisite fibre
quality or simultaneous improvement for lint yield and quality is more desirable.

11.8.2 Early Maturity

Earliness is closely related to determinate growth habit. Earliness in cotton is

difficult to define and measure, since receipt of rain or enough moisture in the soil
induces the cotton plant to flower and continue to set bolls over longer period. In
fact, cotton is a perennial plant induced to annual, with domestication and selection.
Early maturity in cotton has several advantages. Early maturity shortens the crop
duration and reduces management for late appearing insects, pests and diseases. It
also reduces production cost and allows a double-cropping system. Among the other
advantages, it helps to reduce losses from late appearing pests such as boll weevil
and pink bollworm and also facilitate cotton harvesting in a lesser number of manual
pickings and mechanical harvesting.
Earliness in cotton is measured based on the proportion of seed cotton harvested
in the first and second picking which is expressed as percentage of total seed
cotton and the same may be used as an index (generally above 0.8) for practical
measure of earliness. The number of nodes appearing before the first fruiting branch,
smaller plant size, small bolls and seeds and boll sets closure to the ground are some
of the morphological traits associated with early maturity. Early maturity is a varietal
character varying in different varieties and also influenced by environmental factors.
It is a common observation that moisture stress induces early maturity. The com-
mencement of flowering, duration of flowering after appearance of the first flower
and time required for bolls to mature are few more factors that determine varietal
characters and maturity.
11 Cotton Breeding 625

11.8.3 Fibre Quality

Enhancement of fibre quality is an important and inclusive objective of any cotton

breeding programme. Cotton fibre is an outgrowth of a single epidermal cell, an
outer layer of the seed. Cotton seed produces two types of fibres, long and short
fibres. The long fibres form an outer layer and get easily separated from the seed; the
process is referred to as ginning. The long fibres, generally referred to as ‘lint’, are
spinnable, extensively used for spinning yarn and in the textile industry. The short
fibres, inner layer, that remain attached to the seed after ginning are called as ‘fuzz’
or ‘linters’. In cultivated varieties, the proportion of fuzz fibre varies from 1.0% to
10.5%. It is minimal in G. barbadense, 4.3–5.9% in Asiatic cottons and maximum
(up to 10.5%) in G. hirsutum. The fuzz composing of pure form of cellulose are used
in making rayon, writing and photographic papers, currency notes, X-ray films,
explosives and various cellulosic products.
With a stiff competition from synthetic fibres and to sustain its share in the
apparel market, cotton fibre property improvement becomes imperative. Advances
in fibre technology has made it possible to measure the characteristics of cotton
fibres and to compare and facilitate improvement so as to meet the requirements of
the spinners and textile manufacturers. The spinning performance of cotton fibres
depends on its properties; the most important are fibre length, strength, fineness and
maturity.

11.8.3.1 Fibre Length

This has a direct relation with spinning performance. Uniform staple length of fibre
enables to spin yarn with uniform size and strength. Fibre length along with
uniformity of fibres is measured with an optical instrument called Digital
Fibrograph, which scans cotton fibres at 50% and 2.5% span length (SL). The
50% SL is the length that 50% of fibre in the sample equal or exceed; while in
2.5% SL, 2.5% of the fibres in the sample will equal or exceed. The uniformity ratio
for the sample is calculated as the ratio of 50% SL to 2.5% SL expressed as percent.

11.8.3.2 Fibre Strength

This determines yarn strength. Strength is an important fibre attribute essential for
high-speed spinning. Weaker fibres frequently break and do not stand rigours of the
manufacturing process. The Stelometer and the Pressley strength tester are com-
monly used to measure cotton fibre strength of small samples. Strength is expressed
as pounds of force required to break a bundle of fibres with a cross-sectional area and
denoted as tenacity (g/tex). In general, upland and Asiatic cotton varieties have
weaker fibre than the Pima and Acala types. Through normal breeding approaches,
transferring fibre strength trait from G. barbadense varieties to upland cotton is not
easy. Several researchers working with upland cotton reported negative association
between fibre strength and lint yield. However, years of breeding and selection has
helped to improve lint yield and fibre strength simultaneously in upland cotton.
626 V. N. Waghmare

11.8.3.3 Fibre Fineness

This is associated with fibre diameter and thickness of the fibre wall. Fibres of
G. barbadense varieties have small diameter and smooth or fine texture, while fibres
of upland and Asiatic varieties have larger diameter, thicker fibre wall and coarse
texture. Fibres with a well-developed inner wall are said to be matured and provide
good strength. When the average amount of the inner wall fails to develop, the fibre
is said to be an immature fibre. Fibre fineness and maturity is measured by an
instrument called ‘micronaire’. It measures the rate of airflow at a standard pressure
through a known weight of cotton in standard volume chamber. The rate of airflow is
slower with fine fibres than with coarse fibres and is expressed as standard
micronaire units.
The other parameters affecting quality include colour and extent of trash. Cotton
varieties grown across the globe vary in fibre characteristics, and these are inherent
to the variety. Generally, the cotton fibres of cultivated upland and Asiatic cottons
are white with high reflectance, while the Pima or G. barbadense cotton appears
yellow in colour. Insect and fungal infestations also result in discolouration affecting
fibre colour and quality. Normally, dried leaves, leaf hairs and bracts adhering to the
fibres represent a major part of trash affecting fibre quality.

11.8.4 Plant Type

Breeding for plant type has contributed significantly to increase yields in cereals and
other crops. Cotton, being a perennial type, induced to annual, recommending a
plant type for all situations is not possible. Concerted breeding efforts for developing
high-yielding varieties and adoption of mechanization in a cotton production system,
especially harvesting, have resulted in the development of varieties with medium
stature, compact plant with relatively shorter boll bearing branches and short fruiting
period. Such compact varieties have significantly contributed to increasing cotton
productivity to more than 2000 kg lint/ha in countries such as Australia. Developing
such compact plant through rigorous selection procedure and further maintaining
straight varieties become easy than in hybrids. Such compact plant type will help to
adapt higher plant density and facilitate mechanized harvesting. After adoption of
GM cotton, cultivation of hybrid cotton in India has increased to above 90% of its
acreage under cotton. Efforts need to be made to develop varieties or hybrids with
compact plant type, big bolls with fluffy opening and early maturing with short
fruiting period. Varieties with small or deciduous bracts and smooth leaves (free or
less trichome density) would help in the production of cleaner and least trash cotton.

11.8.5 Wide Adaptability

Adaptability refers to the capacity of a variety to produce to its potential in a given

environmental condition. In India, cotton is grown in varied agro-climate in North,
Central and South from 9 N to 31 N latitude and diverse situations ranged from
11 Cotton Breeding 627

irrigated areas characterized by intensive management to assured rainfall and dry

rainfed situation characterized by low rainfall (less than 500 mm) accompanied by
high temperature. Varieties or genotypes adapted to a particular growing condition
may not have good performance under other environmental conditions. This differ-
ential response of genotypes is attributed to genotype-environment (GE) interaction
(Cruz et al. 2012) and one of the reasons for low yields. To avoid multiplicity of
varieties in narrow areas, it is imperative to develop and identify varieties with wide
adaptability. Wide adaptability and stability of varieties recommended for cultiva-
tion across the agro-eco-regions will help to enhance productivity, minimize varia-
tion in fibre quality parameters and better returns to growers.

11.8.6 Biotic Stresses

Cotton crop is attacked by various insects, pests and diseases resulting in consider-
able economic losses each year. To minimize the losses, growers frequently resort to
use of insecticides and pesticides which, in turn, increase cost of production and
increase the risk of development of resistance in insects against chemical insecticides
and exposure of workers and animals to deadly pesticides and risk of life. Host plant
resistance is the best option to reduce economic losses and minimize the use of
hazardous chemical pesticides.

11.9 Insect Pests

In a cotton crop, the presence of 252 arthropod pest species (including insects and
mites), 173 species of predators and 192 species of parasitoids/parasites have been
documented (Nagrare et al. 2022). However, about a dozen species of insects are
identified as major pest causing significant losses to cotton crop, while the remaining
species are occasional, sporadic, localized or minor in nature. The major pests of
cotton in India are bollworms [American bollworm (Helicoverpa armigera), spotted
bollworms (Earias insulana, E. vittella) and pink bollworm (Pectinophora
gossypiella)] and sucking insect pests [leafhopper (Amrasca biguttula biguttula),
aphid (Aphis gossypii), thrips (Thrips tabaci), whitefly (Bemisia tabaci), mealybug
(Phenacoccus solenopsis) and papaya mealybug (Paracoccus marginatus)]. Other
pests such as Indian cotton mirid bug (Creontiades biseratense), stem weevil
(Pempherulus affinis) and tobacco caterpillar (Spodoptera litura) are also
categorized as major pests especially in South India. Prior to introduction of Bt
cotton, the above pests were reported to be attacking cotton crop at different stages of
growth causing losses ranging between 50% and 60% (Puri et al. 1999). Currently,
losses are estimated ranging from 20% to 30%.
In cotton, innate plant characters that suppress insect pest population were
normally explored with considerable success in resistance breeding. These plant
characteristics and their significance are as follows:
628 V. N. Waghmare

1. Hairiness—Leaf and stem hairiness is associated with jassid resistance (Jenkins

1989; Watson 1989); however, hairiness attracts more incidence of bollworm
(H. armigera) and whitefly (Niles 1980) and also results in high trash content
in lint.
2. Glabrous or smooth leaves—The absence of leaf hairs is found to have signifi-
cantly reduced oviposition of bollworm (H. armigera) and larval population than
hairy leaves (Lukefahr et al. 1971). Eggs laid on glabrous leaves do not remain
attached and freely get dislodged by wind. Thin and glabrous leaves were also
found to be tolerant to whitefly (Butter and Vir 1989).
3. Absence of nectarines—Nectaries are normally present on the lower midrib of
leaves and inside the flower bracts. Nectaries secrete nectar which attracts insects.
A significant reduction in oviposition by bollworm has been reported on
nectariless plants and no adverse effect on plant growth in the absence of
nectarines (Jenkins 1989).
4. High gossypol content—Pigmented gossypol glands are normally present on all
parts of cotton plant. Gossypol is a polyphenolic compound with insecticidal
properties. High gossypol content confers resistance to American bollworm,
tobacco budworm and spider mites. However, gossypol content in seed makes
the cotton seed oil unfit for human consumption without gossypol detoxification.
5. Leaf traits—Narrow leaf lobes with hairiness show tolerance to jassids. Okra leaf
character reported a significant reduction in damage by pink bollworm (Wilson
and George 1982; Wilson 1986).

11.10 Cotton Diseases

Cotton crop is also affected by several diseases. The major diseases of cotton include
fungal diseases [root rot, grey mildew (Ramularia areola), Alternaria leaf spots,
Myrothecium leaf spot, Corynespora leaf spot], bacterial diseases [bacterial blight
(Xanthomonas citri pv. malvacearum), inner boll rot] and viral diseases [cotton leaf
curl disease (CLCuD) and tobacco streak virus (TSV)].

11.10.1 Root Rot

Root rot or seedling rot in cotton is caused by soil fungi Rhizoctonia solani,
R. bataticola and Sclerotium rolfsii. It results in sudden wilting and drooping of
plants that can be easily pulled out. Shredded bark of roots gives yellowish appear-
ance. R. solani is one of the most important pathogens of seedling complex of cotton
(Rothrock 1996); infected root becomes brown and wet with sunken lesions on
stems known as ‘sore shin’ (Atkinson 1892). R. bataticola causes black and dry root;
S. rolfsii infection noticed with white mycelial growth on the collar region leads to
the rotting of roots and drying of seedlings. The disease is prevalent in all cotton-
growing zones of India. A sick plot has been maintained at ICAR-CICR, Regional
Station, Sirsa, to screen segregating and advanced materials to identify resistant
11 Cotton Breeding 629

lines. Several resistant lines have been identified and regularly being used in
breeding programme in India.

11.10.2 Grey Mildew

Grey mildew is caused by Ramularia areola. Pale, irregular and angular spots
initially appear on older leaves delimited by veinlets (Chohan et al. 2020). Dirty
white powdery growth spreads on the lower and upper surface of the leaves. As the
disease advances, leaves turn yellow, necrotic and dark brown and dry leading to
premature defoliation and forced boll opening. Grey mildew disease is prominently
occurring in diploid cotton. However, recently, it is being observed in G. hirsutum
cotton in central and south zones of India. In Maharashtra, the grey mildew is
commonly referred to as ‘dahiya’ or ‘dahya’ disease because symptoms resemble
sprinkled curd on foliage (Gokhale and Moghe 1965). A total of 1489 G. arboreum
germplasm accessions were evaluated for grey mildew reaction at ICAR-CICR,
Nagpur, and seven immune accessions (no disease symptoms), namely
Bangladesh (EC 174092), G-135-49, 30805, 30814, 30826, 30838 and 30856; and
17 highly resistant accessions were identified (Mohan et al. 2006). These accessions
are being used in G. arboreum improvement programme.

11.10.3 Alternaria Leaf Spot

The disease is caused by Alternaria macrospora and A. alternata. Initially, the

disease appears as brown or tan spots on cotyledons, leaves, bracts and bolls.
Concentric rings develop within the spots mostly on the upper surface. Later on,
spots coalesce and cause blighting of the leaves. Favourable conditions lead to
severe defoliation. The disease is prevalent in all major cotton-growing tracts of
the country (Rane and Patel 1956). Recently, two genotypes, i.e. GSHV-159 and
GBHV-184, were identified as immune (disease-free) and ten genotypes resistant
against Alternaria leaf spot disease (Patel et al. 2019). These identified genotypes
may be used for breeding host plant resistance.

11.10.4 Corynespora Leaf Spot

The disease is caused by Corynespora cassiicola and C. torulosa. Initially, affected

leaves show circular to irregular, dark red spots which turn to brown lesions
surrounded by a dark border. Later, alternate light and dark brown rings may develop
on the lesions with ‘shot hole’ appearance. Under severe conditions, defoliation may
occur. The disease is prominently emerging in Central India (Salunkhe et al. 2019).
It is an emerging foliar disease, spreads very fast if congenial weather conditions
prevail and may cause severe economic damage to cotton crop. Available
630 V. N. Waghmare

germplasm may be subjected to intensive screening against this disease to identify

sources of resistance.

11.10.5 Bacterial Leaf Blight

Bacterial leaf blight (BLB) is a bacterial disease caused by Xanthomonas citri

pv. malvacearum. BLB is prevalent throughout the world. The disease appears as
water-soaked, light to dark green, small spots measuring 1–5 mm on cotyledons and
lower surface of leaves. The lesions darken and veins also become black with age.
Leaves shed prematurely resulting in extensive defoliation. As symptoms progress
and stage advances, it is known as angular leaf spot, black arm and boll rot (Hillocks
1992). Asiatic cotton varieties of G. arboreum and G. herbaceum are reported to be
tolerant, but upland G. hirsutum varieties are very susceptible to BLB. At least
18 races of bacterial leaf blight of cotton and corresponding genes conferring
resistance have been identified. In India, race 18 is prevalent in all cotton-growing
states. Depending on the prevalence of the pathogenic races, it is pertinent to
combine two or more genes conferring BLB resistance in new varieties. Several
existing varieties are resistant to BLB which may be promoted in hot spot areas for
cultivation and also involved in breeding gene pool.

11.10.6 Boll Rot

Boll rot is caused by several saprophytic fungal and bacterial pathogens. Recent
detailed studies identified Pantoea spp. as the causal organism for inner boll rot
(Nagrale et al. 2020). The infected, apparent green healthy bolls, when cross-
sectioned, the developing seeds and fibres or lint gets discoloured (yellowish orange
to reddish in colour). The developing seeds swell and rot in one or two locules
(Hudson 2000) and occasionally the complete bolls. The disease is emerging and
currently prevalent in Maharashtra and Central India. Developing varieties with
open canopies, okra to super okra leaf types and frego bracts would help to reduce
the boll rot to a greater extent. Incorporating nectariless trait in the varieties may also
reduce entry of fungal pathogen in the developing boll and subsequent boll rot.

11.10.7 Cotton Leaf Curl Disease (CLCuD)

The cotton leaf curl disease is caused by Begomoviruses of the family

Geminiviridae. The prominent symptoms of CLCuD include yellowing and small
veins thickening (SVT) on the lower surface of young leaves and downward or
upward curling of leaves with stunted plant growth. Under severe conditions, a small
leaf like outgrowth on the lower side of the infected leaves (enations) may also be
visible. This disease is transmitted by insect vector whitefly (Bemisia tabaci).
Currently, this disease is prevalent only in Pakistan and North Indian states, viz.
11 Cotton Breeding 631

Punjab, Haryana and Rajasthan (Rajagopalan et al. 2012). In India, a complete set of
G. hirsutum germplasm and introgressed derivatives were screened at multi-
locations in hot spots of CLCuD in Northern India. However, not a single accession
resistant to CLCuD could be identified. Recently, two accessions GSV 8 and GSV 9
obtained from the United States tested for CLCuD incidence showed immune to
tolerant reaction. These two accessions have now extensively been used to transfer
resistant gene in breeding material for the development of G. hirsutum varieties.

11.10.8 Tobacco Streak Virus (TSV) Disease

This disease is caused by Ilarvirus. Initial symptoms include chlorotic growing tip in
young leaves, subsequent bronzing, curling with necrosis of leaves and plants
become stunted (Gawande et al. 2019). It is transmitted by thrips (Thrips tabaci)
and usually prevalent in southern states of India, but recently reported from
Maharashtra and Andhra Pradesh as well. TSV is an emerging disease; studies on
the identification of host plant resistance are required to be taken in areas of its
prevalence.
Sappenfield et al. (1980) suggested two procedures referred to as ‘multiple
disease resistant breeding’ and ‘multiadversity resistance breeding’. It consists of
the sequential inoculation of cotton seedlings grown in controlled environments with
different disease pathogens or infestations with insect pests, followed by selection of
resistant plants. In this procedure, sick plots developed for multiple pathogens can
effectively be made use of. The procedure may differ as per the combination of
insect pests or disease pathogens for which the resistance is being desired. In this
procedure, simultaneously several common disease pathogens and insect pests are
evaluated, and plants with multiple disease resistance can be identified. Resistant
plants are allowed to be grown to maturity to get seeds and for further use.

11.11 Abiotic (Drought, Salinity and Heat) Stresses

Cotton crop suffers from various abiotic stresses during various stages of crop
growth. Abiotic stresses mainly include drought, high temperature (heat) and
salinity.

11.11.1 Drought

In India, of the total acreage under cotton, about 60% cotton is grown under rain-
dependent situation. In such areas, cotton crop often suffers from moisture stress. It
affects the crop growth development and production. Cotton germplasm and
cultivated varieties exhibit genetic variability for various traits that contributes to
resistance for drought. The major plant characteristics that impart drought tolerance
include leaf traits, i.e. small and thick leaves, leaf hairiness, thick cuticle and
632 V. N. Waghmare

waxiness of surface; stomatal characteristics, i.e. small size, sunken type and less in
number per unit area; and a deep root system with increased lateral root growth.
Small and thick leaves, thick cuticle, leaf surface waxiness and hairiness reduce
water loss through transpiration (Eslick and Hackett 1975; Bhatt and Andal 1979)
and contribute towards stress tolerance, but reduced transpiration results in the
reduction in photosynthesis. Stomata, small in size, sunken type and less in number
per unit area are associated with drought tolerance. Control of stomatal aperture and
rapid closing features helps in reducing the evapotranspiration and maintaining high
turgor potential of leaf tissues under drought stress. The ability of a plant to maintain
high turgor potential is considered to be a manifestation of drought tolerance. The
deep root system penetrates deeper in soil extracting more moisture, while increased
lateral root growth extracts moisture from lateral root zone and maintains water
requirement of the plant under drought stress situation. Availability of sufficient
moisture to the plant under stress does not make it drought tolerant, but how
efficiently used by the plant makes it drought tolerant. In other words, water use
efficiency, reduced transpiration and high photosynthetic rate are also considered to
be the reliable parameters of drought tolerance. High proline content in leaves under
moisture stress has been recorded (Singh and Sahay 1989) and can be used as an
indicator of water stress, but it cannot be used as a measure of drought tolerance.
Drought tolerance is governed by polygenes and influenced to a great extent by
several environmental factors. Combining several traits contributing to drought
tolerance is a difficult task. Conventional pedigree and backcross methods may be
used if the desired traits in biparental crosses are to be combined or introgressed. It is
difficult to find a combination of traits in single genotype. Recurrent selection
involving several trait contributing genotypes to develop a source population and
then intensive selection under drought-induced conditions would help to develop
drought-tolerant genotypes.

11.11.2 High Temperature

Temperature and heat stress has become a major problem in cotton production; it
affects the normal plant development, growth and productivity. The degree of
occurrence of heat stress varies greatly across agro-climatic zones and also depends
on the period of high diurnal temperature. Plant response to high temperatures also
varies within and across species, as well as developmental stages. A high night
temperature has been reported to cause excessive square and boll shedding. Devel-
opment of more heat-tolerant cotton needs to be prioritized; however, identification
of sources of heat tolerance in cotton is a challenge due to reduced genetic diversity
for thermo-tolerance in wild-type cotton.
11 Cotton Breeding 633

11.11.3 Soil Salinity

Cotton is considered as a moderately salt-tolerant crop and may be grown with a

salinity threshold level of 7.7 dS/m (Zhang et al. 2013). Most of the varieties are
found sensitive during germination and early growth stages but observed to be
tolerant during late growth stages. Salinity is a serious threat for cotton in irrigated
areas. Salt stress results in delayed flowering, reduced fruiting, fruit shedding and
reduced boll weight that affect seed cotton yield. Excessive sodium exclusion or its
compartmentalization is found to be the main adaptive mechanism in cotton under
salt stress. Seed priming is suggested for improving cotton germination in saline
soils (Bradford 1986). Differential varietal response to varying salt concentration
may be used to identify tolerant sources and to develop salt-tolerant varieties with
the aid of marker-assisted selection.

11.12 Coloured Cotton

Normally, cotton produced worldwide has white lint. Coloured cotton is being
grown and used by mankind since 2500 BC. Coloured cotton varieties known in
diploid cottons were under cultivation in Asia, particularly Indian subcontinent,
China and Central Asian Republics of the former Soviet Union. In India, brown
linted varieties of tree cotton (G. arboreum), namely Cocanada 1, Cocanada 2 and
Red Northerns, were under commercial cultivation mainly on black soils under
rainfed condition in parts of Andhra Pradesh. Red linted types were predominant
and high in demand for their better dying qualities and colour fastness. Coloured
linted varieties lost their glory, mainly because of low productivity, poor fibre
characteristics and non-uniformity of colours (Waghmare and Koranne 1998). In
the cultivated species, brown and green colours are most common. Some of the
genotypes in germplasm collection of the United States and Russian Republics are
reported to have coloured lint with shades of pink, red, blue, green and also black.
Ms. Sally Fox of Vreseis Ltd. claimed to have developed multi-coloured lint,
i.e. development of more than one colour on the same lint strand (Fox 1987).
However, genotypes with multi-coloured lint have not yet been made available to
the researchers nor produced on a large scale.
About 40 coloured genotypes of upland cotton (G. hirsutum), mostly in various
shades of brown and green colour, are available in the National Gene Bank of Cotton
maintained at ICAR-CICR, Nagpur. These genetic stocks are indigenous collections
as well as exotic accessions from the United States, erstwhile USSR, Israel, Peru,
Mexico, Egypt, etc. In Asiatic diploid cottons (G. arboreum and G. herbaceum),
about 10 germplasm lines possessing mostly brown lint colour are also available.
Wild species are important source of coloured lint. As many as 22 wild species of the
genus Gossypium, including putative donors of the present-day tetraploid cotton,
i.e. G. herbaceum race africanum and G. raimondii, and all 4 cultivated species of
Gossypium possess coloured lint.
634 V. N. Waghmare

Development of lint colour starts with accumulation of pigments in the lumen of

lint before boll bursting. In upland cotton, pigmentation starts appearing in the
developing lint 32 days (46–47 days in Asiatic cotton) after fertilization, and it
takes nearly 6 days to develop colour. However, complete expression of lint colour
takes place only when the boll bursts open and lint is exposed to sunlight. It takes
about a week for the lint to develop a complete natural colour. The intensity and the
time taken for complete development of colour vary with the genetic background of
the genotypes. Lint colour is a genetically controlled character and has mostly
monogenic inheritance. Six loci governing lint colour in upland cotton have been
identified and designated with gene symbols Lc1, Lc2, Lc3, Lc4, Lc5 and Lc6 for
brown lint, Dw for dirty white and Lg for green lint colour (Endrizzi and Kohel
1966; Kohel 1985). Lc1 locus governing brown coloured lint was mapped to
chromosome 7 and Lc2 on chromosome 6 (Wang et al. 2014). The breeding methods
for improvement of coloured cotton are the same as applicable to white linted cotton.

11.13 Conventional Breeding Approaches

Cotton, being an often cross-pollinated crop, the breeding methods employed differ
from methods used for self- and cross-pollinated crops. Though cotton is predomi-
nantly self-pollinated, generally, cross-pollination ranges from 3% to 5% owing to
sparse insect populations. With the intensive use of inputs, particularly insecticides
to control invasive insect pests, the natural population of useful insects that serve as
pollinators has drastically been reduced in the cotton ecosystem. However, in some
instances, cross-pollination has been reported as high as 30–50% where insect
population is abundant in high rainfall areas of the South Eastern United States.
Mode of pollination generally affects the genetic makeup of breeding population.
Owing to partial (often) mode of cross-pollination, cotton breeding makes use of
breeding methods relevant to both self- and cross-pollinated crops. In practice,
cotton breeders exercise considerable flexibility in employing breeding approaches
depending upon the extent of available genetic variability and breeding objectives.
The principal objective in cotton breeding is to improve the productivity and fibre
quality with sufficient degree of adaptability and resistance to insect pests and
diseases. Unlike the self-pollinated crops such as wheat, rice and soybean and
cross-pollinated crops such as maize, partial heterozygosity is desired in the cotton
varieties to be vigorous and productive. It is, in this context, cotton breeding method
differs from the self- and cross-pollinated crops.
Several researchers reviewed cotton breeding procedures and methods
(Richmond 1951; Sikka and Joshi 1960; Singh and Raut 1983). For success of any
plant breeding programme, the prerequisite is availability of sufficient genetic
variability in the desired species. To augment the genetic variability, one may
need to assemble it from various sources, i.e. germplasm collection, and, if required,
create the genetic variability. Variation in the plant species can be enhanced through
introduction, hybridization, mutation and combination of these methods. Genetic
variability thus generated is channelized following certain selection procedures to
11 Cotton Breeding 635

obtain improved varieties. Based on the procedure followed for generation of genetic
variability and selection scheme employed, cotton breeding methods may be classi-
fied distinctly that have been described with suitable examples wherever necessary.

11.13.1 Introduction

Introduction of crop species and varieties in new habitat has played an important role
in the development of early cotton varieties. Cultivated tetraploid cotton
(G. hirsutum) originated in America was introduced and now commercially
cultivated in more than 90 countries in the world. It is one of the striking examples
of successful introduction and acclimatization in India (Sethi 1960). G. hirsutum was
first introduced in India in the latter half of the eighteenth century. The upland cotton
from the United States was introduced by East India Company in the middle of the
nineteenth century (Gammie 1908). The Cambodian cotton whose origin could be
traced from Mexico to the Philippines by way of Cambodia and other parts of
Southeast Asia was introduced in Madras state in 1906 (Anonymous 1954). Despite
several attempts since 1931, for introduction of G. barbadense, the variety
‘Andrews’ introduced from West Indies was adapted and directly released for
commercial cultivation in Kerala and Mysore (Kalyanaraman et al. 1955). Several
introduced cotton genotypes, though directly could not be released as varieties, but
used for the development of hybrids. Some of the notable examples are American
nectariless was crossed with the Indian variety G 67 to produce the world’s first
intra-hirsutum hybrid ‘H4’ (Patel 1971). Similarly, Russian introduction of
G. barbadense SB 289E was crossed with the upland variety ‘Laxmi’ to obtain the
first interspecific hybrid ‘Varalaxmi’ (Katarki 1972). Another Russian barbadense
introduction SB 1085-6 was crossed with Acala Glandless for the development of
the interspecific hybrid ‘CBS 156’ released in Tamil Nadu.

11.13.2 Selection

Selection has emerged as the most important breeding method from time immemo-
rial for improvement of crop plants. It is the process of picking up individuals in the
population with naturally occurring variation or the variation created through artifi-
cial hybridization or induced mutations which show marked improvement for one or
combination of characters over the existing population. The various selection
techniques followed in cotton improvement include empirical mass selection, pure
line selection and progeny selection.

11.13.2.1 Mass Selection

This is the simplest type of selection often practised traditionally on an introduced
material during initial stages of crop improvement. It is known that many
introductions, especially landraces and open pollinated varieties, harbour a consid-
erable extent of genetic variability/heterogeneity; on such genetic variability, mass
636 V. N. Waghmare

selection is usually preferred. In mass selection, desirable high-yielding plants with

phenotypic similarity are selected and ginned and the seed is bulked for planting in
the next season. This process is repeated for 2–3 years till an improved bulk with
higher yield and quality than the existing population is obtained. Release of new
variety by this method takes 7–8 years. Few of the released varieties in India include
Bikaneri Narma, F 414, H 777, SRT 1, Narmada, L 147 and PRS 72 in G. hirsutum
and G 27, HD 11, LD 133, Gaorani, Cocanada white and Saraswati in G. arboreum.
But this method is now seldom used because of its less precision than the progeny
selection.

11.13.2.2 Pure Line Selection

This refers to the identification of homozygous plant progeny. Pure lines are
developed by inbreeding, controlled pollination to avoid outcrossing or from double
haploids. Pure line selection leads to complete homozygosity, little or no heritable
variation, reduced vigour and lower yields; hence generally not practised in cotton
breeding. However, modified pure line selection is practised especially for
maintaining lines with specific traits or for the development of pure lines to be
used as parents in hybrid development programme. The varieties developed through
pure line selection include MCU 5 VT, CO2 and LSS in upland cotton; Cocanada
2, Gaorani 22, Gaorani 46 and Lohit in G. arboreum; Western and Selection 69 in
G. herbaceum; and Sujata in G. barbadense.

11.13.2.3 Progeny Selection

This refers to the selection of single plants in a segregating population for pedigree
selection. The progeny of each selected plant is grown separately, and single plants
in the superior progenies are selected again. The process of reselection of superior
plants is repeated until uniform progenies are obtained. Alternately, progeny selec-
tion can be used for maintaining the genetic purity of the variety or progressively
improving the variety, if enough heterogeneity persists. Punjab American cv 320F is
a good example of intra-varietal selection from LSS that led to the development of
superior variety.

11.13.3 Hybridization

Hybridization is the most common method of producing new genetic variability,

exercising selection and developing new improved cotton varieties. Hybridization
(crossing) between two distinct genotypes or varieties of the same (intraspecific) or
different (interspecific) species has widely been used to generate variability for
economic and fibre quality traits and to combine the desirable traits of the parents
involved in crossing. Besides artificial crossing of known parents, in cotton, natural
crossing (open pollination) occurs to a considerable extent either at intraspecific or
interspecific level creating variability in the open population. This is one of the
reasons that open pollinated varieties rapidly get deteriorated depending on insect
vector population in the cotton ecosystem. An excellent example of natural crossing
11 Cotton Breeding 637

in cotton is available, i.e. Acala 1517 lines of upland cotton in the United States got
tolerance to wilt and excellent fibre properties through natural outcrossing with
G. barbadense (Harrison 1950). In India, hybrid between G. hirsutum (tetraploid)
and G. arboreum (diploid) is reported to have been resulted from natural outcrossing
at Sirsa.
Hybridization breeding procedures in cotton slightly differ from the self-
pollinated crops. Artificial hybridization to combine the parental traits in cotton is
explored in two ways, i.e. first, development of varieties through pedigree and
backcross breeding and second through developing F1 hybrids to exploit heterosis.

11.13.3.1 Pedigree Procedure

This is generally followed to select superior genotypes from the segregating
generations. Segregating populations of single cross, double cross, three way and
multiple crosses can be handled following pedigree scheme to develop new varieties.
In cotton, the selection may be terminated at early stages (before attaining complete
homozygosity) so as to retain residual heterozygosity which is considered desirable
in cotton. Using the pedigree method, the majority of cotton varieties have been
developed for commercial cultivation in India.

11.13.3.2 Backcross
This refers to crossing of F1 hybrid to either of its parents. Backcross breeding, a
system of repeated backcrossing, is used to transfer genes for disease or insect pests’
resistance or other simply inherited characters to the well-adapted varieties. The
variety developed through this method resembles more to the recurrent parent
variety except for the character transferred. This method is very effective even to
transfer male sterility or male fertility restorer genes or chromosome transfer from
one compatible background to another. In cotton, several desirable traits have been
transferred through backcrossing from wild and cultivated species in elite varieties.

11.13.4 Recurrent Selection

Recurrent selection refers to the reselection of superior plants generation after

generation with intermating of selected plants to produce population for the next
cycle of selection. The essence of this method is to accumulate desirable alleles in
the breeding population through cyclic selection and intermating of superior
individuals from the population subjected to recurrent selection. The source popula-
tion may be created by crossing among a group of genotypes, varieties, breeding
lines or exotic germplasm with distinct desirable trait. If the number of genotypes
involved to develop source population is large, crossing each genotype in all
possible combinations becomes more tedious, time and resource consuming. More-
over, natural crossing may occur only on a limited scale depending on natural insect
pollinators. An extent of natural cross-pollination may be augmented by introduction
of male sterility genes, especially genetic male sterility, into the population. Once the
source population is created, to operate recurrent selection involves three steps:
638 V. N. Waghmare

1. Identification of superior single plant with improved desired trait(s)

2. Evaluation of selected plant progenies
3. Recombination of superior progenies to form the next cycle

In cotton, recurrent selection has been used to a very limited extent. However, it is
a very useful and effective method to achieve improvement in cotton yield and fibre
quality traits simultaneously. For instance, three cycles of recurrent selection
increased seed cotton yield by 29.7% in upland cotton (Miller and Rawlings
1967a, b), while the same number of recurrent selection cycles increased lint
percentage from 33.8% to 38% in upland cotton (Meredith and Bridge 1973).

11.13.5 Biparental Mating

The concept of biparental mating was originally developed by Comstock and

Robinson (1948, 1952). It refers to crossing among randomly selected plants in F2
or subsequent generations of a cross in a definite fashion. Biparental mating serves
the purpose of releasing additional variability due to opportunity of more recombi-
nation to occur. It also helps in breaking undesirable linkages and concentrating
favourable genes in the population. Singh et al. (1989) reported breakage of negative
association between boll number and boll weight in cotton. This approach has rarely
been used in cotton though it is very effective in reducing linkage drag and realizing
promising transgressants in interspecific crosses between G. hirsutum and
G. barbadense (Palve et al. 2020).

11.13.6 Mutation Breeding

Mutation breeding has successfully been used in cotton and several other crops to
induce genetic variability for qualitative and quantitative characters. As early as in
1911, perhaps for the first time, nectariless mutant was reported by Leake (1911) in
Asiatic cotton. In India, Ramaih and Bholanath (1946) were the first to report
induced mutation for ginning percent and fibre length in American cotton; and
consequently, the first induced mutant variety Indore-2 was released in the same
year. Through the use of X-ray irradiation, a drought-resistant mutant, MA 9, was
identified from variety Co.2 of American cotton by Doraisamy and Iyenger (1948).
A jassid-resistant mutant was obtained through 48 kr X-ray irradiation of dry seeds
by Jagathesan et al. (1963). An early maturing mutant, MCU 7, with higher yield and
increased spinning performance was obtained through X-ray irradiation and released
for cultivation in Tamil Nadu in 1971 (Selvaraj 1976). Among the noted useful
mutations, a photo-insensitive mutant from MCU 5, a photosensitive variety, was
obtained through gamma-ray irradiation and released as variety ‘Rashmi’ in 1976.
Of the 16 varieties developed through induced mutations in cotton, 8 were developed
in India and released for commercial cultivation. Mutation breeding, although not a
preferred method over the other methods of breeding, however, it has distinct
11 Cotton Breeding 639

advantages of creating enormous variability for the numerous traits and even for the
traits not existing in the germplasm.

11.13.7 Heterosis Breeding

Heterosis is the increase in size or vigour of first-generation hybrids over its parents.
The term ‘heterosis’ was first proposed by Shull to denote the simulation in size and
vigour in a hybrid as an expression of heterozygosis. The terms ‘heterosis’ and
‘hybrid vigour’ are synonymous and most often used interchangeably. Hybrid
vigour of first-generation hybrids in cotton was first observed by Mell (1894) for
fibre length and agronomic traits. Cook (1909) suggested the possibility of commer-
cial exploitation of heterosis in cotton. Several researchers observed high heterosis in
F1 hybrids obtained between the distantly related parents than the closely related
ones. In cotton, high heterosis has been reported in both inter- and intraspecific
crosses in diploids and tetraploids.
The first successful attempt to exploit heterosis was made at Cotton Research
Station, Surat, India, and the first commercial hybrid ‘H4’ was released in 1970
(Patel 1971). The hybrid ‘H4’ was obtained from a cross between two hirsutum
parental lines/varieties (intraspecific hybrid) Gujarat 67 (G 67) and American
nectariless (an exotic line from the United States) which recorded 137% heterosis
over the better parent. Subsequently, in 1972, an interspecific hybrid, Varalaxmi,
involving G. hirsutum cv. Laxmi and G. barbadense cv. SB 289E was released from
Cotton Research Station, Dharwad, India (Katarki 1972). Both the hybrids H4 and
Varalaxmi became very popular among the farmers in Central and South India. The
success of both the hybrids provided significant momentum for hybrid research, and
later several intraspecific (intra-hirsutum and intra-arboreum) and interspecific
(G. hirsutum  G. barbadense and G. arboreum  G. herbaceum) hybrids have
been released for commercial cultivation in India.
Production of hybrid seed by hand emasculation and pollination (Doak method)
is successfully practised on a large scale in India. However, huge requirement of
labour for manual emasculation and pollination makes this procedure economically
unfeasible in countries where labour cost is high. The alternative to Doak method of
seed production is the use of genetic or cytoplasmic genetic male sterility.

11.13.7.1 Genetic Male Sterility (GMS)

There are several known sources of genetic male sterility in cotton. Sixteen different
genes controlling genetic male sterility in tetraploid cottons (13 in G. hirsutum and
three in G. barbadense) and two in G. arboreum have been identified (Meshram
et al. 1994; Singh and Kumar 1993). Sterility is conditioned by dominant alleles at
five loci, viz. MS4, MS7, MS10, MS11 and MS12, and by recessive allele at other loci,
viz. msl, ms2, ms3, msl3, msl4 (Dong A), msl5 (Lang A) and msl6 (81A). Genetic male
sterility conditioned by duplicate recessive genes includes ms5ms6 and ms8ms9. The
expression of male sterility among male sterility genes greatly varies in extent based
on genotypic background. In India, Gregg male sterility source is extensively used.
640 V. N. Waghmare

Among them, the male sterility controlled by two recessive genes (ms5ms6) is
preferred for transfer to the desired female parents by repeated backcrossing. The
male sterile lines so produced can be maintained by sib-mating with the heterozy-
gous male fertile sib segregating at only one locus (ms5ms5/Ms6ms6 or Ms5ms5/
ms6ms6). The progeny of such male sterile and fertile sibs will segregate in a 1:1
ratio of sterile and fertile plants. From the progeny of male sterile line, the fertile
plants may be identified at flowering and removed. The male sterile plants in a
hybridization block can be manually pollinated with the pollens of desired male
parent to produce hybrid seed. The use of genetic male sterility eliminates hand
emasculation and thus reduces cost of hybrid seed production than by the Doak
method.

11.13.7.2 Cytoplasmic Genetic Male Sterility (CGMS)

Interspecific hybrids are one of the most common sources of male sterility in crop
plants. Meyer (1971, 1975) obtained a cytoplasmically controlled male sterility in
G. hirsutum by transferring its genome to the cytoplasm of G. harknessii Brandegee.
From the segregating progenies, fertility restoration lines (fertility restorer gene, Rf)
were also identified from G. harknessii (Meyer 1975) and a gene that enhances
fertility restoration (E) from Pima cotton (Weaver and Weaver 1977). The fertility
restoration was attributed to two gene pairs (Meyer 1975), while a single gene shows
partial dominance (Weaver and Weaver 1977). In India, Shroff (1980) transferred
cytoplasmic male sterility of G. harknessii to G. hirsutum cultivars such as Khandwa
2, Bikaneri Nerma and GS23 and produced hybrids using Egyptian (G. barbadense)
restorer lines. G. anomalum as source of CMS has been reported by Rhyne (1971);
when G. arboreum genome is transferred to the cytoplasm of G. anomalum, stamina
column becomes petaloid. Similar observations were made by Tayiab (1983) in a
first backcross population of a cross cv. AK 235 (G. arboreum)  (G. anomalum  cv.
AK 235) at Akola, Maharashtra. He has also identified male sterility restorer in
G. herbaceum cv. V797, Nageri and Russian herbaceum. Identification of CMS and
fertility restoration sources was considered as a significant development towards
exploitation of heterosis and commercial scale cultivation of hybrid cotton. How-
ever, practical difficulties limit the utilization of male sterility in hybrid seed
production: (1) lack of simply inherited restorer gene with stable expression over
the environments, (2) lack of good combiners with CGMS and fertility restorer genes
and (3) lack of controlled and effective pollination system for hybrid seed
production.

11.14 Genomic Tools

11.14.1 Molecular Markers in Cotton

Molecular DNA-based markers can be classified in three categories based on their

working mechanism, i.e. hybridization-based, PCR-based and sequence-based
markers. The hybridization-based markers mainly include restriction fragment
11 Cotton Breeding 641

length polymorphism (RFLP). RFLP markers are the first type of markers used in
cotton genetic studies. It reveals the differences among individuals by variation in
size of DNA fragments produced by restriction enzymes. PCR-based markers
include random amplified polymorphic DNA (RAPD), amplified fragment length
polymorphism (AFLP), simple sequence repeats (SSRs) and inter-simple sequence
repeats (ISSRs). The sequence-based markers include single nucleotide polymor-
phism (SNP) and genotyping by sequencing (GBS). Molecular markers serve as
landmarks in the genome of an organism effectively used to differentiate one from
another. The above DNA-based markers have effectively been used in cotton for
characterization of genetic resources, genetic diversity and DNA fingerprinting
(Rana et al. 2007; Sapkal et al. 2011), linkage and QTL mapping for important
economic traits (Reinisch et al. 1994; Rong et al. 2004; Waghmare et al. 2005),
genome-wide association studies (GWAS) (Abdurakhmonov et al. 2009; Edwards
and Batley 2010) and marker-assisted selection (MAS) (Guo et al. 2003; Fang et al.
2010).
The recent advances in sequencing technologies have resulted in the development
of huge genomic resources for cotton over the last two decades. The publicly
available resources include SSR (109837), SNP (459825), RFLP (4576), RAD
(3984), AFLP (1962) and other scores of markers for genetic studies in cotton
(Yu et al. 2014). To facilitate high-throughput genotyping of the breeding
populations, few SNP arrays such as TAMU CottonSNP63K array (Hulse-Kemp
et al. 2015), NAU 80K SNP array (Cai et al. 2017) and 40K SNP array (Sawant et al.
CSIR-NBRI, Lucknow, India, unpublished) have been developed and extensively
used for genetic mapping and marker-assisted breeding programmes. Using these
genetic resources, about 119 genetic linkage maps involving intraspecific and
interspecific populations have been developed, and more than 6497 quantitative
trait loci (QTL) representing more than 30 agronomically important traits were
mapped on specific chromosomes.

11.14.2 Genetic Diversity

Understanding genetic relationship and extent of genetic variation among genotypes

is important to use them in the improvement programmes. Genetic diversity based on
the molecular markers gives insights into the genetic relationship and structure of a
population. A narrow genetic base is reported to be the reason for stagnation and
decline in global cotton yield. The genetic diversity in cotton using different
molecular markers by several workers has been reported (Tatineni et al. 1996;
Saha et al. 2003; Rana et al. 2007; Rakshit et al. 2010; Sapkal et al. 2011). SSRs
have also been used to assess the genetic purity of the cotton hybrids (Selvakumar
et al. 2010). The SNPs as markers have also been used to detect genetic variations
within and between the species of cotton (Van Deynze et al. 2009).
642 V. N. Waghmare

11.14.3 Linkage and QTL Mapping for Economic Trait

All types of DNA markers can be used for constructing a linkage map. However, the
codominant markers (SSR, SNPs) are more informative and detect heterozygous
condition that may be preferred over the dominant markers (RAPD). Different types
of populations such as F2, backcross populations Bc1 and Bc2, backcross inbred lines
(BILs), recombinant inbred lines (RILs) and multi-parent advanced generation inter-
cross (MAGIC) populations are commonly used in genetic mapping. The first
genetic linkage map of cotton was constructed by Reinisch et al. (1994) using
RFLP markers which included 705 polymorphic loci in 41 linkage groups and a
total map length of 4675 cM. Afterwards, several genetic linkage maps were
constructed (Shappley et al. 1998; Jiang et al. 1998; Zuo et al. 2000; Ulloa et al.
2002; Zhang et al. 2002; Rong et al. 2004; Waghmare et al. 2005; Yu et al. 2012)
with different marker densities.
RFLPs have been widely used to map genes of economic interest in cotton. An
RFLP map of G. hirsutum and G. barbadense was used to map 14 QTLs for fibre-
related traits (Jiang et al. 1998). Genes influencing density of stem and leaf trichomes
(Wright et al. 1998), low seed gossypol contents in seeds and high gossypol in plant
(Vroh Bi et al. 1999), plant adaptation traits including leaf chlorophyll contents
(Saranga et al. 2001) and leaf nectaries (Waghmare et al. 2005) were mapped on an
RFLP map developed using F2 interspecific populations. Using F2:3 population,
26 QTLs were identified for agronomic and fibre quality traits (Ulloa et al. 2002).
In a backcross population of G. hirsutum and G. barbadense, 28 QTLs for fibre
length, nine for length uniformity and eight for short fibre contents were mapped
(Chee et al. 2005) using F2-based RFLP map.
Shen et al. (2005) conducted an extensive SSR genotyping of F2 populations from
three diverse upland cotton genotypes using 1378 markers and identified 39 fibre-
related QTLs. Using recombinant inbred lines (RILs), Wang et al. (2006) reported
several QTLs related to plant architecture, yield and fibre quality in upland cotton.
Qin et al. (2008) used four-way cross populations developed from the 4 inbred lines
of G. hirsutum to map 31 QTLs linked to the yield and fibre quality traits. The
genetic map developed using two F2 populations with 2072 loci covering 3380 cm
was used for QTL analysis, which detects 54 QTLs linked to early maturity (Li et al.
2013). QTL mapping using different genotypes and mapping populations
phenotyped in varying environments yield heterogeneous results. Rong et al.
(2007) compiled 432 QTLs mapped in one diploid and ten tetraploid interspecific
cotton populations, aligned using a reference map and depicted in a cMap resource.
The meta-analysis resulted in more complete picture of the genetic control of a trait
and trait variation. It supported the hypothesis of non-fibre-producing diploid ances-
tor contributed to tetraploid lint fibre gain, and both sub-genomes contribute QTL at
largely non-homeologous locations, suggesting divergent selection acting on many
corresponding genes before and/or after polyploid formation. Several studies dealing
with QTL mapping in cotton are available, and more than 6497 QTLs available in
CottonGen database (https://www.cottongen.org/) promise the future strategy for
marker-assisted breeding (Yu et al. 2014).
11 Cotton Breeding 643

11.14.4 Genome-Wide Association Studies (GWAS)

Genome-wide association study involves rapidly scanning markers across the com-
plete sets of DNA, or genomes, of several individuals to find genetic variations
associated with a particular trait. Association mapping, also referred to as linkage
disequilibrium (LD) mapping, is effectively being used to determine the variation in
complex traits in cotton. With the availability of multiple cotton genome sequence
data (Wang et al. 2012a, b; Paterson et al. 2012; Zhang et al. 2015), a large number
of SNP markers have been identified at the whole-genome level in cotton. In
association studies, natural (nonstructured) populations are phenotyped and
genotyped to identify the trait associated with marker (Barnaud et al. 2006) so as
to capture natural allelic variation (Huang and Han 2014). In cotton, huge genetic
diversity conserved is available in the worldwide collections of cotton germplasm.
Using association studies, many QTLs and candidate genes associated with fibre
quality have been identified (Yu et al. 2013). Though tetraploid genome size is large,
considering the total map length of 5200 cm, Abdurakhmonov et al. (2009) worked
out about 1000 polymorphic markers for successful and reliable association mapping
in cotton.
Sun et al. (2017a) performed a GWAS for fibre quality traits using 719 diverse
accessions of upland cotton and 10,511 polymorphic SNPs using the
CottonSNP63K array and identified 46 significant SNPs associated with five fibre
quality traits. In a combined GWAS and transcriptome analysis, they could identify
19 promising genes related to FL and FS (Sun et al. 2017b). Using a natural
population containing 503 G. hirsutum accessions through CottonSNP63K
genotyping, Huang et al. (2017) detected 79 significant SNPs associated with fibre
quality traits. Ma et al. (2018) resequenced a core collection comprising of 419
accessions. Phenotyping was done across 12 environments and three genes
associated with fibre quality traits were identified using the association mapping,
two GhFL1 and GhFL2 for FL, and Gh_A07G1769 for FS through transgenic
experiments in Arabidopsis. Liu et al. (2020) identified 42 single nucleotide
polymorphisms (SNPs) and 31 QTLs associated with five fibre quality traits in a
genome-wide association study. They also identified two pleiotropic SNPs, SNP
locus i52359Gb and SNP locus i11316Gh, for fibre traits.

11.14.5 Marker-Assisted Selection (MAS)

Plant breeders select plants which appear phenotypically more promising for the
desired traits. Most of the economic traits are controlled by polygenes with complex
non-allelic and environmental interactions. In some instances, the same genotype or
specific locus associated with QTL may not be detected (Edwards et al. 1987). In
such instances, tightly linked loci associated with desired trait, if linked with
molecular marker, can effectively support identification of genotypes for specific
phenotype. Thus, in marker-assisted selection (MAS), a phenotype is selected on the
basis of genotype of a marker (Collard et al. 2005). In the segregating population,
644 V. N. Waghmare

selection of plants with desired gene combinations is important in plant breeding to

realize the desired performance. On the identification of tightly linked markers to the
genes of interest, breeders may use the known identified DNA marker to select the
plants carrying the gene(s)/QTL (Young 1996). The effectiveness of MAS is majorly
dependent on marker types and size of the population being handled.
Application of MAS for the traits with high heritability such as disease resistance
is more effective. Yield-related components are polygenic in nature with low
heritability, which is a major challenge for the utilization of MAS (Elshire et al.
2011). Several QTLs have been identified for seed cotton yield, fibre quality, plant
architecture, resistance to diseases such as bacterial blight and Verticillium wilt
(Bolek et al. 2005), resistance to pests like root knot nematode and flowering date
(Voss-Fels and Snowdon 2015) as well as for abiotic stresses (drought, salt toler-
ance) (Elshire et al. 2011; Wang et al. 2015) in different populations. This provides
an evidence of putative loci related to specific traits. But these identified QTLs,
through either linkage mapping or association mapping-based approaches, have low
resolution and do not serve the purpose to be used for MAS unless QTL regions
identified by flanking markers are subjected to high-density genetic mapping which
is a prerequisite for MAS. A composite fine-mapping approach will help to dissect
the markers close to the target genes and enhance the reliability of MAS. The
genomic sequences of cotton provide precious resources to develop high-density
SSR- or SNP-based genetic maps. Establishing linkage between phenotypic and
genotypic interactions, the identification of stable QTLs lays a basis for fine
mapping.
Zhang et al. (2003) identified a major QTL for fibre strength, QTL(FS1), found to
be associated with eight markers that explained more than 30% of the phenotypic
variation. QTL(FS1) was mapped to chromosome 10, and the markers linked to this
QTL could be used in MAS. RAPD markers were converted into sequence
characterized amplified region (SCAR) markers to screen the BC1F4 population
and successfully used, i.e. SCAR 1920 marker, for improvement of fibre strength
and marker-assisted selection (Guo et al. 2003). The cotton blue disease (CBD)
controlled by single dominant gene was mapped in the telomere region of chromo-
some 10. Screening of the SNP markers laid to identification of three SNP markers
associated with CBD which were employed to efficiently tag a trait enabling MAS
for high levels of blue disease resistance in cotton (Fang et al. 2010).
Recently, two genomic loci for lint yield (ghlyi-A02 and ghlyi-D08) were
identified with the mix of GWAS and gene-based association that provided a
quick method to identify the candidate genes associated with fibre quality (Fang
et al. 2017a, b). Ma et al. (2018) characterized genes related to fibre length (ghfl1 and
ghfl2) and fibre strength (Gh_A07G1769), which may be further used for MAS.
Zhang et al. (2018a) analysed linked SSR marker BNL3232 in the F2 segregating
population of upland cotton following bulked segregant analysis (BSA) and found
that one SNP locus was closely associated with the fruiting branches trait. They
verified that this SNP marker could be used for molecular-assisted selection of cotton
architecture. Kushanov et al. (2017) claimed to have developed two varieties
possessing higher fibre strength and improved length, namely Ravnaq-1 and
11 Cotton Breeding 645

Ravnaq-2. Ravnaq-1 has superior fibre quality with improved fibre strength (37 g/
tex) and staple length (38 mm) compared to its recurrent parent Andijan-35 (32 g/tex
and 35 mm staple length). Similarly in Ravnaq-2, molecular markers effectively
mobilized superior fibre quality loci that improved fibre strength by 17% and staple
length by 9% compared to its recurrent parent Mekhnat. They concluded that the
markers and donors have been proved to be useful in MAS to obtain superior cotton
cultivars.

11.14.6 Genome Sequencing

In view of the economic importance of cotton, intensive efforts were made by the
cotton community to uncover the genome mysteries of cotton species. For sequenc-
ing the cotton genome, the smallest D genome of G. raimondii (D5) was selected,
and a first draft genome assembly was published simultaneously in 2012 (Paterson
et al. 2012; Wang et al. 2012a). Subsequently, in the last one decade, all four
cultivated species of cotton and about 11 wild diploid species have been sequenced;
and sequence data and several thousands of annotated protein-coding genes have
been made available (Paterson et al. 2012; Wang et al. 2012a, 2019; Li et al.
2014a, b, 2015; Zhang et al. 2015; Yuan et al. 2016; Du et al. 2018; Udall et al.
2019; Cai et al. 2019; Hu et al. 2019; Grover et al. 2019, 2020; Chen et al. 2020;
Huang et al. 2020). The availability of the number of whole cotton genome sequence
data provides a major source of candidate genes with potential for genetic improve-
ment of cotton quality and productivity. The integrated whole-genome sequence data
and marker data have been made available on CottonGen database (Yu et al. 2014)
for easy accessibility and retrieval including search and online analysis tools.
The ever-increasing information of DNA sequencing of different Gossypium
genomes enables the discovery of genes, their variants and new markers associated
with different traits, opening new avenues for crop improvement (Edwards and
Batley 2010). Sequencing of new Gossypium genomes allows comparing the extent
of structural and sequence variation among the genomes and displaying the spectrum
of diversity. The genomes of cultivated diploid and tetraploid cottons have been
repeatedly sequenced so as to obtain complete and fine sequences (Pan et al. 2020).
The comparative genome sequence data sets are likely to reveal the evolutionary
history and insights into the formation of present-day cultivated cotton. Repeated
sequencing of genomes is expected to address issues of genome instability involving
structural changes, gene loss, DNA inversion, translocation, illegitimate recombina-
tion, accumulation of repetitive sequences and changes related to the functional
evolution of genes. The whole-genome sequences have paved the way to identify
and clone functional genes (Pan et al. 2020) and to enhance breeding efforts to
develop cotton to produce high yield, superior quality fibres and resisting effects of
climate change.
646 V. N. Waghmare

11.14.7 Genotyping by Sequencing (GBS)

Advances in DNA sequencing technologies enabled researchers to rapidly develop

large numbers of SNP markers at a relatively low cost. The next-generation sequenc-
ing (NGS) technologies have successfully been used for whole-genome sequencing
(Paterson et al. 2012; Wang et al. 2012a, b; Li et al. 2014a), gene expression analysis
(Naoumkina et al. 2014) and SNP discovery in cotton (Byers et al. 2012; Gore et al.
2014). Among the methods used to discover SNPs, a robust and simple approach is
GBS, which facilitates the detection of a wide range of SNPs using several
individuals simultaneously. The GBS protocols usually use methylation-sensitive
restriction enzymes (RE) to get reduced representation of the genome by targeting
the genomic sequence flanking RE sites (Elshire et al. 2011; Poland et al. 2012). The
approach of reduced representation and restriction site-associated DNA construction
of GBS library has been simplified, made extremely specific, highly reproducible,
needing less DNA, with targeted lower copy regions and two- to threefold higher
efficiency. The procedure is completed in only two steps on plates, followed by
polymerase chain reaction (PCR) amplification of the pooled library (Elshire et al.
2011). With the above approach, GBS can be utilized in any polymorphic species or
any segregating population with any number of individuals (Schnable et al. 2013).
Genotyping by sequencing (GBS) is a rapid way to identify single nucleotide
polymorphism (SNP) markers; however, these SNPs may be specific to the
sequenced cotton lines (Islam et al. 2015). GBS technique has been modified and
improved to a large extent (Baird et al. 2008). The restriction enzymes that cut
upstream and downstream of target site (Wang et al. 2012a, b) allows marker
intensity adjustment by producing same length tags and analysis of about all the
restriction sites.
Genotyping by sequencing has several potential applications that include gene
pool maintenance, diversity analysis, genomic selection, gene mapping and other
plant improvement methodologies (Elshire et al. 2011). GBS is cost-effective for
studying populations in association mapping and further to employ genomic selec-
tion on a large scale (Poland and Trevor 2012). In cotton, Gore et al. (2014) detected
SNPs in G. hirsutum RIL population by GBS and constructed SSR-SNP linkage map
for mapping ten agronomic and fibre traits. Fan et al. (2018) constructed one of the
first genetic maps using 3557 GBS SNPs spanning a total genetic distance of
3076.23 cM in a RIL population of G. barbadense and identified 42 QTLs for the
fibre quality and lint yield traits. A BC2F2 population, involving G. tomentosum and
G. hirsutum as the recurrent parent, was genotyped through genotyping by sequenc-
ing (GBS) wherein 10,888 SNPs were generated and used to construct a genetic map
(Magwanga et al. 2018).
Analysis of serine/threonine protein kinases through miRNA targets in the
segregating subfamilies revealed that most of the genes were involved in enhancing
abiotic stress tolerance. Further analysis and qRT-PCR validation revealed 16 puta-
tive genes, which were highly upregulated under drought stress condition, and were
found to be associated with NAC (NAM, ATAF1/2 and CUC2) and myeloblastosis
(MYB), the known stress tolerance genes. Ahmed et al. (2020) reported significant
11 Cotton Breeding 647

QTLs associated with leaf and stem pubescence in F2 intra-hirsutum population and
the response of plant under pest (aphid) infestation. The putative genes were
co-localized on chromosome A06 governing mechanism for trichome development
and host-pest interaction. The identified GBS SNP markers may be explored for
marker-assisted breeding to develop sucking pests’ resistant cotton cultivars.
In a study to determine genetic structure and relationship of G. hirsutum races,
following GBS and phylogenetic analysis revealed that the Latifolium, Richmondii
and Marie-Galante race accessions were more genetically related to the G. hirsutum
cultivars (Zhang et al. 2019). Further, three SNPs were identified located in genes
related to the processes of plant responding to stress conditions which were con-
firmed through genome-wide signals of marker-phenotype association analysis.

11.15 Transgenic Cotton

‘Transgenic’ refers to the introduction of one or more genes or DNA sequences from
another species by artificial means. The recombinant DNA technology allows the
transfer of genetic material across a wide range of species and has removed the
traditional limits of cross-breeding. It involves transfer of desired genes into the plant
genome through genetic transformation and then regeneration of a whole plant from
the transformed tissue/cell. For successful development of transgenic plants, the
essential requirements include an efficient transformation protocol for the specific
crop species, transformation vector and gene to be transferred and suitable target
tissues. Various transformation methods such as Agrobacterium-mediated gene
transfer, particle bombardment (biolistics) method (Klein et al. 1987) and in planta
pollen tube transformation (Kalbande and Patil 2016) are being followed to transfer
genes into cotton genome. Agrobacterium-mediated transformation is a widely used
and reliable method of transformation that involves co-cultivation of explants with
Agrobacterium culture. Cotton is a recalcitrant crop to regenerate from in vitro tissue
cultures. Genotype-dependent genetic transformation is known in cotton. Coker
genotypes, namely Coker 312 and Coker 201, or its introgressed lines (United
States), YZ-1, Simian-3, CRI 24 (in China) and Siokral 1–3 (Australia), are amena-
ble for regeneration in vitro by somatic embryogenesis and are widely used in cotton
genetic transformation (Leelavathi et al. 2004). However, the genetic transformation
frequency is very low.
The first transgenic cotton was produced by transferring Cry1Ac gene encoding
crystal toxin protein from the soil bacterium Bacillus thuringiensis which is harmful
to lepidopteran insects. The genetically engineered cotton with gene from B.
thuringiensis was popularly referred to as Bt cotton. Bt cotton was first approved for
field trials in the United States in 1993 and then for commercial use in 1995.
Subsequently, it spread to several cotton-growing countries. Bollgard II, with two
genes Cry1Ac and Cry2Ab, was introduced in 2003 representing the next generation
of Bt cotton. So far, some 67 transgenic cotton events carrying insect and herbicide
resistance with two to three genes have been released for general cultivation in
various parts of the world (Yu et al. 2014).
648 V. N. Waghmare

Development of GM cotton to control bollworms in cotton was more relied on

toxin producing cry genes from B. thuringiensis. Several variants of Bt genes have
been introduced to cotton and reported their efficacy on target pests, viz.
H. armigera, P. gossypiella and Spodoptera litura. Silencing of CYP6AE14 gossy-
pol detoxifying enzyme in insect midgut using GM cotton RNAi lines for cyp6ae14
gene is observed to reduce the survivability chance of bollworms by the action of
gossypol in cotton plants (Mao et al. 2011). Amaranthus caudatus agglutinin (ACA)
(Wu et al. 2006), Allium sativum agglutinin (ASAL) (Vajhala et al. 2013), Galanthus
nivalis agglutinin lectin (GNA) (Liu et al. 2013) and insecticidal Tma12 gene from
Tectaria macrodonta (Shukla et al. 2016) reported their efficacy against target
sucking pests of cotton.
The transgenic technology has also been explored for improvement of economic
yield and fibre quality traits of cotton. Spatio-temporal regulated expression of the
auxin biosynthesis gene iaaM (Zhang et al. 2011), sucrose synthase gene from
potato (Xu et al. 2012) using FPB7 and S7 promoter, respectively realized
15–30% higher yield compared to control. An increased fibre yield and quality is
reported due to overexpression of sucrose synthase GhsusA1 from superior quality
germplasm line (Jiang et al. 2012). Knockdown lines of phytochrome PHYA1
(Abdurakhmonov et al. 2014b) and overexpression of PHYB (Rao et al. 2011)
were reported to improve fibre yield (10–35%), quality and agronomic traits of
cotton. Significant improvement in fibre strength and micronaire in all transgenic
lines having higher expression of the expansin gene was reported due to the action of
CpEXPA3, an expansin gene from Calotropis procera in cotton (Bajwa et al. 2013).
A number of actin-binding proteins, viz. GhADF1 (Wang et al. 2009) and WLIM1a
(Han et al. 2013), participate in the regulation of actin cytoskeleton dynamics and are
reported to be associated with the regulation of fibre quality traits in cotton.
Overexpression of WLIM1a, a LIM domain protein of elongation and secondary
wall synthesis stages, improved fibre strength and fineness traits through modulation
of actin cytoskeleton dynamics and transcription factor for lignin biosynthesis (Han
et al. 2013). Modification in fibre properties was also reported in transgenic cotton
lines expressing GhXLIM 6 in fibre development and mainly attributed to dual role
of the target protein on F-actin cytoskeleton and transcriptional regulation of cellu-
lose biosynthesis (Li et al. 2018).
The transgenic approach for improvement of abiotic stress tolerance traits
utilizing gene sourced from different species is reviewed in different crop species
including cotton (Ullah et al. 2017; Mahmood et al. 2020). The heterologous
expression of genes coding for transcription factors, viz. NAC transcription factor
(SNAC1) (Liu et al. 2014), StDREB2 (El-Esawi and Alayafi 2019), AtEDT1/HDG11
(Yu et al. 2016), membrane transporters AtNHX1 (He et al. 2005), AtAVP1 (Pasapula
et al. 2011), TsVP1 (Lv et al. 2008, 2009), ROS scavenging system and osmotic
regulation ScALDH21 (Yang et al. 2016), NtOsmotin gene (Parkhi et al. 2009)
enhanced drought and salt tolerance and agronomic performance in transgenic
cotton compared to control. The ultralow gossypol in cotton seed is found to be
associated with reduction of seed-specific δ cadinene synthase expression by
utilizing the seed-specific alpha globulin promoter. The low gossypol transgenic
11 Cotton Breeding 649

event TAM66274 is approved for commercialization in the United States in 2018

(Sunilkumar et al. 2006; Rathore et al. 2020).
Bt cotton is currently occupying the majority of the area under cotton. It occupies
about 85% of the total cotton area in the United States, more than 90% in India and
Pakistan and above 65% in China (Anderson and Rajasekar 2016). Success of Bt
cotton varies across the countries. Bt cotton has greatly impacted on the cotton
cultivation in India. The cotton area increased from 9 million ha to about 13 mil-
lion ha, and the country’s production has almost doubled. The technology has
reduced the pesticide usages, reduced yield losses and increased the profitability of
the farmers. However, field-evolved resistance of pink bollworm against Bollgard
and Bollgard II cotton has been reported in the United States (Dennehy et al. 2002),
China (Tabashnik et al. 2012) and India (Dhurua and Gujar 2011; Naik et al. 2018).
Sucking pests (whitefly and jassids) have emerged as major pests demanding more
attention and resources for management after PBW. For effective working of the
transgenic technology, newer gene sources conferring resistance to PBW and suck-
ing pest need to be involved and stacked to provide durable resistance.

11.15.1 Bt Cotton in India

Genetically modified (GM) cotton was developed as an alternate strategy to the

previously used hazardous concoction of insecticide mixtures to circumvent boll-
worm problem in cotton. Bt cotton was the first of GM technologies introduced in
India in 2002 as Bollgard (cry1Ac gene—Mon531 event) and in 2006 as Bollgard II
(cry1Ac + cry2Ab genes—Mon15985 event). Indian farmers preferred Bt cotton
instead of the hazardous insecticide cocktails for bollworm control. With continued
higher adaption, Bt cotton is being grown on over 90% of cotton area. Bt cotton
effectively controlled bollworms, especially the American bollworm, Helicoverpa
armigera. Yields are estimated to have increased at least by 30% due to effective
protection from bollworm damage. The biggest gain from Bt cotton was in the form
of reduced insecticide usage from 46% to less than 20%. Insecticide usage for
bollworm control decreased from 9410 metric tonnes (worth INR 747.6 crores) in
2001–2002 to 222 metric tonnes (worth INR 96.3 crores) in 2011–2012. The
intensity of bollworms reduced significantly on cotton and also on other host
crops. The number of pesticide sprays in cotton declined rapidly from 15 to
20 applications to very few. Protection of early fruiting parts resulted in earliness
and determinate habit eventually leading to fewer pickings, reduced labour,
improved quality, better price and possibility of second crop after cotton.
In contrast to other countries, Bt technology was introduced in India exclusively
in the form of Bt hybrids. Area under cotton (from 76 to >129 lakh ha) and yields
(from 300 kg to >500 kg lint/ha) increased after adoption of Bt cotton hybrids in
India. This productivity enhancement achieved was said to be a combined result of
exploitation of heterosis (hybrids) and protection from Bt technology. Despite more
than 90% area under Bt hybrids, the cotton productivity in India is lowest than world
average (>750 kg/ha) and remains stagnated at around 500 kg lint/ha. The reasons
650 V. N. Waghmare

for low productivity and stagnation in yield include deployment of long duration Bt
hybrids, less genetic diversity in cultivated hybrids and cultivation of cotton in over
60% area under rain-dependent situation. The majority of Bt hybrids are long
duration that suffer moisture stress at boll formation stage due to poor water retention
of shallow soils in rainfed regions. Productivity enhancement in India can come from
yield improvement in rainfed ecosystems through deployment of climate-resilient Bt
cotton varieties.

11.16 Genome Editing in Cotton: CRISPR/Cas

Precision in transfer and editing of the target gene is of more significance in the
genetic manipulation of crop plants. Engineered nucleases, viz. zinc finger nucleases
(ZFNs), meganucleases, transcription activator-like effector nucleases (TALENs)
and recently introduced clustered regularly interspaced short palindromic repeats-
CRISPR-associated system (CRISPR-Cas)-mediated genome editing, have been
successfully deployed in different crop species. The intrinsic versatility, simplicity
and high efficiency of CRISPR/Cas9 have resulted in an explosion of research using
genome editing as the preferred method to generate precise alterations in the genome
of numerous plant species. CRISPR/Cas9 derives from a microbial adaptive immune
system, and its major components are the Cas9 nuclease capable of producing
double-strand breaks and a small guide RNA (sgRNA) which directs the Cas9
protein to the target site. A number of factors influence the efficiency of the
CRISPR/Cas9 system with strong expression of Cas9 and sgRNA being essential
to obtain high mutation rates (Jiang et al. 2013).
The first report of genome editing in cotton was based on the re-engineered
meganuclease for herbicide and insect resistance in cotton (D’Halluin et al. 2013).
Janga et al. (2017) reported successful targeted knockdown of single copy reporter
green fluorescent protein (GFP) gene in cotton genome using CRISPR-Cas. Gao
et al. (2017) developed a fast and efficient method and validated the functionality of
sgRNAs in cotton using three different genes, GhPDS, GhCLA1 and GhEF1, and a
transient expression system. They demonstrated that multiple gene targeting can be
achieved in cotton with simultaneous expression of several sgRNAs. Targeted
mutagenesis of Cloroplastos alterados 1 (GhCLA1) and vacuolar H+-
pyrophosphatase (GhVP) genes (Chen et al. 2017), GhMYB25-like (Li et al. 2017)
and GhALARP, a gene encoding alanine-rich protein (Zhu et al. 2018) in both A and
D sub-genomes of tetraploid Gossypium hirsutum cotton with no traceable off
targets, demonstrated the possible utilization of tool for precision genome editing
in cotton.
The CRISPR/Cas9 system was successfully utilized to generate two sgRNAs in a
single vector for multiple sites genome editing using Discosoma red fluorescent
protein2 (DsRed2) and an endogenous gene GhCLA1 in allotetraploid cotton (Wang
et al. 2018). Long et al. (2018) optimized the cotton CRISPR/Cas9 system to achieve
vastly improved mutagenesis efficiency by incorporating an endogenous GhU6
promoter that increases sgRNA expression level six to seven times higher and
11 Cotton Breeding 651

mutation efficiency four to six times over the Arabidopsis AtU6-29 promoter.
Recently, a variant of CRISPR-Cas (Cas9 nickase) with base editing ability known
as ‘G. hirsutum-Base Editor 3 (GhBE3) base-editing system’ has been successfully
demonstrated for their ability to create single base mutations in cotton (Qin et al.
2020). Ramadan et al. (2021) used pooled sgRNAs assembly and successfully
targeted multiple genes; 112 plant development-related genes were knocked out
via an optimized CRISPR/Cas9 system. All targeted genes were successfully edited
with high specificity.
The Gh14-3-3d-edited plants free of T-DNA called transgene-clean editing plants
through CRISPR/Cas9 significantly enhanced resistance to Verticillium dahlia, a
serious pathogen in cotton (Zhang et al. 2018b). CRISPR/Cas9 knockout of the
arginase gene significantly enhanced the number of lateral roots and the root surface
area in both normal and nitrogen deficiency conditions (Wang et al. 2017) which
may help in water and nutrient uptake and improve resistance to other abiotic
stresses in cotton.

11.17 High-Throughput Phenotyping

Expression of plant phenotype is the function of genotype and environment interac-

tion. Traditionally, plant phenotype has been used for selection and improvement of
crop plants. Selection of stable phenotype, through experience, was the fundamental
of breeding during early domestications of crops and until rediscovery of Mendel’s
laws of inheritance. Phenotyping on a large population of plants has traditionally
been challenging, both time and resource consuming and sometimes destructive.
Pfeffer (1887) was the first to use an apparatus for plant growth measurement. In the
last two decades, several sensors, automation, quantitative data analysis and vision
tools have been developed that have become pivotal for quantifying the plant traits
with increasing throughput and accuracy (Fiorani and Schurr 2013). Application of
non-destructive and non-invasive technology for plant phenotyping in high through-
put started with the model plant Arabidopsis (Granier et al. 2006). Now, increasingly
mobile and higher-throughput field phenotyping systems using ground- and aerial-
based [satellite imagery and unmanned aerial vehicles (UAVs)] imaging with a
variety of sensors become available that allowed breeders to monitor genotype
performance in breeding plots and crop management.
In cotton, recent studies indicating the application of high-throughput
phenotyping (HTP) using imaging techniques have successfully explored possibility
to improve the efficiency of phenotyping. Li et al. (2016) introduced a region-based
semantic segmentation method for infield cotton boll detection based on colour and
texture features using two-dimensional (2D) colour images. The method was found
superior and could also detect the boll opening stage automatically. However, the 2D
image-based method has a limitation of plant occlusion, and image quality is
significantly affected by variable illumination conditions in the field which limits
automation in data processing (Li et al. 2014b). The use of 3D model-based method
652 V. N. Waghmare

over 2D digital image method for plant phenotyping is getting more prominence as
they permit multiple morphological trait data recording simultaneously.
Jiang et al. (2016) developed and evaluated HTP using depth images for mea-
surement of plant height that correlated (R2 ¼ 0.922–0.987) with the plant height
measured manually and with accuracies of over 92%. Sharma and Ritchie (2015)
tested automated measurements of plant height, ground cover fraction (GCF),
normalized difference vegetation index (NDVI), and canopy temperature
(Tc) using a ground-based platform under ten different irrigation levels and found
high correlations with lint yield.
Revathi and Hemalatha (2012) proposed the use of image processing edge
detection techniques and homogeneous pixel counting technique, neural network,
for cotton foliar diseases. Using the pattern recognition algorithm called
convolutional neural networks, Xu et al. (2018a) confirmed that the system devel-
oped for identifying and automatic counting of cotton flower was comparable with
manual counting. Xu et al. (2019) demonstrated the application of aerial multispec-
tral images captured by a multispectral camera on an unmanned aerial system for
phenotyping of plant height, canopy cover, vegetation index and flower. McCarthy
et al. (2010) succeeded in measurement of internode lengths using an infield
machine vision system in upland cotton and observed that visual occlusion of the
main stem nodes by foliage and variations in natural lighting conditions as principal
reasons for internode lengths not being detected for every plant. An autonomous
ground robot system equipped with real-time kinematics (RTK)-GPS system, iner-
tial measurement unit and waypoint to count the number of cotton bolls was
developed (Xu et al. 2018b). This study demonstrated that opened cotton bolls can
be counted from 3D point cloud with less human intervention. Ritchie and Bednarz
(2005) used a photosynthetically active near-infrared spectrometer to investigate the
relationship of red edge-based NDVI and leaf area index and to quantify cotton
defoliation. Results showed that spectral data based on red edge measurements can
provide accurate defoliation estimates which could possibly improve defoliation
efficiency.
Thermal images by an infrared thermal camera were used for an infield estimation
of the water status of cotton under a range of irrigation regimes as a potential tool for
irrigation scheduling (Cohen et al. 2005). Andrade-Sanchez et al. (2014) developed a
field-based HTP platform with a set of sensors to measure canopy height, reflectance
and temperature simultaneously collecting phenotypic data at a rate of 0.84 ha/h.
Hansen et al. (2014) proposed the use of a time series to monitor the changes in
growth characteristics of cotton over time. Wu et al. (2018) monitored the progres-
sion of cotton root rot based on the extracted NDVI time series profiles.
Light detection and ranging (LiDAR) technology provides an alternative
approach for 3D plant model reconstruction. LiDAR is a remote sensing technology
to measure the distance between the sensor and the object of interest by illuminating
the object with a laser and analysing the time of flight (ToF). LiDAR is also a
potential alternative to image-based methods for phenotyping morphological traits at
plot or plant level under field conditions. French et al. (2016) and Sun et al. (2017a,
2018) prominently used LiDAR to scan cotton plants. Both the studies used a global
11 Cotton Breeding 653

positioning system mounted on a tractor platform. French et al. (2016) succeeded in

achieving high-resolution and low-distortion mapping of cotton heights, width, leaf
area and boll counts. While multiple traits, viz. plant height, projected canopy area
and plant volume, were simultaneously extracted from repeated measurements over
the growing season (Sun et al. 2018).
With the extensive worldwide production of cotton and its importance as a natural
fibre crop, the HTP offers greater potential in improving the accuracy, efficiency,
speed and quality of data acquisition. However, cotton is grown on vast area, due to
the heterogeneity of field plots and variations in environmental conditions in cotton
production, area wide implementation of HTP has the limitation. It is expected that
the future HTP systems with improved robustness, accuracy, effectivity and
affordability will pave the way for its application in cotton production. Hence,
HTP platforms that facilitate to capture the variability across spatial and temporal
scales in cotton fields will be increasingly important.

11.18 Emerging Challenges at National and International Levels

Cotton is a sensitive and challenging crop for management. Cotton production across
the world is constrained by high incidence of insect pests and diseases, weeds, soil
salinity, soil degradation, drought stresses, heat and frequent climatic aberrations.
These constraints may vary with cotton production regions, but all regions experi-
ence one or the other from mild to severe form. Extreme weather conditions during
early and boll development stage present a major challenge for cotton production in
most of the cotton-growing regions. Drought stress in rain-dependent areas affects
the cotton yields to a larger extent. During the summer of 2019 in Alabama, at least
one-third of the state was impacted by drought according to the US Drought
Monitor. This unpredictable, extreme weather is changing the reproductive and
feeding patterns of pests, i.e. tarnished plant bugs, which are moving from their
wild host plants to the cotton crop earlier than expected. In the regions where
planting is undertaken in summer months, germination of seeds and growth of
seedlings get affected due to high temperature and heat. Soil salinity coupled with
high temperature in irrigated areas of Northern India affects germination and seed-
ling stand due to soil crust formation.
Among the major pests of cotton, in recent years, pink bollworm (Pectinophora
gossypiella) has emerged as a major problem on Bt cotton in Southeast Asia. Field-
evolved resistance of pink bollworm against Bollgard and Bollgard II cotton has
been reported in the United States, China and India. Pink bollworm was effectively
controlled in the United States following diverse strategies. However, it is causing
menace and severe crop losses to the extent of 10–30% in India. Sucking pests
(whitefly and jassids) have emerged as major pests on Bt cotton demanding more
attention and resources for management. Whitefly is a significant pest in Northern
Indian states of Punjab, Haryana and Rajasthan and also in Pakistan.
Among the major diseases, cotton leaf curl disease (CLCuD) caused by
Begomoviruses is a major threat to cotton production in North India and Pakistan.
654 V. N. Waghmare

The disease is transmitted by insect vector whitefly (Bemisia tabaci); hence, its
effective control is possible through management of whitefly. Tobacco streak virus
(TSV), caused by Ilarvirus, is normally prevalent in southern states but emerging as
a new challenge in central and northern states of India. Grey mildew (Ramularia
areola), Myrothecium leaf spot and Corynespora leaf spot are the fungal diseases
demanding timely interventions to contain spread and minimize losses. Recently,
inner boll rot is an emerging problem in central and southern states during boll
development stage. Fall armyworm (FAW) Spodoptera frugiperda, a pest of maize,
has become an important pest of cotton in Brazil due to changes in cotton cropping
systems. Since 2017, increasing migratory incidences of FAW on cotton were
observed in India and have become a potential threat to cotton (Arya and Ahmed
2019).
Natural (mainly cotton) fibres face a stiff competition from synthetic or
man-made fibres. Synthetic fibres are generally made from petrochemicals by a
process known as polymerization, which involves combining monomers to make a
long chain or polymer. These fibres are generally longer, stronger and durable and
provide smooth and excellent finishing to the fabrics. At present, the worldwide
consumption of different fibres includes 63% synthetic fibres, 25% cotton, 7%
wood-based fibres and 5% other natural fibres (Garside 2021). Contrary to the
world fibre consumption pattern, the annual consumption of total fibre is to the
tune of 5 million tonnes with a synthetic fibre contribution of 40%, while natural
fibres together contribute 60%. China is the largest producer of synthetic fibres
contributing 66% of the world synthetic fibre production (Ruiz 2019). To increase
the contribution of cotton fibre in textile fabrics, emphasis needs to be given on
increasing strength and length of cotton fibres.

11.19 Breeding Progress/Varietal Development

11.19.1 Conventional Breeding

Conventional breeding has been the base for improvement of lint yield, fibre quality,
adaptation and disease and pest resistance. Initial varieties grown in many of the
countries were mixtures of several types due to cross-pollination that provided much
needed genetic variability to operate selection. Later, diverse germplasm with
adaptability to a wide range of environmental conditions facilitated the development
of numerous varieties worldwide. The development of cotton that matures early and
possesses enhanced host plant resistance received much attention from about 1970
until the mid-1990s (Bourland and Myers 2015). However, with the advent of
transgenic Bt cotton and advancement of molecular tools, emphasis on traits has
changed to high productivity inclusive of quality and resistance.
11 Cotton Breeding 655

11.19.2 Status of Varietal Development in India

The history of cotton cultivation and its use in India puts the dating of early cotton
to 5000 BC (Menon and Uzramma 2017). Until the middle of the nineteenth century,
only the G. arboreum and G. herbaceum varieties of cotton were grown in different
regions of the country. The first attempt of introduction of American cotton in India
was made in 1790 when the seeds of Bourbon cotton from Malta and Mauritius
were distributed in Bombay state, but failed. It was only in Hubli-Dharwar areas in
the 1840s seeds from New Orleans were grown successfully. Dharwar American
cotton soon became popular, and the acclimatized American upland Georgian
cotton variety ‘Buri’ was released for the first time from Nagpur Farm in
1903–1904.
Scientific studies of cotton cultivation started only after the establishment of
the agricultural departments in various provinces and princely states in 1904 and
the Indian Cotton Committee (ICC) in 1917 at Bombay facilitated cultivation
of long-staple cotton in India. This committee established the Indian Central
Cotton Committee (ICCC) in 1921 which assisted the agricultural departments
to develop improved cotton varieties. Until 1947 when India became independent,
predominantly, the diploid Asiatic cottons, G. arboreum and G. herbaceum, were
grown covering 97% of the acreage under cotton. The cotton improvement efforts
got further fillips with the abolition of the ICCC in 1966 and establishment of the
All India Coordinated Cotton Improvement Project (AICCIP) at Coimbatore in
1967 and the ICAR-Central Institute for Cotton Research (ICAR-CICR) at
Nagpur. Since then, 268 high-yielding improved varieties and 109 hybrids
(non-GM) were released for commercial cultivation in different cotton-growing
states.
Some of the prominent landmark varieties and hybrids in India include release of
the world’s first intra-hirsutum cotton hybrid ‘H4’ in 1970 (Patel 1971), the first
interspecific hybrid between G. hirsutum and G. barbadense ‘Varalaxmi’ in 1972
(Katarki 1972), G. barbadense Sea Island cotton variety ‘Suvin’ in 1978 and
‘LRA5166’, a G. hirsutum variety with wide adaptability in all three cotton-growing
zones which occupied >30% area under cotton for about a decade. Successful
development of hybrids led to exploitation of heterosis in cotton for higher yields.
Interspecific hybridization and introgression from wild species resulted in the devel-
opment of several varieties and hybrids, viz. Badnawar 1, Khandwa 1, Khandwa
2 (from G. hirsutum  G. tomentosum); PKV 081, Rajat, Arogya, AKA 8401
(G. hirsutum  G. anomalum); Deviraj, G 67 (G. hirsutum  G. arboreum); Devitej
(G. hirsutum  G. herbaceum); MCU 2 and MCU 5, Varalaxmi, DCH 32, DHB
105, NHB 12, TCHB 213, HB 24 (G. hirsutum  G. barbadense); and DDH 2, DH
7, DH 9 (G. herbaceum  G. arboreum). Some of the popular varieties and
hybrids released for cultivation in different cotton-growing states are given
(Tables 11.4 and 11.5).
656 V. N. Waghmare

Table 11.4 Cotton varieties released for different states of India

Name of state Tetraploid cotton Diploid cotton
Punjab F 1378, LH 1556, LH 900, F 846, F LD 327, LD 491, LD694
1054, LH 1134, F 505, F 1861
Haryana H 1098, H 777, HS 6, H 974, HS HD 107, HD 123
182, H 1117
Rajasthan Bikaneri Narma, RST 9, RST RG 8, RD 18
875, G. Ageti, RS 810
Uttar Pradesh Vikas Lohit, CAD 4
MP Khandwa 2, Khandwa 3, Vikram, Maljari, Jawahar Tapti, Sarvottam
JK 4
Gujarat G.Cot 10, G.Cot 12, G.Cot 16, G. G.Cot 15, G.Cot 19, G.Cot 13, G.Cot
Cot 18, LRA 5166, LRK 516 17, G.Cot 21, G.Cot 23
Maharashtra DHY 286, PKV 081, Rajat, LRA AKH 4, AKA 5, AKA 8401, PA
5166, LRK 516 183, PA 255, AKA 7, Y1, PA
402, CNA 1028, CNA 1032, CNA
1054
Andhra Pradesh MCU 5, LRA 5166, L 389, L Srisailam, Mahanandi, Raghvendra,
603, Kanchana, LK 861 Arvinda
Telangana MCU 5, LRA 5166, LRK 516, L Srisailam, Mahanandi, Raghvendra,
389, L 603, Kanchana, LK 861 Arvinda
Karnataka Sharda, Abadhita, Sahana DB 3-12*, Raichur-51, DLSA 17
Tamil Nadu MCU 7, MCU 5 VT, LRA 5166, K 10, K 11, CNA 1003 (Roja)
LRK 516, Surabhi, Sumangala,
MCU 12, SVPR 2, Suvin
*G. herbaceum

Table 11.5 Popular non-GM hybrids in India

Name of state Tetraploid cotton Diploid cotton
Punjab FHH 209, F 2276, FATEH, LHH 144 DDH 11, Moti (LMDH 8), PAU
626 H (FMDH-3), FMDH-8,
FMDH-9
Haryana DhanLaxmi, OM Shankar AAH1, CICR-2, AAH 32
Rajasthan Maru Vikas RAJH-9
Uttar Pradesh – –
Madhya LAHH 4 and JKHy-1 and JKHy-2, –
JKHY 11
Gujarat H4, H6, H8, H10 DH 7, DH9
Maharashtra PKV Hy 2 and NHH 44, NHH AKDH-7, AKDH-5, PhA 46
250, Savitri, RHH 195, NHH
302, CICR HH 1
Andhra Pradesh LAHH 1, LAHH 4, NHB 80 –
Telangana LAHH 1, LAHH 4, NHB 80 –
Karnataka Varalaxmi, DCH 32, DHB 105 and DDH 2
DHH 11, RAHH 455
Tamil Nadu Savita, TCHB 213, Surya and Sruthi, K9, K10
TSHH 0629, CBS 156, Suguna
11 Cotton Breeding 657

11.19.3 Genomics-Assisted Breeding

Advances in molecular marker technologies and genome sequencing have facilitated

dissection of determinants of various economic traits in crop plants. Transgenic
technology and genomics have made significant contributions in enhancing the
efficiency of cotton breeding. To date, several QTLs associated with economic and
fibre quality traits have been mapped and few of them subjected to fine mapping.
However, the development of products using marker-assisted breeding in cotton are
very few. Two varieties, namely Ravnaq-1 and Ravnaq-2, possessing higher fibre
strength and improved length have been developed through marker-assisted breed-
ing (Abdurakhmonov 2016; Kushanov et al. 2017). Ravnaq MAS cultivars were
tested by State Variety Testing Committee of Uzbekistan across different cotton-
growing soil-climatic zones of the country during 2013 and 2014 and found superior
in agronomic performance over conventional upland cultivars. Using PHYA1 RNAi
GE cotton, a series of varieties viz., Porloq-1, Porloq-2, Porloq-3 and Porloq-4 were
developed (Abdurakhmonov 2016). These RNAi cultivars were successfully tested
for 3 years (2012–2014) in different soil-climatic regions of Uzbekistan. The RNAi
cultivars demonstrated superiority to traditional varieties both in terms of fibre
quality and adaptation to harsh environmental conditions across Uzbekistan.
ICAR-CICR, Nagpur, deployed MON 531 event (cry1Ac gene, used as a gene-
based marker) in elite varieties and developed ten varieties through marker-assisted
breeding, tested under the AICRP system of evaluation and released for commercial
cultivation.

11.20 Modernization of Cotton Improvement Programmes

The conventional breeding is based on the concept of selecting single and best high-
yielding progeny from the segregating populations to develop a cultivar. Conven-
tional breeding helped in the release of high-yielding varieties with superior fibre
quality. With the adoption of improved varieties and hybrids, refined agronomy and
integrated plant protection measures, cotton production has increased manifold until
the beginning of the last decade. However, lately, most of the cotton-growing
countries are facing yield stagnation and uncertainties due to changing climatic
conditions during the past few years. Depending on the availability of resources,
the research programmes may be modulated to meet the pressing needs. At the
current status of cotton research, research gaps and future areas can be identified;
accordingly, the National Research Programmes may be modulated to bridge
the gaps.

11.20.1 Creating Additional Genetic Variability

Conventional breeding has limitation in transferring desired traits from unadapted

exotic accessions to cultivated varieties lacking the trait because of negative linkages
658 V. N. Waghmare

and linkage drag. Continuing use of well-adapted base germplasm in the breeding
programme and selection and evolving varieties with similar genetic base has
resulted in narrow genetic base of the cultivated varieties. In India, about 95% of
the cotton area is under Bt cotton hybrid cultivation. Most of the hybrids have at least
one or both the parental lines possessing Bt gene(s). The parental lines are derived
using Bt base line in Coker background through limited backcrossing. Thus, most of
the hybrids under cultivation have one or other parental line in common contributing
to narrow genetic base of the varieties/hybrids under cultivation.
The major cotton-growing countries maintain huge genetic resources of
cultivated species and wild accessions; however, their utilization is minimal. The
exotic and wild accessions possess numerous potential genes that contribute to
disease and pest resistance, economic traits, fibre quality attributes and resistance
to abiotic stress. Therefore, broadening the genetic base of cultivated cotton by
mobilizing the useful genetic variations from diverse exotic accessions, races of
cultivated species and wild accessions requires to be the top priority. Countries with
cotton as priority crop need to have such exclusive research programme(s) on the
utilization of wild resources.

11.20.2 Use of Speed Breeding

Cotton generally takes 150–180 days to complete a crop cycle that makes difficult to
grow more than one normal crop in the same year. Growing more than one crop a
year of a breeding material will save on time and resources and also speed up the
development of varieties or product with desired introgressed traits.

11.20.3 Greater Access to Genomic Breeding Tools

Continuing improvement of molecular tools and advances in sequencing technology

has resulted in the development of huge genomic resources. However, the gap
between information on available genomic resources and its conversion into a tool
for use in cotton breeding is huge that needs to be bridged through capacity building
and collaboration across the national and international laboratories.

11.20.4 Developing High-Yielding, Stress-Tolerant,

Climate-Resilient Varieties

Prioritization is needed to develop verities or lines that will sustain climate change
and emerging stresses. The use of marker-assisted breeding will help to pyramid
genes for different traits in one background.
11 Cotton Breeding 659

11.21 Maintenance Breeding

Cotton, being an often cross-pollinated crop, genetic makeup of its varieties gradu-
ally changes year after year. Cook, as early as in 1932, reported the problems of
preservation of varieties of cotton. He emphasized ‘selection’ as the approved
method of keeping a variety uniform and of maintaining its productiveness; an
account must be taken of many more features of diversity to preserve the essential
characters of varieties by continued selection (Cook 1932).
The genetic purity of varietal seeds is related to the genetic potential of a variety/
hybrid for realizing yield, quality and resistance to biotic and abiotic stresses. The
genetic purity of a variety may deteriorate during seed production due to various
factors. These include natural outcrossing, spontaneous mutation, residual
variability, adaptive or developmental variation and mechanical mixture. Varietal
deterioration is the most common and serious problem that makes it necessary to
maintain the genetic purity of varieties under cultivation. For varietal maintenance in
cotton, the probable approaches which can be used include:

1. Rouging off-type plants

2. Mass selection
3. Progeny selection
4. Maintaining seed stocks of the original and seed increase

Rouging out off-type plants, also referred to as negative mass selection, is a

widely used procedure for the maintenance of genetic purity. Removal of off-types is
based on plant phenotype which can be identified visually. It reduces the mixture,
provided the off-type plants are removed before flowering, else cross-pollination
involving pollen from off-type plants may build up mixtures. Mass selection
involves identifying true-to-type superior plants of a variety based on phenotype
and mixing the seed of selected plants to grow next generation. Selfing of selected
plants is desirable to eliminate possible cross-pollination with off-type plants. A
large number of plants are selected and bulked to raise the next generation so as to
reduce variability. Inadvertent inclusion of off-type plants in a pool of a small
number of plants may increase variability than in the original population.
The progeny selection method is widely used in the maintenance of varietal
purity. It involves selection of a large number of single plants (500–1000), plant
progenies are evaluated, and only progeny rows confirming to the varietal type are
selected and pooled to produce nucleus seed and further pure seed increase.
Maintaining seed stocks is commonly and increasingly being used for the mainte-
nance of varietal purity. In this method, a huge quantity of original variety seed is
produced and stored in environmentally controlled conditions to maintain germina-
tion and viability for years. If the varietal genetic purity deteriorates, the required
quantity of seed is removed from the reserve to produce nucleus and further seed
increase. In this approach, the genetic changes in the variety are expected to be
minimal over the longer life span of the variety. It also saves breeder’s time for the
660 V. N. Waghmare

production of varietal nucleus seeds every year and also resources invested for crop
cultivation, isolation and regular monitoring of seed plots and seed processing.

11.22 Coordinated System of Testing

India has established a strong system of cotton genotype evaluation developed by its
Research Institutes and Cotton Research Station working under State Agricultural
Universities across cotton-growing states. The establishment of the Indian Central
Cotton Committee (ICCC) in Bombay as a technical advisory body to the govern-
ment in 1921 is considered as a major landmark in the history of cotton research in
India. The ICCC became a statutory body for promoting research in cotton. The
ICCC established the Cotton Technological Research Laboratory (CTRL) [now,
ICAR-Central Institute for Research on Cotton Technology (ICAR-CIRCOT)] at
Bombay in 1924 for conducting tests on fibre properties of cotton samples to relate
fibre properties with the spinning value of cotton. The ICCC was abolished in 1966
and the CTRL was placed under the administrative control of the ICAR. The ICAR
reorganized its research set up and established the All India Coordinated Cotton
Improvement Project (AICCIP) (now, All India Coordinated Research Project on
Cotton (AICRP on Cotton)) in 1967 with its headquarters in Coimbatore (Tamil
Nadu). Prior to the AICCIP, different centres conducting research on cotton were
under the control of PIRRCOM (Project on Intensification of Regional Research
Cotton, Oilseeds and Millets). The AICRP on Cotton has a network of 22 cotton
research centres located in 11 cotton-growing states. The AICRP on Cotton conducts
multi-location and multidisciplinary research on applied aspects of cotton including
varietal development, evaluation/site-specific validation and fine-tuning of agro
technologies and pest/disease management strategies. Since its inception in 1967,
the AICRP on Cotton has played a stellar role in shaping the cotton sector in India
through the development of several varieties/hybrids and fine-tuning agro-eco-
region-specific cotton production and protection technologies. The AICRP on Cot-
ton also acts as a nodal centre for transfer of technologies through Front Line
Demonstrations (FLDs). The entire cotton-growing area has been divided into
three zones, i.e. north, central and south zones, based on agro-climatic conditions
and growing season.
The zone-wise promising top-ranking entries after detailed agronomy studies are
considered for identification by Varietal Identification Committee. If a variety is
intended to be released in a state, it is done by the State Varietal Release Committee.
The proposals of identified varieties for one or more cotton-growing zones are then
submitted to the Sub-Committee on Crop Standards Notification and Release of
Variety of Central Seed Committee where it is released and notified. Further, if a
variety is released by the State Committee, it has to be notified by the Central
Committee (Basu 1999). The denotification of old/obsolete varieties is also done
by the same committee. Through the AICRP on Cotton, 268 high-yielding non-Bt
varieties and 109 non-Bt hybrids of cotton have been developed by the network
partners and released. Cultivation of Bt transgenic cotton was approved for
11 Cotton Breeding 661

commercial cultivation by the Government of India in 2002. The Bt hybrids devel-

oped mostly by private seed companies under licence from Monsanto were approved
by event-based approval mechanism (EBAM) committee under Review Committee
on Genetic Manipulation (RCGM) based on criteria formalized by Genetic Engi-
neering Approval Committee (GEAC). From 2016 onwards, RCGM has entrusted
the responsibility of evaluation and release of Bt cotton varieties/hybrids to ICAR
and AICRP on Cotton. Following the similar system of evaluation, eight Bt varieties
and 57 Bt hybrids have been released through ICAR-AICRP on Cotton.

11.23 Future Prospects

Genetic variability is the base for improvement of any crop plants. Success of
selection and consequently development of varieties is directly associated with the
extent of genetic variability for several component traits contributing to yield.
Cultivated cotton has a narrow genetic base resulting in stagnation of yields the
world over. To continue gains in yield and quality, it is imperative to explore primary
and secondary sources of gene pool to widen heritable genetic variability in the
breeding populations. Countries such as India where yield levels are far below than
world average emphasize on research programmes for enhancing genetic variability
needed.
Wide scale cultivation of Bt transgenics has provided benefits of protection of
cotton crop against bollworms, increased the seed cotton yield and reduced insecti-
cide use during early years of Bt adoption. However, susceptibility of most of the Bt
hybrids to sucking pest and subsequent breakdown of resistance/susceptibility of Bt
hybrids to pink bollworm have resulted in an increased use of insecticides in cotton.
Failure of BGII cotton to pink bollworm is a warning signal for researchers/
policymakers and users alike. For success of such technology, adequate precautions
are a must while implementation. Alternately, newer sources of genes must be
identified, validated and deployed to broaden the horizon of technology.
Advances in next-generation sequencing made the genome sequencing afford-
able, faster and precise. The sequenced and resequenced genomes of diploid and
allotetraploid and also sequencing of about a dozen wild species of cotton provide
valuable information on genomic structure, variation, markers, diversity and numer-
ous genes and biological processes associated with important traits such as fibre
development and stress responses. Several linkage maps were developed; genes and
thousands of QTLs linked to traits of interest were identified. However, large
knowledge gaps still persist concerning with the molecular regulation of the
biological processes. Characterization of essential genes controlling complex traits
is a major challenge for cotton functional genomics studies. Well-characterized
functional components of complex traits will facilitate effective application of
molecular-assisted breeding in cotton.
Emerging genome engineering technologies such as the CRISPR/Cas9 system
have great potential. This technology may be exploited to edit the disease-
susceptible genes, negative regulators of yield and fibre quality-related genes and
662 V. N. Waghmare

genes enhancing adaption and resistant to stress situation in cotton. However,

success of this technology is dependent on the availability of an efficient regenera-
tion system. In cotton, genotype-dependent regeneration is becoming a major bot-
tleneck for use of CRISPR/Cas9. Development of versatile and robust somatic
regeneration protocol suiting to a diverse set of genotypes will provide additional
avenues for transgenic development and efficient application of genome editing
tools across the genotypes for improvement of economic, fibre quality and adapta-
tion traits.
In recent years, the spinning industry is adopting large, almost fully automated
spinning mills to lower yarn manufacturing cost. With this trend, the mills exercise
less flexibility with respect to fibre types (blend composition) and yarn composition
(count and twist factors). The mills requirement is mostly for fibre length
>29–30 mm, matching fibre strength of 29–30 g/tex and micronaire of about 4.0.
The mills offer premium price for better fibre quality cotton. The diploid cottons
suffer on fibre quality parameters and are less in demand. This trend has also resulted
in skewed species composition, G. hirsutum occupying about 97% of the area under
cotton cultivation in India. Considering variation in market prices for cotton and
mills requirement, it is imperative for the cotton breeders to develop varieties with
improved fibre quality, viz. fibre length about 30 mm plus, matching fibre strength
and micronaire of 3.8–4.2. Asiatic diploids are inherently tolerant to insect pests,
diseases and drought stresses than upland cotton. Improved fibre quality parameters
matching with mills requirement can help to retain past glory of diploids in future.

11.24 Conclusions

Cotton is the most important source of natural fibre, meeting the most important
human needs for clothing. Cotton significantly contributes to the cotton growing
economies in terms of export earnings and providing employment to millions in
farms and processing industries. In cotton research, the prime objective is to improve
lint yield and quality through utilization of diverse germplasm resources employing
conventional and recent high-throughput technologies. The phenotypic selection
efficiency of the conventional breeding can be maximized using DNA-based
markers and recent genomic tools for the future breeding strategies. Stagnation of
yields and narrow genetic base of the cultivated cotton is a major issue across the
cotton-growing countries implicating need to use available genetic variability in
unadapted exotic accessions and to develop gene pools. Currently, insect- and
herbicide-resistant transgenic cotton occupy over 80% of world acreage under
cotton. Field-evolved resistance of pink bollworm against Bollgard and Bollgard II
cotton has been reported in some of the countries including India. Sucking pests
(whitefly and jassids) have emerged as major pests demanding more attention and
resources for management after PBW. For effective working of the transgenic
technology, newer gene sources conferring resistance to PBW and sucking pest
need to be involved and stacked to provide durable resistance.
11 Cotton Breeding 663

Application of next-generation sequencing (NGS) permitted whole-genome

sequencing and building draft assembly at a faster rate. The sequence information
across the genomes has become a major source for identifying new SNP markers and
candidate genes with potential for genetic improvement of cotton quality and
productivity. The refinement and fine-tuning of genotyping by sequencing (GBS)
permits scanning of a large number of individuals simultaneously. Cotton genomics
research now entered in the phase of functional characterization of genes related to
economic traits. These advances have paved the way to identify and clone functional
genes (Pan et al. 2020) and enhance breeding efforts to develop cotton so as to
produce high yield, superior quality fibres and resisting effects of climate change.
Precision genome editing technology such as CRISPR/Cas9 has demonstrated
success in gene-targeted mutagenesis in several crops including cotton. This tech-
nology holds promise to develop transgene-free edited plants for economic, quality,
resistance and adaptation traits in cotton and deserves higher investment by
researchers.

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Maintenance Breeding of Pusa Basmati
Varieties 12
Rakesh Seth, A. K. Singh, and S. Gopala Krishnan

Abstract

Genetic gain, achieved by any breeding and varietal development programme,

can be realized only when there is a robust seed production system, underpinned
by a systematic maintenance breeding programme. Breed (variety) and seed are
two facets of the same coin—one without another is irrelevant. The full potential
impact of a new improved variety, however excellent it may be, cannot be
realized, unless it is supported by a strong seed multiplication, distribution and
marketing system. The popularity and complete dominance of the ICAR-IARI
bred Basmati varieties is evident from the increase in percent share of breeder
seed indents of Pusa Basmati varieties in the total breeder seed indents of all
Basmati varieties. The details of maintenance breeding and the success of Pusa
Basmati varieties are described in this chapter.

Keywords
Basmati · Genetic gain · Mechanical mixtures · Outcrossing · Breeder seed
production

R. Seth (*)
ICAR-Indian Agricultural Research Institute Regional Station, Karnal, Haryana, India
A. K. Singh · S. G. Krishnan
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 677
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_12
678 R. Seth et al.

12.1 Introduction

India has achieved significant productivity gains in major cereals post-green revolu-
tion (post-GR) era of 1984–2017. The annual gain in rice productivity in different
phases after green revolution has been computed as 68% and 117% in 1984–2000
and 2001–2017, respectively (Fig. 12.1) (Yadav et al. 2019). Similarly, impressive
genetic gains have also been made in quality and productivity of Basmati varieties, a
speciality group of rice varieties, having great aroma and premium culinary
attributes (Singh et al. 2018a). This progress has largely been attributed to develop-
ment and adoption of improved cultivars and crop management technologies.
Significant efforts go into breeding programmes and development of trait-specific
high-yielding varieties with inbuilt resistance to pests and diseases, besides tolerance
to various biotic and abiotic stresses and quality attributes. Seeds are the carriers of
these genetic gains to farmers and ultimately to the consumers. Quality seed alone
contributes a 15–20% increase in productivity. ICAR-Indian Agricultural Research
Institute (ICAR-IARI) bred Basmati varieties (commonly known as ‘Pusa Basmati’
varieties) have made a significant impact in converting these genetic gains into
economic gains for different stakeholders associated with Basmati rice production,
processing and export. Cumulative foreign exchange earnings of a single landmark
Basmati variety, Pusa Basmati 1121, in one decade (2008–2017) have been to the
tune of US $20.8 billion (Singh et al. 2018a). Pusa Basmati varieties (Pusa Basmati
1121, Pusa Basmati 1509, Pusa Basmati 1, etc.) are dominating the seed chain
(Figs. 12.2 and 12.3).
Basmati rices possess unique organoleptic properties (aroma and taste) due to
which these are very popular in the international markets. However, cultivation of

Fig. 12.1 Rice productivity (kg ha
1) trend since 1950 (Yadav et al. 2019)
12 Maintenance Breeding of Pusa Basmati Varieties 679

Fig. 12.2 Cumulative breeder seed indent of Basmati varieties during the last 10 years, 2010–2019
(Breeder Seed Allocation Plans 2020)

Fig. 12.3 Percentage share of breeder seed indents of Pusa Basmati varieties in total breeder seed
indents of all Basmati varieties (2010–2019)

Basmati is geographically limited to North-Western India and Punjab in Pakistan. In

India, Basmati production is confined only to seven states (Punjab, Haryana,
Himachal Pradesh, Delhi, Uttarakhand, Jammu and Kathua districts of Jammu and
Kashmir and 27 districts of Western Uttar Pradesh). This specific region has been
earmarked as Geographical Indication (GI) for Basmati rices in 2016 by
680 R. Seth et al.

Geographical Indication Registry, Government of India (GI No. 145, Certificate

No. 238 dt. 15.02.2016). Typically, GI conveys an assurance of quality and distinc-
tiveness which is essentially attributable to the fact of its origin in that defined
geographical locality, region or country (Department of Promotion of Industry and
Internal Trade 2021).
Basmati—being one of the most popular speciality rices in the EU and the Middle
East—attracts premium prices and is subject to stringent tests to differentiate
between authentic Basmati from non-Basmati rices (Nader et al. 2019). The authen-
ticity definitions by the UK Code of Practice on Basmati Rice (CoP) of 2017 clearly
stipulate that when the description of the product is ‘Basmati rice’, the non-Basmati
rice content must not exceed 7%. This tolerance is in place to take account of seed
impurity and other segregation issues at origin (http://www.riceassociation.
org.uk). This clearly underscores the critical need for maintaining the supply of high-
quality genetically pure seed for the production of Basmati rice.
Traditional Basmati varieties are tall, lodging and disease prone, photoperiod
sensitive and poor yielders. Pusa Basmati 1, the world’s first evolved, semi-dwarf,
photoperiod-insensitive, high-yielding Basmati variety developed by ICAR-IARI,
New Delhi, in 1989, brought a paradigm shift in Basmati breeding (combining
Basmati quality with higher yield and semi-dwarf stature). ICAR-IARI continues
to play the flagship role in Basmati breeding with the development of several popular
Basmati varieties like Pusa Basmati 1509, Pusa Basmati 6, Pusa Basmati 1637, Pusa
Basmati 1718 and the recently released Basmati variety Pusa Basmati 1692 (notified
in 2020).

12.2 Maintenance Breeding

Maintenance breeding (used synonymously with varietal maintenance) is a basic

technique which primarily deals with the purification and maintenance of varieties.
Notwithstanding its simplicity, this process has a profound impact on the spread and
enhanced productive life of a variety. ‘Variety maintenance’ is the perpetuation of a
small stock of nucleus seed, as the basis of all future multiplication and production of
a variety, either by repeated multiplication of a small stock by a precise procedure,
controlling the relationships of the plants in the stock, or by storage (Laverack 1994).

12.2.1 Why Maintenance Breeding?

‘Thou shall not sow thy fields with mingled seed’, Leviticus 19:19. Thus were the
Hebrews enjoined to sow their fields with unmixed seed. The early farmers were
aware of the fact that varieties of crops deteriorate with time unless directed efforts
are made towards maintaining the integrity of the variety (Kadam 1942). Plant
breeding is often described as ‘plant evolution’ directed by man. One of the principal
constraints of the conventional breeding methods is that selection decisions about the
merits of diverse lines are largely based on their phenotypes. Genotype describes the
12 Maintenance Breeding of Pusa Basmati Varieties 681

allelic constitution of an individual at one or more loci, while phenotype is the

observable expression of one or more traits (Singh and Singh 2017). The various
traits of an organism can be grouped into two categories: (1) qualitative traits,
governed by one or few major genes or oligogenes, each of which produces a
large effect on the trait phenotype, and (2) quantitative traits, governed by several
genes, each having a small individual effect on trait phenotype, which are usually
cumulative. Most of the traits of biological and economic importance are quantita-
tive or metric traits. The phenotypic expression of quantitative traits is significantly
influenced by the environment and, often, an interaction between genotype and
environment.
The phenotype can be expressed by the following equation:

P ¼ μ þ G þ E þ ðG  E Þ

where P is the phenotype of a quantitative trait (governed by multiple genes), μ is the

population mean, G is the effect of genotype of the concerned individual, E is the
effect of the environment on the expression of the trait and (G  E) is the interaction
component. A precise estimation of G, E and G  E components of phenotypic
variation for different quantitative traits is one of the continuing quests for plant
breeding (Singh and Singh 2017; Singh 2012). This is also a challenge in mainte-
nance breeding as the production of different classes of seeds including nucleus and
breeder seed is essentially done based on the phenotype.
A comprehensive study on the importance of maintenance breeding in the first
miracle rice variety IR 8 provided strong justification for continuous maintenance
breeding to counter rapidly evolving biotic and abiotic stresses. Maintenance breed-
ing plays a decisive role in the adaptation of newly developed varieties to changing
environmental conditions, which have a deleterious impact on older varieties (Peng
et al. 2010).

12.2.2 Varietal Deterioration and Maintenance Breeding

Two essential characteristics of a cultivar are (1) identity and (2) reproducibility. In
self-fertilizing crops, a cultivar generated from a single, homozygous genotype will
be uniform in appearance, whereas a cultivar increased from a mixture of genotypes
will exhibit a range of genetic variability according to that present in the mixture.
This is assuming that the plant originally selected is homozygous at all loci—an
assumption plant breeders often make, but this assumption is seldom met (Sleper and
Poehlman 2006). There may be several minor loci still segregating even in the F10
generation leading to the production of off-types in a large population. Kadam
(1942) in his classical paper on varietal deterioration enumerated seven critical
factors responsible for the degradation of varieties over time.
682 R. Seth et al.

12.2.2.1 Developmental Variations

Seed crops which are grown under different environments over consecutive
generations may exhibit differential growth responses leading to the production of
such variation. In order to minimize these variations, it is advisable to restrict the
seed production of the varieties in their areas of adaptation.

12.2.2.2 Mechanical Mixtures

Mechanical mixtures are one of the most important reasons for varietal deterioration
and are mainly attributed to human negligence (Fig. 12.4). These are the leading
causes for litigation between seed producers and farmers. Shattering of grains in rice
(an important source of mixture) results in volunteer plants (self-sown plants). Thus,
care should be taken that the land used for seed production is free from volunteer
plants. This stipulation is a mandatory protocol for seed production as per Indian
Minimum Seed Certification Standards (IMSCS 2013). Proximity of threshing
floors, unclean tarpaulins or the use of the same contaminated seed drills, seed
bins and gunny bags and mistakes in handling seed during seed processing are the
main reasons for mechanical mixtures. These can be avoided by taking utmost care
during every step of seed production and processing.

Fig. 12.4 Mechanical mixtures: major factor for varietal deterioration (result of human
negligence)
12 Maintenance Breeding of Pusa Basmati Varieties 683

12.2.2.3 Mutations
Mutation is a sudden heritable change in the genotype of an organism. The
organisms with such heritable changes are known as mutants. Mutations are of
two types (spontaneous and induced) depending upon their origin. A spontaneous
mutation is one that occurs in nature, while an induced mutation results from a
mutagenic agent. What appears to be a spontaneous mutation may have been
induced, because all plants in nature are subjected to low dosages of natural radiation
(Sleper and Poehlman 2006). In nature, plant mutation rates occur between 10
5 and
10
8 during adaptation and evolutionary processes. These frequencies of natural or
spontaneous mutations are extremely low (Zhon-hua et al. 2014). Mutations per se
do not pose a serious threat in seed production and varietal maintenance of Basmati
rices as well.

12.2.2.4 Natural Outcrossing

The extent of natural outcrossing in rice varies from 0% to 3%, depending on the
cultivar and the environment, with an average of about 0.5% (Sleper and Poehlman
2006). Sometimes there is lag between spikelet opening and bursting of the anther
resulting in outcrossing. Though rare, but outcrossing in rice is not an exception
(Fig. 12.5a, b). In a study on outcrossing (OC) in winter wheat, Martin (1990)
observed that there is no question that OC occurs during the multiplication stages of
cultivar development. It is likely that OC is most serious when experimental lines are
growing side by side in early-generation plant or head rows and, subsequently, in
initial small increase plots. If the incidence of outcrossed seed could be reduced in
seed replanted from such nurseries, the production cost of all classes of certified seed
could be reduced significantly by decreasing the amount of roguing required to meet
purity standards for the cultivar.
An interesting observation has been reported by Kadam (1942) that farmers in
Konkan generally believe that mixtures suddenly appear in the third year of growing
an improved variety. This is due to the fact that in that year natural F1 plants have
segregated for various characters. Perpetuation of such plants, in addition to mechan-
ical mixtures, increases the proportion of dominant types, until in the end a variety
resembles a conglomeration of various types. The natural outcrossing can be with
off-types, diseased or undesirable plants.
Bateman (1947) in an exhaustive work on contamination of seed crops reported
that there are two types of contamination of seed crops: (1) mechanical mixtures and
(2) cross-pollination between varieties (admixture of foreign seed at harvesting or
admixture of foreign pollen at flowering). The degree of genetic contamination in
seed fields due to natural crossing depends upon four variables: (a) the breeding
system of species, (b) isolation distance, (c) varietal mass and (d) pollinating agent.
Contamination generally decreases, as the isolation distance between the varieties is
increased; however, there still may be miniscule traces of contamination over wide
distances. Appropriate isolation of seed crops per se is, therefore, a primary prereq-
uisite for the seed production of crop plants cross-pollinated by winds or insects.
684 R. Seth et al.

Fig. 12.5 (a) Outcrossed plants in rice seed field of Pusa Sugandh 5. (b) Outcrossed plant with
pigmented apiculi in rice seed field of Pusa Sugandh 5

12.2.2.5 Minor Genetic Variations

Varieties appearing phenotypically uniform and homogeneous at the time of their
release may still have minor genetic variations. This could be due to the fact that in a
typical breeding programme, the seed multiplication is done after its identification/
release. Till the identification/release of a variety, the genotypes are grown in smaller
12 Maintenance Breeding of Pusa Basmati Varieties 685

area, and when grown in larger area for seed multiplication, it makes it possible to
identify the off-types in a large population of plants. Some of these minor genetic
variations may be lost during subsequent production cycles due to selective elimi-
nation by the environment (Kadam 1942; Agrawal 1991). Remnant of these genetic
variants can be eliminated to a large extent by careful nucleus and breeder seed
production.

12.2.2.6 Selective Influence of Diseases

The selective influence of diseases is also an important factor in varietal deteriora-
tion. New varieties often become vulnerable to new races of diseases caused by
obligate parasites and are often out of seed production programmes (Kadam 1942;
Agrawal 1991). With the current focus on incorporating disease resistance in
Basmati varieties, a number of disease resistance varieties have been bred by
ICAR-IARI through molecular marker-assisted backcross breeding (MABB)
(Singh et al. 2019)—for example, Pusa Basmati 1718 (a MAS-derived bacterial
blight (BB) resistant Basmati rice variety possessing two genes, xa13 and Xa21)
(Singh et al. 2018b), Pusa Basmati 1637 (a MAS-derived near isogenic line of Pusa
Basmati 1 possessing Pi9 gene for blast resistance) (Singh et al. 2017a) and Pusa
Basmati 1728 (a MAS-derived near isogenic line of Pusa Basmati 6 carrying two
genes for BB resistance, viz. xa13 and Xa21) (Singh et al. 2017b). Taking up
systematic seed production programme of these varieties having inherent resistance
to specific diseases, the selective influence of these specific diseases can be reduced
or eliminated.

12.2.2.7 Segregation Due to Residual Heterozygosity in the Cultivars

Premature release of varieties, still segregating for resistance and susceptibility to
diseases or other factors, is also an important factor of varietal deterioration. In
addition, heritable variations on account of recombination and polyploidization may
occur in varieties during seed production (Kadam 1942; Agrawal 1991). Avoiding
hasty release of varieties and putting in seed chain only the stabilized varieties can
reduce residual segregation or stability issues to a large extent.
It is apparent from the aforesaid discussion that genetic variation may appear
within a seed lot due to multiple reasons, viz. mechanical contamination, undesirable
pollination, residual segregation, recombination and mutations. These diverse
factors ensure that no variety is likely to retain the precise allele frequencies
established by breeder without continuous monitoring (Laverack and Turner
1995). The process of continuous intervention to monitor and maintain the genetic
purity of the variety is termed as maintenance breeding. It is usually the fag end of
varietal development and the first step in the initiation of seed production. Fig-
ure 12.6 depicts an analogy adapted from 0 to 1 (Thiel and Masters 2014). The value
0 to 1 indicates an innovation (variety) and 1 to n is scaling up (seed production).
Maintenance breeding is at the cusp of breeding and seed production. In practice,
most of the issues pertaining to quality, adaptability and yields are encountered at
initial scaling up of the variety and should be sorted out at this stage. Pusa Basmati
686 R. Seth et al.

Fig. 12.6 Maintenance

breeding (M.B.): challenging
cusp of innovation (varietal
development) and scaling up
(seed production). (Adapted
from Thiel and Masters 2014)

1692, a new variety notified in 2020 (Singh et al. 2020), is now at the cusp of
maintenance breeding and its large-scale seed production.

12.3 Basmati Varieties Maintenance Breeding and Breeder Seed

Production

At present, 34 varieties have been notified as Basmati varieties till 15 July 2021
(Notified Basmati Varieties 2021) (Table 12.1). To understand the varietal dynamics
and consumer preferences, a comparison of breeder seed indents of all Basmati
varieties in seed chain in the last decade (2010–2019) has been made in Figs. 12.2
and 12.3. A total of 24 Basmati varieties figured in breeder seed indents in the last
decade. Two varieties Basmati 217 and Mahi Sugandha have zero breeder seed
indent, and three varieties have almost negligible cumulative breeder seed indent of
less than 0.50q each ((Type 3 (0.10q), Ranbir Basmati (0.37q), Punjab Basmati
4 (0.32q)) during this decade. Top three peaks were occupied by Pusa Basmati
varieties viz., Pusa Basmati 1121, Pusa Basmati 1509 and Pusa Basmati 1 (Fig.
12.2). This complete dominance of Pusa Basmati varieties gives an idea about
demand pull of these varieties, implicitly indicating that varieties per se are not
only excellent, but also gives an insight about IARI’s ability to consistently saturate
the seed markets with genetically pure high-quality seeds which is produced from
nucleus seed (product of maintenance breeding).
All the IARI (Pusa) bred Basmati varieties undergo systematic maintenance
breeding at ICAR-IARI, Regional Station, Karnal (dedicated to maintenance breed-
ing and seed production). A brief description of some important Basmati varieties
(Pusa Basmati 1121, Pusa Basmati 1509, Pusa Basmati 6, Pusa Basmati 1718) along
with specific comments on the maintenance breeding and breeder seed production is
discussed in following sections.
 12

Table 12.1 Notified Basmati varieties as per APEDA (The Agricultural and Processed Foods Exports Development Authority)
S. no. Varietya Notification no. and date S. no. Variety Notification no. and date
1 Basmati 217 4045—24.09.1969 18 Malviya Basmati Dhan 10–9 2817 (E)—19.09.2013
361 (E)—30.06.1973 (IET 21669)
2 Basmati 370 361 (E)—30.06.1973 19 Vallabh Basmati 21 2817 (E)—19.09.2013
786—02.02.1976 (IET 19493)
3 Type 3 (Dehraduni Basmati) 13—19.12.1978 20 Pusa Basmati 1509 2817 (E)—19.09.2013
(IET 21960)
4 Punjab Basmati 1 (Bauni Basmati) 596 (E)—13.08.1984 21 Basmati 564 268 (E)—28.01.2015
5 Pusa Basmati 1 615 (E)—06.11.1989 22 Vallabh Basmati 23 268 (E)—28.01.2015
6 Kasturi 615 (E)—06.11.1989 23 Vallabh Basmati 24 268 (E)—28.01.2015
7 Haryana Basmati 1 793 (E)—22.11.1991 24 Pusa Basmati 1609 2680(E)—01.10.2015
8 Mahi Sugandha 408 (E)—04.05.1995 25 Pant Basmati 1 (IET 21665) 112 (E)—13.01.2016
9 Taraori Basmati 1 (E)—01.01.1996 26 Pant Basmati 2 (IET 21953) 112 (E)—13.01.2016
(HBC 19/Karnal Local)
Maintenance Breeding of Pusa Basmati Varieties

10 Ranbir Basmati 1 (E)—01.01.1996 27 Punjab Basmati 3 3540 (E)—24.11.2016

11 Basmati 386 647 (E)—09.09.1997 28 Pusa Basmati 1637 3540 (E)—24.11.2016
12 Improved Pusa Basmati 1 1178 (E)—20.07.2007 29 Pusa Basmati 1728 3540 (E)—24.11.2016
13 Pusa Basmati 1121 1566 (E)—05.11.2005 30 Pusa Basmati 1718 2805 (E)—25.08.2017
After amendment 2547 (E)—29.10.2008
14 Vallabh Basmati 22 2187 (E)—27.08.2009 31 Punjab Basmati 4 1379 (E)—27.03.2018
15 Pusa Basmati 6 (Pusa 1401) 733 (E)—01.04.2010 32 Punjab Basmati 5 1379 (E)—27.03.2018
16 Punjab Basmati 2 1708 (E)—26.07.2012 33 Haryana Basmati 2 3220 (E)—05.09.2019
17 Basmati CSR 30 1134 (E)—25.11.2001 34 Pusa Basmati 1692 3482 (E)—07.10.2020
After amendment 2126 (E)—10.09.2012
a
Notified till 15 July 2021
687
688 R. Seth et al.

12.3.1 Pusa Basmati 1

Pusa Basmati 1 was released for commercial cultivation in 1989 (Fig. 12.7). It is the
first evolved Basmati variety having semi-dwarf stature, high yield potential and
photoperiod insensitivity. Development of this variety by ICAR-IARI was a turning
point in Basmati breeding in India. Pusa Basmati 1 is a product of cross between
Pusa 150 and Karnal Local. It combines unique traits from diverse lineage. Pusa
150 is a breeding line derived through a convergent breeding approach involving
many high-yielding non-aromatic rice varieties (Taichung Native 1, IR 8, IR 22, etc.)
and traditional Basmati rice variety (Basmati 370) used as quality trait donor. Karnal
Local was a selection from the traditional Basmati rice collection, Haryana Basmati
Collection 19 (HBC 19) from the Karnal district of Haryana (with better grain and
cooking quality), which was later released as Taraori Basmati in 1996 (Singh et al.
2004). Pusa Basmati 1 is still in demand as regular breeder seed indents of this
variety are received till date. It is being maintained at ICAR-IARI, Regional Station,
Karnal, since 1989 (notification year). Maintenance breeding comment: kind of
variants observed in nucleus/breeder seed plots: (1) awn less off-types; (2) flowering
variants.

Fig. 12.7 Pusa Basmati 1: outstanding example of maintenance breeding (notification year 1989)
12 Maintenance Breeding of Pusa Basmati Varieties 689

12.3.2 Pusa Basmati 1121

Pusa Basmati 1121 is an exquisite Basmati rice variety with exceptional grain and
cooking quality notified for commercial cultivation in 2005 and subsequently (after
the amendment) for the states of Delhi, Punjab and Haryana in 2008 (Table 12.1).
The superior linear cooked kernel elongation of this unique variety was derived from
parents Basmati 370 and Type 3 (used as donors for grain and cooking quality traits).
Accumulation of favourable loci for extra-long grain and exceptionally high linear
cooked kernel elongation was possible through transgressive segregation, due to
selective inter-mating of the sister lines showing better linear kernel elongation in the
segregating generations. As many as 13 rice varieties/enhanced germplasm (includ-
ing Basmati 370 and Type 3) were used to bring together the favourable alleles at
multiple loci for agronomic, grain and cooking quality characteristics in the devel-
opment of Pusa Basmati 1121 (Fig. 12.8) (Singh et al. 2018a).
Modern varieties being the products of complex lineage and multiple crosses,
consequently the varietal maintenance of these varieties also becomes quite arduous.
Different types of variants do crop up in these varieties during repeated cycles of
seed production. Many times it becomes very difficult to keep the exact combination
of the favourable alleles brought together by breeder, almost intact in repeated cycles

Fig. 12.8 Pusa Basmati 1121 pedigree showing contribution of several varieties. Years in
parentheses indicate the year in which crossing was initiated (1966) and the year of release of
variety (2003) (Singh et al. 2018a)
690 R. Seth et al.

of multiplication. Pusa Basmati 1121 is a typical example of a difficult variety to

maintain due to its complex ancestry (Fig. 12.8) various types of variants have been
observed (Fig. 12.9a, b). Consistent and recurrent cycles of varietal maintenance,
nucleus and breeder seed production (Fig. 12.10) have enabled this variety to make a
significant contribution in farmer prosperity. Maintenance breeding comment: chal-
lenging variety to maintain. Kind of variants observed in nucleus/breeder seed plots:
(1) tall off-types; (2) dwarf off-types; (3) grain size off-types; (4) awned off-types.

12.3.3 Pusa Basmati 1509

Pusa Basmati 1509 is a very popular Basmati rice variety notified in 2013 for
commercial cultivation. It has semi-dwarf plant stature (a plant height of
95–100 cm), sturdy stem and non-lodging and non-shattering habit as compared to
Pusa Basmati 1121. It is suitable for multiple cropping systems with a seed-to-seed
maturity of around 115–120. It has an average yield of 4.1 t/ha with potential yield as
high as up to 7.0 t/ha under good management conditions. Pusa Basmati 1509
possesses aromatic extra-long slender grains (8.41 mm) and good kernel length
after cooking (19.1 mm) (Singh et al. 2014). Its area is fast increasing, and this
variety has significant export potential (Fig. 12.11). Maintenance breeding com-
ment: kind of variants observed in nucleus/breeder seed plots: (1) tall off-types;
(2) grain size off-types.

12.3.4 Pusa Basmati 6

Pusa Basmati 6 is very popular in niches of southern Punjab and north-western

districts of Haryana. The major chunk of breeder seed of this variety is used in these
districts (Fig. 12.12). Pusa Basmati 6 is also popularly known as Pusa 1401. It has
semi-dwarf plant stature with sturdy stem. This variety has a kernel that retains
uniform shape after cooking, as against kernel shape of Pusa Basmati 1121 (tapering
end after cooking). Pusa Basmati 6 possesses strong aroma along with minimum
chalkiness (<4%) (Singh et al. 2018a). Maintenance breeding comment: kind of
variants observed in nucleus/breeder seed plots: (1) grain size off-types; (2) tall
off-types; (3) dwarf off-types.

12.3.5 Pusa Basmati 1718

Pusa Basmati 1718 is a product of marker-assisted backcross breeding having two

genes (xa13 and Xa21) governing bacterial blight (BB) resistance. It is a
MAS-derived near isogenic line of popular variety Pusa Basmati 1121. Pusa Basmati
1718 has been released for Basmati-growing states of Haryana, Punjab and Delhi.
With a seed-to-seed maturity of 136–138 days, it has an average productivity of 4.6 t/
ha (maximum yield potential 6.0 t/ha) (Singh et al. 2018b). It possesses long slender
12 Maintenance Breeding of Pusa Basmati Varieties 691

Fig. 12.9 (a) and (b) Pusa

Basmati 1121 maintenance
and purification. Variants in a
paired row, raised from single
true-to-type panicle
692 R. Seth et al.

332q

162q
144q
115q 121q 123q 139q 121q 135q
118q 102q 100q 97q
85q 99q
74q 90q
70q 69q 66q
45q
50q 51q
23q 45q
0q 4q 25q
0q 5q
2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019

Br. Seed Indent (q) Br. Seed Producon (q)

Fig. 12.10 Journey of Pusa Basmati 1121. An established brand. Breeder seed indent and
production from 2005 onwards

139q 135q

121q

69q 66q
57q
62q 65q
53q
48q
25q

0 22q
0

2013 2014 2015 2016 2017 2018 2019

Breeder Seed Indent (q) Breeder Seed Producon (q)

Fig. 12.11 Journey of Pusa Basmati 1509: a brand in making. Breeder seed indents and production
from 2013 (notification year) onwards

grains (8.1 mm) and very good kernel length after cooking (17.0 mm). It also has
very less grain chalkiness, intermediate amylose content (22.2%) and strong aroma
(Singh et al. 2018a). This variety is becoming quite popular and in the near future is
likely to occupy significant area under Basmati cultivation. Maintenance breeding
comments: (1) tall off-types; (2) grain size variants.
12 Maintenance Breeding of Pusa Basmati Varieties 693

44q
41q
37q

25q 25q
22q
20q
19q 20q
21q
15q 19q
17q 13q 13q
10q
11q
9q
0q
0q
2010 2011 2012 2013 2014 2015 2016 2017 2018 2019

Br. Seed Indent (q) Br. Seed Producon (q)

Fig. 12.12 Journey of Pusa Basmati 6: breeder seed indents and production from 2010 (notifica-
tion year) onwards

12.4 Basmati Varieties Maintenance Breeding Procedure

The procedure adopted is panicle to row method:

• Single ‘true-to-type’ panicles (350–500 in number) are selected.

• Selected ‘true-to-type’ panicles are threshed individually. Each threshed panicle
is critically screened for seed characteristics.
• For Basmati varieties, a small portion of seed of each panicle is subjected to grain
and cooking quality testing.
• Seeds of panicles not conforming to seed characteristics or not performing well in
cooking quality are rejected.
• In the case of varieties developed through MABB, an additional step is
undertaken. Seedlings are raised from part of the seed from each panicle used
for cooking, for screening the presence of target alleles of the genes incorporated
using either gene-based or gene-linked markers (Fig. 12.13). Any panicle having
any inadvertent plant without possessing the R-allele of the disease resistance
genes is summarily rejected.
• Seeds of remaining 200–250 panicles are raised in panicle rows. A slight modifi-
cation is raising of paired rows from a single panicle. Raising of paired rows from
single panicle helps in better comparison amongst the selected panicles
(Figs. 12.14a, b).
694 R. Seth et al.

Fig. 12.13 Amplification profile of the molecular analysis of panicles of Pusa Basmati 1718 for
the presence of BB resistance genes, xa13 and Xa21, using gene-based marker, xa13 prom and
pTA248, respectively. All the panicles amplified 500 bp fragment for xa13 prom and 950 bp with
pTA248 corresponding to the resistance alleles of xa13 and Xa21. Hence, all these panicles which
were possessing desirable grain and cooking quality are only considered for raising panicle to row
progenies for nucleus seed production. M, 100 bp ladder; P1, Pusa Basmati 1121 (susceptible
check); and P2, Improved Pusa Basmati 1 (resistant check); 1–22, panicles harvested from nucleus
seed plot for further maintenance, nucleus and breeder seed production

• Generally, the row length is kept 5 m long. Spacing between the rows (30 cm) and
between two paired rows (60 cm). The plant-to-plant spacing is kept 20 cm. Thus,
a 5 m long paired row raised from a single panicle would be having 50 plants
(i.e. 25 plants/row and 50 plants/paired row). The wider spacing of 60 cm
between two paired rows helps in the proper expression of individual plants
and critical observation and screening of different paired rows. This layout can
be modified as per availability of seedlings per panicle for transplanting for each
paired row.
• A thorough screening of panicle rows at different crop growth stages is done.
Diagnostic characteristics based on DUS guidelines (PPV&FRA 2007) for con-
duct of test for distinctiveness, uniformity and stability on rice are very useful in
screening.
• Panicle rows not conforming to ‘true-to-type’ plant type or showing off-types are
totally discarded as and when observed.
• Remaining selected panicle rows are harvested and threshed individually. And
again harvested and threshed seed of each individual panicle row is critically
examined.
• Finally, seeds of all retained ‘true-to-type’ panicle rows are bulked to get geneti-
cally pure high-quality nucleus seed.

Integration of cooking and grain quality test and screening for disease resistance
genes in the maintenance breeding programme itself has significantly enhanced the
consumer preference of these varieties. Maintenance breeding plots of specific
varieties are raised in such a way that these are surrounded by the breeder seed
plots of the same variety. This simple intervention (nucleus seed plots surrounded by
breeder seed plots) not only prevents outcrossing with undesirable pollen as breeder
seed plots act as buffer but also helps in visual comparison providing both micro and
macro views of the variety (Fig. 12.14a, b).
12 Maintenance Breeding of Pusa Basmati Varieties 695

Fig. 12.14 (a) Pusa Basmati 1121 nucleus seed production (panicle paired rows). (b) Pusa
Basmati 1121 maintenance breeding plots (nucleus seed) surrounded by breeder seed plots
(to prevent outcrossing)
696 R. Seth et al.

12.5 Maintenance Breeding, Seed Production, Off-Types

and Rogues

Adequate understanding of terminology, namely maintenance breeding, generation

system of seed multiplication, seed chain, off-types and rogues, helps in conceiving
and executing a proper seed production programme. There are three recognized
classes of seed in the Indian generation system of seed multiplication (i.e. breeder,
foundation and certified seed), and seed supply chain follows a three- to four-tier
system of multiplication (Breeder seed ! Foundation seed ! Foundation/Certified
seed ! Certified seed). The seed multiplication cycle starts with ‘breeder seed’,
which is dependent upon availability of high-quality nucleus seed (a product of
varietal maintenance). Any issue with the genetic purity of the breeder seed lot
(presence of contaminants/off-types/mixtures) gets multiplied and results in an
exponential increase in these contaminants in succeeding generations. The presence
of these contaminants may lead to loss of identity and requisite traits of the variety
for which it has been specifically bred.

12.5.1 Off-Types

Off-types are defined as plants showing a distinct phenotype from the sown variety
and are unknown as a variety (Lee et al. 2013). The proportion of off-types in any
particular population or seed lot depends on four factors: (a) rate of addition of plants
in each generation and the number of generations of multiplication, (b) proportion of
progeny of off-types which are also off-types (i.e. the stability of these off-types in
subsequent multiplications), (c) relative rate of multiplication of off-type plants and
(d) effectiveness of removal of off-types by roguing at each generation (Laverack
and Turner 1995). Bateman (1946) described contamination as ‘obvious’ and ‘cryp-
tic’ in the deterioration of certain British vegetable seed stocks when isolation
distances were inadequate. He classified off-types produced by cross-pollination
with other varieties into ‘obvious’ types, where a distinct phenotype was produced,
and ‘cryptic’ where the resulting variant genotype was not easily seen from pheno-
typic characters. Obvious off-types would be seen more easily and removed. Cryptic
off-types would be more difficult to detect and so could spread in the population with
potentially serious consequences for yield and quality. This description of obvious
and cryptic contamination is very aptly delineated by the famous optical illusion
(Fig. 12.15) titled ‘The Young Girl—Old Woman’ (Attneave 1971). The cryptic
off-types are generally camouflaged in larger seed production plots. These can only
be removed effectively in maintenance breeding plots, where limited numbers of
panicle rows are being critically observed, as against larger seed production plots
(Figs. 12.16 and 12.17).
12 Maintenance Breeding of Pusa Basmati Varieties 697

Fig. 12.15 Obvious or cryptic. The optical illusion ‘The Young Girl—Old Woman’ (the young
woman’s chin is also the old woman’s nose). (Adapted from Attneave 1971). Cryptic off-type
plants are often camouflaged

Fig. 12.16 Obvious (tall off-type)

698 R. Seth et al.

Fig. 12.17 Cryptic (grain size off-type)

12.5.2 Roguing

Roguing may be defined as the selective removal of undesirable plants from a seed
crop on the basis of visual inspection in the field in order to improve one or more
quality attributes of the seed lot to be harvested. Roguing for genetic purity is an
attempt to maintain the original genetic base of a variety. By defining the limits of
phenotypic variation and removing non-conforming plants, it seeks to achieve
uniformity expected or required. Roguing represents a continuation of the mainte-
nance process in order to restrict variation within an acceptable level, but it is
necessarily imprecise because judgments about genotype (G) are made from the
phenotype, which is the result of genotype and environment (G  E) interaction
(Laverack and Turner 1995). Proper understanding of rice plant morphology and its
descriptive features helps in undertaking effective roguing. DUS guidelines of Rice
gives the descriptors of rice plant (62 characteristics; 29 asterisk characteristics)
(PPV & FRA 2007). These guidelines are very helpful in identifying off-types from
true-to-type plants in maintenance breeding plots as well as for undertaking roguing
operations in large-scale seed production plots (Figs. 12.16 and 12.17).
The point to be understood here is that in maintenance breeding plots (nucleus
seed plots), we never undertake roguing. It is the summary rejection of panicle rows
expressing any sort of variants. Roguing operations are undertaken only in large-
scale seed production plots (breeder, foundation, certified or truthfully labelled
seed).
12 Maintenance Breeding of Pusa Basmati Varieties 699

12.6 Conclusions

Putting together all the disparate components discussed above (maintenance breed-
ing, seed chain, seed production, true-to-type, off-type and roguing), it can be
concluded that varietal development, maintenance breeding and seed production
represent a continuum. For any effective crop varietal development programme,
maintenance breeding plays a pivotal role in its ability to saturate the area under
cultivation with genetically pure seed. Basmati export trade in international markets
is going to have a bigger and wider footprint in the coming years. If this sector is to
be developed, akin to software industry with a potential to generate more than
Rs. 50,000 crores forex in next 3–5 years (Basmati Rice-Life in Science with Pallava
Bagla 2020), then the Basmati rice exports have to be tailor-made to meet
consumers’ preferences. Global Basmati markets are now becoming mature with
very discerning buyers in the EU, North America and the Middle East, where
authentic Basmati rice gets a premium price. Nader et al. (2019) clearly depict the
kind of scrutiny and pedigree checks these markets undertake for authenticity testing
of this premium Basmati grain (Fig. 12.18). Another interesting and insightful
indicator is UK Code of Practice on Basmati Rice (CoP) of 2017, which clearly

Tradional varieties Evolved variees

1. generaon 2. generaon 3. generaon

Pant Basmati 1
Taraori (HBC-19,
Karnal location) Pusa Basmati 1
Pusa 1637

Basmati 386 Punjab Basmati 3 Pusa Basmati

1460
Pusa Basmati 6 Pusa Basmati
Ranbir Basmati (1401) 1728
Type3 (Dehradun)
Haryana Basmati
Pusa Basmati
Mahi Sugandha 1509
Pusa Basmati
Kasturi 1121
Pusa Basmati
1718
Basmati 370 Niab Basmati 2016

Kernel (Pakistani
Basmati) CSR-30 (Yamini)

Punjab Basmati
Basmati 217 (Bauni)

Basmati 198/ D98

Ranbir
Basmati 385

Super Basmati Basmati 2000

Basmati 320
Basmati 515 Shaheen Basmati

Fig. 12.18 EU strict authenticity checks: pedigree of Basmati rice varieties based on information
about their breeding history, which was available in the public domain. (Adapted from Nader et al.
2019)
700 R. Seth et al.

stipulates that when the description of the product is ‘Basmati rice’, the non-Basmati
rice content must not exceed 7%. This tolerance is in place to take account of seed
impurity and other segregation issues at origin (http://www.riceassociation.org.uk/
content/1/47/2017-basmati-code-of-practice.html). This type of rigorous scrutiny of
Basmati rice is an explicit imperative for a very strong varietal maintenance
programme for all the Basmati varieties in seed chain, to keep India’s dominance
in Basmati markets.

Acknowledgements The authors would like to put on record their gratitude to Dr. S. S. Atwal,
Ex-Head, IARI Regional Station, Karnal, and Dr. V. P. Singh, Ex-Principal Scientist, IARI, New
Delhi, for initiating the systematic maintenance breeding work of Basmati rice varieties at IARI
Regional Station, Karnal. This legacy is being continued, with the hope that systematic maintenance
breeding will become a national mandate for all the breeding and seed production units working on
various field and vegetable crops.

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rice. PPV&FR Authority, GOI, New Delhi
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basmati-code-of-practice.html. Assessed 25 Jan 2021
Singh BD (2012) Plant breeding, principles and methods, 9th edn. Kalyani, New Delhi
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Singh BD, Singh AK (2017) Marker assisted plant breeding: principles and practices. Springer,
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Singh AK, Gopala Krishnan S, Nagarajan M et al (2014) Basmati rice variety Pusa basmati 1509.
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(13)60188-2
Maintenance Breeding
13
R. N. Yadav, Priya Ranjan Kumar, Zakir Hussain, Sangita Yadav,
Sandeep K. Lal, Atul Kumar, P. K. Singh, Amit Bera, and Shiv K. Yadav

Abstract

The improved varieties play a pivotal role in agricultural development and

economy of a country. These developed varieties are evaluated in All India
Coordinated Trials prior to identification, release and notification. As per the
provisions of Seed Act (1966), only the notified kinds or varieties are eligible for
multiplication under certified seed production programme. The Indian seed
programme largely adheres to the limited generation system for seed multiplica-
tion. The system recognizes three generations, namely breeder, foundation and
certified seeds, and provides adequate safeguards for quality assurance in the seed
multiplication chain to maintain the purity of the variety as it flows from the
breeder to the farmer. However, one of the major constraints in enhancing crop
productivity is deterioration of varieties when they are multiplied in subsequent
generations. The maintenance of a variety in its original and purest form is
referred to as ‘maintenance breeding’, where a breeder and/or seed technologist
maintains the genetic identity and purity of a released variety, as it undergoes
production year after year. The terms ‘maintenance breeding/varietal mainte-
nance’ and ‘nucleus seed production’ are synonymous. There are different
procedures for variety maintenance and nucleus seed production for various

R. N. Yadav
ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India
P. R. Kumar
ICAR-Indian Agricultural Research Institute, Barhi, Jharkhand, India
Z. Hussain · S. Yadav · S. K. Lal · A. Kumar · P. K. Singh · S. K. Yadav (*)
ICAR-Indian Agricultural Research Institute, New Delhi, India
e-mail: shiv.yadav@icar.gov.in
A. Bera
ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 703
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_13
704 R. N. Yadav et al.

forms of cultivars in different crops. There is paucity of literature pertaining to the

maintenance and multiplication of improved open-pollinated varieties (OPVs)
and hybrids in cross- and often cross-pollinated crops. This chapter provides
appropriate, user-friendly procedures as well as guidelines for maintenance of
inbred lines and varieties or nucleus seed production, which can be helpful for
maintaining varietal uniformity and purity applicable to some of the important
cross- and often cross-pollinated crops like maize, pearl millet, sunflower, castor,
rapeseed and mustard, pigeon pea, sorghum, safflower and cotton.

Keywords
Cross-pollinated crops · Generation system · Inbred lines · Maintenance
breeding · Variety maintenance · Reserve seed method · Plant row method ·
Nucleus seed production · Often cross-pollinated crops · Seed quality

13.1 Introduction

Over the last five decades, India has experienced an impressive growth trajectory,
thus transforming from a food scarce country to a food sufficient and to a food
surplus one. Having experienced a situation of ‘ship to mouth’, India has emerged as
the largest producer of milk, spices, cotton and pulses and the second largest
producer of wheat, rice, fruits and vegetables (DoAHD&F 2019). This became
possible with infusion of new technologies, innovative institutional engineering
and proper incentives. However, as we look forward, these food systems face
many challenges ranging from increasing pressure on natural resources (soils,
water, air, forests, etc.) to climate change, fragmented landholdings, increasing
urbanization and malnutrition among children (Gulati et al. 2021). Hence, India
further needs a right mix of policies from subsidy driven to investment driven, and
from price policy to income policy approach, promoting agricultural production and
diversification towards more nutritious food to mitigate these problems.

13.2 Development of New Varieties

The improved varieties play a critical role in agricultural development of a country.

Hence, the primary objective of crop improvement research is the development of
improved/superior varieties. The mode of reproduction (breeding system) of crop
plants influences the level of genetic variability present in the crop population as well
as the breeding and selection methods suitable for crop improvement. In addition,
the particular type of reproduction behaviour can impose practical limits on the
efficiency of certain breeding and selection procedures. For this reason, breeders
have sought to genetically alter the breeding system of crops. The use of cytoplasmic
male sterility and the modification of self-incompatibility are examples of alterations
that have been affected in breeding systems to produce new methods for crop
13 Maintenance Breeding 705

improvement (Ahmar et al. 2020). In addition, the breeding system must be

manipulated to produce hybrid cultivars to overcome the stagnation in production
potential of varieties. Present-day crop breeding and selection methods are based on
the genetic principles propounded in Mendel’s laws of inheritance (Allard 2010).
The readers are requested to refer to the basic genetics and/or plant breeding and/or
plant biotechnology texts to seek explanation of the terminologies and methods,
since a complete coverage in the context of chapter is not possible.

13.3 Identification, Release and Notification of New Varieties

In order to reduce the dependence on foreign countries and to ensure the food and
nutritional security of burgeoning population, the Indian government established All
India Coordinated Research Projects (AICRPs) and other institutes in a systemic
manner to produce a large number of varieties with assured seed quality in all major
crops. The production of high-quality seeds was one of the pillars to change the
position of Indian agriculture into the new world order. The ultimate intention was to
introduce the newly evolved high-yielding cultivars to the resource-poor farmers for
cultivation in the area of their adoption (Chand et al. 2021b).
In pursuance of these objectives, the Government of India acknowledged seed as
an essential commodity under the Essential Commodities Act, 1955. During October
1964, Varietal Release System (VRS) came into existence with the formation of the
Central Variety Release Committee (CVRC) at the national level and State Variety
Release Committees (SVRCs) at each state level. A Central Seed Committee (CSC)
was established under the then Ministry of Agriculture as per the provisions of the
Seeds Act, 1966. The functions of the CVRC were taken over by the CSC in 1969 to
ensure the notification of the kinds/varieties and regulate the quality of seeds being
offered for sale. Further, the CSC constituted a Central Sub-Committee on Crop
Standards, Notification & Release of Varieties for Agricultural Crops and Horticul-
tural Crops to perform the functions related to release/notification, provisional
notification and de-notification of cultivars at the central level, whereas State Seed
Sub-Committee (SSSC) was constituted to perform similar functions at the state
level (Mohan and Nigam 2013).
In India, new improved varieties of crops are developed by Crop Research
Institutes of Indian Council of Agricultural Research, State Agricultural Universities
and few Private Seed Companies. These varieties are tested (evaluated) for a
minimum period of 3 years, before identification and consideration of release for
cultivation. The official testing of candidate varieties for identification on national or
zonal basis is carried out by the All India Coordinated Research Project (AICRP) of
a given crop. The AICRP conducts the trials under its supervision at experimental
centres of ICAR Research Institutes, State Agricultural Universities and officially
recognized Private Seed Companies (Tonapi et al. 2015a).
After due deliberations, the candidate entry is released for general cultivation, if
found promising. Once a variety is accepted for release, it can be notified in the
gazette. After official release (at state as well as central levels), the cultivars are
706 R. N. Yadav et al.

notified under the Seeds Act so that the quality of seeds can be regulated. The main
purpose of notification is to bring the seeds of a particular crop/variety under the
purview of Seed Law Enforcement, mainly to empower the seed inspectors to verify
the quality of its seeds by sampling and analysis. The notification is made by the
central government on the recommendation of the Central Seed Committee. The
proposals for notification of a state variety are forwarded in the prescribed format by
the state government after its release in a particular state to the Central Seed
Committee for consideration. At this stage, details about All India trials need to be
furnished even for state released varieties. Once notified, a variety can be multiplied
under certified seed production (Chand et al. 2021b).

13.4 Seed Multiplication Chain

The variety comes into seed multiplication chain soon after its gazette notification.
The commercial seed production involves management of complete seed chain
which includes three stages of seed, viz. breeder seed, foundation seed and certified
seed. Nucleus seed, of course, is not an official class of seed in India, but is the
source for production of breeder seed and therefore has highest genetic purity. It is
the end product of the maintenance breeding programme. Breeder seed is produced
from nucleus seed under the supervision of a qualified plant breeder in a research
institute or agricultural university which has developed the variety. This provides for
initial and recurring increase of foundation seed. Breeder seed is monitored by a joint
inspection team of scientists and officials of certification agency and National Seed
Corporation. Breeder seed shall be genetically so pure as to guarantee that in the
subsequent generation, i.e. certified foundation class shall conform to the prescribed
standards of genetic purity. Foundation seed is the progeny of breeder seed and is
produced by National Seed Corporation, State Seed Corporations and SAUs under
technical control of qualified plant breeders or technical officers. Its production is
supervised and approved by state seed certification agency (SCA). The minimum
standards for genetic purity and other quality parameters are available in Indian
Minimum Seed Certification Standards for foundation as well as certified seed
classes. Foundation seed may also be produced from foundation seed which can
be clearly traced to breeder seed. Certified seed is the progeny of foundation seed or
certified seed produced from foundation seed, and its production is also supervised
and approved by certification agency. The seed of this class is normally produced by
the State and National Seeds Corporation and Private Seed Companies on the farms
of progressive growers. This is the commercial seed which is made available to the
farmers (Kumar et al. 2017a).
In India, seed certification standards have been prescribed for foundation seed and
certified seed only. There are two types of standards, i.e. field standards and seed
standards. The field standards apply to the seed production plots and standing crops,
whereas seed standards are applicable at the seed level. Field standards include land
requirements, isolation requirements, maximum permissible level of off-type, insep-
arable other crop plants, pollen shedders (in male sterile line), plants infected by
13 Maintenance Breeding 707

seed-borne diseases, etc. Seed standards include genetic purity, physical purity,
germination, other crop seeds, moisture content, etc. (Tunwar and Singh 1988).
In the generation system of seed multiplication, the production of a particular
class of seed from specific class up to certified seed stage is carried out (Agarwal
2008). The choice of a proper seed multiplication model is the key to further success
of a seed programme which basically depends upon:

(a) The rate of genetic deterioration.

(b) Seed multiplication ratio.
(c) Total seed demand.

13.5 Genetic Deterioration

One of the main constraints in the availability of quality seed is deterioration of the
variety during multiplication over years primarily due to the lack of knowledge of
variety maintenance methodology. There may be several reasons for variety deterio-
ration (Kadam 1942) as listed below:

• Developmental variations.
• Mechanical mixtures.
• Natural crossing.
• Genetic shifts.
• Selected influence of pests and diseases.
• The techniques of the plant breeder.
• Mutations.

The variety deterioration in its physical and physiological traits may also lead to
genetic aberrations. The frequency of chromosomal aberrations induced during seed
ageing gradually increases with the increase in the time of ageing. The factors like
moisture, temperature, relative humidity and activity of insect pests are related to the
retention of seed quality and thus the deterioration of variety in storage. High
temperature, relative humidity and moisture in the storage environment appear to
be the principal factors involved in the deterioration of physiological seed quality
(Dahuja and Yadav 2015).

13.6 Seed Production Models

Seed multiplication ratio (SMR) is the number of seeds to be produced from a single
seed (broadly ratio of seed yield to seed rate). One of the key elements of a seed
production system is estimation of actual demand considering factors like SMR,
weather, market, farmers’ skill to maintain seed and sources of seed. Fair demand
assessment is crucial for actors engaged in the system including government,
producers, importers and distributors. Based on actual demand, seed multiplication
708 R. N. Yadav et al.

models may be derived for each crop, and the seed multiplication agency should
decide how quickly the farmers can be supplied with the seed of novel varieties for
faster variety replacement, subsequent to the supply of breeder seed to the concerned
agency, for faster variety replacement (Kumar et al. 2017a). In view of these basic
factors, the chain of seed multiplication models could be:

(a) Three-generation model—breeder seed-foundation seed-certified seed.

(b) Four-generation model—breeder seed-foundation seed (I)-foundation seed
(II)-certified seed.
(c) Five-generation model—breeder seed-foundation seed (I)-foundation seed (II)-
certified seed (I)-certified seed (II).

13.7 Principles of Maintaining the Genetic Purity During Seed

Production

The important safeguards for maintaining genetic purity during seed multiplication
(Singhal 2003) are:

(a) Control of seed source.

(b) Preceding crop requirement.
(c) Providing adequate isolation to prevent contamination by natural crossing or
mechanical mixtures.
(d) Roguing of seed fields, prior to the stage at which they could contaminate the
seed crop.
(e) Periodic testing of varieties for genetic purity through grow-out test.
(f) Avoiding genetic shift by growing crops in areas of their adaptation only.
(g) Certification of seed crops to maintain genetic purity and quality seed.
(h) Strictly adhering to the generation system.

The above mentioned principles will take care of prevention of factors responsi-
ble for deterioration of a variety. However understanding of characteristics of
specific varieties and their expression in various environments is essential for
breeders and or seed technologists involved in seed production and maintenance
breeding.

13.8 General Principles of Raising Crops for Maintenance

Breeding

Seed production in general and nucleus seed production in particular differ from
commercial crop production in several aspects (Pandita et al. 2017). Some important
principles in the production of quality (nucleus/breeder) seed that are to be taken into
consideration have been discussed below.
13 Maintenance Breeding 709

13.8.1 Land Requirement

The land selected for seed production should be well fertile, levelled and with proper
drainage. It should be completely free from volunteer plants (self-sown plants).
Volunteer plants are a big problem, e.g. in Brassica sp., legumes, sorghum, pearl
millet, etc. The self-sown plants may continue to appear even up to 3–4 years. There
is no problem of volunteer plants in maize and wheat. The volunteer plants may
contaminate directly by producing seed, if not removed. They may also contaminate
through crossing with the main variety, particularly in cross-pollinated crops.
In addition, there should be no weed plants in the field or within isolation distance
which are cross compatible to the seed crop, e.g. Johnson grass in sorghum.
Selection of proper land for seed production is quite helpful in the prevention of
the deterioration of variety through mechanical mixtures and natural outcrossing
with volunteer plants (Agrawal 2015).

13.8.2 Isolation Requirements

The seed production plot should be isolated from various sources of contamination
by a certain minimum distance, known as isolation distance. Isolation from contam-
ination source is much more important for cross-pollinated crops to prevent genetic
contamination through pollen. The contamination source may be volunteer plants in
the field, other varieties in nearby fields or same variety not conforming to genetic
purity and other cross-compatible species (may be crops or weed plants) that need to
be kept at a minimum distance (Tunwar and Singh 1988) as mentioned (Table 13.1).
The figures in the parenthesis are isolation distance from different kernel coloured
plants and teosinte in the case of maize and from Johnson grass and high tillering
forage sorghum with grassy panicle in the case of sorghum. It may be noted that in

Table 13.1 Isolation requirements for different seed crops for certified seed classes
Isolation distance (m) for
Crop Foundation seed Certified seed
Cotton 50 30
Maize (inbreds and foundation single cross) 400 (600) –
Maize (composites, synthetics, OP) 400 200
Maize (hybrids) – 200 (300)
Pearl millet (comp, syn and OP) 400 200
Pearl millet (hybrids) 1000 200
Pigeon pea 200 100
Rapeseed and mustard (self-compatible types) 200 100
Rapeseed and mustard (self-incompatible types) 50 50
Sorghum (OP varieties) 200 (400) 100 (400)
Sorghum (hybrids) 300 (400) 200 (400)
Sunflower 400 200
710 R. N. Yadav et al.

any case the isolation for nucleus seed production/maintenance breeding plot should
not be kept less than the recommended distance for foundation seed production.

13.8.3 Harvesting, Threshing and Processing

Harvesting and threshing of seed crop needs more care as any damage to seed may
lead to loss in germinability. The threshers/combine harvesters should be thoroughly
cleaned to avoid mechanical mixing. The crop should be harvested at proper stage
and moisture content to minimize mechanical damage to seed. In hybrid/MS line
seed production, where two parents are used, harvesting requires special attention.
All the male parent rows should be harvested first and moved away from the field.
The plot is then inspected for the presence of any male parent plants or ears/panicles.
The female parent rows are then harvested as hybrid seed/MS line seed (Benaseer
et al. 2018). After harvesting, proper threshing would be of vital importance to avoid
any physical impurity. Subsequently the seed has to be conditioned that may involve
pre-cleaning, drying and treatment etc. and it should be packed and labeled in the
manner that no mixing happens and the seed maintains highest of its quality in
storage.

13.8.4 Storage

Storage losses of seeds/grains due to insect pests have been recorded throughout the
world. Seed security is the key to attain food security. Before its utilization for
sowing purpose, seeds may require storage for some period depending on a particu-
lar purpose of seed production. Like most biological materials, nucleus seed is also
vulnerable to various factors that can cause the deterioration of seed quality during
storage. Apart from temperature and relative humidity of the storage environment,
infestation of insects or rodents can contribute to loss of seed quality (FAO 2018).

13.9 Maintenance Breeding/Variety Maintenance

At the time of release of a variety, a small quantity of seed is available with the plant
breeder. Commercial quantity of seed is produced after a series of multiplication
steps, and it starts with the maintenance breeding programme in which nucleus seed
is produced. The nucleus seed is used for the initiation of seed multiplication chain
where breeder, foundation and finally certified seed are produced. Maintenance of a
variety is required for continuous supply of quality seed to the farmers in sufficient
quantity. The maintenance breeding programme helps in:

(a) Purification and maintenance of variety and consequent nucleus seed

production.
13 Maintenance Breeding 711

(b) Reduction in the amount of roguing required in large breeder seed production
plots.
(c) Removal of certain specific off-types which can be detected only at nucleus seed
production stage.
(d) Extension of useful life of varieties.

Maintenance breeding is the branch/area of plant breeding which deals with

principles and methods of nucleus seed production and variety maintenance. The
terms maintenance breeding/varietal maintenance and nucleus seed production are
synonymous. Laverack (1994) defined variety maintenance as ‘the perpetuation of a
small stock of parental material through repeated multiplication following a precise
procedure’. The precise procedure refers to plant row method ‘Evaluation of
selected (true to the type) plants on the basis of performance of their progenies’.
Here, performance does not mean yield per se, but trueness to the variety. Plant row
method is suitably modified depending upon growth habit and reproduction
behaviour of the crop.

(a) Self-Pollinated Crops

In most of the self-pollinated crops like chickpea, garden pea, green gram,
soybean, field pea, etc., plant row method as such is used for variety mainte-
nance, where it is easy to take out entire single plants. In the case of tillering and
closely planted crops like wheat, barley rice, etc., single ear/panicle is selected,
and the method is termed ear row or panicle row method. Cowpea plant has a
twining growth habit, so the method is modified to cluster row method (Yadav
et al. 2003), where single cluster is selected instead of single plant. The part of
the plant selected for planting in single rows should have a sufficient number of
seeds to be used for evaluation. The plant row method is described below:
• Single plants (true to the variety) are selected, harvested and threshed
individually.
• Individual plant seed is screened for seed characteristics. Seed lots having
variant seed or seeds are rejected.
• Individual plant seed is planted in single rows (one plant seed-one row).
• Plant rows are critically screened at different growth stages.
• Variant rows or rows with variant plant(s) are discarded as and when
detected.
• Single plants typical of the variety are again selected from the remaining rows
(for the next cycle of maintenance breeding).
• The rows are harvested and threshed individually. The seeds are again
screened for varietal traits.
• Seed packets typical of the variety may be bulked to constitute NSS-I or may
be used for sowing in NSS-II plots, if nucleus seed requirement is high.
(b) Cross-/Often Cross-Pollinated Crops
In often cross-pollinated crops, there is a certain amount of outcrossing
depending upon flower structure and pollination agents. Therefore, the produce
of single plant rows cannot be taken as nucleus seed, as there might be some
712 R. N. Yadav et al.

cross-contamination from adjoining variant rows detected after pollination. So

the plant row method is further modified to reserve/rest seed method where
single plant seed, after screening, is divided into two parts maintaining its
identity. One part is used for evaluation in plant rows, while the other one is
kept in laboratory as reserve seed. The reserve seed packets of the plants which
have true-to-type progeny (as evaluated in plant rows) are bulked to constitute
nucleus seed. This method has been found very effective in purification and
maintenance of pigeon pea and mustard varieties. In highly cross-pollinated
crops, the cultivars are mainly open-pollinated varieties or synthetics or
composites; a certain level of gene frequency for desirable traits is maintained
following the Hardy-Weinberg principle. So, the cultivars are maintained in
isolation with random mating (no selection of single plants). In such crops, some
amount of variation is tolerated as it is a part of the variety. Nowadays, the
majority of cultivars in cross-pollinated crops are hybrids, where maintenance
procedure is applied on parental inbred lines as purity of hybrids is governed by
purity of its constituting inbreds. The inbred lines are maintained by selfing.
Inbred lines showing extreme inbreeding depression may be maintained by
sib-mating or a combination of selfing and sib-mating.

13.9.1 Reserve Seed Method of Variety Maintenance

(a) A large number (300–500) of single plants typical of the variety are selected
from an initial seed crop plot. The number of single plants depends upon the age
of the variety. However, higher numbers of plants are selected in a newly
released variety as compared to an established variety.
(b) These selected single plants are harvested and threshed individually. The
threshed seed is examined critically for colour, shape and size. The seed packets
that are not true representative of the variety are rejected. The selected individual
plant seed is divided into two parts maintaining their identity (the serial number
of the selected plant is written on both of the packets).
(c) In the next season, one part of the seed from selected plants is sown in plant rows
(3–5 m long depending upon the number of seeds) for evaluation. The
remaining seed (rest part) of each plant is stored. It is very important to maintain
the identity of the plant row and the reserve seed (e.g. for a particular plant seed,
the row planted from one part of the seed and the reserve seed stored should be
given the same number).
(d) The individual plant progeny rows are examined critically throughout the
growing season. Any row with one or more off-types is rejected as and when
detected. The rejection is recorded in the notebook also.
(e) At the time of flowering, it should be examined daily or at alternate days to
minimize genetic contamination from off-type plants. All the rejected rows
should be removed as and when detected.
(f) Plant rows true to the variety for morphological characters are retained. These
rows are harvested separately.
13 Maintenance Breeding 713

(g) Seed from individual plant progeny rows is again examined for colour, shape
and size. The seed of plant rows not conforming to the variety is rejected.
(h) Reserved seed (kept in stores) of single plants representing true-to-type
progenies is bulked to constitute the nucleus seed. For the next cycle of variety
maintenance, single plants are selected from crop grown using this reserve seed.

In areas with very low pollinator frequency or covered plots, the single plant progeny
row (used in evaluation) produce may also be used as nucleus seed, but priority
should always be given to reserve seed.
This bulked seed is planted in isolation for further multiplication or breeder seed
production.
The reserve seed method is cumbersome and requires more efforts from the
maintenance breeder. So after two to three cycles of reserve seed method when the
variety gets purified, one may opt for two to three cycles of mass selection. In mass
selection method, the large number of true-to-type plants is selected from the central
part of the field (as border areas of plot have more cross-contamination). After a
thorough screening of the single plants’ seed, the true-to-type plant seed is bulked to
constitute nucleus seed. After two to three cycles of mass selection, there may be a
need for purification, and we may go for variety maintenance through reserve seed
procedure.

13.9.2 Maintenance of Varieties Derived Through Marker-Assisted

Selection (MAS)

The successful adoption of marker-assisted selection (MAS)-derived varieties

depends on the appropriate after-release follow-up, particularly in maintenance
breeding. Unlike other varieties, the maintenance breeding of MAS-derived varieties
involves testing genetic purity of the seeds through gene-based/gene-linked markers
for the homozygosity of the target allele(s) for tolerance or stress resistance. This
follow-up step is very important not only at the nucleus and breeder seed production
levels but also during the certified seed production, for the maintenance of seed
quality (Singh et al. 2019).

13.9.3 Reserve Stocks

It is always desirable to retain a reserve stock to safeguard against loss from crop
failure. These stocks must be stored under cold storage for at least 2 years. Seed
stores should be dry and cool with proper sanitation. The seeds should be dried
to 8–12% moisture content for storage in moisture impermeable; polythene or
poly lined/tin containers and cloth/jute bags, respectively. The recommended
temperatures and relative humidity (Smith 1992) are as follows:
714 R. N. Yadav et al.

1. Short term (Up to one year): 20
C/60% RH.

2. Medium term (One year to 2–3 years): 15
C/40% RH.
3. Long term (<5 years): 5
C/30% RH.

13.9.4 Grow-Out Test

The quality of nucleus seed can be assured by conducting grow-out test. GOT is also
conducted to monitor the genetic purity of the breeder seed lots. A sample of
nucleus/breeder seed lot is drawn and subjected to grow-out test as per the proce-
dure. The GOT for nucleus seed acts as pre-control while that of breeder seed as
post-control plots for genetic purity of breeder seed (Prasad et al. 2017).
Maintenance breeding/nucleus seed production of major cross- and often cross-
pollinated crops has been described in this chapter.

13.10 Maintenance Breeding of Crops

13.10.1 Maize

Maize is a diploid (2n ¼ 20) annual plant belonging to the family Gramineae and the
tribe Maydeae. Unlike other grass species, maize plants are fairly tall with height
ranging from 1.5 to 3 m. Based on endosperm characteristics, maize can be classified
(Kumar et al. 2012) as:

Pop type: small smooth kennels with hard endosperm.

Flint type: large smooth kernels, mainly hard endosperm but often with a small
floury centre.
Floury type: large smooth kernels with floury endosperm.
Dent type: large kernels with a central core of floury endosperm, which on drying
shrinks more than the surrounding hard tissue denting the kernel.
Sweet type: carbohydrates stored largely as sugars, kernels wrinkle and turn trans-
lucent when dry.

13.10.1.1 Floral Biology and Pollination

The knowledge of the reproductive biology of maize enables scientists to carry out
selfing and sibbing—the two main ways of effecting inbreeding in maize. It also
helps in carrying out hybridization by way of crossing desirable parents. The plants
are monoecious where the tassels (male flowers) emerge at the top and the female
flowers (the cobs) are borne in the axils of the lower leaves. The stigmatic surfaces of
the female flowers (called silks) emerge from the leaf axils shortly (after 2–5 days)
after tassel emergence, making the crop protandrous in nature. The seeds are formed
on the cobs, which are compact stalks of female inflorescences. The male inflores-
cence is a loose terminal panicle, which has a central rachis bearing lateral branches
spirally. The spikelets are arranged in rows, and each spikelet has two glumes which
13 Maintenance Breeding 715

are equal in size. Lemma is oval and contains palea. Spikelets are lodiculate and
staminate (bear three stamens). Palea is membranous and flat with intruded margin.
Lodicules are two in number, fleshly and truncated. Pistillate (female) inflorescence
is borne at the end of a short axillary branch called shank. Leaves are reduced to leaf
sheath, which constitutes husk covering the ear. Ear is modified spike and has a thick
central axis called cob, on which numerous paired spikelets are arranged in a series
of longitudinal rows. The ovary is superior; superior style is terminal, long and
filiform. Stigma is bifid; entire style is hairy and receptive. The ovary has one ovule
with basal placentation, fruit is a caryopsis and seed is monocotyledonous with
endosperm.
Within the grass family, maize produces the largest pollen grains
(90–125 μ  85 μ). The pollen volume and weight are approximately
700  109 cc and 250  109 g, respectively. Maize pollen principally travels
through air, but due to its larger size and gravity, the pollen cannot travel long
distances as compared to other members of the Maydeae tribe of Poaceae family.
Pollen remains viable from a few hours to several days. Higher temperature and low
relative humidity adversely affect pollen viability.
Maize is a typically cross-pollinated species because of its monoecious and
protandrous nature. It is an anemophilous crop, where pollination is facilitated by
wind. The degree of male and female floral synchrony is specific and sensitive to
plant population, soil fertility and environmental stress. A tassel sheds pollen for
2–14 days (depending on genotype and environment with major shedding between
5 and 8 days, where pollen is released for approximately 4–5 h, commencing 1 h
after sunrise. This period may be delayed by 1–2 h, if the weather is cool and cloudy.
Each plant, depending upon the genotype, is capable of producing 9000–50,000
pollens per kernel set. Antlers with a minimum overlap result in approximately 5%
self-fertilization. Silks emerge on the ear over a period of time, which grow continu-
ously and are receptive throughout its length. The silks are receptive at emergence
and remain receptive up to 10 days. After fertilization, the silks stop elongation and
desiccate rapidly. If not fertilized, the silk continues to elongate until it is fertilized or
cell elongation is complete (Kumar et al. 2012).

13.10.1.2 Important Diagnostic Characteristics

The characteristics of maize (UPOV 2009) are detailed in Table 13.2 below to help
the seed technologists and breeders to identify true-to-type plants/progeny rows and
eliminate the off-type/undesirable plants/progenies.

13.10.1.3 Maintenance and Nucleus Seed Production of Inbred Lines

Maize is a cross-pollinated crop; however, it is self-compatible; as a result, up to 5%
natural selfing occurs in maize. Practically, it is possible to encourage inbreeding in
maize by pollinating with pollen from same (selfing) or related plants (sibbing).
Inbreeding leads to homozygosity. This is attainted much faster in the case of selfing,
while to a lesser extent by sib-mating. Maize being a cross-pollinated species, it
exhibits inbreeding deficiencies. However, over the past few decades, population
716 R. N. Yadav et al.

Table 13.2 Important diagnostic characteristics of maize

Stages of
Characteristics States observations
Anthocyanin coloration of Absent/weak/strong Seedling
sheath
Anthocyanin coloration of Absent/present Reproductive
brace roots
Width of leaf blade Narrow/medium/broad Vegetative
Angle between main axis and Small/medium/large Reproductive
lateral branches
Number of primacy and lateral Absent/few/many Vegetative/
branches reproductive
Plant height Short/medium/long Vegetative/
reproductive
Time of silk emergence Early/medium/late Silk emergence
Anthocyanin coloration at the Absent/present Reproductive
base of glume
Time of anthesis Very early/early/medium/late/very late Reproductive
Anthocyanin coloration of Absent/present Reproductive
anthers
Density of spikelets Lax/medium/dense Reproductive
Anthocyanin coloration of silk Absent/present Silk emergence
Length of peduncle Short/medium/long Reproductive
Anthocyanin coloration of White/light purple/dark purple Reproductive
glumes of cob
Ear diameter Small/medium/large Reproductive
Ear shape Conical/cylindrical Reproductive
Number of rows of grains Few/medium/many After harvest
Type of grains Flint/semi-flint/semi-dent/pop/waxy/ After harvest
opaque/opaque tinge/sweet
Row arrangement of grains Straight/spiral/irregular After harvest
Grain shape Shrunken/round/indented/pointed After harvest
Grain size Small/medium/bold After harvest

improvement programme, especially recurrent selection, has increased the vigour of

inbred lines to a considerable extent.
Inbred lines are derived through rigorous selfing and/or sib-mating (seven to eight
cycles). They are considerably homozygous. The goal in inbred line maintenance is
to maintain the performance and appearance (physical and genetic purity) of original
lines, which includes proper isolation, rigorous elimination of off-types (roguing),
care in pollination procedures (selfing or sibbing) and using accurate pedigree
records and labels. Inbred line maintenance can be accomplished through self-
pollination, sib-pollination or a combination of these. Selfing helps in maintaining
inbreds in homozygous condition, while sib-mating tends to prevent excessive loss
of vigour. In selfing, representative plants of the inbred lines are self-pollinated, and
those with uniform characteristics with the inbred description are harvested
13 Maintenance Breeding 717

individually. Ears consistent with inbred characteristics are shelled separately. In the
next year, parts of the seeds of individually shelled ears are sown as ear to progeny
rows. Off-type rows are eliminated and rows with characteristics consistent are
selected and self-pollinated. Self-pollinated cobs are harvested individually, and
off-types are rejected. Ears are shelled separately. A portion of seeds is retained
separately, to be used for future progeny testing, and the rest is bulked as
nucleus seed.
Alternatively, out of bulked seeds, inbred line is planted. Off-type plants are
rogued out before flowering. This is followed by sib-mating, which is pollination
between plants within a row. Moreover, both plant-to-plant as well as bulk
sib-pollination are practised. Plant-to-plant sib-pollination is safer.
Inbred lines can also be maintained in isolation, allowing for open pollination
after thorough roguing of off-types. True-to-type plants are retained and involved in
sib-mating. Off-type ears are rejected after harvest. True-to-type cobs are shelled in
bulk. Seeds from best cobs are retained and used as nucleus seed, whereas the rest is
used as breeder seed.
The most convenient way of maintaining inbred lines is to grow them in a big
seed plot in isolation and execute rigorous roguing at four stages of crop growth,
i.e. at knee-high stage, flowering, post-flowering and at harvest. The cobs of all
plants are covered with silk bag before silk emergence. Once the breeder is sure that
all off-type plants are rogued out of the seed plot, the silk bags are removed and open
pollination is allowed to take place. After harvest, selection is made on the basis of
ear and grain characters. One hundred best representative ears constitute breeder’s
seed after bulking the seeds. Out of the selected 100 ears, 50 to 75 seeds are bulked to
make up nucleus seed. The rest of the ears harvested from the seed plot are bulked to
constitute breeder seed. In the whole process, extreme care is taken to rogue out
off-type plants to encourage homogeneity in the material (Singh et al. 2003).

13.10.1.4 Maintenance of Composites/OPVs

Open-pollinated varieties (OPVs) refer to a collection of individuals which share a
common gene pool. Synthetics have been derived through interbreeding of lines
with good general combining ability, while composite varieties are interbred
populations in advanced generation of promising genotypes without any knowledge
of their combining ability. Open-pollinated varieties (OPVs) are easier to develop
than hybrids; their seed production is simpler, relatively inexpensive and is adapted
to the local environment. The subsistence farmers who grow them can save and
exchange own seed for planting in the following season, reducing their dependence
on external sources. OPVs are particularly suitable for tribal and hilly regions, where
seed replacement rate is very low.
In the case of OPVs, care must be taken for actual representation of the variety.
Only off-type plants should be removed to minimize inbreeding depression.
The number of plants to be used to advance generation is dependent on two factors:
the number of plants required to adequately represent the variety and the quantity of
the seed required to meet the future seed requirements. Mild selection during seed
production and multiplication is inevitable; however, it should be minimized.
718 R. N. Yadav et al.

Varietal maintenance is normally done in isolation following half-sib method. Fifty

to 100 seeds are to be bulked from each cob from representative plants of the variety
to form nucleus seed. About 5000–10,000 seeds are normally sufficient to represent
OPVs and provide adequate quantity of nucleus seed (Singh et al. 2003).

13.10.2 Pearl Millet

Pearl millet, commonly known as bulrush millet (Pennisetum glaucum (L.) R. Br.),
also classified as P. typhoides, P. americanum or P. spicatum, is a cultivated, small-
grain, tropical cereal grass. Vernacular names include ‘bajra’ (India), ‘gero’ (Nigeria,
Hausa language), ‘hegni’ (Niger, Djerma language), ‘sanyo’ (Mali), ‘dukhon’
(Sudan, Arabic) and ‘mahangu’ (Namibia). It is a diploid (2n ¼ 2x ¼ 14) with a
large genome (2450 Mbp) (Taylor 2004). Pearl millet is quantitatively the most
important millet, with a world annual production of about 15–25 million tonnes
(Mt). It is cultivated mainly in the semi-arid tropics, almost exclusively by subsis-
tence and small-scale commercial farmers.
India is a major pearl millet-producing country with 43% of world acreage. It is
an indispensable food crop and important source of fodder for drier areas of India
where no other cereals can be cultivated economically. It is the fourth most important
cereal after rice, wheat and sorghum. Five states (Rajasthan, Maharashtra, Gujarat,
Uttar Pradesh and Haryana) account nearly 90% of the total of around 10 m ha
cultivated pearl millet areas in India. Increasing area under cultivation of improved
varieties and hybrids necessitates the production of large quantities of hybrid seed,
which should meet high quality standards. Improved pearl millet varieties and
hybrids are being released by the ICAR institutes and the State Agricultural
Universities. The genetic purity of nucleus and breeder seed is a prerequisite for
maintenance of high standards of seed quality of a variety/hybrid, which can be
maintained only if sound scientific methods of seed production are meticulously
practised for nucleus and breeder seed production (Satyavathi et al. 2021).

13.10.2.1 Floral Biology and Pollination

Pearl millet inflorescence is a compound terminal spike or panicle. It consists of a
central rachis. It bears fascicles on rachillae, arranged in a spiral form. Each fascicle
contains one to two spikelets surrounded by a whorl of bristles (i.e. involucre). A
spikelet consists of two glumes and two florets. The lower is staminate, whereas the
upper is hermaphrodite. The ovary is free and exposed and monocarpellary. The
styles are free or adnate at base and bifid, terminating in brush-like stigmas. There
are three stamens with penicillate and versatile anthers.
Pearl millet is a protogynous species. The styles start protruding 2–3 days after
the emergence of the panicle. The stylar branches protrude first from the florets in the
upper middle region of the panicle and then proceed both upwards and downwards.
In the hermaphrodite flowers, the stigmas emerge faster than the anthers, and hence
stigmas receive pollen from inflorescence of other plants. The time required for
complete stigma emergence varies from 2 to 3 days, depending on the environment
13 Maintenance Breeding 719

conditions. The two stigmas separate and diverge only after complete exertion on the
styles. They remain fresh and receptive for 2–3 days, depending upon the environ-
ment. The sequence of flowering practically excludes self-pollination in the same
inflorescence, but it may occur within the inflorescence of the same plant (Mangat
et al. 1999).
By the time anther emergence commences, all stigmas will have emerged,
been already pollinated, which avoids selfing under open-pollination conditions.
The emergence of the first anther usually begins about 3–4 days after the first stigma
has emerged. The protogyny in pearl millet is exploited for controlled cross-
pollination without resorting to emasculation. The inflorescence to be used as a
female or male is covered with the glassine paper bag before any stigma is visible.
Generally, the safest stage is when about one-third of the inflorescence is out of the
flag leaf sheath. When all stigmas have emerged, the panicle can be considered ready
for cross-pollination. If selfed seed of the male parent is not required, pollen from it
can be collected by bagging even that inflorescence in which stigmas have
completely emerged. Fresh pollen from dehiscing anthers, visible as yellow powder
in the transparent selfing bags, is collected by tapping the bagged inflorescence. The
pollination is carried out by quickly removing the bag from the female inflorescence,
dusting the pollen collected from the male inflorescence and then rebagging the
pollinated inflorescence again.

13.10.2.2 Important Diagnostic Characteristics

To facilitate easy roguing of the off-type plants from a seed plot, knowledge of the
diagnostic characters of a variety is very important. These diagnostic characters
should have high heritability so that their expression does not change under the
varying environments. In pearl millet, characteristics (UPOV 2010) given in
Table 13.3 below are important which should be observed during the crop season
or at the seed level.

13.10.2.3 Nucleus Seed Production

The salient features of the procedure for the maintenance breeding/production of
nucleus seed of OPVs, male sterile line, maintainer line and restorer line in pearl
millet (Bhatnagar et al. 2003) is described below:

Open-Pollinated Variety

Season I
• Basic seed of open-pollinated variety is grown in an area of 0.1–0.2 ha
maintaining a strict isolation of at least 1000 m from any other plot of pearl millet
or wild millet.
• One-third of the commercial plant population should be maintained keeping at
least 3000–5000 plants.
• Carefully observe at critical stages (tillering, pre-flowering, flowering, dough
stage and maturity) and select 500–1000 plants with characters identical/typical
to the released variety.
720 R. N. Yadav et al.

Table 13.3 Important diagnostic characteristics of pearl millet

Stages of
Characteristics States observations
Plant: anthocyanin Absent/present Seedling
coloration of the first leaf emergence
sheath
Plant: growth habit Erect/intermediate Vegetative/
spike
emergence
Plant: time of spike Very early/early/medium/late/very late Spike
emergence emergence
Leaf: sheath pubescence Absent/present Spike
emergence
Plant: node pubescence Absent/present Spike
emergence
Spike: anther colour Yellow/brown/purple Anthesis
Plant: node pigmentation Whitish/green/brown/red/purple Reproductive
Spike: exertion Partial/complete Reproductive
Spike: length Very small/small/medium/long/very long Reproductive
Spike: anthocyanin Absent/present Reproductive
pigmentation of glume
Spike: bristle Absent/present Reproductive
Spike: bristle colour Green/brown/red/purple Reproductive
Spike: shape Cylindrical/conical/spindle/candle/lanceolate/ Reproductive
dumb-bell/club/oblanceolate/globose
Plant: height Very short/short/medium/tall/very tall Reproductive
Spike: density Very loose/loose/semi-compact/compact/very Harvest
compact maturity/lab
Seed: colour Whitish/cream/yellow/grey/deep grey/grey Harvest
brown/yellow brown/purple/purplish black maturity/lab
Seed: shape Obovate/elliptical/hexagonal/globular Harvest
maturity/lab
Seed: size Very low/small/medium/bold/very bold Harvest
maturity/lab

• Harvest and keep seed of each selected plant separately. Evaluate each plant for
seed characters.
• Keep half of the seed of each selected plant progeny as remnant seed.

Season II: Progeny Evaluation

• Plant unreplicated progeny rows along with checkrows (grown from the basic
bulk seed of OPV) after every 15–20 rows.
• Compare progeny rows at critical stages and select 30–50% progenies confirming
to the varietal characters.
• Bulk the remnant seed of selected progenies.
13 Maintenance Breeding 721

Season III: Nucleus Seed Plot

• From the bulked remnant seed, grow nucleus seed nursery in isolation (1000 m).
• The harvested seed is bulked, can be divided into five to six lots and kept under
cold storage.
• One of these lots can be used as base seed for nucleus seed production when
required, and the rest may be used for breeder production in the subsequent years.

13.10.2.4 Nucleus Seed Production of Parental Lines of Hybrids

The nucleus seed production of hybrids essentially involves the seed production of
their parental lines. In the case of pearl millet, especially single cross hybrids are in
vogue; thus, an account of production of nucleus seed of single cross hybrids, i.e. A
line (male sterile), B line (maintainer) and R line (restorer), is given below.

Maintainer Line (‘B’ Line)

Season I
• Grow a large number of plants of B line (0.05 ha).
• Select and self about 1000 plants at the time of flowering.
• Finally, select about 200 selfed plants confirming to the characters of
maintainer line.

Season II
• Grow plant to row progeny of selfed plants in two replications, retaining the
remnant seed.
• The progeny rows are studied for the diagnostic characters, and rows not
confirming to the characteristics of the line are rejected and uprooted.
• Identify the best progeny rows (25–30%).
• Bulk the remnant seed of selected best lines.

MS Line (‘A’ Line)

Season IV
• Grow A and B lines in alternate rows. Seed of B line will be obtained from
rejuvenation as given in the maintenance of B lines.
• Make 200–250 paired crosses between A and B plants.
• Care is taken to cross A and B plants confirming to the line standards only.
• Paired crosses among A and B lines should be labelled, viz. A1  B1, A2  B2,
etc., and harvested seed of each pair should be kept separately.

Season V
• Grow the pairs, respective A line (crossed seed) and B line (selfed seed) in
alternate rows.
• Retain a portion of seed as remnant seed.
722 R. N. Yadav et al.

• Observe critically pairs of A and B lines for all the characters including height,
flowering and typical morphological characters. Off-type and undesirable types
should be rejected.
• Observe for pollen shedders in A line. The A line progenies showing pollen
shedders and corresponding B lines should also be rejected.
• Identify uniform pairs of A and B lines which confirm to the standards of parental
lines.
• Remnant seed of the A lines of the selected pure pairs is bulked. This forms
nucleus seed bulk of A line.

Restorer Line (‘R’ Line)

Season I
• Grow a large number of plants of R line (0.05 ha).
• Self a number of plants (about 1000) confirming to the standards of line at the
time of flowering.
• Finally, select about 200 selfed plants based on field studies as well as
observations in laboratory for seed character like colour, shape, etc.

Season II
• Grow plant to row progeny of selfed plants in two replications.
• Retain a portion of selfed seed of each plant as remnant seed.
• The progeny rows are studied for the diagnostic characteristics of the line.
• Evaluate the rows for yield and agronomic score for other economic characters.
• Identify the best progeny rows (30–50%) based on all characteristics mentioned
above. In the progeny row testing if an adequate number of progeny rows
confirming to the line standards are not obtained, selfing for one or more
generations will be required. These selfed plants of R line should also be tested
for their restoration ability.
• Bulk the remnant seed of best lines.

Season III
• Grow the bulk seed of remnant seed in isolation.
• Bulk the seed of all the plants after the harvest.
• This forms the nucleus seed bulk of R line.

13.10.3 Sunflower

The genus Helianthus (Compositae family) contains 60 annual and perennial species
originating from America. Among them two have been improved for nutritional use,
H. tuberosus L., for its succulent tubers, and H. annuus L., the cultivated sunflower,
the oil from whose seed, and protein-rich oil cakes are utilized. The basic number of
chromosomes is X ¼ 17. Helianthus contains diploid species, the cultivated sun-
flower (H. annuus) with 2n ¼ 2x ¼ 34, tetraploid species (H. hirsutus, H. laevigatus)
13 Maintenance Breeding 723

with 2n ¼ 4x ¼ 68 and hexaploid species (H. resinosus, H. tuberosus) with

2n ¼ 6x ¼ 102. Sunflower is a global oilseed crop of economic importance,
introduced in India in 1970 for commercial cultivation. Poor quality of seed is one
of the important factors responsible for low productivity in India, which necessitates
maintenance of genetic purity of varieties and parental lines of hybrid cultivars
(Jonard and Mezzarobba 1990).

13.10.3.1 Floral Biology and Pollination

The flowering process begins with unfolding of outer ray florets. The outer whorl of
disc flowers opens first proceeding gradually towards the centre of the head. In
general, two to four whorls open daily and complete flowering within a head in
5–8 days. Anthesis takes place in the morning between 06 and 08 AM on warm
sunny days. Anthesis is delayed if weather is cool, cloudy or wet. The sunflower is
protandrous. Pollen is dehisced within the anther tube. As the style elongates and
pushes up through the anther tube, the pollen is mechanically forced out. The style
continues to elongate until the stigmas emerge from the anther tube and the lobes
separate, exposing their pollen receptive surfaces. Pollination and fertilization occur
when the spiny viable pollen is transferred to stigmatic surface. Cross-pollination is
favoured by insects, in particular honeybees (Giriraj and Reddy 2003).

13.10.3.2 Diagnostic Characteristics

Following major characteristics of sunflower (UPOV 2000) as listed in Table 13.4
below should be taken into consideration for identification of true-to-type plants/
rows and elimination of off-types in nucleus/breeder seed plots/fields.

Table 13.4 Important diagnostic characteristics of sunflower

Stages of
Characteristics States observations
Leaf size Very small/small/medium/large/very large Vegetative
Leaf colour Light green/medium green/dark green Vegetative
Leaf blistering Absent/medium/strong Vegetative
Fineness of Fine/medium/coarse Vegetative
serration
Flowering Early/medium/late Start of flowering
Ray flower Ivory/pale yellow/yellow/orange/purple/red brown/ Flowering
colour multi-coloured
Head diameter Small/medium/large Harvest maturity
Head shape Concave/flat/convex/mis-shape Harvest maturity
Plant height Very short/short/medium/tall/very tall Vegetative/
reproductive
Seed length Short/medium/long After harvest
Seed base colour White/grey/brown/black After harvest
Stripes on seed Absent/present After harvest
724 R. N. Yadav et al.

13.10.3.3 Nucleus Seed Production of Open-Pollinated Varieties

Pustovoit method of breeding has been recommended for the maintenance of
commercially grown open-pollinated varieties (Giriraj and Reddy 2003) as detailed
below:

• A total of 5000–8000 individual plants are selected in the base population raised
under isolation. (Selection is based on uniform plant and shape of head.)
• Selected plants are evaluated for seed yield, oil content, test weight and hull
content, and 20–25% of the best plants are advanced for progeny testing.
• A single row of selected progenies is raised, and for every 10–20 progenies, a
check is included which is the best cultivar most similar to the progenies being
evaluated.
• Retain a portion of selfed seed of each plant as remnant seed.
• After harvest of progeny trial, laboratory evaluation is undertaken again for seed
yield, oil content and other agronomic attributes.
• Finally, select 150–200 superior progenies.
• The remnant (reserve) seeds of selected progenies from the original plants are
identified and bulked to form nucleus seed.
• Part of this seed is grown for the next cycle as detailed above, and the other part is
channelled into breeder seed production chain.

13.10.3.4 Nucleus Seed Production of Parental Lines of Hybrids

• Performance of released hybrid cultivar over the years is mainly dependent on the
initial maintenance of genetic purity of parental lines. Maintenance of parental
lines ensures genetic purity in subsequent seed production chain for increasing
seed quality. Parental lines have to be purified under the direct supervision of the
breeder who has developed the hybrid.

A single cross hybrid involves production and maintenance of:

• ‘A’ line or CMS line (male sterile)

• ‘B’ line or maintainer line (male fertile)
• ‘R’ line or restorer line (male fertile).

Maintenance of ‘A’ and ‘B’ Lines

Season I
• Grow ‘A’ and ‘B’ lines obtained from original population or nucleus seed source
in alternate row of 4–5 m length. Raise at least 300 rows in each ‘A’ and ‘B’ line.
• Tag the plants in both ‘A’ and ‘B’ lines considering uniformity for plant height,
flowering and morphological characteristics prescribed for the line.
• Cover (before flowering) the plants tagged in A and B lines and transfer manually
pollen from B line to A line. Label all the capitula of A  B crosses as A1  B1,
A2  B2 . . . A500  B500.
• About 400–500 A  B crosses should be ensured.
13 Maintenance Breeding 725

• Individual selected ‘B’ lines are harvested first and threshed for seed characters in
lab. Undesirable types should be rejected. Seeds of true types should be stored in
separate packets after drying.
• After the harvest of ‘B’ lines, ‘A’ lines are harvested which received pollen from
corresponding ‘B’ line.
• After threshing and drying, the seeds are stored in packets with proper labelling.

Season II
• Grow plant to progeny line of A  B crosses—A line alternated with
corresponding B line.
• Retain a portion of seed as remnant seed for all the A  B crosses and B lines.
• Progeny rows are studied for diagnostic characters. The lines (A and B) which do
not conform to prescribed norms are rejected.
• After flowering, observe individual plants carefully for pollen shedders (male
fertile) in A line. The lines in which pollen shedders are observed should be
rejected. The corresponding B line should also be rejected.
• Identify the best progenies (about 100).
• The remnant (reserve) seeds of selected best progenies from the original plants are
identified (A and B) and bulked separately.
• The bulk seeds of ‘A’ and corresponding bulk seed of ‘B’ line form the
nucleus seed.

13.10.4 Rapeseed and Mustard

Rapeseed-mustard is a unique group of crops having different kinds of breeding

behaviour. Some of them are self-compatible (self-pollinated) crops like yellow
sarson (Brassica rapa var. yellow sarson), gobhi sarson (Brassica napus) and
Ethiopian mustard (Brassica carinata), while others are self-incompatible (cross-
pollinated) crops including toria (Brassica rapa var. toria), brown sarson (Brassica
rapa var. brown sarson) and taramira (Eruca sativa). In Indian mustard (B. juncea),
the major crop of the group, cross-pollination ranges from 5% to 15%. Brassica spp.,
commonly known as rapeseed-mustard, plays a significant role in the Indian econ-
omy by providing edible oils, vegetables, condiments and animal feed. Globally,
India holds the second and third position in rapeseed-mustard area under cultivation
and production, respectively. However, anthropogenically accelerated climate
change thwarts yield potential of rapeseed-mustard by employing abiotic (drought,
flood, temperature variation and salinity) and biotic (disease and insects) stresses
(Chauhan et al. 2011).
Historically, the cultivation of Brassica spp. has been quoted in numerous ancient
scriptures and believed to be cultivated on or prior to 5000 BC. It has also been
reported that mustard crop was in cultivation around Channhu-daro of Harrapan
ancient civilization during 2300–1750 BC. There is ambiguity in the history as the
origin of B. juncea is concerned. It had been believed that the centre of origin for
B. juncea is the Middle East, where putative parents, i.e. B. nigra and B. rapa, would
726 R. N. Yadav et al.

Table 13.5 The common names, types of pollination, chromosome number, genome and size of
different Brassica spp.
Genome
Common Type of Chromosome size
Species name pollination no. (2n) Genome (Mb)
B. juncea (L.) Indian mustard Often-self 36 AABB ~922
Czern.
B. carinata Karan rai or Often-self 34 BBCC –
A. Braun Ethiopian
mustard
B. napus L. Gobhi sarson Self and cross 38 AACC ~1130
B. nigra (L.) Black mustard Cross 16 BB ~558
Koch
B. oleracea L. Cabbage, Cross 18 CC ~630
cauliflower,
etc.
B. rapa L. var. brown Lotni type: 20 AA ~485
sarson crossTora type:
self
var. toria Cross
var. yellow Self
sarson
Eruca sativa Taramira Self 22 EE –
B. alba Rab. White mustard Self 24 SS –
(syn. Sinapis
alba)

have crossed with each other. Later on, it had been disseminated to other parts of the
world such as Europe, Asia and Africa. Today, there are two centres of diversity, i.e.
China and Eastern India, based on the prevalence of their wild progenitors and
relatives. At present, it has been proved that there are two geographical races,
i.e. Chinese and Indian, of B. juncea based on molecular and biochemical studies.
In 1935, Nagaharu U proposed a theory known as U’s triangle to show genetic
relationships based on artificial interspecific hybridization experiments among six
species, namely B. rapa, B. nigra, B. oleracea, B. carinata, B. napus and B. juncea.
As per theory, three allotetrapolyploid species (B. napus, B. juncea and B. carinata)
were derived by natural hybridization of three basic diploid species (B. rapa,
B. nigra and B. oleracea), followed by genome doubling (Chand et al. 2021a).
Nowadays, with the accomplishments of genome sequencing of Brassica taxa, this
hypothesis has been increasingly accepted. Furthermore, it has been scientifically
proved that allotetraploid B. napus and B. juncea had been derived from their diploid
parents based on comparative genomic analysis, and the results were in accordance
with ‘U’ triangle (Nagaharu 1935) (Table 13.5).
13 Maintenance Breeding 727

13.10.4.1 Floral Biology and Pollination

The mustard inflorescence is an aggregate of yellow florets at the apex of the raceme
that give a field a deep golden appearance when fully open. The structure of the
flower, as given under ‘Cole Crops’, applies equally to the mustard flower. The two
outer nectarines may be somewhat functional or inactive. Mustard is an excellent
source of nectar and pollen for honeybees. The floret opens between 9 a.m. and noon
and remains open for 3 days. Usually, the stigma projects about 2 mm beyond the
petals the afternoon preceding opening of the flower and is immediately receptive.
Soon afterwards, however, the corolla begins to grow and re-engulfs the stigma.
Thereafter, the stamens lengthen so that the anthers are in level with the stigma, but
when the corolla opens, they turn half around. At this period, nectar secretion by the
inner nectaries begins. Just before the flower closes, the anthers turn to their former
position, and if any degree of self-fertility exists, selfing can result (Yadava and
Singh 2003).
The position of the anthers in relation to the nectaries and stigma makes cross-
fertilization likely but by no means inevitable on the visit of pollinating insects. The
flower is so constructed that pollen from another flower is likely to be transported to
it before its own pollen comes in contact with the stigma. Mustard is basically an
insect-pollinated type of crop, with ample pollen and nectar to attract pollinating
insects. Some of the self-pollen may contact the stigma without the aid of insects, but
this contact can be abetted by the bees’ visit to the flower. The compatibility varies
with species, cultivar and even the age of the plant. Yellow mustard (B. hirta) is a
cross-pollinated crop, while B. juncea is self-fertile but can be abetted by wind
and/or bees. Bees can help achieve more than double seed production, e.g. in B. alba.
The flowers are highly attractive to bees for both nectar and pollen, so there is no
problem in getting visitation if sufficient bees are in the area and the weather permits
floral visitation. Rapeseed-mustard is adversely affected by heat stress (35/15
C) at
the early stage of flowering. Drought can adversely affect plant growth at various
stages from seed germination to reproduction and flowering to harvesting and
ultimately results into oil and yield penalty.

13.10.4.2 Important Diagnostic Characteristics

Oilseed brassicas have a lengthy taproot system. Leaves are dark green, serrated,
pinnatifid and either sessile (rapeseed) or petiolate (mustard). In B. rapa, syn.
campestris, the upper leaves are auriculate and clasp the stem closely. In B. napus,
only the lower leaves are partially clasping, whereas in B. juncea they are petiolate.
The inflorescence is elongate raceme, borne terminally on the main stem as well as
on the branches carrying bright yellow flowers (colour may vary from dark to cream
yellow). The fruit is a long narrow pod or siliqua, usually consisting of two carpels
separated by a false septum, which shatters after maturity and is a varietal character
detrimental to an oilseed strain. They produce dark brown (black), light brown or
yellow coloured seeds. The important characteristics of rapeseed and mustard
(UPOV 2013) which may help the seed technologists and breeders to identify
true-to-type plants/rows and to eliminate off-type plants during maintenance breed-
ing/seed production are given in Table 13.6 below.
728 R. N. Yadav et al.

Table 13.6 Important diagnostic characteristics of rapeseed and mustard

Stages of
Characteristics States observations
Leaf shape Serrated/non-serrated Vegetative
Leaf type Sessile/petiolate Vegetative
Leaf colour Light green/medium green/dark green/purple Vegetative
green/purple
Leaf hairiness Present/absent Vegetative
Calyx colour Green/light green Vegetative
Corolla colour Dark yellow/yellow/cream yellow/white Flowering
Petal shape Narrow/broad Flowering
Plant type Erect/semi-erect/spreading Vegetative/
reproductive
Plant height Dwarf/medium/tall Vegetative/
reproductive
Main shoot Short/medium/long Vegetative/
length reproductive
Siliqua Appressed/semi-appressed/spread Maturity
arrangement
Siliqua surface Smooth/intermediate/constricted Maturity
Siliqua beak Short stout/long slender Maturity
Seeds/siliqua Less/average/more Maturity
Pod locule Unilocular/bilocular/trilocular/tetralocular Maturity
Seed colour Yellow/dull grey/reddish brown/brown/black Maturity/post-
harvest
Seed size Small/medium/bold Post-harvest
Oil content Low/medium/high/very high Post-harvest

13.10.4.3 Nucleus Seed Production of Open-Pollinated Varieties

The procedure of nucleus/breeder seed production varies from crop to crop
according to their breeding behaviour. The field should be selected where no
Brassica species had been grown for the last 3 years, unless the crop was raised
for nucleus seed production of the same variety. Field should be properly isolated
from the other field of any Brassica species. An isolation distance of 200 m is
recommended for production of nucleus and breeder seed of self-incompatible
(cross-pollinated) crops, including B. rapa var. toria, B. rapa var. brown sarson
and E. sativa (taramira), and self-compatible (self-pollinated) crops, including
B. juncea (Indian mustard), B. rapa var. yellow sarson and B. carinata (Karan
rai). For maintenance of varieties in mustard, typical reserve seed method
(as outlined above) is followed. As the procedure is somewhat cumbersome, we
may also go for plant row method in self-compatible group, if the frequency of
pollinators is negligible (Yadava and Singh 2003).
13 Maintenance Breeding 729

13.10.4.4 Nucleus and Breeder Seed Production of Parental Lines

Hybrids developed in rapeseed-mustard are based upon the cytoplasmic-genetic
male sterility (CMS) system. Parental lines are multiplied in different plots. The
seed parent (A line) is maintained by growing the rows of A and B lines in a specific
ratio. Normally, a 3:1 ratio of seed parent (A line) and maintainer (B line) is
followed. The maintainer rows (B line) are harvested first. Later on, the remaining
rows of seed (A line) parent are harvested and bulked. Strict roguing is advised
during flowering to rogue out the fertile plants from seed parent. The seed production
of B and R lines is similar to any other varietal seed production. The commercial F1
hybrid seed is produced by growing seed parent (A line) and restorer (R line) in a 3:1
ratio as followed in the case of maintenance of seed parent. The rows of restorer
parent (R lines) are harvested first and bulked, followed by harvesting of seed parent.
The seed from the seed parent is processed and packed as hybrid seed. Honeybees
play an important role in enhancing the transfer of pollen; hence, 3–4 honeybee
boxes/ha may be kept to ensure proper pollination and good seed set (Yadava and
Singh 2003).

13.10.5 Pigeon Pea

The name pigeon pea was first used in Barbados during 1692 where pigeons were
fed with the seeds of Cajanus cajan. Wide genetic variability exists in India,
therefore it is considered as the centre of origin for cultivated pigeon pea. This
crop is also been widely cultivated in many African countries, Egypt, and a bunch of
Asian countries since prehistoric times. Eastern Africa was considered as centre of
origin of pigeon pea by several workers owing to its occurrence in wild form. Based
on the occurrence of wild relatives and diversity, it was inferred that India is the
primary centre of origin and Africa is the secondary centre of origin for pigeon pea
(Kumar et al. 2017b).
Pigeon pea (Cajanus cajan (L.) Millspaugh) is the second most important pulse
crop in India, next to chickpea, covering an area of 4.42 m hectares. Bestowed with
several unique characters, it finds an important place in the cropping systems being
adopted by the farmers. The highest production of pigeon pea is from Maharashtra
which is around 30% of national production. More than 90% of production contri-
bution of Tur is from 8 states, namely Maharashtra, Karnataka, Madhya Pradesh,
Uttar Pradesh, Gujarat, Jharkhand, Telangana and Andhra Pradesh. The existing
productivity of pigeon pea (806 kg/ha) can be doubled with the adoption of
improved production technology. Seed is a basic input, and unless pure seed is
used, the application of other inputs such as fertilizers, irrigation and plant protection
measures becomes less effective. However, non-availability of quality seed remains
a major constraint in meeting the targeted increase. The genetic identity of a pigeon
pea variety/hybrid can be maintained in foundation and certified seed stages if sound
scientific methods are meticulously practised at nucleus and breeder seed stage.
730 R. N. Yadav et al.

13.10.5.1 Floral Biology and Pollination

Pigeon pea is an important legume crop of the Papilionaceae family. It is an often
cross-pollinated crop, and breeding principles of both self- and cross-pollinated
crops are highly effective in its genetic enhancement. Pigeon pea is a hard woody
shrub, extensively adaptable to a range of soil types, temperature and rainfall. It has a
deep taproot system extending up to 2 m and can grow to a height of 4 m. Pigeon pea
roots form a symbiotic association with Bradyrhizobium spp. and perform biological
nitrogen fixation. The branching pattern of stem may vary from bush type to compact
upright type and is of determinate, semi-determinate and non-determinate types
based on the flowering pattern. The primary leaves are simple, opposite and cadu-
ceus, while the latter ones are pinnately trifoliate with lanceolate to elliptical leaflets.
Pigeon pea flower is bisexual and zygomorphic, borne on terminal or auxiliary
racemes and is normally yellow in colour with some variations. Stamens are 10 in
number and diadelphous (9 + 1) with light or dark yellow anthers. The ovary is
superior with a long style attached to a thickened, incurved and swollen stigma. The
male and female parts of the flower are covered by corolla which consists of standard
petal, wing petal and keel petal. Anthers are dorsifixed and light or dark yellow in
colour. The ovary is superior, subsessile densely pubescent with two to nine ovules.
The stigma is capitate and style is long filiform and glabrous. The floral structure of
pigeon pea was initially adapted to self-pollination, which changed over time to
partial outbreeding. In 90% flowers, pollination takes place before the opening of the
flower (Singh et al. 2016).
Pigeon pea is an often cross-pollinated crop with a range of 3–40% cross-
pollination. In a fully developed bud, anthers surround the stigma and dehisce a
day before the flower opens. The duration of flower opening varies according to
climate and the environment. Anthesis in pigeon pea starts from 06.00 AM and
continues till 04.00 PM. Maximum anthesis takes place between 10:30 a.m. and 12:
30 p.m. Flowers that open in the evening usually remain open throughout the night
and are closed before noon on the following day. The receptivity of stigmas starts
68 h before anthesis and continues for 20 h after anthesis. The duration of flower
opening also depends on the weather and the environment. This varies from 6 to
36 h. Fertilization occurs on the day of pollination. The fruit of pigeon pea is called
pod, which is of various colours, with and without deep constrictions. Seeds (with
20–22% proteins and amino acids) can be round or lens shaped, in shades of white
and brown colour with yellow colour cotyledon. Pigeon pea is a widely consumed
multi-utility pulse crop; thus, the knowledge about the crop botany is vital for
modifying it according to future challenges and goals.

13.10.5.2 Important Diagnostic Characteristics

For identification and production of true-to-type seed, some of the important mor-
phological characters of pigeon pea (PPV&FRA 2007) to help the seed technologists
and breeders have been listed below (Table 13.7).
13 Maintenance Breeding 731

Table 13.7 Important diagnostic characteristics of pigeon pea

Stages of
Characteristics States observations
Plant type Compact/semi-spreading Vegetative
Growth habit Determinate/indeterminate/semi-determinate Flowering
Pigmentation on Green/purple Vegetative
stem
Leaf shape Oblong/obovate/sesamum Flowering
Days to flowering Early/medium/late Start of
flowering
Colour of the base Light yellow/yellow/orange yellow/purple/red Flowering
of petal
Pattern of streaks Absent/sparse/medium/dense Flowering
Pod colour Green/green with brown streaks/green with purple Premature pods
streak/purple/dark purple
Pod pubescence Absent/present Full podding
Seed colour Cream/brown/dark brown/grey/purple Maturity
Seed shape Oval (egg shape)/globular (pea shape)/(angular)/ Maturity
elongate
Seed size Small/medium/large/extra large Ripe seeds

13.10.5.3 Nucleus Seed Production of Varieties and Male Parents

Variety maintenance and nucleus seed production in varieties and fertile inbred lines
(B and R lines) are done following reserve seed method (as described above). We
may use produce of individual plant progeny rows (as grown for evaluation purpose)
as nucleus seed where insect/pollinator’s activity is very low. During nucleus seed
production, it is very important to provide sufficient isolation distance and avoid
volunteer plants by selection of seed plot (Dhar et al. 2003).

13.10.5.4 Nucleus Seed Production of Female Parent

Nucleus seed production of genetic male sterile (GMS) line constitutes an important
part of seed production and determines the purity and quality of seed in the
subsequent years of seed production. The important precautions are:

• Use the original seed of the genetic male sterile or female parent available with
the breeder to produce nucleus seed.
• For nucleus seed production of genetic male sterile lines, pair-wise selection of
male sterile and male fertile plants with characteristics similar to each other and to
the original genetic male sterile line is carried out for crossing of male sterile plant
with the fertile one for maintenance.
• The crossing is carried out manually under caged conditions to avoid any chance
of pollination with alien pollen. At least 50 such pair-wise crosses of male sterile
and fertile plants having similar characteristics are made under caged conditions
in the original genetic male sterile line.
732 R. N. Yadav et al.

• Harvest the seeds from male sterile plant of each pair separately and raise plant
progeny rows along with the original genetic male sterile line after every ten
progenies as a check.
• This enables the evaluation of progenies for different morphological
characteristics and determination of segregation ratio of male sterile and fertile
plants.
• Cover the uniform individual progenies exhibiting similarity for different traits
with the check and segregating for 1 MS: 1 MF plants with the nylon net cages
separately at flower initiation stage and maintain them by crossing of male sterile
plants with fertile sib counterparts by hand pollination.
• Harvest and thresh the male sterile plants of all the selected progeny rows
separately for screening with respect to seed yield and seed characteristics.
• Bulk the seeds of the progenies exhibiting similarity with the check and giving
higher seed yield than the check to form the nucleus seed. The progenies with
off-type plants are discarded at flowering stage itself.
• The selection of progenies of genetic male sterile lines for nucleus seed produc-
tion should be very strict and hence bulk the seed uniform from only genetically
pure lines to maintain originality in the subsequent generations.

The present-day pigeon pea hybrids are developed using a CMS system. Seed
production of parental lines in the CMS system is much easier than the GMS system
(Dhar et al. 2003).

13.10.6 Sorghum

Sorghum (Sorghum bicolor (L.) Moench) is grown worldwide for food, feed, fodder,
fuel and industrial products. Cytogenetically, sorghum is a diploid of 2n ¼ 2x ¼ 20,
where 2n is the somatic chromosome number having two complete sets (2x) of
chromosomes and a chromosome number of 20. It has a haploid chromosome
number of 10, containing approximately 800 Mb with 34,000 protein-coding
genes. The genome contains a high level of repeats (61%). In India, sorghum is
the most important cereal crop for poor people in the semi-arid zones. The sorghum
hybrids were developed and released in India, which resulted in quantum jump in
productivity from 570 kg/ha in 1970 to >1000 kg/ha in recent times. However, it is
still the lowest among the major sorghum-producing countries in the world, though
the world average is 1435 kg per hectare. The purity of commercial seed depends on
the genetic purity of parental lines in nucleus, breeder and foundation seeds. Hence,
the quality of maintenance breeding is the prerequisite to ensure high genetic purity
in multiplication chain during seed production programme (Reddy et al. 2006).

13.10.6.1 Floral Biology and Pollination

In sorghum, the panicle may be short and compact or loose and open. It may be
4–25 cm or more in length and 2–20 cm or more in width. The inflorescence is a
raceme, which always consists of one or several spikelets. Racemes vary in length
13 Maintenance Breeding 733

depending upon the number of nodes and length of internodes. The sessile spikelet
varies in shape from lanceolate to almost round and ovate and is sometimes
depressed in the middle. The lower glume is usually somewhat flattened and
conforms more or less to the shape of the spikelet, while the upper one is more
convex or boat shaped. The seed may be enclosed by the glume or may protrude
from the glume. The seed may be just visible or almost completely exposed. In
sessile spikelets, there are two lemmas, two lodicules and a palea. The pedicelled
spikelets are much narrower than the sessile spikelets, usually lanceolate in shape.
They are male or neutral in sex, but may rarely have a rudimentary ovary. The
lemmas are much reduced in size and only rarely does the upper lemma have an awn.
Sorghum has two pistils and three stamens. Each fluffy stigma is attached to a short
stout style extending to the ovary. The anthers are attached to long thread-like
filaments.
The floral initial forms 30–40 days after germination (but may range from 19 to
70 days or more). Floral initiation marks the end of the vegetative growth due to
meristematic activity. Sorghum usually flowers in 55–70 days in warm climates, but
it could be as early as 30 days or as late as 100 days or more. The flowering (anthesis)
in a panicle starts from the top, and it travels to successively lower whorls. Flowering
is completed over a period of 4–5 days (6–8 days under cooler conditions). Pollen is
usually available for a period of 10–15 days because the heads in a field do not
flower at the same time. Sorghum is predominantly a self-fertilized crop, but the
cross-pollination may occur to the range of 2–10%. At flowering, the glumes open
and the three anthers fall free, while the two stigmas protrude, each on a stiff style.
Flowering occurs just before or just after sunrise, but may be delayed on cloudy
damp mornings. The anthers dehisce when they are dry. For selfing, the panicle is
merely covered with a paper bag. Pollen is shed freely and can always be collected in
bags enclosing the spikes. When crossing is made before 10 AM, it generally set the
maximum amount of seed per inch of head (Tonapi et al. 2015b).

13.10.6.2 Important Diagnostic Characteristics

The characteristics of sorghum (UPOV 2015) are given in Table 13.8 below to help
the seed technologists and breeders to identify the true-to-type plants and to rogue
out the off-types or undesirable plants.

13.10.6.3 Maintenance Breeding

The maintenance breeding of sorghum (Babu and Seetharama 2003) involves the
purification of:

• Cytoplasmic male sterile line (A line).

• Maintainer line (B line).
• Restorer line (R line).
• Open-pollinated variety.
734 R. N. Yadav et al.

Table 13.8 Important diagnostic characteristics of sorghum

Stages of
Characteristics States observations
Plant height Tall/medium/dwarf Vegetative
Plant colour Pigmented (grey brown groups)/tan (yellowish) Vegetative
Juiciness Juicy/corky Vegetative
Leaf Erect/semi-erect/droopy Vegetative
Leaf midrib White/dull green/yellow/brown/purple Vegetative
colour
Leaf colour Dark green/green/light green Vegetative
Stem Thin/medium/thick Vegetative
thickness
Days to Early/medium/late Reproductive
flowering
Panicle Very lax/very loose with erect primary branches/very Reproductive
compactness and shape loose drooping primary branches/
loose erect primary branches/loose drooping primary
branches/semi-loose erect primary branches/semi-loose
drooping primary branches/semi-compact elliptical/compact
elliptical/compact oval/half broom corn/broom corn
Glume colour White/straw/brown/light red/red/yellow/purple/black Maturity
Seed covering 25% grain covered/50% grain covered/75% grain covered/ Maturity
grain fully covered/glumes longer than grain
Awns Awned/awnless Maturity
Days to Early/medium/late Maturity
maturity
Shattering Low/medium/high Maturity
Seed colour White/pale yellow/yellow/orange Maturity
Seed lustre Lustrous/medium/non-lustrous Maturity
Seed sub-coat Present/absent Maturity
Seed Dimple/plump Maturity
plumpness
Seed form Single/twin Maturity
Endosperm Completely corneous/mostly corneous/intermediate/starchy Maturity
texture
Endosperm White/yellow Maturity
colour
Endosperm Normal/waxy/sugary Maturity
type

13.10.6.4 Nucleus Seed Production of ‘A’ and ‘B’ Lines

Seed quality with all its ramifications must be cardinal virtue in the seed chain. The
purity of commercial seed depends on the genetic purity of parental lines in nucleus,
breeder and foundation seeds. The success of hybrid depends on the maintenance of
genetic purity of parental lines, which is essential to obtain high yields in farmer’s
fields.
13 Maintenance Breeding 735

Season I
Select the individual plants of A and B lines from good quality breeder seed or plots
grown with the breeder in large areas (0.5–1.0 acre) based on distinguishing mor-
phological traits for characterizing the genotypes that are not influenced by the
environment.

• Raise 200–300 rows (each 5 m length) from each A and B line obtained from
above seed source.
• Examine the panicle morphological traits especially those which are not
influenced by genotype  environment interactions, such as compactness from
top to bottom and secondary branch distribution, number of whorls, shape of
apex, panicle branch distribution at the bottom, middle and apex, glume
characteristics (shape, size and colour) and awn characteristics, etc.
• Tag the individual A and B lines which are true-to-type plants. Self the individual
tagged plants in B lines and mark the paired crosses between A and B plants
during flowering. The ear head of B lines and A  B crosses should be labelled
properly such as A1  B1, A2  B2,. . . A200  B200. Harvest the individual plants
as per labelling. The A lines should be harvested after B lines. After proper
threshing and drying, store the properly labelled packets.
• Carefully examine the seed of each plant on the table for uniformity in colour,
shape and size of seed. Discard the seed of ear head appearing deviant from
original true-to-type seed characters.

Season II
• Raise plant to progeny rows such as B line and A  B crosses form the selected
200–300 plants. Retain some portion of seed as remnant seed for all the B line
plants and A  B crosses.
• Observe the individual plants in progeny rows for diagnostic characters. Uproot
the rows not confirming to the characteristics of the line. The A lines showing
pollen shedders and the corresponding B lines should also be rejected.
• Examine the seed characters in laboratory as per the descriptors of parental line.
Discard the seed of progeny row in the case of doubtful deviants, if any.
• Identify the best progenies (about 50) of A and B lines which confirm to the
standards of the parental lines. The remnant seeds of selected best progenies from
the original A and B plants are identified and bulked separately, which forms the
nucleus seed.

13.10.6.5 Nucleus Seed Production of ‘R’ Line

Season I
• Grow a large number of plants of R line.
• Self about 1000 plants conforming to the standards of the line at the time of
flowering.
• After harvest, rejection may be done based on seed colour, shape, size, etc.
736 R. N. Yadav et al.

• Finally, select about 200 plants based on field observations as well as

observations in the laboratory.

Season II
• Grow plant to row progeny of the selected plants in the two replications. Retain a
portion of selfed seed as remnant seeds.
• The progeny rows are studied for the diagnostic characters. The lines not
confirming to the characters of the parental line should be rejected. If an adequate
number of progeny rows confirming to the lines are not found, selfing for one
more generation will be required. It is desirable to test selfed plants of R lines for
their restoration ability.
• Evaluate lines for economic traits and disease resistance characters.
• Identify the best progeny rows (about 50) based on all the diagnostic descriptors
of R line.

Season III
• Grow the bulk seed of remnant seeds in isolation.
• Ensure adequate pollination during flowering.
• Bulk the seed of all the plants after the harvest.
• This forms the nucleus seed of R line.

13.10.6.6 Nucleus Seed Production of Varieties

Season I
• Grow a large number of plants of a variety.
• Self about 500 confirming to the standards of the cultivar at the time of flowering.
Finally, select about 200 plants based on field observations.
• After the harvest, rejection may be done based on laboratory examination for seed
colour, shape, size, etc.

Season II
• Grow head to row (5 m length) progeny of the selected plants in two replications.
Retain a portion of selfed seed as remnant seeds.
• The progeny rows are studied for the diagnostic characters. The lines not
confirming to the characters of the variety are rejected. Variation of plants may
be with regard to plant height, leaf traits, flowering and maturity period, insect
pests and disease reactions and panicle types. If an adequate number of progeny
rows confirming to the lines are not found, selfing for one more generation will be
required.
• Evaluate lines for economic and disease resistance traits.
• Identify the best progeny rows (about 50) based on all the diagnostic descriptors
of the variety.
• These rows should be harvested separately with labels, and the seed of individual
ear to rows should be cleaned and table examined. The deviants should be
discarded, if any.
13 Maintenance Breeding 737

Season III
• Grow the bulk seed of remnant seeds in isolation.
• Ensure adequate pollination during flowering.
• Bulk the seed of all the plants after the harvest.
• This forms the nucleus seed of a variety.

13.10.7 Cotton

The genus Gossypium includes ~45 diploid (2n ¼ 2x ¼ 26) and five tetraploid
(2n ¼ 4x ¼ 52) species. Diploid species fall into eight genomic groups (A–G and K)
(Percival et al. 1999). The African clade (A, B, E and F genomes) occurs naturally in
Africa and Asia, while the D-genome clade is indigenous to the Americas. A third
diploid clade (C, G and K genomes) is found in Australia. Allotetraploids arose in
the New World from interspecific hybridization between an A-genome-like African
species and a D-genome-like American species, which occurred 1–2 million years
ago. The closest relatives of the original tetraploid progenitors are the A-genome
species Gossypium herbaceum L. (A1) and Gossypium arboreum L. (A2) and the
D-genome species Gossypium raimondii (D5) Ulbrich. Two of five allotetraploid
species, Gossypium hirsutum L. and Gossypium barbadense L., are domesticated
and cultivated. Interestingly, the A-genome species produce spinnable fibre and are
cultivated on a limited scale, whereas the D-genome fibre is rudimentary and not
useful (Applequist et al. 2001). The fibre in allotetraploids is much longer and
stronger, suggesting activation or silencing of homoeologous fibre-related genes
by genetic and epigenetic mechanisms, leading to hybrid vigour. Most production
(>97%) in the USA is upland cotton (G. hirsutum L., AD1), and the remainder is
Pima cotton (G. barbadense L, AD2) with extra-long fibre that is sought after for
high-quality textiles. Cotton is one of the most important commercial crops of India.
Even though India ranks first in the world in respect of total cotton area, it ranks only
third in respect of production, next to China and the USA.
India is unique where all the four cultivated species of cotton, viz. Gossypium
hirsutum, G. barbadense, G. arboreum and G. herbaceum, are grown commercially.
During 2020–2021, the production of cotton was 371.0 lakh bales cultivated under
an area of 129.57 lakh hectares with a productivity of 487 kg per hectare as per the
estimates of Cotton Corporation of India. Nearly 65% of the cotton crop is cultivated
under rainfed conditions in the country. Seed plays a major role as a basic input to
cotton productivity and sustained production. Studies indicated that the use of good
quality seeds alone could increase production by up to 20%. Good seeds enable the
farmers to maintain uniform and vigorous stand of crop, which serve as a catalyst to
make other inputs productive and cost-effective.

13.10.7.1 Floral Biology and Pollination

Cotton flowers are extra-axillary, terminal and solitary and are borne on the sympo-
dial branches. The flower is subtended by an involucre of usually three unequal leaf-
like bracts. Bracteoles, alternating with the bracts on the inside of the involucre or
738 R. N. Yadav et al.

standing on either side of the small bract, may be present. The calyx, consisting of
five undiverged sepals, is persistent and shaped as a shallow cup. The calyx adheres
tightly to the base of the boll as it develops (Manickam and Prakash 2016).
The corolla is tubular, consisting of five obcordate petals alternating with calyx
lobes and overlapping the next one in the series in a convolute manner. On the first
day after anthesis, the corolla changes into pinkish hue and then into red during
succeeding days. It withers and falls off on the third day, together with the staminal
column and stigma leaving the ovary, calyx and involucre intact.
The stamens are numerous and united to form a tubular sheath which surrounds
the pistils, except for the exposed portion of style and stigma at the tip. Under normal
conditions, the pollen grains are viable up to 24 h and thereafter lose potency and fail
to effect fertilization. The time taken by the pollen tube to traverse the style varies
according to the variety and the environment. In general, 10–13 h duration is
required to traverse the entire length of style. Generally, the interval between
pollination and fertilization varies from 36 to 40 h. The pollen grains of cotton are
heavy, sticky and warty, leaving little chance for wind pollination. The insects are
the natural agents for the pollen transfer.
The pistil consists of three to five undiverged carpels corresponding to the locular
composition of a fully mature dehisced boll. The ovules are attached to the parietal
placenta of each locule. The style varies in length and splits near the apex into three,
four or five parts depending on the number of carpels. The dehiscence of the boll is
along the dorsal sutures.

13.10.7.2 Important Diagnostic Characteristics

The characteristics of cotton (UPOV 2018) are given in Table 13.9 below to help the
seed technologists and breeders to identify the true-to-type plants and to rogue out
the off-types or undesirable plants.

13.10.7.3 Nucleus Seed Production of Varieties

To start a nucleus seed programme, a base source is a prerequisite. For released
varieties, it may be breeder seed or nucleus seed, whereas it may be AVT II seed
material for new varieties. Sufficient single plants (minimum 200 plants) may be
selected from the base source. The selected plants should conform to the basic
morphological (phenotypic) characters given at the time of release of variety. The
selected plants are individually observed for various distinguishing morphological
characters as mentioned in the table above and are selfed. Mean and standard
deviation for various agronomic characters are to be worked out, and the plants
that lie within the mean  SD for all the characters are selected. Individual plant
selection is made on morphological characters identical or typical to released variety
in the field. The selected plants are subjected to fibre quality evaluation to determine
2.5% span length, micronaire, uniformity ratio and bundle strength. Plants which
conform to the basic fibre characters given in the release proposal or which lie within
mean  SD are selected (Manickam et al. 2003).
The selfed seeds from the selected plants are grown in a randomized replicated
design. The row length of plants may be determined based on the availability of
13 Maintenance Breeding 739

Table 13.9 Important diagnostic characteristics of cotton

Stages of
Characteristics States observations
Hypocotyl Absent/present Seedling
pigmentation
Stem pigmentation Absent/present Vegetative/
reproductive
Stem hairiness Absent/medium/strong Vegetative/
reproductive
Plant height Dwarf/medium/tall Vegetative/
reproductive
Leaf shape Palmate (normal)/digitate (okra)/semi-digitate (semi- Vegetative/
okra)/lanceolate (super okra) flowering
Leaf size Small/medium/large Vegetative/
flowering
Leaf colour Light green/green/light red/dark red Vegetative/
flowering
Leaf pubescence Absent/medium/strong Vegetative/
flowering
Leaf nectaries Absent/present Vegetative/
flowering
Leaf petiole Absent/present Vegetative/
pigmentation flowering
Bract type Normal/frego Vegetative/
flowering
Sepal pigmentation Absent/present Flowering
Petal colour White/cream/yellow/pink/red/bicolour Flowering
Petal spotting Absent/present Flowering
Position of stigma Embedded/exserted Flowering
Anther colour White/cream/yellow/purple Flowering
Boll size Small/medium/large First boll
bursting
Boll shape Rounded/elliptical/ovate First boll
(longitudinal bursting
section)
Boll tip prominence Blunt/pointed First boll
bursting
Boll surface Smooth/pitted First boll
bursting
Boll opening Close/semi-open/open First picking
Fibre length Very short/short/medium/long/extra-long First picking
Fuzz colour White/grey/brown/green Harvest
maturity
Fibre colour White/off-white/brown/green Harvest
maturity
Fibre strength Weak/medium/strong Harvest
maturity
Ginning percent Low (<31)/medium (31–35)/high (36–40)/very high After ginning
(>40)
Density of fuzz Naked/semi-fuzzy/fuzzy After ginning
740 R. N. Yadav et al.

seeds. Normally, two rows of two replications per progeny are grown. Appropriate
spacing should be adopted to enable full expression of characters. It will be better to
take up nucleus seed production in areas where the variety is most adopted and
during the best growing season.
Normally, the progeny rows should be grown in compact fields with proper
isolation. The nucleus seed production plot should be critically observed by the
breeder for all the morphological characters during different growth periods. If any
progeny or a plant is found to be deviant at any stage for any character, the whole
progeny should be rejected. The lines unusually susceptible to insect pests and
diseases may also be rejected. Selfing is to be done to maintain the purity. The
progenies are studied for various morphological characters, and the data are analysed
statistically. The progenies that fall within the mean  CD at 5% are selected. The
fibre test and micro-spinning test are conducted, and only progenies that conform to
the original fibre characters are selected. Equal quantity of selfed seeds of selected
progenies is bulked to constitute the nucleus seed. If a large quantity of breeder seed
is required, the next stage of progeny bulk seed may be taken as nucleus seed stage
II. If required, the cycle of selection could be repeated again to further ensure
uniformity.

13.10.7.4 Nucleus/Breeder Seed Production of Parental Lines

of Conventional Hybrids
The nucleus and breeder seeds of parental lines of hybrids are produced in a similar
way as described above for varieties. However, female and male parents are
maintained separately in isolation. At final stage, the selected lines should be tested
for heterosis and SCA; the seeds of those lines having highest SCA and heterosis for
yield and fibre quality traits are utilized for further multiplication and hybrid seed
production. This procedure is repeated in the maintenance of parental lines of
hybrids to retain the original productivity and fibre quality of hybrids (Manickam
et al. 2003).

13.10.7.5 Nucleus Seed Production of A, B and R Lines in the CMS

System
• Production of ‘B’ line: The scheme of production of nucleus and breeder seeds of
‘B’ line is similar to that of female parental line of conventional hybrids.
• Production of ‘A’ line: The ‘A’ and ‘B’ lines are grown in alternate rows, and
paired crosses are effected between ‘A’ and ‘B’ plants during flowering. Care
should be taken to cross A and B plants confirming to the original characters of
the female parent. Simultaneously, selfing is done in the B line. In the next year, a
portion of the selfed and crossed seeds are sown in pair (A and B) while retaining
the portion of remnant seeds. Both A and B lines are evaluated for all the
morphological characters. Apart from this, the A lines are also observed for
pollen shedders. The A lines showing pollen shedders are rejected, and uniform
A and B lines are identified which confirm to the standards of the parental lines.
The remnant crossed seeds are bulked to constitute the nucleus seed of A line
from which the breeder seeds are produced by sib-matting between A and B lines.
13 Maintenance Breeding 741

• Production of ‘R’ line: About 200 single plants may be selected based on the
morphological characters matching the original R lines. They are simultaneously
selfed and test crossed with A lines. In the next year, both test crosses and the
progenies from the selfed seeds are raised. A part of selfed seed is retained as
remnant seeds. Critical observations are recorded in the progenies for conformity
with morphological characters of the original parent. The crosses are observed for
the fertility restoration. In those crosses, wherein fertility restoration is incom-
plete, their corresponding progenies are rejected. Also, the progenies not
confirming to the morphological characters of the parents are rejected. The
remnant seeds from the selected progenies are bulked to constitute the nucleus
seed of R lines. The breeder seed is produced from the nucleus seed as discussed
earlier for varieties (Udaya Bhaskar et al. 2016).

13.10.7.6 Nucleus Seed Production of GMS Line

About 200 heterozygous fertile plants are selected in the base population, based on
morphological characters matching the original female parental line of the hybrid.
Sib-mating is done between the sterile and selected fertile plants. In the next year,
progeny rows of each selected single plant are raised from a portion of sib-mated
seeds. The progeny rows are evaluated for various morphological and fibre quality
characters for confirmation. The segregation for fertile and sterile plants in sib-mated
progenies is also observed. Only those progenies which segregate in a 1:1 ratio for
sterile and fertile plants and confirm to original morphological characters are
sib-mated, while the others are rejected. The remnant sib-mated seeds of the selected
progenies are bulked to constitute the nucleus seed. The breeder seed is produced
from the nucleus seed by sib-mating sterile plants with their fertile counterparts
(Singhal 2003).

Acknowledgements The authors duly acknowledge all the resources consulted and text referred
from various books, manuals, papers and resources on the Internet for the preparation of this
chapter.

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Efficient Breeding of Crop Plants
14
Pawan L. Kulwal, Reyazul Rouf Mir, and Rajeev K. Varshney

Abstract

In crop breeding programs, the rate of genetic gain which is achieved using the
traditional breeding is insufficient to meet the increased demand of food for the
rapidly expanding global population. The main constraint with the conventional
breeding is the time which is required in developing crosses, followed by
selection and testing of the experimental cultivars. Although, using this tech-
nique, lot of progress has been made in increasing the productivity, the time has
come to think beyond this and integrate the recent advances in the area of
genomics, phenomics and computational biology into the conventional breeding
program for increasing its efficiency. While doing this emphasis on proper
characterization and use of plant genetic resources, defining the breeding
objectives and use of recent advances in holistic way are also essential. Therefore,
in this chapter, we first highlight the importance of plant breeding followed by
significance of the plant genetic resources in the breeding program, need of
ideotype breeding and the breeding objectives for important traits including
resistance against various biotic and abiotic stresses. We then discuss the

P. L. Kulwal (*)
Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth (Agricultural University), Rahuri,
Maharashtra, India
R. R. Mir
Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir,
Jammu and Kashmir, India
R. K. Varshney
Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for
the Semi-Arid Tropics, Patancheru, Hyderabad, Telangana, India
State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute,
Murdoch University, Murdoch, WA, Australia

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 745
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_14
746 P. L. Kulwal et al.

limitations of conventional breeding and advantages of genomics-assisted breed-

ing. While doing this, we also discuss various molecular breeding tools and
genomic resources as well as different approaches for efficient breeding including
marker-assisted selection, marker-assisted recurrent selection and genomic selec-
tion. This is followed by importance of other non-conventional approaches
including the recent one on gene editing, speed breeding and role of integrated
data management and bioinformatics in the breeding programs. We also discuss
the significance of phenomics and phenotyping platforms in the crop breeding as
well as role of computational techniques like artificial intelligence and machine
learning in analysing the huge data which is being generated in the breeding
programs. Finally, we conclude with a brief note on the emerging challenges in
breeding which need to be addressed and the thrust areas of research for the
future.

Keywords
Plant breeding · Efficient breeding · Ideotype breeding · Genomics · Plant genetic
resources · Phenomics · Gene editing · Artificial intelligence

14.1 Importance of Crop Breeding

The history of plant breeding has been very promising, and plant breeding has
contributed immensely in consistently increasing the productivity of the crop plants
during the last several centuries. This has helped in addressing the issue of hunger
and malnutrition to larger extent. The achievements of plant breeding have been
manifold and have resulted in tremendous increase in yield either by directly
improving the yield component traits or through resistance breeding. The Green
Revolution is the best example of this, through which the productivity of cereals has
increased remarkably by introducing dwarf genes into wheat varieties responsive to
fertilizers (Tester and Langridge 2010). In several countries including India, self-
sufficiency has been achieved in almost all the major crops in the last few decades
using the practices of conventional breeding coupled with better agronomic
practices. However, these methods are not sufficient to produce enough food for
the growing population in the coming years, particularly with the growing
challenges of environmental changes (Godfray et al. 2010; Tester and Langridge
2010).
In order to achieve the breeding objectives, plant breeders often use various
methods and techniques. Although the application of techniques in conventional
breeding is often straight forward, they need to be refined from time to time
according to the existing needs. It is under such circumstances that modern and
efficient breeding approaches involving use of genomics tools should become part of
the breeding programs (Kulwal et al. 2012). However, before implementing any
such technique, it is essential that the breeding objectives are clearly defined.
14 Efficient Breeding of Crop Plants 747

The science of plant breeding has evolved over the years. Recently, the timeline
of the plant breeding has been partitioned into four different phases (Ramstein et al.
2019). Breeding 1.0 focused on selection with unknown loci during the first
10,000 years before 1900 (early domestication phase), Breeding 2.0 relating to the
Mendelian genetics and selection by controlled crosses, Breeding 3.0 involving use
of genomics techniques like marker-assisted breeding and Breeding 4.0 focusing on
ideotype-based selection and use of techniques like genetic transformation and gene
editing (Wallace et al. 2018; Ramstein et al. 2019). Broadly speaking, we can
categorize Breeding 1 and 2 as conventional approaches while Breeding 3 and
4 as efficient approaches. While we are already in the phase 4.0, the real potential
of genomics tools (phase 3.0) has not yet been fully exploited in all the crops.
Nevertheless, the success these efficient breeding techniques have shown (see later)
has provided new dimensions to the crop improvement programs.

14.2 Importance of Plant Genetic Resources in Crop Breeding

Efficiency of any breeding program is directly dependent on the availability of the

plant genetic resources (PGRs) for that crop. These PGRs include cultivated and
wild species and valuable germplasm including landraces (Bošković et al. 2012). In
order to deal with the complex traits and to respond to the challenges of climate
change, particularly biotic and abiotic stresses, breeders need to exploit as much
genetic diversity as they can (Galluzzi et al. 2020). This diversity can be exploited
through use of the PGRs (landraces, crop wild relatives and other available germ-
plasm) which are generally conserved in the gene banks. Often, the breeders use
superior performing lines, albeit with limited diversity in their breeding programs.
Although substantial progress has been made for yield improvement with this
approach, the time has come when breeders need to exploit the true potential of
the PGRs to address the challenges of the future. There are different ways through
which PGRs are used in crop breeding programs. However, this depends on the
breeding objective, the trait being studied and the genetic resources available
(Bidinger 1992).
The three most common ways through which PGRs are being used in the
conventional breeding are the (1) introgression (transfer of one or few genes from
PGRs), (2) incorporation (widening of the genetic base) and (3) pre-breeding (use of
exotic materials or wild relatives) (Haussmann et al. 2004). Besides this, PGRs can
also be effectively used (1) as a parental genotype in developing a mapping popula-
tion to be used in QTL mapping and (2) simultaneous identification and transfer of
desirable QTLs from wild or unadapted germplasm into the cultivated one through
advanced backcross QTL mapping and (3) for identification of genes/QTLs through
the approach of association mapping/genome-wide association studies (GWAS) and
allele mining (Kulwal 2016; Kulwal and Singh 2021). Large numbers of studies
have been carried out in different crops, and hundreds of marker-trait associations
(MTAs) have been identified for a variety of traits through GWAS (Gupta et al.
2019). In situations when all the PGRs for a crop cannot be utilized for GWAS, then
748 P. L. Kulwal et al.

Table 14.1 Plant genetic resources available in different gene banks of CGIAR institutes
S. no. Crop Institute Number of accessions
1 Wheat CIMMYT and ICARDA 199,248
2 Rice IRRI and Africa Rice 151,765
3 Barley ICARDA 32,790
4 Maize CIMMYT and IITA 30,055
5 Sorghum ICRISAT 41,582
6 Bajra ICRISAT 23,841
7 Small millets ICRISAT 11,797
8 Chickpea ICRISAT and ICARDA 36,513
9 Pigeon pea ICRISAT 13,783
10 Soybean IITA 4841
11 Groundnut ICRISAT 15,622
12 Forages CIAT, ICARDA and ILRI 70,514

core and mini-core collections are developed by identifying most diverse but
representative set of germplasm from the total collection for further analysis.
There are quite a few examples where PGRs from the gene banks have been used
to identify and introgress important genes/QTLs for abiotic stresses in different
crops. For instance, in rice, a landrace FR13A was identified for its resilience to
complete submergence. The submergence QTL (Sub1) from its derivatives has
successfully been introduced into several lines leading to the development of
many rice varieties with improved tolerance to submergence (Bailey-Serres et al.
2010). Similarly, in chickpea genotype ICC 4958 available at the ICRISAT gene
bank was identified as having a profuse root system and was used in many QTL
mapping studies which had led to the identification of QTL-hotspot for drought
tolerance-related traits (Varshney et al. 2014). This QTL region was subsequently
transferred in the genetic background of chickpea variety Pusa-372 leading to the
development and release of drought-tolerant variety Pusa Chickpea-10,216 follow-
ing the approach of marker-assisted selection (MAS). In addition, the QTL-hotspot
has been introgressed in several genetic background, and many introgression lines
have been developed (Roorkiwal et al. 2020; Bharadwaj et al. 2021). These
examples clearly demonstrate the vital role PGRs play in the plant breeding
programs. There are many more such examples in different crops where PGRs
have been used for the improvement of the varieties.
The gene banks are invaluable treasures which contain large number of PGRs and
provide an opportunity to utilize these resources to breed for the uncertainties posed
by climate change (Bohra et al. 2020; Khan et al. 2020). Large numbers of
accessions have been conserved at different gene banks across the world. These
include major gene banks of CGIAR (https://www.genebanks.org) which house
thousands of accessions collected from world over for the important crops
(Table 14.1). The number of accessions per crop which are conserved in different
gene banks in the CGIAR institutes is also available at https://www.genebanks.org/
resources/crops/ (verified March 04, 2021). In addition, there are several national
14 Efficient Breeding of Crop Plants 749

gene banks in different countries which also conserve different accessions. In India,
National Bureau of Plant Genetic Resources (NBPGR) at New Delhi is the main
gene bank entrusted with this responsibility. In addition, there are several crop-
specific gene banks at different institutes of ICAR. While conserving the germplasm
is an important step, it is equally important to characterize and utilize these PGRs
effectively for use in the crop improvement programs for addressing the issue of the
world’s future food requirements (McCouch et al. 2020). In order to utilize this
treasure of PGRs available with the national gene bank in India, recently the
Department of Biotechnology, Government of India, has funded several projects
for the utilization of these germplasm for their characterization and use in the
breeding programs. There is no doubt that utilization of these PGRs in the breeding
programs can help in achieving the Sustainable Development Goals as outlined by
the United Nations (Halewood et al. 2018).

14.3 Ideotype Breeding

The concept of ideotype breeding was proposed for the first time by Donald (1968)
in wheat. The concept given by Donald presumed that most of the plant breeding
programs are based on two main objectives including (1) defect elimination and
(2) selection for yield. The term defect elimination is appropriately used when the
disease resistance trait is introduced into a susceptible variety or when early maturity
trait is introduced into a variety prone to water stress in late season (Donald 1968).
The defect elimination involves correction of physical imperfections like fragile skin
in tomatoes, weak malting performance in barley, poor flavour in potatoes and weak
straw in cereals. The elimination of these defects ultimately led to the increase in
yield and quality. On the other hand, selection and improving yield is considered
ultimate objective of any breeding program in the world. The improvement of yield
can be done through hybridization that involves crossing of superior genotypes
having broad genetic base. Therefore, in summary, ideotype-based approach in
plant breeding improves the efficiency of the selection (Gauffreteau 2018). The
process of ideotype breeding involves (1) defining the varietal specifications;
(2) designing and building an ideotype; and (3) selecting varieties according to the
ideotype and assessing their ability to meet the specifications.
In ideotype breeding, the theoretical models are being developed based on our
understanding, knowledge, experience and imagination. The models thus developed
are known as “the breeding of model plants or ideotypes”. Through this type of
breeding, it is possible to design a plant that is capable of greater production in a
target environment than the genotype it is to replace. For efficient ideotype breeding,
we need to choose model characters. These model characters are presumably very
important. For instance, in cereals stout stem is a “model character” and provides
lodging resistance. Similarly, presence of awns is another model character and has a
role in photosynthesis and yield. Another model character is erect foliage (upright
leaves) which have shown advantage in photosynthesis. The concept of crop
ideotype initially formulated for wheat crop by Donald has been used for several
750 P. L. Kulwal et al.

other crop species including barley (Rasmusson 1987), chickpea (Siddique and
Sedgley 1987), forest trees (Dickmann 1985) such as spruce and pine (Kärki and
Tigerstedt 1985) and fruit trees like mango and apple (Dickmann et al. 1994). The
attributes of ideotypes are morphological characters based on physiological consid-
eration. The concept of ideotype first relied primarily on the morphological traits.
However, later the ideotype definition was extended, and traits like physiological,
biochemical, anatomical and phenological traits have been included in defining a
particular crop ideotype. However, before including any new parameter or a trait for
a plant type, it is important to check its contribution towards crop yield. Thus, study
and understanding the concept of plant ideotype for a given crop can prove to be an
efficient in the breeding of that crop.

14.4 Breeding Objectives for Important Traits

14.4.1 Breeding Objectives for Yield

Grain yield is one of the most complex quantitative traits known in crop plants, and
this trait is significantly influenced by the environment. The genetics of grain yield
over the years suggested that grain yield is controlled by large number of genes/
QTLs with minor effect. The gene controlling grain yield is often influenced by the
environment. Therefore, it is important to study genotype  environment interaction
while studying genetics of this complex quantitative trait. In addition, extensive
studies of grain yield have uncovered that genes responsible for grain yield are often
interacting with other genes. This phenomenon is popularly described as “epistasis”.
Different kinds of gene  gene interactions and gene  gene  environment
interactions have also been discovered for grain yield. The complexity of grain
yield as a trait can be realized by the fact that grain yield can be dissected into
several component traits with higher heritability. In addition, it has been reported in
earlier studies that individual traits showing correlation with grain yield are most
often controlled by the same set of QTLs/genes.
The most important component traits of grain yield included number of
spikelet’s/spike, number of grains per spike and 1000 grain/kernel weight (Mir
et al. 2021b). For example, in bread wheat, the important reproductive organ
harbouring grains is the spike, and therefore traits related to wheat spike are
considered very important for manipulating grain yield. The published literature
showed strong and positive correlation between different spike traits like spike
length with grain yield and yield-related traits including 1000 grain/kernel weight
(Mir et al. 2012a). Therefore, from a breeding point of view, genes/QTLs already
identified or to be identified in the future for traits related to wheat spike are of
importance for wheat molecular breeding programs aimed at enhancing grain yield.
The domestication genes/loci like Q, C and S are also considered important and
influence several yield component traits including rachis fragility, spike length, spike
compactness, grain morphology traits, grain number, seed shape and glumes of a
wheat spike.
14 Efficient Breeding of Crop Plants 751

The genetic dissection of grain yield has been attempted using a variety of
approaches including QTL interval mapping and association mapping and have
led to the discovery of genes/QTLs for grain yield component traits in several
crops. The QTL/genes that have been identified over years need to be deployed
into breeding programs through modern and efficient breeding methods including
MAS (see later).

14.4.2 Grain Quality Characters

Grain quality traits are very important in any crop because the market price of the
end produce is directly related to the quality parameters. A lot of emphasis is thus
being given on the improvement of the quality parameters. While there are some
quality parameters which are common to majority of the grain crops (e.g. grain size,
shape, protein content, etc.), some are unique (e.g. pre-harvest sprouting tolerance in
wheat, sorghum, mungbean; milling quality in rice, etc.). List of some important
quality traits in different crops is given in Table 14.2. While a lot of breeding efforts
have been made for the improvement yield of crop plant, it is now necessary that
focus should be shifted towards quality parameters. Breeding for quality parameters
is difficult because their nature of inheritance is complex and they are controlled by
polygenes. Moreover, measuring the trait precisely is most of the time technically
demanding and expensive. However, with the development of novel, rapid and cost-
effective screening techniques, breeders have taken renewed interest in the breeding
for quality parameters (Munck 2009).
Any breeding program aimed at improving the quality traits relies most impor-
tantly on the availability of the known sources containing genes for these traits
(Varshney et al. 2021). The PGRs (germplasm, landraces, wild relatives) can prove
very useful in this regard. Genes/QTLs for these traits can be identified in a mapping
population developed for this purpose by crossing two genotypes differing for the
trait or using germplasm collection and natural population. Several studies have been
carried out in different crops where QTLs have been identified for important quality

Table 14.2 Key important quality traits in different crops

S. no. Crop Quality traits
1 Wheat Grain protein content; gluten strength; pre-harvest sprouting tolerance;
grain size; grain weight; kernel colour; dough making properties
2 Rice Grain size; grain shape; aroma; whiteness; long and thin uncooked grains;
amylose content; milling, physical appearance, cooking, sensory,
palatability, and nutritional value
3 Maize Protein content; amino acid content; fatty acid content; starch quality
4 Sorghum Amylose content; starch content; crude protein; gross energy; tannin
content; polyphenol content
5 Chickpea Protein content; grain size; fibre content; carotenoid composition
6 Soybean Seed weight; seed protein; sucrose concentration; oil content; oil
composition
752 P. L. Kulwal et al.

traits (Kulwal et al. 2005, 2010). Some of these QTLs have also been transferred into
the desirable genotypes using efficient breeding programs like MAS (Varshney et al.
2021). However, success of any such program also depends on the variation
explained by the identified QTL. One of the concerns in breeding for quality traits
is that it is often considered that improvement in some trait (e.g. protein content)
comes with yield penalty, although not always (Kulwal and Mhase 2017). For this
purpose, understanding the nature of gene action and genotype  environment
interaction is also essential. In recent years, the techniques like genetic engineering
and gene editing offer tremendous scope for improving the quality.

14.4.3 Resistance to Biotic Stresses

Biotic stresses (pests and diseases) are known to cause significant losses to the crop
plants resulting in reduction in the yield as well as quality of the produce. Depending
on the existing circumstances, the degree of losses caused can vary from minor to
severe. It has been reported that almost half of the total yield losses in the world are
due to biotic stresses (Balconi et al. 2012). Therefore, breeding for biotic stresses is
the major objective in any crop improvement program. While use of chemical
pesticides is effective in controlling these stresses, they can add to the cost of
production and cause significant damage not only to human and animal being but
to the environment as well (Bainsla and Meena 2016). With the issues concerning
climate change, the threat of new pests and diseases has also increased in recent
years. In order to address this issue in a sustainable way, use of resistance sources in
the breeding program coupled with deployment of efficient and precise techniques
like MAS, marker-assisted gene pyramiding, genetic engineering and gene editing
are very promising. MAS not only has simplified the breeding programs but has also
accelerated the process of gene transfer in the desired genetic background (see later).
The sources of resistance can be identified by screening large number of germplasm
accessions against particular disease/pest. Exploitation of PGR can prove useful
under such circumstances.
Although the conventional breeding relying on the principle of back crossing
using resistant sources has proved successful in incorporating resistance, it is time-
consuming and not very efficient technique. Other limitation is that it is effective
only when the R genes are used one at a time, thus limiting gene pyramiding. There
are many successful examples where the technique of MAS has successfully been
used to transfer resistance genes/QTLs against various pests and diseases in the crop
plants as well as in gene pyramiding (Dormatey et al. 2020). It has also been reported
that the resistance achieved through pyramiding of the resistant QTL is at par or
better than that conferred by the R genes (Richardson et al. 2006). However, MAS is
useful only when the resistance source which is being used in the crossing program is
compatible with the recipient genotype. In cases when the compatible resistant
sources are not available, the technique like genetic engineering and gene editing
(see later) can prove very effective (Dong and Ronald 2019). Several successful
examples are available where these techniques have been used for incorporating
14 Efficient Breeding of Crop Plants 753

resistance against particular pest (Varshney et al. 2021). One thing which is very
important in resistance breeding is that with the constant pressure of emerging pests
and diseases, the breeders need to keep themselves well equipped with the recent
tools and one step ahead of the pest and disease in question so that new varieties with
durable resistance can be developed.

14.4.4 Resistance to Abiotic Stresses

The yield of crop plants is mostly influenced by a variety of biotic and abiotic
stresses, climatic and agronomic factors. The major abiotic stresses limiting crop
yields include drought, heat, cold, freezing, salinity and metal stresses. All these
abiotic stresses create adverse effects on morphology, physiology and biochemistry
which ultimately lead to the adverse effects on growth and yield of plants. Both
vegetative and reproductive phases of plant growth are influenced by the abiotic
stresses like heat, drought, cold and freezing. It is estimated that an average of 50%
yield losses in agricultural crops is caused by abiotic stresses, and among these
abiotic stresses high temperature stress causes 40% loss followed by salinity (20%),
drought (17%) and cold/freezing (15%) (Meena et al. 2017). For example, in
chickpea, one of the most important grain legume crops in the world the significant
economic losses due to drought/heat (1.3 billion US dollars), cold (186 million US
dollars) and salinity (354 million US dollars) have raised major concerns among the
chickpea-growing countries (Jha et al. 2014; Mir et al. 2021a). This situation is
further exacerbated by climate change which may cause higher intensities and
frequencies of abiotic stresses, thereby necessitating the identification and develop-
ment of climate-resilient cultivars having region-specific traits, which can perform
well under stress.
Several physiological changes are induced in plants in response to different
abiotic stresses. For instance, the physiological changes induced in plants in
response to abiotic stress included wilting and abscission of the leaf, transpiration,
etc. The most important abiotic stress “drought” results in decrease in turgor pressure
and thus affects cell growth. It also creates disruption to water flow from xylem to
neighbouring elongating cells and thus stops cell elongation. The visible changes
include reduction in leaf area as well as plant height. The different mechanisms
adapted by plants during abiotic stress include escape, avoidance and tolerance
mechanisms. Like drought and heat stress, cold and freezing stress also adversely
affects plant growth and development, membrane structure and photosynthetic
activity (Mir et al. 2021a). Low temperature stress is an important issue for winter-
sown crops like chickpea, lentil, pea, wheat, barley, etc. in the countries surrounding
the Mediterranean Sea, the tropical highlands and temperate growing areas. The
most affected regions are northern South Asia and parts of the Australia, where crop
faces low-temperature stress (<15  C) which limits growth and vigour at all
phenological stages but particularly during vegetative and reproductive stages lead-
ing to chlorosis and necrosis of leaf tips, substantial loss of flowers and pod abortion,
754 P. L. Kulwal et al.

reduced pollen viability and pollen tube growth and, thus, reduced seed quality and
yield potential by 30–40% (Rani et al. 2020; Mir et al. 2021a).
Keeping in view the losses due to abiotic stresses, the breeding for climatic
resilient varieties having tolerance against abiotic stresses has emerged as one of
the important subject areas of crop research and a major goal in plant breeding
programs worldwide (Meena et al. 2017). Different breeding methods have been
used to breed for different abiotic stresses in different crop plants. The methods of
breeding adopted in different crop plants depend on their mode of reproduction (self-
pollination, cross-pollination or asexual) and the genetic control of trait of interest.
The breeding methods for drought are usually the same as that of yield. In general,
the conventional breeding methods like pedigree and bulk method could be used for
self-pollinated crop species, and recurrent selection could be used for cross-
pollinated crop species.
In some cases if one wishes to transfer more than one trait related to drought into a
high yielding variety, then back cross breeding method is considered the most
appropriate. The varieties for salinity tolerance were developed through pedigree,
modified bulk pedigree and anther culture approach. The different genetic resources
including landraces, wild relatives, released varieties, pre-breeding lines, advanced
breeding lines and mutants also serve as important sources of resistance against
abiotic stresses. Wild species of crop plants serve as an important source and
reservoir of genes for abiotic stress tolerance. For instance, in wheat crop, Aegilops
kotschyi, Ae. Squarrosa and Triticum urartu serve as an excellent source of drought
tolerance and Aegilops tauschii as source of salinity tolerance. In chickpea, Cicer
microphyllum, Cicer reticulatum and Cicer echinospermum serve as excellent
sources of cold tolerance. The genetics of abiotic stresses is considered very complex
and controlled by large number of small effect genes/QTLs.
Although conventional breeding methods have been used to address the issues of
abiotic stresses, to breed more efficiently, scientists all over the world are now
adopting integrated genomics-based tools in their breeding pipelines. A variety of
genomics, physiology and breeding approaches have been extensively deployed for
the genetic dissection of abiotic stress adaptation (Mir et al. 2012b). Several geno-
mics approaches including QTL interval mapping, GWAS, transcriptomics, etc.
have been deployed for the discovery of genes/QTLs/transcripts/markers for their
use in genomics-assisted breeding for development of abiotic stress-tolerant crop
varieties.

14.5 Crop Breeding in the Era of Genomics

14.5.1 Limitations of Conventional Breeding

While the conventional breeding is being practiced since centuries and has
immensely helped in development of large number of varieties in different crops,
it has its own limitations. Since the conventional breeding programs are dependent
on phenotypic selection, which basically is more of an art than science, the
14 Efficient Breeding of Crop Plants 755

effectiveness of such program is less. The major limitations which hamper the
success of conventional breeding are (a) the time required for improvement of a
trait is very long; (b) the accuracy with which the desirable genotypes could be
selected is very less (this happens mainly due to linkage drag when many traits are
transferred along with the trait(s) of interest—including those traits that have
undesirable effects); and (c) the efficiency with which the selection for the trait
can be done is also very less. These three limitations not only increase the time and
cost required for development of a variety, but many times, the new genotype
becomes susceptible to new pest or disease by the time it is ready for release as a
new variety.

14.5.2 Advantages of Molecular Breeding/Genomics-Assisted

Breeding

The three key limitations associated with the conventional breeding discussed above
can effectively be overcome by the use of molecular breeding/genomics-assisted
breeding (GAB). This can also be called as precision breeding (Kulwal et al. 2012).
The three key advantages of molecular breeding over the conventional breeding are
the following.

14.5.2.1 Time Saving

Using molecular breeding, the time and labour savings may arise from the substitu-
tion of difficult or time-consuming field trials (that need to be conducted at particular
times of year or at specific locations or are technically complicated) with DNA
marker tests. This is an important advantage of the molecular breeding, since lesser
time will also curtail the cost of the breeding program and selections can be done any
time during the year.

14.5.2.2 Increased Efficiency

Molecular breeding can greatly increase the efficiency and effectiveness of breeding
compared to conventional breeding because it is simpler compared to phenotypic
screening, selection may be carried out at seedling stage and single plants may be
selected with high reliability. These key advantages may translate into greater
efficiency or accelerated line development in the plant breeding programs.

14.5.2.3 Increased Accuracy

It is well-known that effect/influence of environmental factors on field trials is more,
thereby limiting the accuracy of selection. However, selection based on DNA
markers is more reliable as effect of environment is not there. Moreover, the total
number of lines that need to be tested may be reduced, and specific genotypes can
easily be identified and selected.
With the advances in the area of genomics coupled with the availability of large
number of genomic resources in different crops (see next section), molecular
756 P. L. Kulwal et al.

breeding or GAB has now become an integral part of the crop improvement program
(Varshney et al. 2021).

14.5.3 Molecular Breeding Tools for Efficient Breeding

As already discussed in the above section that there are several advantages of
molecular breeding over conventional plant breeding, the traditional/conventional
crop improvement techniques are now being replaced by GAB approaches. Recent
advances in genomics tools and techniques have facilitated the development of large
number of different types of molecular markers, genetic and physical maps, high-
throughput and precise genotyping platforms and rapid discovery of genes using
different approaches in almost all important crop plants (Bohra et al. 2020). There-
fore, efficiency and precision of crop improvement could increase using these
genomic tools and techniques. This has become primarily possible due to the
advances in the next-generation DNA sequencing technologies and development
of large numbers of molecular markers. The efficient breeding program today thus
relies on several tools which are described in the following sections.

14.5.3.1 Molecular Markers

The recent years have witnessed the development of large-scale genomics and
genetic resources including variety of molecular markers, expressed sequence tags
(ESTs) or transcript reads, bacterial artificial chromosome (BAC) libraries, genetic
and physical maps and genetic stocks with rich genetic diversity, such as core
reference sets and introgression lines in majority of the crop plants (Varshney
et al. 2010). The DNA-based markers also known as molecular markers are being
used for the detection of genome sequence level differences between two or more
than two individuals. The discovery of molecular markers has revolutionized crop
improvement programs by providing quick and sophisticated/reliable crop improve-
ment tools and techniques. The marker technology although discovered in the 1980s
with the discovery of RFLPs has witnessed continuous evolution from hybrization-
based markers to GBS-based markers (Mir et al. 2013; Mir and Varshney 2013;
Gupta et al. 2013a, b; Kumar et al. 2021; Tyagi et al. 2019, 2021). A number of
classifications have been proposed to classify molecular markers. Some of the
classifications of markers include hybridization-based vs. non-hybridization-based,
first-generation vs. second-generation vs. third-generation markers,
past vs. present vs. future, low-throughput vs. medium-throughput vs. high-
throughput markers, sequence based vs. non-sequence based and array-based vs. non-
array-based markers (Gupta et al. 2008; Mir et al. 2013; Mir and Varshney 2013).
The advances in genomics has not only resulted in development of large numbers
of markers in important crops but also in in the once considered orphan and resource
poor crops like chickpea, pigeon pea and groundnut. Now in these crops, thousands
of all important types of molecular markers including SSR, diversity arrays technol-
ogy (DArT), single nucleotide polymorphism (SNP), different SNP platforms,
micro-array-based markers, GBS, InDel markers, etc. are available. For instance,
14 Efficient Breeding of Crop Plants 757

over the years, >2000 SSRs in chickpea, >3000 in pigeon pea and >2500 in
groundnut have become available using different approaches of marker develop-
ment. Similarly, thousands of DArT and SNP markers are available in these crops.
Several genotypic platforms including Kompetitive Allele Specific PCR (KASP)
assays, GoldenGate assays, Vera Code assays and 60 K SNP chips using Affymetrix
SNP platform and Axiom SNP array with thousands of SNPs uniformly distributed
across the genome are available now (Thudi et al. 2021). These marker resources
have been used in the study of genetic diversity, population structure, development
of genetic maps and QTL mapping/GWAS for key traits in all major food crops. The
genes/QTLs once identified are being deployed into molecular breeding programs
aimed at enhancing targeted traits in different crop plants through MAS, marker-
assisted recurrent selection (MARS) and genomic selection (GS). It is expected that
the improved versions of next-generation crop varieties could be developed with
enhanced quality traits, better yield and disease resistance.

14.5.3.2 Genetic/Linkage Maps

The molecular genetic map or linkage map refers to linear arrangement of genetic
markers (loci) on the genome obtained on the basis of estimates of recombination
fractions among the markers. The genetic map may be thought of as a “road map” of
the chromosomes developed for a mapping population derived from two different
parents. It indicates the position and relative genetic distances between markers
along chromosomes, which is analogous to signs or landmarks along a highway. The
concept of genetic linkage is known since the studies of Morgan 1911 and Sturtevant
published genetic map of chromosome X of Drosophila in 1913. The first partial
genetic map of maize was published by Emerson and colleagues in 1935. These
linkage maps were prepared by analysing segregating populations derived from
crosses of genetically diverse parents and estimating the recombination frequency
(RF) among genetic loci. The distance between the markers on a genetic map is
related to the RF between the markers. Lower the frequency of recombination
between two markers, the closer they are situated on a chromosome, and hence
greater the frequency of recombination, more is the genetic distance. Markers that
have a recombination frequency of 50% are described as “unlinked” and assumed to
be located far apart on the same chromosome or on different chromosomes. Different
chromosomal regions vary in their recombination frequency. Because of this, genetic
maps cannot be used to measure physical distance between markers on the genome
and only provide an approximation of physical distance, as well as a representation
of marker order along the chromosome. Genetic maps have in general several
functions including (1) providing an insight into genome organization, (2) the
evolution of species, (3) synteny between related species, (4) rearrangement across
taxa and more importantly (5) identification of genes/QTL for a trait of interest.
The molecular genetic maps based on DNA markers are now available in almost
all plants of significant academic and economic interest, and the list of plants is
growing regularly. Different types of molecular markers have been used for devel-
opment of genetic maps, and sometimes genetic maps of only individual
chromosomes have been constructed on the basis of needs of researchers. However,
758 P. L. Kulwal et al.

development of whole genome maps covering all the chromosomes in genome is

always desirable. Initially RFLP-based genetic maps were developed, but with the
discovery of markers of choice like SSRs and SNPs, now almost all maps are based
on these markers (Thudi et al. 2021). More recently, several high-throughput
genotyping platforms have been developed based on SNP markers, and the use of
these genotyping platforms has facilitated the development of high-resolution and
high-density genetic maps. These high-density genetic maps prove useful in fine
mapping of genes. The different maps developed over the years have been used for
mapping, tagging, cloning and characterization of large number of genes/QTLs in all
important crop plants, and the information so generated can facilitate efficient
breeding.

14.5.3.3 Use of Genome Sequence Information for Crop Breeding

The science of plant genomics research had its beginning with the publication of
genome sequence of Arabidopsis thaliana in the year 2000. Nowadays, the genome
sequence of almost all the major crop plants including cereals and legumes have
become available (Thudi et al. 2021). After sequencing of Arabidopsis genome, rice
genome was sequenced in year 2005. After sequencing of rice genomes, draft
genomes of several cultivars among ssp. japonica and ssp. indica have also become
available. Draft genomes of Australian wild A genome taxa including O. rufipogon
and O. meridionalis, other wild species, core collections and mini-core core
collections have also become available in recent years (for a review, see Thudi
et al. 2021).
The other most important cereal crop “maize” genome was sequenced using a
most widely used female parent “B73” for developing maize hybrids and study of
maize genetics (Schnable et al. 2009). Followed by the sequencing of B73 genome,
draft genome sequence of other maize inbred including Mo17, W22, HZS, SK and
K0326Y were also generated. Bread wheat, one of the most important cereal crops
with complex and huge genome size, has also been sequenced by the International
Wheat Genome Sequencing Consortium (IWGSC) more than a decade after the
initial drafts of the rice genome (International Wheat Genome Sequencing Consor-
tium, IWGSC, http://www.wheatgenome.org/). Similarly, barley genome was also
sequenced using six-row malting cultivar Morex (Mascher et al. 2017) followed by
sequencing of Tibetan hulless barley (Zeng et al. 2015, 2018) and wild barley
species AWCS276.
Like cereals, major legume genomes have also been sequenced. For instance,
draft genome of cultivated soybean Williams 82 (Schmutz et al. 2010) and undo-
mesticated ancestor of G. max, the G. soja (Kim et al. 2010), have become available.
The genome sequence of two diploid progenitor species of groundnut (A. duranensis
V14167 and A. ipaensis K30076) was reported by the International Peanut Genome
Initiative (IPGI) through the Peanut Genome Consortium (PGC) (Bertioli et al.
2016). This was followed by sequencing of several other groundnut genomes
(Chen et al. 2016; Lu et al. 2018; Yin et al. 2018; Bertioli et al. 2019; Zhuang
et al. 2019). The common bean genome sequence has also become available for
Andean inbred landrace “G19833” (Schmutz et al. 2014). For grain legume crop
14 Efficient Breeding of Crop Plants 759

chickpea, a draft genome sequence for Kabuli genotype, CDC Frontier was
generated by Varshney et al. (2013b) and for desi chickpea genotype ICC 4958 by
Jain et al. (2013). For pigeon pea, draft genome assembly was developed for variety
Asha (ICPL 87119) (Singh et al. 2012; Varshney et al. 2012).
The sequencing of these plant genomes has played very crucial role in discover-
ing important genes and understanding their biological functions. Due to advances in
genome sequencing technologies, the speed of sequencing has increased, and cost of
sequencing has drastically decreased. This has resulted in the sequencing of draft
genome of >800 plant species, and the number is continuously increasing (Thudi
et al. 2021). The sequencing of crop genomes and the information derived have been
utilized in both basic and applied research. For instance, this information has been
utilized in working out evolutionary relationships, developing better phylogenetic
classification and discovery of genes, alleles, markers, etc. The sequencing of large
number of genomes has also resulted in the introduction of the concept of plant pan
genome, each composed of “core genome” and “dispensable genome”. The recent
advances in genomics tools and techniques have helped in the development of
genomics resources in all major crop plants in the world. Several databases like
Legume Information System (LIS https://legumeinfo.org/; LegumeIP, https://plan.
tgrn.noble.org/ LegumeIP; and Know Pulse, https://knowpulse.usask.ca) have been
developed for providing genomic information.

14.6 Approaches for Efficient Breeding

14.6.1 Genomics-Assisted Breeding

With the advances in the area of genomics in last few years coupled with the
availability of large numbers of genomic resources in terms of mapping populations,
different types of molecular markers, genome sequence, linkage maps and identified
QTLs/MTAs have changed the way plant breeding is being practiced. The important
advantage the science of genomics has brought is the increased efficiency of the
breeding programs leading to the proper understanding of the genetic architecture of
the traits and incorporating this information in the varietal development programs.
There are different ways through which this can be accomplished and are discussed
below.

14.6.1.1 Marker-Assisted Selection (MAS)

The simple meaning of MAS is the use of molecular marker linked with the
QTL/gene of interest as the substitute for making selection for a desirable genotype
under laboratory conditions rather than cumbersome field-based phenotypic screen-
ing. However, before using the markers in the breeding program, there are few key
things which need to be satisfied. These are (1) identification of the marker
(s) associated with the trait of interest, (2) validation or testing suitability of these
markers in the desirable genetic background and (3) use of these markers in
the breeding program though marker-assisted backcrossing (MABC) for transfer
760 P. L. Kulwal et al.

of the required QTL/gene in the desirable genetic background (Kulwal et al. 2012).
The general pre-requites for undertaking MAS have also been discussed elsewhere
(Jiang 2015). The success of MAS entirely depends on the accuracy with which
MTAs are identified. This can be accomplished by the development of linkage maps
(preferably high-density maps) using the genotypic data of large numbers of markers
generated for a biparental mapping population developed by crossing two genotypes
differing for the trait of interest. The biparental mapping populations which can be
used for this purpose are F2, doubled haploids (DH) and the recombinant inbred
lines (RILs). The advantage of having linkage maps is that, one can place the
markers on different chromosomes in linear order and assign distances between
these markers. When development of biparental mapping population is not possible/
feasible (particularly in case of tree species), one can use the germplasm or natural
population and genotype them using molecular markers for identification of the
QTLs/MTAs following the approach of association mapping (AM) or GWAS.
It is equally important that the population for which genotypic data has been
generated is phenotyped precisely for the trait of interest so that the data can be used
in conjunction with the genotypic data for the identification of QTLs/MTAs. Ideally,
phenotypic data recorded over seasons and locations is desirable so that QTL  envi-
ronment interactions can also be worked out. Several approaches of QTL analysis
have been proposed for the analysis of the data (reviewed by Kulwal 2018). Large
numbers of studies have been carried out following the approach of biparental QTL
mapping and GWAS in different crops for variety of traits (Gupta et al. 2011, 2014,
2019). However, not all the markers linked with these identified QTLs can be used in
the MAS program. The underlying criterion for this therefore is that the QTL which
is to be transferred through MAS must be a major effect QTL. However, in recent
years with the availability of wealth of data generated through large numbers of QTL
and GWA studies as well as meta-analysis, it has become easy to identify major QTL
and choose the type of marker for the MAS program. The advantage which MAS
offers is that it can effectively be utilized for traits having low heritability. Large
numbers of studies are now available where MAS has been utilized for the transfer of
useful QTL in the desirable genetic backgrounds in different crops leading to the
development of superior breeding lines and varieties (Varshney et al. 2013a). Given
the fact that there has been tremendous reduction in the costs of marker genotyping
and the advantages which MAS offers, it is anticipated that MAS will be used on
large scale by the breeders for crop improvement in the future.

14.6.2 Marker-Assisted Recurrent Selection (MARS)

It is well established that majority of the traits of interest are polygenic in nature and
are controlled by many genes/QTLs, each having minor effect. The problem with
deployment of these minor QTLs in the breeding program through MABC is that
they are not expressed consistently over different seasons. It therefore become
difficult to introgress multiple QTLs in a common background. Although in conven-
tional breeding recurrent selection has been suggested as an effective strategy for
14 Efficient Breeding of Crop Plants 761

improving the polygenic traits by accumulating the favourable alleles in the popula-
tion, the strategy is not very effective due to effect of environment on the phenotype
and the long time required for genotypic selection (typically 2–3 crop seasons per
cycle) (Godiki et al. 2016). In order to address this issue and to utilize these minor
effect QTLs in the breeding program, MARS has been proposed and allows geno-
typic selection and intercrossing in the same crop season (Bernardo and Charcosset
2006).
MARS utilizes markers initially for the identification and then selection of several
genomic regions associated with the complex trait(s). This then can be used to
assemble the best-performing genotype within a single or across related populations
(Ribaut et al. 2010; Jiang 2015). The advantage of MARS over MABC is that the
genetic gain achieved through the former method are more as compared to the later
since MARS deals with transfer of several QTLs as against that of only selected QTL
in the MABC. There are several successful examples in crop plants where MARS
has shown increased efficiency of selection in the breeding programs. Some of these
examples include in maize for yield improvement (Johnson 2004), for improving
grain yield under drought stress (Beyene et al. 2016), in wheat for bread making-
related traits (Charmet et al. 2001) and crown rot resistance (Rahman et al. 2020).
There are many other examples where MARS has been successfully utilized in
different crops.

14.6.3 Genomic Selection (GS)

Although conventional breeding coupled with modern breeding techniques have

helped in increasing the genetic gain to a considerable extent, it is necessary that the
rate of gain should be increased further to address the challenges of food security
(Xu et al. 2020). Genomic selection (GS) also referred to as genome-wide selection
(GWS) or genomic prediction is one of the forms of MAS, in which large numbers of
markers covering the entire genome are used to predict the genetic value of a trait or
individual. Selection for the desirable individuals is based on computing the geno-
mic estimated breeding values (GEBVs) using the markers across the genome
(Meuwissen et al. 2001; Crossa et al. 2017). This in contrast to MAS in which
only the markers tightly linked with the trait are used in the breeding program

Fig. 14.1 Figure depicting the difference between marker-assisted selection and genomic selec-
tion; the horizontal bar represent the chromosome on which mapped markers are shown in black
vertical lines, while position of QTL is shown with red rectangle
762 P. L. Kulwal et al.

(Fig. 14.1). The underlying criteria in GS is that rather than focusing on only
important or major QTLs in the breeding programs, it utilizes all the QTLs (minor
and major) by using the genome-wide markers while making the prediction. In order
to increase the accuracy of GEBV and GS, large number of markers across the
genome is thus essential so that all the QTLs are in LD with at least one marker
(Meuwissen 2007; Jiang 2015).
For undertaking the GS, a training population (TP) for which genotypic and
phenotypic data is generated is essential so that a prediction model for understanding
the relationship between the two can be developed. The genotypic data of the
breeding population is then fed into this model to calculate GEBVs for these lines
(Heffner et al. 2010). There are different ways through which these GEBVs can be
calculated. The GEBVs calculated represents the sum of the effects of all QTLs
across the genome. GS thus outperforms MAS in terms of its effectiveness (Kulwal
et al. 2012). Since there are different statistical models to estimate the breeding
values, each having its own superiority and limitations under the given scenario, one
model cannot fit all the situations (Rahim et al. 2020). It is therefore difficult to
suggest which model will work under the given scenario.
Although the technique of GS was initially proposed for use in animal breeding
(Meuwissen et al. 2001), in recent years, emphasis is given on the use of GS in the
breeding of many crops. It has also been reported that the cost per unit gain was
lower up to 55% using GS than the phenotypic selection (PS) in case of oil palm and
that GS was superior to MARS and PS (Wong and Bernardo 2008). Similarly,
superiority of GS over PS has also been reported in many crops (reviewed by
Jiang 2015; Pandey et al. 2020; Rahim et al. 2020). Although the technique of GS
appears to be promising, its success primarily depends on the size of the TP which is
used for identifying the associations. This TP should be updated frequently by
incorporation of new genotypes in the analysis so as to maintain the prediction
accuracy (Rahim et al. 2020). However, given the fact that not many breeders are
trained in the use of molecular markers on large scale and computer programs
dealing with estimation of breeding values, it is necessary that breeder friendly
software packages should be developed for such purpose. In addition, developing
the efficient models which can involve genotype  environment interaction and
achieve greater prediction accuracy are therefore required (Xu et al. 2020). It is
expected that with the reduction in the cost of marker genotyping due to advances in
the next-generation sequencing techniques, accompanied with advances in the
computational analysis, GS will become an integral part of the crop breeding
programs (Desta and Ortiz 2014).

14.6.4 Gene Editing in Plant Breeding

Crop improvement is a continuous process for ensuring food and nutritional security
for burgeoning world population. Great success has been achieved through conven-
tional plant breeding and through use of transgenics. The advantages, success stories
and limitations of transgenic technology have been reviewed in detail in several
14 Efficient Breeding of Crop Plants 763

earlier publications (see Datta et al. 2004; Husaini et al. 2011; Ahmar et al. 2020).
Due to several concerns associated with transgenic technology, new plant breeding
techniques including RNA interference (RNAi), gene silencing and gene editing are
gaining worldwide attention in different crop improvement programs. Among the
different new breeding technologies, gene/genome editing (GE) making use of site-
directed nucleases (SDNs) is considered the most important and one of the
promising technologies that can overcome the inherent limitations associated with
classical/conventional plant breeding and transgenic technology. The GE tools and
techniques are considered effective for modifying the target genome and creating
desired and novel new traits/phenotypes in crop plants. The breakthrough technol-
ogy started with sequence-specific nucleases including zinc-finger nucleases
(ZFNs), transcription activator-like effector nucleases (TALENs) and now the
most important and emerging clustered regularly interspaced short palindromic
repeats, CRISPR/Cas technology (Lloyd et al. 2005; Cermak et al. 2011; Mahfouz
et al. 2011; Li et al. 2013; Nekrasov et al. 2013; Shan et al. 2013; Tan et al. 2020).
Discovered by Emmanuelle Charpentier and Jennifer A. Doudna (Nobel
Laureates in chemistry for the year 2020), CRISPR/Cas9 genetic scissor is consid-
ered one of gene technology’s sharpest tools that can help to change the DNA of crop
plants with extremely high precision. The noble prize winning technology
“CRISPR/Cas9” can help to change the code of life of crop plants over the course
of a few weeks. CRISPR technology has been used extensively in plant genome
editing over the past few years and has a great potential for precision breeding
(Zhang et al. 2020). However, this system is also subject to some technical
limitations and some other main obstacles including consumer preference of gene-
edited food product that may hinder its application in food crops (Ahmar et al. 2020).
The progress and perspectives of the use of genomic editing tools and technologies
for their use in plant breeding have been extensively reviewed (see Varshney et al.
2019; Zimny et al. 2019; Zhang et al. 2019, 2020).
The technology has been mostly used for improvement of crop yields, quality and
stress resistance by simply knocking out one or more than one genes that control a
particular trait (Zhang et al. 2018). For instance, knocking out of genes (Gn1a, DEP1
and GS3) in cereal crop rice led to the increase in grain number, dense erect panicles
and increased grain size (Zhang et al. 2020). Similarly, in maize disruption of waxy
gene “Wx1” resulted in increase in concentration of amylopectin with enhanced
digestibility of grain. In wheat and tomato, knocking out of gene/allele “MLO”
resulted in the development of powdery mildew-resistant wheat and tomato plants
(for a review, see Zhang et al. 2020). The technology has recently revolutionized
agriculture by helping in fixing heterosis in rice hybrids (Khanday et al. 2019; Wang
et al. 2019), which is otherwise lost in subsequent generations due to segregation of
alleles in F1 hybrids.
In these studies involving fixing heterosis in rice, a genotype known as MiMe
(Mitosis instead of Meiosis) was produced by targeting important genes responsible
for meiosis, and thereby haploid plants were developed using CRISPR technology.
When MiMe genotype was combined with haploidy in hybrid rice, the clonal
progeny maintained genome-wide parental heterozygosity that demonstrates the
764 P. L. Kulwal et al.

possibility of asexual reproduction through seed propagation in crops (Khanday

et al. 2019; Wang et al. 2019). The technology of fixing heterosis in rice hybrids will
allow the maintenance of rice hybrids during propagation to subsequent generations.
This revolutionary process can reduce the cost of hybrid seed production as well will
allow farmers to produce their own hybrid seeds, reducing dependence of subsis-
tence farmers on commercial seed producers. In a study in wheat, A3A-PBE-
mediated cytidine base editing was used for editing of all the six TaALS alleles
that resulted in the development of nicosulfuron-resistant wheat lines (Zong et al.
2018). In an another study considered one of the best examples of the use of
CRISPR/Cas technology for crop improvement is CRISPR-mediated gene regula-
tion in tomato, where CRISPR technology was used to mutate the promoters of
genes responsible for controlling the most important quantitative traits including
fruit size, inflorescence branching and plant architecture (Rodriguez-Leal et al.
2017). In summary, the technique has already been used in ~20 crop species
improvement programs for the development of crops that possess high yield and
withstand biotic and abiotic stresses. The list will keep on increasing in more crops
involving improvement of important traits in the near future.

14.6.5 Role of Bioinformatics in Breeding

Bioinformatics is multi-disciplinary science, integrating biology, statistics, mathe-

matics, computer science, etc. that helps in solving the biological problems. The
need for the science of bioinformatics was strongly felt with the evolution of next-
generation sequencing technologies that helped in sequencing of genomes of almost
all important crop species. The sequencing of genomes through genome sequencing
projects led to the explosion of sequencing data produced and hence demands
conception/creation of novel discipline called “bioinformatics”. The aim of bioin-
formatics is primarily storage, acquisition, analysis, distribution and modelling of
various types of sequence data (Aslam et al. 2004). Therefore, computational
biology and bioinformatics have their roots in life science and helps to find out the
function of macromolecules, biological sequence data and genome content/genes.
In the last two to three decades, the science of bioinformatics has emerged as a
significant tool for the use of large volumes of data that have been generated using
different omic-technologies. The analysis of data through different software
programs provided vital role in extracting useful information, interpretation of data
and future decision-making process (Batley and Edwards 2008, 2009; Aslam et al.
2004). The analysis of genome sequencing data and other genotyping data through
bioinformatics tools have helped in discovery of thousands of genes in important
crop species. The identified genes will prove useful in plant breeding programs
aimed at enhancing trait performance of varieties leading to the development of next-
generation crop varieties.
The huge volume of genome sequencing data generated required development of
databases for its storage, and therefore in 1986 largest sequence databases were
developed in association of GenBank with European molecular biology laboratory
14 Efficient Breeding of Crop Plants 765

(EMBL). A number of bioinformatics online databases including crop-specific

databases are now available including BGI Rice Information System, Gateway of
Brassica Genome, ChloroplastDB, EMBL, GRAINGENES, GRAMENE, GRIN,
NCBI, LIS, KOME database, KEGG PLANT, OryGenesDb, TAIR, TREP, etc. The
complete list has been tabulated elsewhere (Aslam et al. 2004). The details of
classification of databases, databases for transcription factor in plants, small RNA
databases, genomic databases, crop-specific databases and list of different bioinfor-
matics tools for analysis of NGS data, dbEST available in different crops, etc. are
also available in different review articles (see Vassilev et al. 2005; Agarwal and
Narayan 2015; Aslam et al. 2004; Kushwaha et al. 2017). In general, there are three
primary sequence databases including GenBank (NCBI), the Nucleotide Sequence
Database (EMBL) and the DNA Databank of Japan (DDBJ). These databases are
actually repositories used for storing of raw sequence data. However, each data entry
is also extensively annotated, and important properties and features of each sequence
are also highlighted. These three important databases exchange data routinely.
Similarly, databases are also available for storing protein sequence like SWISS-
PROT and TrEMBL. The constant serge in the omics data and the emergence of
molecular breeding technologies coupled with advances in genomics and computa-
tional biology provide ample opportunities for bioinformatics to develop efficient
approaches for plant breeding.

14.6.6 Integrated System of Data Management and Delivery

With the challenges posed by the varying environments, the activities of plant
breeding have expanded in the last few decades. This has resulted in multi-
disciplinary and multi-institutional collaborations and generation of large-scale
phenotypic data, typically collected over different environments having increased
dimensionality due to use of sensors and techniques like phenomics. This is in
addition to the large-scale genomics information which is being generated routinely
due to the availability of high-throughput techniques resulting in big data. This big
wealth of data on one hand has increased the capabilities of the breeders in achieving
their goals and on the other hand has made it necessary to think about proper
management of the information. While the scientific community spends most part
of their time on generation of valuable data, only limited time is spent on proper
documentation, analysis and interpretation process.
Although there is no doubt that the key to success for any breeding program is
careful collection of the data, it is equally important that there should be proper
integration of the other parameters in the analysis process leading to the meaningful
interpretation of the results. Any wrong decision or improper interpretation of the
data can cause huge loss to any breeding program. It is therefore very important that
there should be an integrated system of data management and delivery in a plant
breeding program so that one can access, analyse and recombine the vast wealth of
data (Kuriakose et al. 2020). The advantage with this system is that, the information
generated in the experiment is not only stored carefully, but can be retrieved at any
766 P. L. Kulwal et al.

given time as per the need. This generally is not possible in the traditional way of
collecting the data. Therefore the success of any future breeding program will
depend on how strong the data management and delivery system is in place. An
excellent overview of this aspect is discussed by Kuriakose et al. (2020).
This type of setup is generally seen in many private seed companies, but lacked in
the public sector breeding programs in developing countries. It is therefore
envisioned that the primary challenge for the plant breeders in coming years will
be to design the efficient system to handle and analyse the massive amounts of
multifarious data that is generated in the breeding programs rather than access to the
modern technology (Cobb et al. 2019).

14.6.7 Speed Breeding

Ideally, any conventional breeding program involve crossing and/or selection for
successive generations (typically 4–6) followed by yield evaluation trial before a
variety is released for cultivation. Majority of the varieties so far in the world have
been released using the same approach during the last several decades. Generally
1–2 generations/cycles are possible per year in majority of the crop plants. With this
slow speed, the time required in a breeding process is too long and also slows down
the process of variety development. Although the alternate techniques like shuttle
breeding and doubled haploid can be used to shorten the time required in a breeding
program, they have their own limitations. Therefore, in order to accelerate the
process of breeding and generation advancement, a technique called speed breeding
was proposed recently (Hickey et al. 2019). As the name suggests, speed breeding
relies on use of environment-controlled growth chambers equipped with artificial
lights which can accelerate the plant growth and development so that multiple
generations of crop plants can be advanced per year (Ahmar et al. 2020). This is
very much required in today’s context because in order to produce more to feed the
growing world population, there is an urgent need to accelerate the rate of genetic
gain. While the molecular breeding techniques are efficient in introgression of the
desired gene/QTL, their utility will be enhanced only if more number of generations
are advanced per year. Speed breeding enhances the growth of the plant by
regulating light and temperature, thereby promoting early flowering and rapid
generation advancement (Bhatta et al. 2019).
Since each crop plant has differential requirement of photoperiod for normal
growth and development, the protocol established for one crop plant may not be
suitable for the other. The proper understanding of the physiology of the plant is thus
necessary. Ideally, in speed breeding, vegetative growth is enhanced by increasing
the temperature in the chamber, while it is lowered during the reproductive growth
(Hickey et al. 2019). However any such improvement comes with a cost. For
instance, flowering can be hastened in the environment-controlled chambers; how-
ever, the total biomass and yield will be impacted due to this (Bhatta et al. 2019).
However, the success achieved in achieving four to six generations per year in crops
like wheat, barley and canola (Hickey et al. 2017; Ghosh et al. 2018; Watson et al.
14 Efficient Breeding of Crop Plants 767

2018) using speed breeding shows the great promise this technique offers in the crop
improvement programs and in accelerating the speed of variety development. How-
ever, one need to weigh the cost involved in developing the facility and the
associated gains through it before investment is made on this technique.

14.7 Advances in High-Throughput Phenotyping

One of the major factors limiting progress in GAB is lack of precise phenotypic data.
Therefore, plant phenomics is considered one of the most important factors for
translating the progress made in the area of plant genomics. The area of plant
phenotyping has made huge progress in the last decade by replacing invasive or
destructive methods of phenotyping by the high-throughput precise non-destructive
methods of phenotyping (Mir et al. 2019). The advancement made has
revolutionized crop phenomics and allowed screening of large germplasm (mapping
populations, core collections and breeding material) with high precision/accuracy
with less efforts, time and labour. These advances not only have generated huge
amount of information but have also necessitated use of novel techniques for the
analysis of the big data. These issues have been discussed in the following sections.

14.7.1 Plant Phenotyping Platforms

The non-destructive high-throughput phenotyping (HTP) platforms developed and

used routinely include infrared cameras, fluorescent microscopy/spectroscopy,
three-dimensional camera, lidars (light detection and ranging), magnetic resonance
imaging (MRI) and positron emission tomography (PET), canopy spectral reflec-
tance (SR) and infrared thermography (IRT), nuclear magnetic resonance (NMR)
and digital imaging (see Mir et al. 2019 for review). The use of these HTP platforms
helps in recording trait data on thousands of plants in a single day similar to next-
generation sequencing technology in the field of plant genomics (Finkel 2009). A
number of state-of-the-art international phenomics centres/facilities have been
developed for precisely recording high-throughput phenotyping data in cost-
effective manner. Some of the important phenomics facilities include the Plant
Accelerator in Adelaide, Australia (http://www.plantaccelerator.org.au/); High Res-
olution Plant Phenomics Centre (http://www.plantphenomics.org/HRPPC) in South
Australia; the Jülich Plant Phenotyping Centre (http://www.fz-juelich.de/ibg/ibg-2/
EN/methods_jppc/methods_node.html) in Jülich, Germany; Leibniz Institute of
Plant Genetics and Crop Plant Research in Gatersleben, Germany; and the National
Plant Phenomics Centre (http://www.phenomics.org.uk/temp-site/about.html) in the
UK to name a few (Gupta et al. 2012; Mir et al. 2015, 2019). The relevant
information about plant phenotyping is being provided by the world’s major plant
phenotyping centres “International Plant Phenotyping Network (IPPN)” (https://
www.plant-phenotyping.org/). In addition, different private companies like
LemnaTec, Phenokey, PhenoSpex, Photon System Instruments, Wiwam and We
768 P. L. Kulwal et al.

Provide Solutions are offering large-scale, custom high-throughput phenotyping

platforms for the field and laboratory (Mir et al. 2019).
The different HTP phenotyping platforms that have been developed for recording
data on variety of traits in almost all crop species include “LEAF-E” developed and
used for the analyses of leaf growth parameters, “Zeppelin NT aircraft” used aerial
phenotyping “Phenovator” and “GROWSCREEN FLUORO” used for phenotyping
for photosynthesis and growth “TRiP (Tracking Rhythms in Plants)” used for
determination of circadian period. Similarly, image-based phenotyping methods
have been developed and used for measuring plant stresses including cold tolerance
and spikelet anthesis. The other phenomics platforms like” PHENOPSIS” was used
to dissect plant responses to soil water deficit, and “Unmanned Aerial Platforms
(UAP)” was used for measuring low-nitrogen (low-N) stress tolerance. The
“Hyperspectral Imaging (HIS)” was used to determine spectral changes on the leaf
and cellular level in plants during resistance reactions/host-pathogen interactions.
Like phenotypic platforms, a number of different software programs have been also
developed for recording trait data on variety of traits. A list of software programs and
phenotyping platforms for high-throughput precise phenotyping being used in
several laboratories across the world are available elsewhere (see Mir et al. 2019).
The different precise high-throughput phenomics methods/platforms already
developed have been used for trait phenotyping of variety of traits including growth
traits, phenological traits, physiological traits, scoring disease incidence, insect
damage, drought tolerance and recording data on different plant organs like roots,
seeds and shoots (for review see Mir et al. 2019). For instance, in crops like rice,
wheat, barley, maize, pea, Arabidopsis, potato, soybean, etc., different phenotyping
platforms have been used, and data has been recorded for spikelet anthesis, circadian
period, plant height, leaf growth parameters including leaf area, area phenotyping of
canopies, photosynthesis, photosynthesis efficiency, chlorophyll content, leaf nitro-
gen content and canopy height (see Mir et al. 2019 for more details). Phenomics has
also been used for the study of plant responses to various abiotic stresses including
drought, heat, cold tolerance, salinity and nutrient-starving. For drought tolerance,
trait phenotyping either in glasshouse or in field have been conducted and
approaches like osmotic balance in hydroponics to conveyer systems in glass
house to rainout shelters in the field have been used very extensively.
Several important methods and platforms that are now routinely being used for
precise high-throughput phenotyping of drought tolerance have been discussed in
detail elsewhere (Mir et al. 2012b). These methods are based on imaging, robotics
and computers that allow recording of trait data of thousands of plants in a day in
non-destructive manner. Like abiotic stresses, phenomics platforms have been also
used for recording trait data on biotic stresses like insect pests. For instance,
automated video tracking “a phenomics platform” has been developed and used to
record the aphid feeding behaviour on leaf discs that is helpful to measure plant
resistance. This platform of automated video tracking can be also used to measure
data on aphids and other piercing-sucking insects in plants in high-throughput
manner. Like insects, the platforms can be used for recording data on disease
reactions and for characterization/selection of resistant plants against fungal
14 Efficient Breeding of Crop Plants 769

pathogens. In summary, the phenomics platforms/methods/software have been used

to record data in high-throughput fashion for variety of traits in almost all important
crops, and the trait evaluation has also led to the genetic dissection leading to
discovery of genes/QTLs for several traits including root system architecture traits,
seed shape, osmotic tolerance and biomass traits in crops like rice, wheat, barley and
mustard.

14.7.2 Applications of Artificial Intelligence (AI) and Machine

Learning (ML) in Crop Breeding

Classical plant breeding techniques mainly focus on estimation of genetic diversity,

analysis of stability for different traits over different seasons and environments,
hybrid prediction using different parental combinations and related things and rely
on routine statistical methods for analysis of the data (Niazian and Niedbała 2020).
Besides this, in order to identify the desirable plant, breeder often needs to take
repeated observations in the field and make careful selection. This not only requires
lot of time, but skill and experience of a breeder. It has now been realized that in any
plant breeding program, rapid and precise phenotyping for the desired trait is very
essential. Since this involves recoding thousands of data points in shorter time, in
recent years a shift from traditional way of phenotyping to use of sensor based
phenotyping has been seen. This has been facilitated by the advances in the area of
phenomics and phenotyping platforms as discussed above. The important advantage
with these techniques is that it can enable collection of enormous and high-
dimensional data in a very short span of time. Similarly, with the advances in the
omics techniques (genomics, proteomics, metabolomics, epigenomics), the volume
of data which is being generated in any such experiment is huge. In order to handle
this huge amount of data efficiently in a breeding program and to make meaningful
interpretations, the methods which involve minimal human efforts are required for
analysing the data with increased precision (Harfouche et al. 2019).
Modern technology has been of great help to the breeders in this endeavour. For
instance, digital images of standing crop in the fields are taken from the surface or
through air with the help of drones or unmanned aerial vehicles (UAVs). This not
only saves time in recording the data but also reduces the error associated with the
manual way of recording observations. The large numbers of images or data points
so captured can be analysed using computer tools for understanding the traits and
interpreting the results. Artificial intelligence (AI) and machine learning (ML) and
variants thereof (neural networks, deep learning, etc.) are considered as the impor-
tant breakthrough in dealing with this big-data. The ML tools can collectively
analyse the phenotypic, genetic and environmental data to help breeders better
understand the relationships between genetics, environment and plant performance.
While doing this, ML method uses approximations to find out the patterns which are
embedded in the data so that it can be used to predict the future data (Murphy 2012).
Thus, AI and ML can be used practically in all aspects of breeding (including
prediction of phenotype, image identification, disease identification and genomics
770 P. L. Kulwal et al.

experiment including GWAS and GS studies) (Harfouche et al. 2019). This not only
will accelerate the process of breeding but will allow screening of large number of
accessions in a breeding experiment with increased precision in shorter span of time.
This can enable breeders in identifying the desirable plant suited for a particular
climate and soil type and identifying desirable cross combination of genes for
increased yield (Beans 2020). In recent years, different approaches of ML have
been proposed and used in plant breeding programs (Parmley et al. 2019; Kuriakose
et al. 2020; Niazian and Niedbała 2020).
Although sensors and machines can increase the volume of data, they cannot
replace experience of a breeder. Moreover, since breeders generally are not experi-
enced in the algorithms which are used in ML, therefore, any such experiment
requires close cooperation between statisticians, IT specialists and experienced
breeders. It is expected that with the growing awareness about AI and ML and
quest for better algorithms involved in analysis and interpretation of the data, they
will become an integral part of breeding programs in the future.

14.8 Emerging Challenges at National and International Level

Although plant breeding has contributed immensely and resulted in achieving self-
sufficiency in many crops in several countries, with the pressure of ever-growing
world population and the impact of climate change resulting in uncertain
environments, the task of plant breeders has become more challenging. In the future,
the main task before the breeders will be to develop varieties with higher productiv-
ity having better adaptability to the changing climates. The important challenge
which breeders need to address is to develop the varieties which are suited to the
specific agroecological regions rather than developing mega-varieties. In addition,
emphasis need to be given on varieties which offer better nutrient use efficiency and
requiring less resources so that they can offer economic benefits to the farmers.
Similarly, another challenge before the breeders will be to develop varieties which
can offer food security for the increasing world population and sustainable
agriculture.

14.9 Future Thrust Areas and Conclusions

While plant breeding is often considered as an art and science of genetically

improving plants and no technique can substitute plant breeding, it needs to adapt
to the advances in digital revolution so as to integrate it with molecular techniques
for the benefit of humankind. For this purpose, plant breeders need to sync them-
selves with the advances in the area of genomics and phenomics and embrace
modern techniques like AI and ML to increase its effectiveness and to address the
challenges of the future. Although the impact of plant breeding in increasing the food
productivity is known to everyone, it is still necessary that the subject should be
considered as priority by all. Integration of promising techniques like MAS and GS
14 Efficient Breeding of Crop Plants 771

Fig. 14.2 Figure depicting different breeding schemes from conventional to efficient using
genomic resources

in the breeding program can offer increased genetic gains. This probably seems to be
the only way through which we can ensure/achieve food security in more sustainable
way. In addition, emphasis on exploiting the potential of the PGRs is very essential.
Moreover, the novel methods like speed breeding and genome editing technique like
CRISPR/Cas can allow rapid generation advancements of a breeding cycle and
development of genetic diversity for breeding purpose, respectively, and are very
promising if used in proper manner. To conclude, rather than using technologies in
isolation, integration of modern and efficient techniques in the breeding program can
help in achieving food security in a sustainable manner in long run (Fig. 14.2).

Acknowledgements PLK would like to thank Department of Biotechnology, Govt. of India for
the research grants during the course of writing this article. RKV thanks Bill and Melinda Gates
Foundation, USA, for supporting several projects related to genomics-assisted breeding at
ICRISAT and acknowledges Science and Engineering Research Board (SERB), Department of
Science and Technology, Government of India, for awarding JC Bose National Fellowship.

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Brassica Breeding
15
Devendra Kumar Yadava, Yashpal, Navinder Saini,
Joghee Nanjundan, and Sujata Vasudev

Abstract

Rapeseed-mustard belongs to Brassicaceae (syn. Cruciferae) family, is the third

major oilseed crop globally. It is the second most important edible oil crop and
ranks first in terms of contribution (>30%) to the indegenous edible oil produc-
tion in India. Though significant progress has been made in India in terms of area
(1.5 times), production (3.4 times), and productivity (2.2 times) of rapeseed-
mustard since the launching of the National Mission on Oilseeds during
1985–1986, there is a need to increase the productivity vis-à-vis production to
check the increasing import bills on edible oils. The global programmes on
Brassica are more focused on Brassica napus and B. rapa, whereas Indian
programme is concentrating more on Brassica juncea which is occupying around
90% of the total area under rapeseed and mustard. The chapter highlights the
historical importance of rapeseed-mustard in the global oil economy, its origin,
and evolutionary process, floral biology, breeding objectives, progress made in
the varietal improvement, and future targets with the strategies to achieve them.
Conservation of enormous genetic diversity of the different coenospecies of
Brassica and its use in the pre-breeding/breeding activities have also been
highlighted. A good number of varieties have been developed, and some of
these varieties like Pusa Bold, Pusa Jai Kisan, Pusa Agrani, Varuna, RH
30, Laxmi, Pusa Mustard 30, and Pusa Mustard 25 have been the land mark

D. K. Yadava
Crop Science Division, Indian Council of Agricultural Research, Delhi, India
Yashpal · N. Saini · S. Vasudev (*)
Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
J. Nanjundan
Indian Agricultural Research Institute, Regional Station, Wellington, Tamil Nadu, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 779
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_15
780 D. K. Yadava et al.

varieties contributing significantly to the national edible oil production. Presently

more focus is being given in developing hybrids, climate resilient varieties, and in
improving the oil/meal quality traits. A series of low erucic acid and canola
quality varieties of B. juncea and B. napus have been developed which meet
the global standards for erucic acid and glucosinolates. Short-duration varieties
developed during the last decade have impacted the oilseed area expansion in
non-traditional areas and also helped in crop diversification in traditional
mustard-growing belts. Heat tolerance at seedling and reproductive stages, toler-
ance to salinity, and drought are the focused areas of research under the changing
climatic scenarios, and a good number of climate resilient high-yielding varieties
are in the seed chain. Biotic stresses like Sclerotinia stem rot, Alternaria blight,
Orobanche, and aphids are required to be addressed on priority in the future
programmes through the use of modern biotech tools including genome editing.
Marker-assisted selection for introgression of quality and white rust resistance
traits is already in progress which needs to be augmented further.

Keywords
Rapeseed-mustard · Breeding objectives · Improved varieties · Genetic resources ·
Brassica species

15.1 Introduction

Rapeseed-mustard group of crops belonging to Brassicaceae (syn. Cruciferae) fam-

ily, is the third major oilseed crop at the global level, after soybean and palm oil.
China, Canada, India, Germany, the UK, France, and Australia are the major
producers of rapeseed-mustard. Brassicaceae (syn. Cruciferae) family currently
includes 3709 species and 338 genera (Warwick et al. 2006) and is one of the
most economically important plant families (Rich 1991). At the end of the fiscal year
2019, India produced more than nine million metric tons of rapeseed and mustard
(https://www.statista.com/statistics/769713/india-rapeseed-and-mustard-produc
tion-oilseeds; Statista.com). In India, rapeseed-mustard is the second most important
oilseed crop after soybean. Rapeseed-mustard commonly falls under the genus
Brassica which constitute a group of crops that are used as vegetables (Brassica
oleracea cv. cabbage, cauliflower, and broccoli), condiments (Brassica nigra,
i.e. mustard/rai seeds), and the edible oil (Brassica juncea, Brassica rapa, Brassica
napus, and Brassica carinata) extracted from their seeds. These crops are the chief
sources of edible oil in the Indian diet, and the de-oiled cake with a high concentra-
tion of proteins and minerals is a rich source of animal feed. Among these oleiferous
Brassica spp., Brassica juncea (Indian mustard) is a predominant crop, occupying
around 90% area of rapeseed-mustard per se.
Though the area in the country has been static with minor fluctuations over the
years, there has been a significant 33% increase in the production (from 6.28 million
tons in 2014–2015 to 9.34 million tons in 2018–2019) and a 38% increase in the
15 Brassica Breeding 781

productivity (from 1083 kg/ha during 2014–2015 to 1499 kg/ha in 2018–2019), due
to the modern scientific interventions, concerted efforts of the breeders and other
stake holders. During 2018–2019, Rajasthan emerged as major mustard-growing
state with a lion’s share of ~60% (Agricultural statistics 2019). Mustard has been
introduced in several non-traditional states like Assam, Meghalaya, Tripura, Sikkim,
and Arunachal Pradesh in northeast and Andhra Pradesh, Telangana, Karnataka, and
Tamil Nadu in the south during the last decade. The short duration varieties, viz.
Pusa Agrani, Pusa Mahak, Pusa Mustard 25, Pusa Mustard 27, Pusa Mustard
28, Pant Rai 20, etc., have given encouraging performance in these
non-conventional mustard-growing areas. With the development and introduction
of short duration (100–110 days) Indian mustard varieties, some area of B. rapa
cv. toria has also been replaced by B. juncea in plains as well as in northeastern
states.

15.2 Origin, Evolution, and Distribution of Species, Forms and

Wild Relatives

The tribe Brassiceae can be split into eight distinct lineages or clades (Arias et al.
2014). Three of these clades diverged earlier from the others, while the rest are
generally thought of as the core Brassiceae. The genus Brassica itself contains three
distinct lineages: lineage A comprises species with ten chromosomes (B. rapa),
lineage B comprises species with eight chromosomes (B. nigra), and lineage C
(B. oleracea) comprises species with nine chromosomes. Some Brassica species
have also undergone another round of polyploidization and interspecific
hybridization, leading to the rise of new Brassica allopolyploid species: B. juncea,
B. napus, and B. carinata. Their progenitor species all come from different lineages:
B. juncea (n ¼ 18) stems from B. rapa (lineage A) and B. nigra (lineage B), B. napus
(n ¼ 19) stems from B. rapa and B. oleracea (lineage C), and B. carinata (n ¼ 17)
stems from B. nigra and B. oleracea. These relationships were discovered very early
on by Morinaga (1934) and Nagaru (1935). These six species have been known as
the U’s Triangle species ever since Nagaharu (1935) demonstrated that Brassica crop
species comprise three diploid species and three amphidiploid species.
It was believed that the three diploid species originated from one common
ancestor. However, molecular investigations summarized by Gómez-Campo and
Prakash (1999) point to a common origin for B. rapa and B. oleracea, while
B. nigra evolved from a separate progenitor. The cytogenetic relationship between
the Brassica species established by Nagaharu (1935) was later confirmed by chro-
mosome pairing and artificial synthesis (Axelson et al. 2000), nuclear DNA content,
DNA analysis, and by the use of genome-specific chromosome markers (Hasterok
et al. 2001).
Brassica juncea (L.) Czern. and Coss., known as oriental, brown, or Indian
mustard, is believed to be one of the earliest domesticated plants. It is described in
Sanskrit texts as early as 3000 BC (Hemingway 1995). B. juncea spread to Europe as
a medicinal crop during the middle ages. Today, B. juncea is used worldwide as an
782 D. K. Yadava et al.

oilseed, a condiment, and a vegetable (Edwards et al. 2007) crop. Wild forms of
Brassica juncea have been found in the near east and southern Iran. According to
Vavilov (1949), Afghanistan and its neighbouring regions (Central Asia) were the
primary centre of the origin of Brassica juncea. Multiple centres of origin for
B. juncea have been proposed by others, where the putative progenitors,
B. campestris (syn. rapa) and B. nigra, had geographic sympatry, leading to
conflicting views about the origin of B. juncea (Bhowmick 2003). The Middle
East has been proposed as the most probable place of origin of B. juncea as wild
forms of its progenitor species B. rapa and B. nigra occur together in this region
(Olsson 1960a, b; Mizushima and Tsunda 1967; Prakash and Hinata 1980; Gómez-
Campo and Prakash 1999). The regions of south-western China and North Western
Himalayas may constitute two secondary centres where there is enormous diversity
in B. juncea forms. Biochemical studies support this finding of the diversity in these
regions (Vaughan et al. 1963) and further provide evidence for the existence of two
geographical races of B. juncea, the Chinese pool and the Indian pool (Vaughan and
Gordon 1973). This evidence is supported by Song et al. (1988) through RFLP
studies which suggest two centres of origin: (a) the Middle East and (b) China.
However, Rakow (2004) had opined that China cannot be considered as a centre of
origin for B. juncea because the two-parent species B. nigra and B. campestris (syn.
rapa) were never found as wild species in that country.
B. juncea is an annual crop that grows as cultivated, weedy escapes, or wild forms
in coastal lowlands, sandy beaches, plateaus, and mountainous regions. It has a wide
geographical range, spanning the continents of Europe, Africa, Asia, America, and
Australia. B. juncea is closely related botanically to canola (B. napus) and turnip
rape (B. rapa) and has a similar growth habit (Hemingway 1976). The genera
Brassica display enormous diversity, and a range of wild and weedy species occur
in nature which are related to the cultivated genus. However, most of these species in
the wild germplasm belong to secondary and tertiary gene pools, reproductively
isolated, and invariably show strong incompatibility barriers. A list of economically
important species of genus Brassica and its close allies along with their uses is
presented in Table 15.1, and those grown in India are given in Table 15.2.

15.3 Genetic Resources: Improvement of Cultivated Species

Successful varietal development program needs continuous supply of resource genes

for crop yield, quality, and various biotic and abiotic stress tolerance traits. A major
shift in yield level of any crop plant with increased tolerance to biotic and abiotic
stresses is possible only with the extensive genetic manipulation through breeding.
This requires systematic efforts in the management of global crop genetic resources
in the face of emerging challenges like climatic change, resource degradation, habitat
destruction, species invasion, deforestation, etc. There are many unaddressed issues
where genetic solutions are possible by systematic use of available genetic resources.
Despite attaining many highs in rapeseed mustard crop improvement with the release
of 203 varieties for different situations, still there exists a gap between the achieved
15 Brassica Breeding 783

Table 15.1 Economically important Brassica species

Botanical Chromosome
name Common name Genome no. Usage
Brassica rapa (syn. B. campestris) AA 20
spp. oleifera Turnip rape Oilseed
var. brown Brown sarson Oilseed
sarson
var. yellow Yellow sarson Oilseed
sarson
var. toria Toria Oilseed
spp. rapifera Turnip fodder Vegetable (root)
spp. chinensis Bok choi Vegetable (leaves),
fodder (head)
spp. Chinese cabbage Vegetable (leaves)
pekinensis
spp. – Vegetable (leaves)
nipposinica
spp. – Vegetable (leaves)
parachinensis
Brassica nigra Black mustard BB 16 Condiment (seed)
Brassica CC 18
oleracea
var. acephala Kale Vegetable, fodder
(leaves)
var. capitata Cabbage Vegetable (head)
var. sabauda Savoy cabbage Vegetable (terminal buds)
var. Brussels sprouts Vegetable (head)
gemmifera
var. Kohlrabi Vegetable, fodder (stem)
gongilodes
var. botrytis Cauliflower Vegetable (inflorescence)
var. italic Broccoli Vegetable (inflorescence)
var. fruticosa Branching bush Fodder (leaves)
kale
var. Chinese kale Vegetable (stem, leaves)
alboglabra
Brassica Indian mustard AABB 36 Oilseeds, vegetable
juncea
Brassica AACC 38
napus
spp. oleifera Rapeseed, gobhi Oilseed
sarson
spp. rapifera Rutabaga, swede Fodder
Brassica Ethiopian mustard BBCC 34 Vegetable, oilseed
carinata
Eruca sativa Rocket, taramira EE 22 Vegetable, non-edible
oilseed
Raphanus Radish RR 18 Vegetable, fodder
sativus
Sinapis alba White mustard SS Oilseed
784 D. K. Yadava et al.

Table 15.2 Rapeseed and mustard crops grown in India

Botanical Botanical
name Common name name Common name
Brassica Indian mustard, sarson, Rai, Raya, B. tournefortii Panjabi rai, Jangali rai
juncea Laha, Rayda, Banga sarson
B. juncea var. Vegetable mustard, Rai B. nigra True mustard, black
cuneifolia mustard, Banarasi rai
B. rapa spp. Turnip B. pekinensis Chinese cabbage-
oleifera heading
B. rapa var. Brown sarson, Kali sarson B. napus Gobhi sarson
brown sarson
B. rapa var. Yellow sarson, Pili sarson B. carinata Karan rai, Ethiopian
yellow sarson mustard
B. rapa var. Toria, Rai, Lahia, Magni achara rai Eruca sativa Taramira, rocket salad
toria
Source: Mishra and Kumar (2008)

and achievable (Nanjunadan et al. 2020). From 1998 onwards, a good number of
genetic resources including genetics stocks, varieties, and germplasm lines for
different important traits have been procured, developed, released, and registered
with NBPGR. At present, more than 11,119 mustard accessions are being conserved
at the National Bureau of Plant Genetic Resources, New Delhi. An equal number is
being maintained at the Directorate of Rapeseed-Mustard Research, Bharatpur, and
different AICRP centres located at various State Agricultural Universities and ICAR
Institutes. Good success has been made in the development of quality Indian mus-
tard cultivars, where stable donors like Heera and EC 597325 for low glucosinolates
were used and the first Double Zero variety Pusa Mustard 31 was released from
ICAR-IARI in 2016. Later RLC-3 (2017), Pusa Double Zero Mustard 33 (2021), and
hybrid RCH 1 were released. Varieties like Pusa Karishma (LES-39), LES-1-27
(Pusa Mustard 21), LET-17 (Pusa Mustard 22), LET-18 (Pusa Mustard 24), LET-36
(Pusa Mustard 29), LET-43 (Pusa Mustard 30), LES-54 (Pusa Mustard 32), RLC
1, and RLC 2 for low erucic acid are currently available for cultivation. As far as
abiotic stresses are concerned, a good number of varieties like CS-52, CS-54, CS-56,
CS-60 (salt tolerant), Pusa Vijay (NPJ-93), Pusa Mustard 25 (NPJ-112), Pusa
Mustard 27 (EJ-17), Pusa Mustard 28 (NPJ-124) (heat tolerant), and RGN-13,
RGN-48 (frost tolerant) have been developed and are available in the public domain.
Well-established short duration genotypes, viz. Pusa Agrani (SEJ-2), Pusa Mahak
(JD-6), Pusa Tarak (EJ-9912-13), Pusa Mustard 25 (NPJ-112), Pusa Mustard
27 (EJ-17), Pusa Mustard-28 (NPJ-124), Kranti, NDRE-4, PR-2006-1, Divya
(IC-553910), Pant Rai 19, etc., with 100–120 days maturity have been developed
which can be further exploited for breeding early maturing and high-temperature-
tolerant Brassica juncea varieties. For white rust resistance breeding Bio-YSR,
BEC-144, BEC-286, EC-399299, EC-399301, RC-781, JM-1, Heera, etc. are stable
sources and are being used widely in the national programme.
15 Brassica Breeding 785

15.4 Floral Biology: Emasculation—Pollination Techniques

B. juncea is an annual herbaceous plant. The plants are tall (90–200 cm), erect and
branched. The fruits (siliquae) are slender, 2–6.5 cm long, strongly ascending, or
erect with short and stout beaks. The colour of the seed is yellow or brown. The seed
coat is rough. Figure 15.1a–d provides the structure of flower, inflorescence, and
silique of B. juncea.
The leaves are alternate (rarely opposite), and maybe coriaceous, very often
pinnately incised, and do not have stipules. The inflorescence is corymbose raceme
type. Flowering is indeterminate, beginning at the lowest end on the main shoot and
continues upward. Flowers are ebracteate, pedicillate, complete, hypogynous, and
actinomorphic. Calyx comprises four sepals in two whorls each. Anteroposterior
sepals form the outer whorl, whereas lateral ones form the inner whorl. Sepals are
pale green in colour. Corolla comprises four cruciform petals. These are clawed and
regular. Two functional nectaries are located at the base of the short stamens and two
non-functional nectaries are at the base of the long stamens. The androecium is
tetradynamous and consists of six stamens arranged in two whorls. The longer four
stamens form the inner whorl and are arranged in anteroposterior pairs. The two
shorter stamens form the outer whorl and are present in a lateral position. Anthers are
bithecus and basifixed. The gynoecium is usually bicarpellary, syncarpus, and
superior with carpels transversely placed. It is bilocular due to the presence of a
false septum. Placentation is parietal; the ovary is usually sessile with many ovules,
short style, and bifid stigma.
The mature bud flowers within 2 h after sunrise. The stigma becomes receptive
2–3 days before the flower opens and thus facilitates selfing by bud pollination
(Kumar 2001). The dehiscing side of anther sacs faces the stigma, but as the time of
dehiscence approaches, the inner whorl of two anthers undergoes a twist of 60 –
180 which results in extrose dehiscence in the case of the self-incompatible types.
The dehiscence of all the anthers in self-compatible types is introse. B. juncea is a
predominantly self-pollinated crop (Labana et al. 1992). However, in some
environments out crossing varies from 7.6% to 22% (Dhillon and Labana 1988;
Ram et al. 1991; Abharam 1994). Pollen can live up to 4 or 5 days when the

A B C D (brown and Yellow seeded)

Fig. 15.1 (a) Flower (b) inflorescence (c) siliquae (d) seeds of Brassica juncea
786 D. K. Yadava et al.

temperature is low and humidity is high. With warm temperatures and low humidity,
survival time may drop to 1 or 2 days (Mayers 2006). Brassica pollen is viable even
after 4 h of stress at 60  C (Rao et al. 1992) however, under experimental conditions,
it has been observed that pollen could remain functional for a year or more in dry
storage at 20  C (Brown and Dyer 1990).
Pollination is carried out both by insects and wind. Wind can carry pollen over
long distances as pollen counts of up to 22 pollen grains/m3 were observed 1.5 km
away from the source field and were sufficient to affect the seed set on bait plants
(Timmons et al. 1995). The extent of wind pollination was recorded up to 11–17.5%
(Singhal et al. 2005). Bees however are the primary pollen vector because the pollen
is heavy and sticky and is not carried to great distances in the absence of wind
(Labana and Banga 1984). Bees visit flowers for nectar; the positioning of nectaries
is such that in self-incompatible types, the body of the bee gets smeared with pollen
and in self-compatible types, the bee affects self-pollination by pressing the inner
whorl of introrsely dehisced anthers while extracting nectar thus bringing them in
contact with the stigmatic surface (Kumar 2001). The stigmas remain receptive
3 days before opening to 3 days after opening of the flowers (Singh and Rai
2004). Bees may carry pollen over long distances and have been found foraging in
fields more than 4 km away from the hive (Eastham and Sweet 2002), resulting in an
outcross seed set. Besides the physical carrying of pollen grains, bee visitations also
cause pollens to become airborne. Airborne pollen grains can then be carried by the
wind, leading to cross-pollination. Cross-pollination of nearby plants can also result
from physical contact with the flowering racemes.
The extent of wind pollination in B. juncea cv. Pusa Bold was studied in New
Delhi, India. Dispersal of pollen grains by the wind was noticed up to 35 m from the
pollen source (Balasubramanian 2011). Airborne pollen grains may pass through
insect-proof nets, and effective pollination may occur. The commonly used method
of reproductive isolation in the case of B. juncea is spatial isolation. The
recommendations made on isolation distance for production of foundation seed
and certified seed of 96% purity of self-fertile B. juncea are 200 and 50 m, respec-
tively (Anonymous 2013).

15.5 Breeding Objectives

In general, plant breeding has four fundamental steps:

• Goal setting: Taking a cue from economic and biological factors, methodologies
are selected.
• Generating new diversity: Continuous breeding for a particular set of desirable
traits has eroded genetic variability. Sufficient genetic variability must be avail-
able for any trait and the crop to be improved. If necessary, the genetic base of the
breeders’ gene pools can be widened through mutation breeding using gamma
rays or EMS techniques. Introgression of single genes or traits or by a large-scale
15 Brassica Breeding 787

infusion of new germplasm through base broadening/wide hybridization can also

be used for generating diversity.
• Selection: The improvement of a character or a crop is achieved through selection
after the crosses are made between the chosen parents with desirable traits. The
selection methods used in plant breeding differ between inbreeding,
crossbreeding, and vegetatively propagated crops.
• Cultivar release: After the rigourous cycles of selection and testing, the
improved genotype is released and marketed (Nanjundan et al. 2020; Tandon
et al. 2015).

B. juncea breeders aim to make simultaneous improvements of agronomic per-

formance, disease resistance and quality traits, and developing suitable varieties for
non-traditional areas (southern states) and rice-fallows in eastern and northeastern
states. Agronomic performance includes yield, lodging, maturity, herbicide toler-
ance, drought tolerance, shattering resistance, and seed size. Disease resistance
efforts may include Sclerotinia stem rot (Sclerotinia sclerotiorum), white rust
(Albugo candida), Alternaria blight (Alternaria brassicae), downy mildew
(Peronospora parasitica), and powdery mildew (Erysiphe cruciferarum) resistance.
Improvements in quality traits will depend on whether the aim is to develop canola
or conventional mustard varieties. For canola, high oil content, low glucosinolate
content (<30 ppm), high protein content, and a fatty acid profile with low erucic
(<2%) and low saturated fatty acid content (~7%) are desired. For conventional
mustard varieties, high oil content, high glucosinolate content, and a fatty acid
profile with a moderate level of erucic acid are aimed commonly (Yadava et al.
2014).
The major breeding objectives for mustard crop are as follows

15.5.1 Increased Seed and Oil Yield

In oilseed crops, oil content determines the economic yield and market rate of the
produce. In rapeseed-mustard the oil content ranges from 35% (E. sativa/
B. carinata) to 46% (B. rapa spp. yellow sarson); thus, despite the fact that the oil
content is a complexly inherited trait, there is ample scope for raising its present level
in largely cultivated species like B. juncea and B. napus.

15.5.2 Abiotic Stresses

High-temperature stress at the time of sowing leads to high seedling mortality and
thus poor seedling establishment and plant stand. Plants exposed to high-temperature
stress at the reproductive stage show high pollen mortality, increased flower drop,
decrease in the number of siliquae, and decreased seeds per siliqua. High tempera-
ture also affects the translocation of photosynthates; thus plants exposed to high
temperature have shriveled/small seeds with reduced oil content. The problem is
788 D. K. Yadava et al.

more severe in the late sown crops. Frost is another abiotic stress that occurs after
every 57 years and causes massive losses; hence, breeding for frost tolerance needs
to be addressed. Soil with salinity and sodicity is also occupying significant area;
hence the ongoing efforts need to be continued on breeding varieties for salinity
tolerance too.

15.5.3 Biotic Stresses

Sclerotinea stem rot, white rust caused by Albugo candida, and Alternaria blight are
major diseases and need to be addressed. Likewise, Orobanche a parasitic weed
creates havoc on this crop in some regions. Breeding for tolerance to Orobanche
should be undertaken on priority. Mustard aphid (Lipaphis erysimi) and painted bug
(Bagrada hilaris) are insects of economic importance and cause huge losses to the
rapeseed-mustard crop at various stages of growth. Breeding for resistance to these
two insects also needs to be undertaken.

15.5.4 Seed and Oil Quality

Erucic acid and glucosinolates are two major antinutritional components in the oil
and seed meal cake of conventional Brassica varieties being grown in India. Low
erucic acid with increased oleic acid and a balanced proportion of omega-3 and
omega-6 fatty acids and enhanced oil content (>42%) are desirable features in
quality Indian mustard varieties. Having achieved the development and release of
“00” canola quality (erucic acid < 2% in seed oil and glucosinolates < 30 μmoles/g
in defatted seed meal) Indian mustard varieties, the Indian breeding program now
has to think of “Triple Zero” quality rapeseed mustard varieties ie. genotypes with
high oleic acid (>60%) and low fibre content in addition to the “00” traits.

15.5.5 Early Maturity

Short duration varieties are needed to fit into different cropping systems of the
country especially in eastern and northeastern regions. Toria is low yielder and
vulnerable to most of the biotic and abiotic stresses; therefore, Indian mustard
varieties like Pusa mustard 25 and Pusa mustard 28, that mature in about
100 days, are a good substitute of toria. Indian mustard varieties that can mature in
80 days without compromising the yield should be targeted for fitting this crop in
multiple cropping systems and also as a real substitute to B. rapa ssp toria.
15 Brassica Breeding 789

15.5.6 Plant Type

More concerted efforts are needed to identify suitable plant types for different crop
geometries and cropping systems. Dwarf plant type (<120 to 150 cm) with basal
branching and amenable to mechanical harvesting is need of the hour for making this
crop more competitive and less labour-intensive. To achieve this, the plant type has
to be tailored with required component traits including determinate growth habit.

15.5.7 Exploitation of Heterosis and Commercial Hybrid

Development

Unlike in most other crops, no natural cytoplasmic male sterility and fertility
restoration (CMS-FR) system was available in B. juncea. The major emphasis during
the initial phase of hybrid breeding was towards the development of CMS-FR
systems using alloplasmic variation. Cytoplasmic male sterile lines could be devel-
oped by backcross substitution of B. juncea genomes in the cytoplasmic background
of wild crucifers. CMS lines originating from sexual hybridizations possess unal-
tered organelle genomes because of exclusive maternal inheritance.
With the availability of a highly effective hybrid seed production mechanism,
heterosis is being exploited commercially in oilseed Brassica. A number of
cytosterility sources from Brassica coenospecies, viz. Diplotaxis siifolia (Rao
et al. 1994), Raphanus sativus (Bannerot et al. 1974; Kirti et al. 1995a),
B. tournefortii (Banga et al. 1994; Rawat and Anand 1979), B. oxyrrhina (Prakash
and Chopra 1990), Trychystoma ballii (Kirti et al. 1995b), Moricandia arvensis
(Prakash et al. 1998), D. catholica (Prakash et al. 2001), Enarthrocarpus lyratus
(Banga et al. 2003a; Janeja et al. 2003), Erucastrum canariense (Prakash et al. 2001;
Banga et al. 2003b), synthetic B. napus ISN-706 (Sodhi et al. 2006), D. erucoides
(Bhat et al. 2006), and D. berthautii (Bhat et al. 2008), were identified and used for
the development of CMS lines and restorers. A number of such CMS systems are
now available for use in the active hybrid development (Table 15.3).
Varying degrees of leaf chlorosis were found to be associated with Raphanus/
Ogu, Oxyrrhina, Tournefortii, Moricandia, and Enarthrocarpus systems. Floral
abnormalities in male sterile plants included petaloid anthers (nigra, muralis,
trachystoma, raphanus, tournefortii, canariense); poor or absent nectarines
(tournefortii and raphanus); crooked style (tournefortii, raphanus); thick pistil
(raphanus); and low seed fertility (raphanus, tournefortii, enarthrocarpus, and
trachystoma). Fertility restorers for Moricandia, Ogura, catholica, and erucoides
and lyratus CMS systems could be developed by introgressing gene(s) for fertility
restoration from donor wild species cytoplasm (Prakash et al. 2009). Fertility restorer
for the mori CMS could also restore fertility in eru CMS system (Bhat et al. 2005).
Mainly, two CMS sources, Moricandia and Ogura, are being used in the Brassica
hybrid development programme in India. In addition, two more CMS systems,
viz. erucoides and berthautii, in which fertility is restored by common restorer line
with that of Moricandia are also being used in IARI, New Delhi. With an objective
790 D. K. Yadava et al.

Table 15.3 Various CMS systems reported in Brassica spp

Cytoplasm Technique Restoration
donor Code used status Crops References
Diplotaxix sif Intergeneric Not B. juncea Rao et al. (1974,
siifolia cross available 1994)
Raphanus ogu Interspecific Available B. napus Bannerot et al.
sativus cross, B. juncea (1974), Kirti
protoplast et al. (1995a),
fusion Ogura (1968)
B. tournefortii tour - Unstable, B. napus Banga et al.
genotype- B. juncea (1994), Rawat
specific and Anand
partial (1979)
restoration
B. oxyrrhina oxy Interspecific Not B. juncea Prakash and
cross, available Chopra (1990,
protoplast Kirti et al.
fusion (1993)
Trachystoma trachy Protoplast Incomplete B. juncea Kirti et al.
ballii fusion (1995b)
Moricandia mori Protoplast Available B. juncea Prakash et al.
arvensis fusion (1998), Malik
et al. (1999),
Prakash (2001),
Bhat et al.
(2006)
D. sietiana Sie Intergeneric Not B. juncea Prakash et al.
cross available (2001)
D. catholica cath Intergeneric Available B. juncea Prakash et al.
cross (2001), Pathania
et al. (2007)
Enarthrocarpus lyr Intergeneric Available B. juncea Deol et al.
lyratus cross B. napus (2003), Banga
et al. (2003a, b),
Janeja et al.
(2003)
Erucastrum can Intergeneric Available B. juncea Prakash et al.
canariense cross B. napus (2001), Banga
et al. (2003a, b)
Synthetic 126-1 Interspecific Available B. juncea Sodhi et al.
B. napus cross (2006)
ISN-706
D. erucoides Eru Intergeneric Available B. juncea Malik et al.
cross (1999), Bhat
et al. (2006,
2008), Prakash
et al. (2001)
D. berthautii bar Intergeneric Available B. juncea Bhat et al.
cross (2008)
Brassica fruticulosa – Available B. juncea Kaur Atri et al.
fruticulosa (2016)
Source: Kumar et al. (2020)
15 Brassica Breeding 791

of nuclear diversification of different CMS sources into the desired genotype,

backcrosses have been attempted at IARI, New Delhi; DRMR, Bharatpur; PAU,
Ludhiana, and CCSHAU, Hisar. A total of around 200 CMS lines in different
genetic backgrounds have been converted using mori, eru, ber, and ogu cytosterlity
sources. Heterotic combinations are being evaluated at multiple locations, and
potential hybrids are expected to be identified soon.

15.6 Breeding Approaches: Conventional

and Non-conventional Including Use of Genomic Tools

Being a heterogeneous group of crops in terms of their pollination control, almost all
breeding methods are being employed for the genetic improvement of different
Brassica spp.

15.6.1 Different Varieties Developed by Following Various Breeding

Methods Are Given Below

• Pureline Selection: Gobhi Sarson—GSL-1, Neelam, NUDH-26-11; Yellow

sarson—Benoy, Jhumka, Ragini, etc.
• Mass selection: Black mustard-Surya; Yellow sarson—YSPb-24; Taramira—
ITSA, RTM-314, T-27; Toria—Agrani, Bhawani, TL-15, M-27, PT-303,
RAUTS, ITSA, T-9.
• Pedigree Method and Its Modifications: B. juncea—Aravali, RGN-48, RGN-13,
NRCDR-2, CS-54, Pusa Mahak, Jagannath, Pusa Agrani, Pusa Bold, RH-781,
RH-819, RL-1359, Vasundhra, Vardan, Vaibhav, Ashirwad, Pusa Mustard
24, Pusa Mustard 25, Pusa Mustard 26, Pusa Mustard 27, Pusa Mustard
28, Pusa Mustard 29, Pusa Mustard 30, Pusa Double Zero Mustard 31, Pusa
Mustard 32, Pusa Double Zero Mustard 33 etc.; B. napus—GSC-5, GSC-6,
GSC-7, GSL-2, Sheetal; Karan rai-PC-5, Pusa Swarnim, Pusa Aditya; Yellow
sarson—Subinoy, Gujrat Sarson-1.
• Recurrent Selection: Toria—PT-30.
• Synthetics and Composites: Composites: Toria—Jawahar toria-1, Panchali,
PBT-37, PT-507, TH-68; Synthetics: Toria-Sangam, Brown sarson-Pusa
Kalyani.
• Backcrossing: B. juncea—JM-1, JM-2, JM-3, Pusa Karishma, Pusa Mustard
21, Pusa Mustard 22; B. napus—OCN-3. Modifications of backcross methods,
such as limited backcrossing followed by pedigree selection, help in defect
elimination and generating larger genetic variation simultaneously.
• Mutation Breeding: B. juncea—Geeta, RLM-619, RLM-514, TM-2, TAM
1028-1, Birsa Bhabha Mustard 1 (BBM1), Trombay Him Palam Mustard-1
(THPM-1); Toria—Anuradha, Parbati; Yellow sarson—Narendra sarson-2.
• Hybrids: At present, Raphanus sativus (ogu), Moricandia arvensis (mori), and
synthetic B. napus ISN-706 (126-1) cytosterility systems are being used for the
792 D. K. Yadava et al.

Table 15.4 Hybrids of rapeseed-mustard released in India

Year of Brassica CMS
S. No Hybrid release spp Institute/organization system
1 PGSH-51 1996 Brassica PAU, Ludhiana Tournefortii
2 Hyolla 401 (PAC 1997 napus Advanta India Ltd. Ogura
401)
3 PGSH 1699 (GSH 2021 PAU, Ludhiana Ogura
1699)
4 NRCHB 506 2008 Brassica DRMR Bharatpur Moricandia
5 Coral 432 (PAC 2010 juncea Advanta India Ogura
437)
6 Coral 437 (PAC 2012
437)
7 Dhara Mustard 2010 NDDB, Delhi University CMS,
Hybrid-I (DMH-I) “126-1”
8 SVJH 108 2021 Shakti Vardhak Hybrid Ogura
Seeds Pvt., Ltd., Hisar
9 RCH 1 2021 PAU, Ludhiana Ogura
10 PHR 126 2021 PAU, Ludhiana Ogura

development of commercial hybrids in Brassica. Seven hybrids of B. juncea

(NRCHB 506, DMH 1, RCH-1, PAC 437, PAC 432, PHR 126, SVJH 108) and
three of B. napus (PGSH 51, PAC 401, PGSH 1699) have been released for
commercial cultivation in India (Table 15.4). Possibility of using genetic male
sterile (GMS) lines in GMS Facilitated Recurrent Selection in self-pollinated
species can be explored with the availability of stable and good outcrossed
seed-producing GMS system.
• Tissue Culture: Alloploid Brassica species were artificially resynthesized by
crossing the respective diploid Brassica species followed by embryo rescue.
This led to development of a short duration variety Pusa Agarni in Brassica
juncea at IARI, New Delhi. Using synthetic B. juncea, short duration varieties,
viz. Pusa Mustard 25, Pusa Mustard 26, and Pusa Mustard 28, were developed.
Most of the breeding programmes are directed towards improvement of mega
varieties, and due to repeated cycles of such breeding, there is great loss of
variability, and the gene pool becomes narrow. Somaclones are important source
of variation when the genetic variability is limited in the germplasm. Pusa
Jaikisan (Bio 902), a somaclone of cultivar Varuna developed at NIPB, New
Delhi, released for commercial cultivation is one of the best examples.

15.6.2 Development of Altered Plant Type

To amenable the brassica crop suitable for mechanised harvesting efforts are going
on for the development of determinate type Brassica juncea and B. carinata. Efforts
15 Brassica Breeding 793

are also going on for developing newer plant types in these species which are dwarf
and possess basal branching.

15.6.3 Embryo Rescue Technique for Interspecific Crosses

Abraham et al. (2000) at BARC, Mumbai, reported somaclonal variants from

mesophyll protoplast in B. juncea cv. Rai 5 which showed 3–5 days early flowering.
Optimization of regeneration protocols has been achieved for most of the Brassica
species using different explants such as cotyledons, hypocotyls, leaf segments,
protoplasts, cotyledonary petiole, and shoot apex (Narasimhulu et al. 1989; Kirti
and Chopra 1989). Somaclonal variation as a tool for creating in vitro variability
offers a unique opportunity for desirable attributes. A somaclone of Varuna,
Bio-902, has been released as a variety which possesses shattering resistance
along with high yield (Katiyar and Chopra 1995). Prakash et al. (2004) reported
regeneration of normal plants by culturing anthers of CMS line of B. juncea carrying
Diplotaxis erucoides cytoplasm.
Somatic cell fusion of sexually incompatible species has also been made possible
through the production of somatic hybrids which have been utilized for the transfer
of desirable traits from parents to hybrids. Interspecific hybrids were produced by
fusing mesophyll protoplast of B. juncea and B. spinescens (Kirti et al. 1991).
Prakash et al. (1998) developed a male sterility and fertility restoration system in
B. juncea by protoplast fusion with Moricandia arvensis. These CMS lines were
found to be chlorotic. Protoplast fusion of chlorotic male sterile B. juncea with green
male sterile B. juncea resulted in green male sterile plants (Kirti et al. 1997). Stable,
fertile somatic hybrids between Sinapis alba and Brassica juncea were successfully
developed which show resistance to Alternaria brassicae and heat stress (Kumari
et al. 2018). Kumari et al. (2020) developed stable allohexaploids of
B. juncea + S. alba and their backcross progeny which provides new insights into
the genetic inheritance of traits such as the resistance to Sclerotinia stem rot and
yellow seed colour. As these allohexaploids have been confirmed for their crossabil-
ity with diploid and amphidiploids of cultivated Brassica, introgression of
Sclerotinia stem rot and yellow seed colour into other Brassica spp. could be
exploited. Singh et al. (2021) identified quantitative trait loci governing resistance
to Alternaria blight introgressed from S. alba to the backcross population of stable
S. alba + B. juncea somatic hybrids (2n ¼ 60; AABBSS), and the identified QTLs
explaining 5.51–10.87% of the phenotypic variations for the resistance to Alternaria
brassicae in the backcross progeny of Sinapis alba + Brassica juncea somatic
hybrids.
794 D. K. Yadava et al.

15.7 Precise and High-Throughput Phenotyping Protocols

for Key Traits

To combat the increasing challenges of climate change, a highly reproducible and

rapid protocol for screening against high temperature at the seedling stage has been
standardized which is proving very helpful in the identification of donors for high-
temperature tolerance (Singh et al. 2012a). This protocol has helped in the develop-
ment of high-temperature-tolerant varieties which can establish even under very high
temperatures (up to 40  C) during plant establishment stage. In case of quality
breeding programme, a new method for methyl esterification of fatty acids in
Brassica seed oil has been developed which helps in phenotyping of large number
of samples for analysis of fatty acids (Sujata et al. 2008). This new method has
revolutionized the quality breeding programme, and as a result series of low erucic
acid and double low varieties, viz. Pusa Mustard 29, Pusa Mustard 30, Pusa Mustard
31, Pusa Mustard 32, and Pusa Mustard 33, have been developed.
Sclerotinea stem rot (SSR) caused by Sclerotinea sclerotiorum (Lib.) de Bary is
becoming a havoc in mustard-growing areas of India. A rapid and reliable screening
technique standardized for the first time in Brassica napus has demonstrated that a
cotyledon assay can be successfully applied to rapidly differentiate the reactions of
B. napus genotypes against S. sclerotiorum (Garg et al. 2008). Mei et al. have
reported a “detached stem assay method” under a controlled environment for
screening Brassica crops for resistance against Sclerotinia sclerotiorum. Gupta
et al. (2020) reported a field-based non-injury method of inoculation technique for
SSR in oilseed Brassica, caused by Sclerotinia sclerotiorum (Lib.) de Bary

15.8 Development of Molecular Markers and Linkage Maps

The discovery of high levels of inter as well as intra-specific DNA polymorphism in

RFLP profiles, obtained with random genomic DNA clones used as probes, by
Figdore et al. (1988) encouraged molecular mapping of Brassica genomes and
tagging of genes for several useful traits. Different mapping populations at F2 or
later stages (F3, F4, or recombinant inbred lines) have been used to construct genetic
maps in B. oleracea (Slocum et al. 1990; Kianian and Quiros 1991), B. nigra (Truco
and Quiros 1994), B. campestris/B. rapa (Chyi et al. 1992; Kole et al. 1997),
B. napus (Hoenecke and Chyi 1991; Landry et al. 1991), and B. juncea (Sharma
et al. 1994; Mohapatra et al. 2002; Sharma et al. 2002). Backcross mapping
population has been used to generate maps for B. nigra (Lagercrantz and Lydiate
1995), and doubled haploid (DH) mapping population has been used to construct
maps of B. oleracea (Voorrips et al. 1997; Li and Quiros 2001; Saal et al. 2001),
B. napus (Ferreira et al. 1994; Uzunova et al. 1995; Foisset et al. 1996), and
B. juncea (Cheung et al. 1997; Axelson et al. 2000). Apart from these, a combination
of mapping populations has also been used. Ramsay et al. (1996) and Kearsay et al.
(1996) have used backcross individuals of DH lines to generate maps of B. oleracea.
Some maps were also constructed using RAPD, AFLP, and SSR markers (Sharma
15 Brassica Breeding 795

et al. 2002; Pradhan et al. 2003, 2011). Pradhan et al. (2003) constructed a high-
density genetic linkage map of B. juncea (2n ¼ 36) using AFLP and RFLP markers
in an F1-derived doubled-haploid population. The number of publicly available
Brassica microsatellite primers is increasing as a result of publicly funded interna-
tional initiatives (http://www.Brassica.info/ssr/SSRinfo.htm).
The release of a set of robust, highly polymorphic, mapped SSR markers span-
ning the entire B. napus genome into the public domain greatly assisted in genome
mapping and gene tagging. To enrich the SSR resource further, Federico et al. (2008)
developed 587 new primer pairs flanking SSRs using sequence information from
3500 genomic clones mainly from B. oleracea to identify di-, tri-, tetra-, and penta-
nucleotide repeats. Yadava et al. (2009) evaluated the cross-transferability and
polymorphic potential of the genomic SSRs to assess their utility across Brassica
species and related genera. The study revealed that the available SSR markers can be
used effectively in monitoring gene introgression. Nevertheless, a large set of
markers should be used to overcome the low level of intra-specific polymorphism
(Koundal et al. 2008). Sun et al. (2007) used sequence-related amplified polymor-
phism (SRAP) to construct an ultra-dense genetic recombination map for a doubled
haploid population in B. napus. Gao et al. (2007) constructed a high-density genetic
map of B. oleracea adding over 1000 new markers to Brassica molecular tools.
Panjabi et al. (2008) designed and tested the efficacy of PCR-based intron polymor-
phism (IP) markers to analyse genome-wide synteny between the oilseed B. juncea
and A. thaliana and analysed the arrangement of 24 genomic block segments in
the A, B, and C Brassica genomes to study the evolutionary events contributing to
karyotype variations. These recently reported SRAP and IP markers should find
application in tagging of useful genes in oilseed Brassica crops.

15.8.1 Molecular Markers Studies in Decoding Genetic Diversity

and Assisting Selection of Superior Genotypes

With the development of genomic resources in oilseed Brassica species, emphasis

had been focused on using DNA/molecular markers for multiple purposes. Several
studies have advocated the use genetically diverse genotypes or genotypes of
different geographical regions to harvest high heterosis in comparison to the local
or closely related genotypes. This in turn emphasized the importance of genetic
diversity evaluation in the plant material for the selection of the most appropriate and
promising parents for breeding programmes. The molecular/DNA markers have
found profound use in genetic diversity analysis because of their reproducibility,
abundance, and distribution, and they are free from the environmental factors’
influences, proving them to be a better marker system over morphological marker.
Molecular marker-based approach is more likely to generate an unbiased picture of
diversity than that obtained by employing agro-morphological traits. Genetic diver-
sity analysis using various types of molecular markers, such as randomly amplified
polymorphic DNA (RAPDs), inter-simple sequence repeats (ISSRs), restriction
fragment length polymorphisms (RFLPs), amplified fragment length
796 D. K. Yadava et al.

polymorphisms (AFLPs), simple sequence repeats (SSRs), expressed sequence tags

(ESTs), and single-nucleotide polymorphisms (SNPs), provides unique
opportunities to accurately evaluate the genetic variability present in a given popu-
lation for various traits. Several studies carried out till date are presented in
Table 15.5.

15.8.2 Disease Resistance

Molecular markers have been generated for the genes conferring resistance to
Leptosphaeria maculans, Plasmodiophora brassicae, Xanthomonas campestris,
Sclerotinia sclerotiorum, Verticillium wilt, turnip mosaic virus, and white rust in
different Brassica spp. Cheung et al. (1997) identified one co-segregating dominant
RFLP marker x140a, mapped on LG7 in B. juncea and designated as Acr. In the
same year, white rust resistance locus Ac21 present in an Eastern European source
that was effective against a Canadian isolate of the pathogen was mapped using
RAPD markers (Prabhu et al. 1998). Mukherjee et al. (2001) mapped a locus
designated as Ac2(t) effective against Indian isolate of the white rust pathogen.
Varshney et al. (2004) developed a tightly linked marker using AFLP, and a
PCR-based cleaved amplification polymorphic sequence (CAPS) marker for closely
linked RAPD marker for white rust resitance. Two independent loci for conferring
resistance to Albugo candida in the east European germplasm of Indian mustard
were reported (Panjabi et al. 2010). Several transgenic approaches to incorpo-
rate resistance have also been applied. Borhan et al. (2010) used WRR4 gene to
develop white rust resistance through Agrobacterium-mediated transformation.
Chhikara et al. (2012) transferred antifungal genes chitinase and ribosome-
inactivating gene to develop Alternaria blight resistance. Hada et al. (2015) used
Agrobacterium-mediated transformation for the LETgene thaumatin and developed
improved resistance to salinity, drought, and Alternaria blight in Brassica. Ali et al.
(2017) developed enhanced resistance to Erysiphe cruciferarum using over-
expression of BjNPR1.

15.8.3 Oil Content and Fatty Acid Composition

Both oil quantity and quality traits have been studied using molecular markers. Ecke
et al. (1995) mapped three loci on different linkage groups in B. napus using RFLP
markers. In B. juncea, Sharma et al. (1999) identified three loci based on segregation
of RAPD markers in a recombinant inbred population. Zhao et al. (2006) reported
mapping of QTLs for oil and protein content in rapeseed. Delourme et al. (2006)
reported that additive effects are the main factors contributing to variation in oil
content. Two RAPD markers, K-011100 and 25a, were generated and linked to the
linolenic acid concentration (Hu et al. 1995; Tanhuanpaa et al. 1995). RAPD
markers linked to oleic, linolenic, and linoleic acid were identified in B. napus
(Hu et al. 1999). Markers linked to genomic regions controlling linolenic acid
15 Brassica Breeding 797

Table 15.5 Role of molecular markers in revealing genetic diversity in Indian mustard (Brassica
juncea)
S. No. Plant material used Markers used Significant results References
RAPD marker
1 12 Indian and 32 RAPD primers 595 total alleles, Jain et al.
11 exotic B. juncea 500 polymorphic (1994)
genotypes of canola alleles, average of
quality 11.8 polymorphic
alleles per primer
2 52 B. juncea 30 RAPD markers 198 polymorphic Rabbani
germplasm including amplicons, a low et al.
41 accessions from level of (1998)
Pakistan, 6 oilseed polymorphism
cultivars, and between the oilseed
5 Japanese vegetable accessions collected
cultivars from Pakistan
3 30 Indian and exotic 4 RAPD markers 21.54–59.36% level Ali et al.
germplasm of genetic (2007)
accessions of polymorphism
B. juncea
4 45 B. juncea 15 RAPD markers A total of 92 RAPD Khan et al.
genotypes fragments, of which (2008)
comprising 81 (88%) were
37 germplasm polymorphic, each
accessions, primer produced 4–9
5 advanced breeding amplified products
lines, and 3 improved with an average of
cultivars 6.13 bands per primer
5 9 varieties of 4 RAPD markers In total, Saha et al.
4 Brassica spp 59 reproducible DNA (2008)
including B. rapa, bands generated, of
B. napus, B. juncea, which 58 bands were
and B. oleracea polymorphic with a
size range from
212 to 2272 bp. The
UPGMA cluster
analysis divided all
the varieties into two
distinct groups
6 9 varieties of 4 RAPD markers In total, Ghosh
Brassica species 59 reproducible DNA et al.
bands generated, of (2009)
which 58 (98.03%)
bands were
polymorphic; cluster
analysis divided the
9 accessions into
2 major groups
7 4 RAPD markers A high degree of Khan et al.
genetic (2011)
(continued)
798 D. K. Yadava et al.

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
15 B. juncea lines of polymorphism
exotic and local among the Brassica
origin lines with average
genetic distance
ranging from 14.45 to
25.43%; a high level
of genetic
dissimilarity reported
among the
14 genotypes
8 34 B. juncea lines 12 RAPD markers A total of 57 DNA Gami et al.
comprising 6 parental fragments obtained, (2013)
genotypes and their out of which 48 were
28 F1 hybrids polymorphic showing
84.63%
polymorphism; the
genetic resemblance
ranged from 0.32 to
0.96, showing that
significant genetic
variation exists
among various
combinations of
mustard lines; the
dendrogram grouped
all the parental
genotypes into one
cluster and all F1s in
the other cluster
9 50 diverse genotypes 10 agro- 100% polymorphism Singh et al.
of B. juncea morphological traits for all the 12 primers; (2013)
including 12 exotic and 11 RAPD a lack of association
and 38 indigenous markers between genetic and
genotypes phenotypic diversity
10 30 B. juncea lines and RAPD markers A total of 104 loci Tahira
varieties with an average of 8.6 et al.
bands per primer and (2013)
size range between
300 bp and 3 kb; on
an average, 84%
similarity was
observed among all
the genotypes
11 5 varieties of 4 RAPD markers A total of 20 alleles Yousuf
B. juncea reported with a et al.
genetic (2013)
polymorphism level
of 0–66.66%
(continued)
15 Brassica Breeding 799

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
12 4 Brassica cultivars 6 RAPD markers Out of 43 fragments Sharma
(2 of B. juncea and generated, 38 were et al.
1 each of B. nigra and found to be (2015)
B. rapa) polymorphic; cluster
analysis grouped
B. juncea and B. rapa
cultivars in one group
and B. nigra cultivars
in the second group
13 Seven individuals of 3 RAPD markers Result of cluster
introgressed Brassica analysis indicated
lines (Binasarisha-5/ that the nine
Daulot) and two of accessions were
their parental lines classified into two
major groups—one
consists of only one
parent Daulot
(Brassica juncea)
while another
consists of
Binasarisha-5
(Brassica napus) and
all introgressed lines
of C6 generation
(treated with
colchicine in C1
generation) resulted
from the cross
B. napus and
B. juncea
14 Ten mustard varieties 10 RAPD markers The RAPD cluster Wani et al.
pattern showed four (2017)
major clusters,
cluster-1 comprised
of Rohini and
Varuna, cluster-II
Narendra Rai and
Maya (EC-98),
cluster III Kanti and
Urvashi. Similarly
cluster IV including
Pusa Jaikisan and
Pusa Agrani. The
varieties Pusa Tarak
(EJ9912-13) and
GM-3 occupied
distinct places in the
dendrogram, thereby
indicating its
(continued)
800 D. K. Yadava et al.

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
distinctiveness from
other varieties
15 6 Brassica genotypes 20 primers A total of 231 scored Raza et al.
band, generated 87% (2020)
polymorphic bands.
Average PIC, MRP,
RP, MI, and EMR
values were 0.088,
0.65, 6.7, 0.78, and
8.9, respectively
ISSR markers
1 93 genotypes from 8 ISSR markers A total of 86 highly Huangfu
24 wild populations reproducible ISSR et al.
bands; most of the (2009)
variation (54.09%)
occurred among the
population and the
remaining (45.91%)
variance was
attributed to
differences among
individuals within
populations
2 30 Indian mustard 20 ISSR markers A total of 156 bands Yadav and
genotypes with an average of 7.8 Rana
bands per primer, out (2012)
of which 115 were
polymorphic
RAPD markers
1 Forty-two genotypes RAPD, ISSR, and Combination of Kalita
of different oilseed Anchored-SSR 11 informative et al.
Brassica spp. markers primers belonging to (2007)
including 28 of all the 3 DNA marker
B. juncea, 4 of profiles could
B. carinata, 3 of precisely identify all
B. napus, 1 of the 28 B. juncea
B. nigra, 5 of genotypes. These
B. campestris, and informative primers
1 of Eruca sativa can be employed in
varietal identification
in oilseed Brassica
species
2 20 varieties of RAPD and ISSR Mean PIC value Ahmad
B. juncea markers greater for RAPD et al.
(0.419) with an (2012)
average of 9.3 alleles
per primer, whereas
in the case of ISSR
markers, 0.261 as
(continued)
15 Brassica Breeding 801

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
average PIC value
with an average
number of 6.8 alleles
per primer
3 15 varieties of 43 RAPD and Out of 43 amplified Sankhla
B. juncea 31 ISSR markers RAPD primers, et al.
42 were found to be (2015)
polymorphic with an
average of 6.09
alleles/primer, while
30 out of 31 ISSR
markers resulted in
polymorphic
amplicons; 2 main
clusters of varieties
RFLP markers
1 5 accessions of Indian SDS-PAGE and one A polymorphism Mir et al.
mustard RFLP marker level of 28.57% (2015)
obtained by protein
profiling, whereas
RFLPs exhibited a
comparatively very
high level of
polymorphism
(87.5%)
AFLP markers
1 21 established and 21 AFLP markers A 62.2% Srivastava
9 synthetic varieties polymorphism; a total et al.
and lines of B. juncea of 1251 scorable (2001)
originated from Asia, fragments, of which
Australia, Canada, 778 bands were
Europe, and Russia polymorphic with an
average of
37 polymorphic
bands per primer pair;
3 distinct clusters
2 77 breeding lines of 10 AFLP markers A total of Burton
B. juncea from 751 scorable et al.
Canada, Australia, fragments with an (2004)
and 15 lines of average of
quality mustard from 26 polymorphic
India, China, Russia, bands per primer pair
and Australia (35%); 5 major
clusters
3 16 Chinese vegetable 14 AFLP markers A total of 66 scorable Qi and
mustard (B. juncea fragments, of which Zhang
var. tumida) 29 bands were (2008)
accessions polymorphic with an
average of 21.1%
(continued)
802 D. K. Yadava et al.

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
polymorphic bands
per primer
combination; 2 main
groups
Cross-transferability studies of SSR markers
1 All the species of U’s 100 genomic STMS 87.5% cross- Yadava
triangle, Eruca sativa markers developed transferability in et al.
and Arabidopsis earlier in B. napus, 3 genotypes of (2009)
thaliana B. oleracea, B. rapa, B. juncea
and B. nigra
2 75 germplasm 25 SSRs derived A cross- Sadia et al.
accessions of from B. napus, transferability rate of (2010)
B. napus, B. rapa, B. nigra, B. oleracea, more than 90%
B. nigra, B. juncea, and B. rapa obtained in various
and B. carinata Brassica species
3 11 different species 161 Brassica Out of 161 SSR Singh et al.
of Brassica and allied species-derived markers, only 70 of (2012b)
genera genomic-SSRs them (43.5%)
demonstrated their
transferability to at
least 1 of the
11 species
4 12 varieties of 124 SSRs derived 81 cross-transferable Thakur
B. juncea from B. nigra, SSRs in B. juncea et al.
B. rapa, B. oleracea, background with an (2015)
and B. napus average of 2.17
alleles/locus; an
overall cross-
amplification
efficiency of 84.8%
of SSR loci
5 All the three primary 124 SSRs derived A 100% cross- Thakur
diploids and three from B. nigra, transferability rate et al.
amphidiploids B. rapa, B. oleracea, obtained for (2018)
species of U’s and B. napus B. juncea and three
triangle subspecies of
B. rapa; the average
percentage of cross-
transferability across
all the 7 species was
98.15%
6 21 accessions 460 EST-SSRs A total of Singh et al.
representing 200 amplicons, of (2018)
19 species from which 150 (75%)
8 different genera of exhibited cross-
Brassicaceae family transferability; of
which 121 (80.67%)
EST-SSRs were
found to be
(continued)
15 Brassica Breeding 803

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
polymorphic with
PIC value ranging
from 0.09 to 0.66
7 An international 15 genomic and Almost similar Batley
germplasm collection 10 novel polymorphism levels et al.
of 86 B. napus and EST-derived SSR found in both the (2003)
43 B. juncea lines markers species, with an
average of 11.1
alleles/locus (4–31)
in B. napus and 10.6
alleles/locus (2–24)
in B. juncea;
EST-SSRs showed
lesser polymorphism
than genomic-SSRs
with an average of 6.5
alleles/locus as
compared to12.6
alleles/locus with
genomic-SSRs
8 Resynthesized 46 A- and B- A total of 198 alleles Bansal
B. juncea (11), genome-specific SSR with 2–12 alleles/ et al.
diploid progenitor markers locus and PIC values (2009)
genotypes (B. nigra, from 0.2 to 0.89, the
B. rapa, 19) and dissimilarity
natural B. juncea coefficient ranging
(4 genotypes) from 0.13 to 0.74
9 120 different 39 SSR markers A total of Turi et al.
accessions of 162 scorable bands, (2012)
Brassica species in which 105 were
including B. napus, polymorphic
B. juncea, and
B. rapa of Pakistan
origin
10 37 genotypes of 10 Brassica-derived 41 alleles with Chandra
Indian mustard for SSR markers 97.56% et al.
Alternaria blight polymorphism; (2013)
tolerance 5 separate groups
11 44 Indian mustard 12 morphological 134 SSRs reported Vinu et al.
genotypes including traits and 143 SSR polymorphism and a (2013)
varieties/purelines markers total of 355 alleles
from India and few amplified; 4 clusters
exotic genotypes
from Australia,
Poland, and China
12 27 genotypes of 15 RAPD and RAPD markers Gupta
Brassica species 3 EST-SSR markers resulted in >91% et al.
(23 B. juncea polymorphism (2014)
varieties, 2 B. napus percentage with an
(continued)
804 D. K. Yadava et al.

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
genotypes, and 1 each average PIC value of
of B. campestris and 0.31, 4.44 marker
B. oleracea) index, and 6.89
average resolving
power; for
EST-SSRs, 86.66%
polymorphism
percentage reported
along with average
PIC value of 0.28,
marker index of 0.94
and resolving power
of 0.269; all the
genotypes of
B. juncea grouped
into one cluster and
other B. species
formed a separate
cluster
13 30 genotypes 24 B. rapa-derived 72% polymorphism Prajapat
belonging to SSR markers with a total of et al.
B. juncea, B. rapa, 84 alleles, with 0.933 (2014)
B. napus, and highest allele
B. carinata frequency and PIC
values in the range of
0.12–0.79
14 A diversity fixed 158 nuclear-SSRs 158 nuclear-SSRs Akhtar
foundation set and 9 chloroplast amplified 241 alleles, et al.
(DFFS) of B. juncea SSR markers while 9 chloroplast- (2015)
comprising specific SSRs could
48 accessions amplify 34 cpSSR
alleles; the different
diversity groups
obtained did not
show full compliance
with structure
analysis, especially
for the nuclear
genetic variation
15 20 Indian mustard 65 Brassica-derived 25 polymorphic SSRs Pratap
genotypes SSRs with 3.52 average et al.
(14 advanced number of alleles/ (2015)
breeding lines, locus and 0.351
4 tolerant germplasm average PIC value;
accessions, 1 tolerant 2 distinct clusters
check PAB 9511, and separating resistant
a susceptible check and susceptible
Varuna) for genotypes
Alternaria blight
tolerance
(continued)
15 Brassica Breeding 805

Table 15.5 (continued)

S. No. Plant material used Markers used Significant results References
16 25 genotypes of 25 EST-SSRs 2–5 alleles per locus Singh et al.
B. juncea and wild detected with PIC (2016a, b)
relatives values ranging from
0.22 to 0.66
17 Indian and exotic 32 genomic-SSRs 16 polymorphic Sudan
genotypes of and EST-SSRs markers; 54 alleles et al.
B. juncea derived from B. rapa with an average of (2016)
2.37 alleles per locus
and 0.31 as the
average PIC value;
3 distinct clusters
18 Indian mustard Two CAPS markers The developed CAPS Saini et al.
genotypes markers for FAE1.1 (2016)
and FAE1.2 used in
B. juncea for
differentiating
between LEA and
HEA lines
19 27 Indian mustard Promoter-based The markers based on Saini et al.
genotypes markers developed promoter (2019)
polymorphism
distinctly
differentiated the
genotypes between
LEA and HEA group
20. 48 mustard genotypes 20 SSR markers 50% polymorphism Baghel
was detected. et al.
48 genotypes were (2020)
divided into 3 major
groups, group ‘I’
contained
17 genotypes, group
‘II’ hold
24 genotypes, and
core group ‘III’
included 7 genotypes
Source Singh et al. (2020)

concentration in B. napus corresponding to fad3 (omega-3-desaturase) gene in

A. thaliana (Arondel et al. 1992) were also identified (Jourden et al. 1996a, b;
Thormann et al. 1996). In another study, a single QTL containing six markers
associated with oleic, palmitic, and linoleic acid content was detected in B. rapa
(Tanhuanpaa et al. 1996). In B. juncea, Sharma et al. (2002) mapped two major
QTLs influencing oleic acid level using both single factor analysis of variance and
interval mapping. Erucic acid loci have been linked to RFLP markers by Ecke et al.
(1995), Thormann et al. (1996), Jourden et al. (1996c), and Barret et al. (1998) in
B. napus. Two QTLs underlying the variation of seed erucic acid content were
assigned to two linkage groups of B. juncea map using double haploid mapping
806 D. K. Yadava et al.

populations derived from high  high erucic acid hybrid (Gupta et al. 2004). Qiu
et al. (2006) constructed a genetic linkage map consisting of 277 loci and identified
reproducible QTL for seed oil and erucic acid content. The SRAP markers based on
B. napus FAE1 gene developed by Rahman et al. (2008) were expected to be highly
useful in MAS for erucic acid content.
Several SNPs have been reported to distinguish FAE1.1 and FAE1.2 in LEA and
HEA genotypes of B. juncea (Gupta et al. 2004). These SNPs were converted into
CAPS markers and have been successfully used in marker-assisted breeding of
B. juncea (Saini et al. 2016). The complete co-segregation between SNPs at position
591 and 1265 in CDS of FAE1.1 gene and at position 237 in case of FAE1.2 with
erucic acid content was reported by Saini et al. (2016).
The sequence comparison of the promoter region of FAE1 of different Brassica
species (Zeng and Cheng 2014; Chiron et al. 2015; Li et al. 2017) provides insight
into the differences in regulation of genes controlling the erucic acid content in the
seed. Yan et al. (2015) identified the polymorphism in the promoter region of
FAE1.1. The FAE1 promoter is a seed-specific promoter (Zeng and Cheng 2014;
Chiron et al. 2015), phylogenetically conserved in related species of Brassica. The
B. oleracea and Capsella rubella promoter region were found to be 48.7% similar
compared to 84.9% between coding regions (Li et al. 2017). The allelic variation
based on length polymorphism in the promoter region was exploited to develop the
polymorphic markers to be used in the breeding programme to develop the low
erucic genotypes in B. juncea. These markers were validated in diverse genotypes
and are highly efficient (Saini et al. 2019).
A reduced erucic acid in the total fatty acid profile increases the oleic acid (C18:1)
fraction, as a malfunction of FAE1 genes results in the failure of conversion of C18:1
to C20:1 or C22:1 (Yashpal et al. 2020). This in turn results in a better ratio of
linoleic and linolenic fatty acids in the oil (Jagannath et al. 2011). A series of
hypomorphic and null mutations in the FAD2.A5 isoform were characterized, and
four of these were combined with null mutations in the other two isozymes, FAD2.
C5 and FAD2.C1, in Brassica napus. The resulting mutant lines contained 71–87%
oleic acid in their seed oil, compared with 62% in wild-type controls (Shuangyi et al.
2019). In yet another attempt to improve oleic acid content, by performing chemical
mutagenesis using ethyl methanesulfonate, mutant winter rapeseed breeding lines
were developed that can produce oil with a high content of oleic acid (C18:1, more
than 75%) and a low content of linolenic acid (C18:3, less than 3%) (Spasibionek
et al. 2020). However, all these studies have been academic exercises and have yet to
perform in the field.

15.8.4 Seed Glucosinolate Content

Ripley and Roslinsky (2005) reported an ISSR marker tightly linked to high level
of 2-porpenyl glucosinolate. It has a good potential to be used for MAS for low
glucosinolate in the canola breeding programme. Ramchiary et al. (2007) used a
recurrent backcross selection (RSB) method with a doubled haploid
(DH) interspersing backcross generations for the introgression of low glucosinolate
15 Brassica Breeding 807

alleles from an east European B. juncea line, Heera into an Indian variety, Varuna. A
validation study on a population of low glucosinolate DH lines derived from all the
backcross generations of the RSB breeding programme revealed that the QTL
detected in BC4DH were the ‘true’ QTL. This study was extended by Bisht et al.
(2009) who mapped a total of six QTLs for this trait. Hasan et al. (2008) reported
four genes involved in the biosynthesis of indole, aliphatic, and aromatic
glucosinolates that might be associated with known quantitative trait loci for total
seed glucosinolate content in B. napus. In association with mapping of seed
glucosinolate (GS) content using the 60K Brassica Infinium single-nucleotide poly-
morphism (SNP) array in 520 oilseed rape accessions, a total of 11 peak SNPs
significantly associated with GS content were detected and validated by the
qRT-PCR analysis of their expression profiles (Qu et al. 2015). In another study,
the QTLs for 2-propenyl glucosinolates (GSLs) colocalized with the QTLs for
3-butenyl GSLs between At1g26180 and BnapPIP1580 on LG08 and accounted
for an average of 42.3% and 42.6% phenotypic variation for 2-propenyl and
3-butenyl GSLs, respectively. Joint QTL mapping and RNA-sequencing analyses
revealed one candidate gene of IIL1 (LOC106416451) for GSL metabolism in B.
juncea (Khattak et al. 2019).

15.8.5 Seed Coat Colour

RFLP markers linked to seed coat colour in B. napus were identified using the BSA
approach (Van Deynze et al. 1995). Seed coat colour trait in B. campestris was
tagged with RAPD markers using B. campestris-oleracea addition lines (Chen et al.
1997). Two RFLP markers flanking one of the interacting loci were identified. Negi
et al. (2000) tagged the seed coat colour trait using AFLP markers through BSA in
B. juncea. Bulked segregant RNA-Seq (BSR-Seq) of BC9 population of yellow
mustard and brown mustard was used to identify the candidate genes controlling the
yellow seed colour in Brassica juncea L., and the seed coat colour gene was mapped
to chromosome A09 (Huang et al. 2020). Twenty thousand nine hundred fifty four
DEGs from transcriptome comparisons of seeds sampled from a pair of B. rapa
accessions with different seed size, seed colour, and oil content at seven seed
developmental stages identified a group of cell cycle-related genes whose expression
was positively correlated with SZ increase and identified a conserved TT8-involved
complex which may determine the seed colour through downregulation of the key
TF gene TT8 and its targets TT3, TT18, and ANR in the flavonoid pathway (Niu et al.
2020).

15.9 Biotechnological Developments

in Brassica/Genomics-Assisted Breeding

To address the new emerging challenges biotechnological interventions have also

been made in the Indian mustard breeding programme with the available tools and
techniques. Many attempts have been made by scientists to improve Brassica using
808 D. K. Yadava et al.

molecular markers like amplified fragment length polymorphism (AFLP), simple

sequence repeat (SSR), single-nucleotide polymorphism (SNP)-based maps (Raman
et al. 2014), etc. Molecular markers such as random amplified polymorphic DNA
(RAPD), restriction fragment length polymorphism (RFLP), AFLP, and SSR have
been used for improving selection efficiency and selecting plant genotypes with the
desired combinations of traits. Markers linked with white rust resistance (Prabhu
et al. 1998), fatty acids, oil content, yellow seed colour, and fertility restoration have
been reported. Transgenic approaches have been followed to develop the transgenic
for aphid resistance, male sterility, AB tolerance, herbicide resistance, and drought
tolerance. Bar, barnase, and barstar based herbicide resistance and genetic male
sterility have been used in the development of experimental hybrids (Jagannath et al.
2002). Lectin gene for aphid resistance and DREB gene construct for drought
tolerance are being used. Osmotin (from tobacco) for drought and salt tolerance,
annexin gene for stress tolerance, chitinase and glucanase (from Arabidopsis) for
tolerance to Alternaria blight disease, and FAE1 gene for low erucic acid mustard
cultivar are other transgenes being used in rapeseed-mustard.

15.10 Progress in Genetic Enhancement

Up to 1970, mass and pure line selection were the main breeding methods used in
breeding programmes, and 26 varieties were developed. The first variety was
released in 1936. After 1980, varieties developed through hybridization increased,
and 22 varieties were released in each of the eighth and ninth decade of the twentieth
century. This number further increased to 41 during the first decade of the twenty-
first century. Simultaneously, 12 varieties have been developed through mutation
breeding. It is believed that most of the Indian mustard varieties were the pure line
selections derived from a very few common ancestors, and a limited number of
donors were utilized in the breeding programme resulting in a narrow genetic base.
Since the early 1980s, systematic and vigorous recombinant breeding has been
followed, and a large number of varieties have been identified and released. The first
notified variety was ITSA of toria (B. rapa) in 1973 after the adoption of official
notification of varieties in 1969 under the Seed Act 1966 (Section 5). The major
objectives of the varietal improvement programme have been genetic enhancement
for seed and oil yield through developing varieties for early, timely, and late sown
conditions to cater to the need of diverse agroecological situations of the country,
improvement of oil (low erucic acid), and seed meal (low glucosinolate) quality,
introgression of resistance/tolerance against major biotic (white rust, Alternaria
blight, Sclerotinia rot diseases, and aphid and painted bug insects) and abiotic
stresses (drought, high temperature, frost tolerance, and salinity), many other situa-
tion-specific varieties have been developed under the programmes.
A total of 35 novel genetic stocks of rapeseed-mustard with important
traits (CMS, restorer, low erucic acid and low glucosinoltes, high oil content, high
oleic acid and low linolenic acid, dwarf, earliness, long main shoot, bold seed,
yellow seed, tetralocular siliquae, white rust resistance, tolerance to high temperature
15 Brassica Breeding 809

and salinity during juvenile stage, high temperature tolerance during terminal stage,
and high water use efficiency) have been registered with NBPGR, New Delhi, till
January 2021. Several varieties/hybrid of different Brassica spp. and Eruca sativa
have been developed. Among these varieties/hybrids, the historical achievement is
the development of first (0) single zero (<2% erucic acid in oil) B. juncea variety
Pusa Karishma released in 2005, first (00) double low (<2% erucic acid and
<30 ppm glucosinolate) Brassica juncea Pusa Mustard 31 released in 2016, and
first double low (00) B. juncea hybrid RCH 1 released in 2021. Ten single zero or
low erucic acid (0) varieties, viz. Pusa Karishma (LES-39), LES-1-27 (Pusa Mustard
21), LET-17 (Pusa Mustard 22), RLC 1, RLC 2, LET-18 (Pusa Mustard 24), LET-36
(Pusa Mustard 29), LET-43 (Pusa Mustard 30), and LET-54 (Pusa Mustard 32), and
3 canola quality varieties/hybrid, viz. Pusa Double Zero Mustardd 31, Pusa Double
Zero Mustard 33, RLC 3, and RCH 1, have been released (Table 15.6). In addition,
ten hybrids of B. napus and B. juncea have also been released (Table 15.4).

Table 15.6 Donor sources and breeding methods used in the development of quality varieties
S. no. Variety Pedigree Breeding method
B. juncea (single low i.e. low erucic acid)
1. Pusa Karishma Pusa Barani/Zem 1 Backcross method
2. Pusa Mustard 21 Pusa Bold/Zem-2 Backcross method
3. Pusa Mustard 24 Pusa Bold/LET 15//LES 29 Pedigree selection
4. Pusa Mustard 22 Pusa Barani/Zem-2 Backcross method
5. ELM 079 (RLC 1) QM-4/Pusa Bold Pedigree selection
6. ELM-123 (RLC 2) QM-4/Pusa Bold Pedigree selection
7. Pusa Mustard 29 ZEM-2/Pusa Barani//EC Pedigree selection
287711
8. Pusa Mustard 30 Bio-902/ZEM-1 Pedigree selection
9. Pusa Mustard 32 LES-1-27/EC-597325 Pedigree selection
B. juncea (Double low i.e. low erucic acid and low glucosinolates)
10. Pusa Double Zero Mustard 31 LES-1-27 (PM21)/NUDHYJ-3 Pedigree selection
11. RLC 3 JM06003/JM06020 Pedigree selection
12. Pusa Double Zero Mustard 33 Pusa Agrani/Heera Pedigree selection
13. RCH 1 CMS- ZM 20  OCRE-4NR CMS-based
hybrid
B. napus (Double low)
14. GSC 5 Hyola 401//Agat GSL-8888 Pedigree selection
15. OCN-3/GSC 6 NECN 13/Tribute//NECN-13 Backcross method
16. GSC 7 Rivette/RR001 Pedigree selection
17. PAC-401 44002A/4154 R CMS-based
hybrid
18. NUDH 26-11 Selection from germplasm Pure line selection
19 PGHS 1699 (GSH 1699) CMS-AG7  FR-ZY 005 CMS-based
hybrid
810 D. K. Yadava et al.

15.11 All India Coordinated Research Project

on Rapeseed-Mustard

Systematic research work on rapeseed-mustard was initiated after the constitution of

the Indian Central Oilseed Committee. This committee was designated as Oilseed
Development Council in 1966. In 1967 an All India Coordinated Research Project
on Oilseeds was initiated under the leadership of Project Coordinator which included
five crops, viz. groundnut, rapeseed-mustard, sesame, linseed, and castor. In 1981, a
separate All India Coordinated Research Project on Rapeseed and Mustard was
established at HAU, Hisar, and 14 research centres were established for research
work on rapeseed and mustard. On October 20, 1993, National Research Centre on
Rapeseed-Mustard was established at Sewar, Bharatpur, in Rajasthan. The Indian
Council of Agricultural Research raised the NRC on Rapeseed-Mustard to Director-
ate of Rapeseed-Mustard Research in February 2009. Presently there are 11 main
and 12 sub-centres under the AICRP Rapeseed-Mustard. In addition, there are
22 verification centres also for evaluation of the advanced material in different
zones under AICRP trials. The country has been divided into six agro-climatic
zones for evaluation and release of the material.
Since the inception of All India Coordinated Research Project on Rapeseed-
Mustard (AICRP-RM) in 1967, a total of 212 varieties (Indian mustard-131; toria-
28; yellow sarson-16; gobhi sarson-16; brown sarson-6; karan rai-5; taramira-8 and
black mustard-1) including 11 hybrids of rapeseed-mustard have been released till
now. Details of varieties released since 2010 are presented in Table 15.7. Rapeseed-
mustard varieties having tolerance to biotic (white rust, Alternaria blight, powdery
mildew), abiotic stresses (salinity, high temperature), and quality traits have been
recommended for specific growing conditions.

15.12 Future Thrust Areas

• Enhancing level of heterosis of hybrids through proper utilization of genetic

resources and focused breeding options for their better commercial adoption.
• Developing early maturing, dwarf, and determinate type varieties for enhancing
crop intensity, suitable for different cropping systems and amenable to mechani-
cal harvesting.
• Development of varieties resistant to biotic stresses especially Sclerotonia stem
rot, white rust, Alternaria blight, aphids, and Orobanche for stabilizing the
productivity.
• Development of varieties with enhanced water and nutrient use efficiency for
optimum utilization of the available soil moisture and nutrients.
• Tailoring varieties tolerant to abiotic stresses such as drought, high temperatures
at sowing and/or maturity, salinity, and frost in rapeseed-mustard.
• Developing double zero varieties (erucic acid <2% and glucosinolate <30 μmol/
g of defatted seed meal cake) with high oleic acid.
• Improving the oil content of present-day varieties from 40% to 45%.
 15

Table 15.7 Different varieties/hybrids of rapeseed-mustard released during 2010–2021

Year of Oil Average
release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
Brassica juncea (Indian mustard)
Pusa mustard 2010 107 ICAR-Indian Agricultural 39.6 14.07 Delhi, Haryana, Punjab, Suitable for early sown
25 Research Institute, New Jammu and Kashmir, (September sowing)
Brassica Breeding

(NPJ-112) Delhi Rajasthan irrigated conditions,

tolerant to high
temperature at seedling
stage, a potential
substitute of toria and
wheat can be taken after
its harvest
Pusa mustard 2011 125 ICAR-Indian Agricultural 37.6 16.04 Delhi, Haryana, Punjab, Suitable for late sown
26 Research Institute, New Jammu and Kashmir, (November sowing)
(NPJ-113) Delhi Rajasthan irrigated conditions,
moderately tolerant to
high temperature at
seedling and maturity
stage
Pusa mustard 2011 115 ICAR-Indian Agricultural 41.7 15.35 Madhaya Pradesh, Uttar Suitable for early sown
27 (EJ-17) Research Institute, New Pradesh, Uttarakhand, and (September sowing)
Delhi Eastern Rajasthan irrigated conditions,
tolerant to high
temperature at seedling
and maturity stage
RH 0119 2011 147 CCS, Haryana 40.0 19.00 Timely sown conditions Erect plant type with
Agricultural University, in rainfed areas of long siliqua having
Hisar (Haryana) Haryana thermo-tolerance
(continued)
811
Table 15.7 (continued)
812

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
Coral PAC 2012 140 Adventa India Ltd., 40.0 25.00 Delhi, Haryana, Punjab, Hybrid, tolerant to white
437 (Hybrid) Hyderabad (Telangana) Jammu, and parts of rust
Rajasthan
PBR-357 2012 146 Punjab Agricultural 39.7 25.50 Delhi, Haryana, Punjab, Suitable for timely sown
University, Ludhiana Jammu, and parts of irrigated condition
(Punjab) Rajasthan
RH 0406 2012 144 CCS, Haryana 40.5 22.50 Delhi, Haryana, Punjab, Tolerant to high
Agricultural University, Jammu, and parts of temperature and salinity
Hisar (Haryana) Rajasthan at seedling stage;
suitable for timely sown
rainfed condition
Pant Rai-19 2012 117 G. B. Pant University of 41.3 20.69 Jammu and Kashmir, Tolerant to high
(PR 2006-1) Agriculture and Punjab, Haryana, and temperature during early
Technology, Pantnagar Delhi stages, suitable for early
(Uttarakhand) sowing
Pusa Mustard 2012 107 ICAR-Indian Agricultural 41.7 19.93 Rajasthan, Haryana, Suitable for early sown
28 (NPJ-124) Research Institute, New Punjab, Delhi, Plains of conditions (first week of
Delhi J&K, HP, and Western September), moderately
UP tolerant to high
temperature at seedling,
tolerant to salinity up to
12 dS/m and powdery
mildew
RH 0749 2013 147 CCS, Haryana 39.5 26.00 Timely sown conditions Suitable for timely sown
Agricultural University, in rainfed areas of irrigated conditions,
Hisar (Haryana) Haryana, Punjab, Delhi, bold seeded with more
and parts of Rajasthan seeds/siliqua
D. K. Yadava et al.
 15

RGN-229 2013 146 Rajasthan Agricultural 40.7 23.60 Rajasthan, Punjab, Suitable for rainfed,
University, Zonal Haryana Delhi, and timely sown conditions
Research Station, Jammu tolerance to high
Sriganganagar (Rajasthan) temperature as well as
salinity
RGN-236 2013 127 Rajasthan Agricultural 39.1 16.36 Rajasthan, Punjab, Suitable for late sown
Brassica Breeding

University, Zonal Haryana, Delhi, and irrigated conditions.

Research Station, Jammu Tolerant to high
Sriganganagar (Rajasthan) temperature at terminal
stage
Pusa Mustard 2013 143 ICAR-Indian Agricultural 37.2 21.69 Delhi, Haryana, Jammu, Single zero (<2% erucic
29 (LET-36) Research Institute, New Punjab, and northern acid) variety
Delhi Rajasthan
Pusa Mustard 2013 137 ICAR-Indian Agricultural 38.0 18.24 Uttar Pradesh, Single zero (<2% erucic
30 (LES-43) Research Institute, New Uttarakhand, Madhya acid) variety
Delhi Pradesh, and eastern
Rajasthan
RVM-2 2013 131 Rajmata Vijayaraje 40.0 17.00 Delhi, Haryana, Jammu, Suitable for rainfed as
Scindia Krishi Viswa Punjab, and northern well as irrigated
Vidyalaya, Zonal Rajasthan conditions
Research Station, Morena
(Madhya Pradesh)
Giriraj 2013 145 ICAR-Directorate of 42 25.5 Rajasthan, Punjab, Timely sown irrigated
(DRMRIJ 31) Rapeseed-Mustard Haryana, Delhi, and conditions
Research, Bharatpur Jammu
(Rajasthan)
Gujarat 2015 110 Sardar Krushinagar 39 20.4 Gujarat Timely sown irrigated
Dhantiwada Dantiwada Agricultural conditions
Mustard 4 University, Sardar
Krushinagar (Gujarat)
813

(continued)
Table 15.7 (continued)
814

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
Albeli 2015 145 Shakti Vardhak Hybrid 40 20.7 Rajasthan, Jammu, Uttar Timely sown irrigated
Seeds Pvt. Ltd., Hisar Pradesh, Madhya conditions
(Haryana) Pradesh, and Uttarakhand
Pant Rai 20 2015 124 G. B. Pant University of 40 19.7 Uttarakhand Timely sown irrigated
Agriculture and conditions
Technology, Pantnagar
(Uttarakhand)
PBR 357 2015 145 Punjab Agricultural 39.5 26.6 Punjab, Haryana, Delhi, Timely sown irrigated
University, Ludhiana Jammu and Kashmir, conditions
(Punjab) parts of Rajasthan,
Western Uttar Pradesh
RGN 298 2015 143 Rajasthan Agricultural 40.0 22.7 Punjab, Haryana, Delhi, Timely sown rainfed
University, Zonal Jammu and Kashmir, conditions
Agricultural Research parts of Rajasthan,
Station, Sri ganganagar Western Uttar Pradesh
(Rajasthan)
GM-3 2016 107 Sardar Krushi nagar 38.8 19.90 Gujarat Timely sown irrigated
Dantiwada Agricultural (Irrigated); and rainfed conditions
University, Sardar 12.10
Krushinagar (Gujarat) (Rainfed)
Pusa Double 2016 144 ICAR-Indian Agricultural 40.56 23.79 Punjab, Haryana, Delhi, Timely sown irrigated
Zero Mustard Research Institute, New Jammu and Kashmir, conditions.
31 (PDZ-1) Delhi parts of Rajasthan, It is the first double zero
Western Uttar Pradesh (low erucic acid <2%
and low glucosinolates
<30 ppm) Indian
mustard variety in the
D. K. Yadava et al.
 15

country. It is a yellow
seeded variety with
improved oil and seed
meal quality (canola
quality) making this
variety beneficial for
Brassica Breeding

farmers, traders, and

consumers
RLC 2016 149 Punjab Agricultural 37.6 21.7 Delhi, Haryana, Punjab, Timely sown irrigated
2 (IC 511615) University, Ludhiana Jammu, and parts of conditions; low erucic
(Punjab) Rajasthan acid (<2%)
PBR 378 2016 146 Punjab Agricultural 40.5 24.5 Punjab Timely sown rainfed
University, Ludhiana conditions
(Punjab)
Gujarat 2016 144 Sardar Krushinagar 40.5 22.2 Punjab, Haryana, Delhi, Timely sown irrigated
Dhantiwada Dantiwada Agricultural Jammu and Kashmir, conditions
Mustard University, Sardar parts of Rajasthan,
5 (GDM 5) Krushinagar (Gujarat) Western Uttar Pradesh
Raj Vijay 2016 108 Rajmata Vijayaraje 41.7 17–18 Madhya Pradesh Early sown, rainfed
Mustard 1 Scindia Krishi Vishwa conditions
Vidyalaya, Zonal
Research Station, Morena
(Madhya Pradesh)
JK Samriddhi 2016 125–130 JK Agri Genetics Ltd., 39.5 23.00 Uttar Pradesh Tolerant to salinity and
Gold (JKMS Hyderabad (Telangana) white rust
2)
Bayer 2016 130–135 Bayer Bio Science Pvt., 39.9 28.00 Uttar Pradesh Quality oil
Mustard 5450 Hyderabad (Telangana)
RLC 3 2016 149 Punjab Agricultural 41.4 18.2 Punjab Timely sown rainfed
University, Ludhiana conditions, low erucic
815

(Punjab) and low glucosinolate

(continued)
Table 15.7 (continued)
816

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
CS-58 2017 135 ICAR-Central Soil 39 19.5 Punjab, Haryana, Suitable for timely
Salinity Research Rajasthan, Uttar Pradesh sown, irrigated, salinity,
Institute, Karnal conditions
(Haryana)
Pant Rai 2017 122–127 G. B. Pant University of 40 12.2 Uttarakhand Timely sown irrigated
21 (PRB Agriculture and conditions
2008-5) Technology, Pantnagar
(Uttarakhand)
RH 725 2018 141 CCS, Haryana 40.2 20.0 Punjab, Haryana, Delhi, Timely sown rainfed
Agricultural University, Jammu and Kashmir, conditions
Hisar (Haryana) parts of Rajasthan,
Western Uttar Pradesh
CS 60 2018 134 ICAR-Central Soil 41 18.0 Punjab, Haryana, Suitable for timely
Salinity Research Rajasthan, Uttar Pradesh sown, irrigated, salinity,
Institute, Karnal and water-logged
(Haryana) conditions
RSPR-69 2019 135–145 Sher-e-Kashmir 39.4 19.9 4 Jammu Suitable for early sowing
(MCN-04-35) University of Agricultural under irrigated and
Sciences and Technology, rainfed, low fertility
Jammu (Jammu and areas during rabi season.
Kashmir) Resistant to white rust
and moderately resistant
to Alternaria blight and
major pests
RH 761 2019 141 CCS, Haryana 40.4 28.6 Jammu, Punjab, Haryana, Suitable for timely sown
Agricultural University, Delhi, and Northern and rainfed conditions in
Hisar (Haryana) Rajasthan rabi season
D. K. Yadava et al.
 15

SVJ-64 2020 130 Shakti Vardhak Hybrid 39.1 23.2 Haryana Suitable for irrigated
Seeds Pvt. Ltd., Hisar conditions under both
(Haryana) high and low fertility
conditions
DRMR 1165- 2020 141 ICAR-Directorate of 39.8 23.00 Jammu, Punjab, Haryana, Suitable for timely sown
40 Rapeseed-Mustard Delhi, and Rajasthan rainfed condition, heat
Brassica Breeding

Research, Bharatpur tolerant at seedling

(Rajasthan) stage and moisture stress
tolerant
Pusa Mustard 2020 147 ICAR-Indian Agricultural 38.0 27.10 Rajasthan (Northern and Suitable for timely sown
32 (LES 54) Research Institute, New Western Parts), Punjab, irrigated, quality
Delhi Haryana, Delhi, Western mustard (low erucic acid
Utter Pradesh, Plains of content in oil)
Jammu and Kashmir,
Himachal Pradesh
Kesari Gold 2020 100 Bayer Bio Science Pvt., 41.0 17.92 West Bengal Timely sown irrigated
(31J3403) Hyderabad (Telangana) conditions; resistant to
lodging; moderately
resistant to fungal
disease and white rust;
resistant to aphid
infestation
Kesari 5111 2020 104 Bayer Bio Science Pvt., 41.5 14.81 West Bengal Timely sown irrigated
(PCJ03-401) Hyderabad (Telangana) conditions, moderately
resistant to fungal
disease and white rust,
and moderately resistant
for aphids infestation
(continued)
817
Table 15.7 (continued)
818

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
Bayer 2019 118 Bayer Bio Science Pvt., 39.1 16.78 West Bengal Timely sown irrigated
Mustard 5222 Hyderabad (Telangana) conditions, resistant to
lodging, moderately
resistant to white rust
and resistant to aphid
infestation
TBM-204 2019 110 Bidhan Chandra Krishi 41 13.4 Bihar, Jharkhand, Odisha, Timely sown irrigated
(Trombay Visvavidyalaya, Nadia Assam, and Manipur conditions, moderately
Bidhan (West Bengal) resistant to Alternaria
Mustard-204) leaf spot
Kesri 5111 2020 115 Bayer Bio Science Pvt., 42 10–12 Uttar Pradesh, Madhya Early maturing, dark
(PRO 5111) Hyderabad (Telangana) Pradesh, Uttarakhand, and brown mustard, tolerant
east Rajasthan to white rust
DRMR 2020 114 ICAR-Directorate of 39.8 18.28 Bihar, Jharkhand, Odisha, Suitable for rainfed
150-35 Rapeseed-Mustard West Bengal, Assam, condition with
(Bharat Research, Bharatpur Chhatisgarh, Manipur protective irrigation
Sarson 7) (Rajasthan) during rabi season,
moderate resistance to
Alternaria blight and
powdery mildew,
moderate resistance to
aphid infestation
Azad Mahak 2021 122 C.S.A University of 41.5 20.50 Uttar Pradesh Suitable for irrigated
[(KMR Agricultural and conditions
(E) 15-2)] technology, Kanpur (Uttar
Pradesh)
D. K. Yadava et al.
 15

Radhika 2021 131 ICAR- Directorate of 40.7 17.88 Jammu, Punjab, Haryana, Suitable under late sown
(DRMR Rapeseed-Mustard Delhi and Rajasthan irrigated conditions with
2017-15) Research, Bharatpur tolerance to terminal
(Rajasthan) heat stress
Brijraj 2021 132 ICAR-Directorate of 39.9 17.33 Jammu, Punjab, Haryana, Suitable under late sown
(DRMRIC Rapeseed-Mustard Delhi, and northern irrigated conditions with
Brassica Breeding

16-38) Research, Bharatpur Rajasthan tolerance to terminal

(Rajasthan) heat stress
SVJH-108 2021 143 Shakti Vardhak Hybrid 41.3 25.5 Haryana Irrigated conditions
(Hybrid) Seeds Pvt., Ltd., Hisar under both high and low
(Haryana) fertility
Pusa Double 2021 141 ICAR-Indian Agricultual 38.0 26.40 Rajasthan (Northern and A canola quality (low
Zero Mustard Research Institute, New Western parts), Punjab, erucic acid content in oil
33 Delhi Haryana, Delhi, Western and glucosinolates in
Uttar Pradesh, Plains of defatted seed meal cake)
Jammu and Kashmir, and variety with high seed
Himachal Pradesh yield. Suitable for timely
sown irrigated
conditions
RCH 2021 145 Punjab Agricultural 38.5 26.70 Rajasthan (Northern and First canola quality (low
1 (Hybrid) University, Ludhiana Western parts), Punjab, erucic acid content in oil
(Punjab) Haryana, Delhi, Western and glucosinolates in
Uttar Pradesh, Plains of defatted seed meal cake)
Jammu and Kashmir, and hybrid with high seed
Himachal Pradesh yield. Suitable for timely
sown irrigated
conditions
PHR 2021 145 Punjab Agricultural 40.2 22.70 Punjab Timely sown irrigated
126 (Hybrid) University, Ludhiana ecologies
(Punjab)
(continued)
819
Table 15.7 (continued)
820

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
TAM 1028-1 2021 101 Dr. Panjabrao Deshmukh 40.0 14.00 Maharashtra (Vidarbha Suitable for timely sown
Krishi Vidyapeeth, Region) condition in rabi season
College of Agriuculture, under restricted
Nagpur (Maharastra) irrigation. Early
maturing variety
Birsa Bhabha 2021 118 Birsa Agricultural 40.0 15.50 Jharkhand Suitable for rainfed
Mustard University, Ranchi timely sown condition
1 (BBM1) (Jharkhand) with tolerance to
moisture stress
Trombay Him 2021 153 CSK Himachal Pradesh 39.9 10.80 Himachal Pradesh Timely sown, irrigated
Palam Krishi Visvavidyalaya, conditions in low and
Mustard-1 Palampur (Himachal mid-hill zone
(THPM-1) Pradesh)
Brassica rapa ssp Yellow sarson
JK Pukhraj 2016 117 JK Agri Genetics Ltd., 45.0 15.5 Uttar Pradesh Bold seed, high oil
(JKYS 2) Hyderabad (Telangana) content
Pant Sweta 2017 115 G. B. Pant University of 45.0 14.5 Uttarakhand Timely sown irrigated
(PYS-2007- Agriculture and conditions
10) Technology, Pantnagar
(Uttarakhand)
Pant Girija 2020 110 G. B. Pant University of 45.3 14.4 Uttarakhand Timely sown irrigated
(PYS-2012-6 Agriculture and conditions resistant to
Technology, Pantnagar lodging; moderately
(Uttarakhand) resistant to fungal
disease and white rust;
resistant to aphid
infestation
D. K. Yadava et al.
 15

Sanchita 2020 96 Pulses and Oilseed 44.5 15.0 West Bengal Suitable for medium
(YSWB- Research Station, maturity, timely sown
2014/2) Berhampore (West irrigated condition
Bengal)
Anushka 2020 85 Pulses and Oilseed 44.5 15.0 West Bengal Suitable for early
(YSWB- Research Station, maturity, timely sown
Brassica Breeding

2011-10-1) Berhampore (West irrigated condition

Bengal)
Brassica rapa ssp Brown sarson
HPBS 80 2018 147 CSK Himachal Pradesh 40 11.50 Himachal Pradesh Timely sown, rainfed
Krishi Vishvavidyalaya, conditions
Palampur (Himachal
Pradesh)
Shalimar 2019 210 Sher-e-Kashmir 42.7 16.00 Jammu and Kashmir Suitable for irrigated
Sarsaon – University of Agricultural conditions of J&K at
2 (KBS-49) Sciences and Technology, 1500–1800 m above
Srinagar (Jammu and MSL
Kashmir)
Shalimar 2019 205 Sher-e-Kashmir 41.3 16.00 Jammu and Kashmir Suitable for irrigated
Sarsaon – University of Agricultural conditions of J&K at
3 (KBS-3) Sciences and Technology, 1800–2000 m above
Srinagar (Jammu and MSL
Kashmir)
Brassica rapa ssp Toria
Uttara 2011 97 G. B. Pant University of 41.7 13.30 Uttarakhand Moderately resistant to
(PT 2002-25) Agriculture and WR, DM, and PM
Technology, Pantnagar diseases
(Uttarakhand)
(continued)
821
Table 15.7 (continued)
822

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
Sushree 2016 75 Odisha University of 44.1 13.80 Odisha Late sown conditions,
Agriculture and non-lodging type
Technology,
Bhubneshwar (Odisha)
TL-17 2016 90 Punjab Agricultural 42.1 13.00 Punjab Early maturing and
University, Ludhiana suitable for multiple
(Punjab) cropping system
Pant Hill 2017 128 G. B. Pant University of 42.1 7.50 Uttarakhand Spring type Toria (Sept-
Toria-1 Agriculture and Oct sowing)
(PT-2006-4) Technology, Pantnagar
(Uttarakhand)
Pant Toria 2017 93 G. B. Pant University of 42.1 12.40 Uttarakhand Suitable for multiple
508 Agriculture and cropping system
Technology, Pantnagar
(Uttarakhand)
Raj Vijay 2017 100 Rajmata Vijayaraje 43.4 12.80 Madhya Pradesh Early sown, irrigated,
Toria 1 Scindia Krishi Vishwa and rainfed conditions
Vidyalaya, Zonal
Research Station, Morena
(Madhya Pradesh)
Tapeshwari 2018 92 CSA University of 41.6 14.00 Uttar Pradesh Early sown, irrigated,
(TK 06-1) Agriculture and and rainfed conditions,
Technology, Kanpur drought tolerant
(Uttar Pradesh)
Tripura Toria 2018 86 ICAR Research Complex 42.6 9.500 Tripura Rainfed, upland, and
1 for NEH Region, Tripura lowland after Kharif rice
Centre, Agartala (Tripura)
D. K. Yadava et al.
 15

RSPT-6 2019 88 Sher-e-Kashmir 42.6 11.30 Jammu Early sowing under

(TCN 13-9) University of Agricultural irrigated and rainfed,
Sciences and Technology, low fertility areas during
Jammu (Jammu and rabi season
Kashmir)
Raj Vijay 2020 91 Zonal Agricultural 42.0 13.88 Madhya Pradesh Suitable for irrigated and
Brassica Breeding

Toria 3 (RVT Research Station, Morena rainfed conditions,

3) (RTM (Rajmata Vijayaraje resistant to white rust,
08-6) Scinedia Krishi Vishwa Alternaria leaf blight,
Vidyalaya), Madhya powdery mildew, downy
Pradesh mildew, and Sclerotinia
stem diseases
Jeuti (JT 90- 2020 91 Assam Agricultural 42.5 4.76 Assam Suitable for normal
1) University, Jorhat condition during rabi
(Assam) season
Azad Chetna 2021 93 C.S.A. University of 42.0 14.0 Uttar Pradesh Suitable for early sowing
(TKM 14-2) Agricultural and during mid-September
technology, Kanpur (Uttar
Pradesh)
Raj Vijay 2021 108 Zonal Agricultural 42.0 11.5 Madhya Pradesh Suitable for double
Toria 2 (RMT Research Station, Morena (Irrigated); cropping systems (Toria-
08-2) (Rajmata Vijayaraje 9.0 Wheat/Onion; Mung-
Scinedia Krishi Vishwa (Rainfed) Toria-Vegetable; Early
Vidyalaya), Madhya bajra-Toria-wheat/
Pradesh vegetable)
(continued)
823
Table 15.7 (continued)
824

Year of Oil Average

release/ Maturity content yield
Variety notification (days) Source institute (%) (q/ha) Area of adoption Salient features
Eruca sativa (Taramira)
Jobner Tara 2017 140 SKN College of 39.7 11.60 Rajasthan, Haryana, Rainfed conditions
(RTM 1351) Agriculture, SKN Punjab, Uttar Pradesh,
Agriculture University, Gujarat, Delhi,
Jobner (Rajasthan) Uttarakhand,
and Maharashtra
Jwala Tara 2017 134 SKN College of 38.9 13.70 Rajasthan and Haryana Rainfed conditions and
(RTM 1355) Agriculture, SKN marginal lands
Agriculture University,
Jobner (Rajasthan)
B. carinata (karan rai or African sarson)
BJC 1 (PC 6) 2016 157 Punjab Agricultural 40.0 19.00 Punjab Suitable for mechanical
University, Ludhiana harvesting
(Punjab)
Brassica napus (Gobhi sarson)
RSPN 25 2015 150 Sher-e-Kashmir 39 15.90 Jammu and Kashmir Subtropical regions of
University of Agricultural Jammu and Kashmir,
Sciences and Technology, moderately resistant to
Jammu (Jammu and diseases
Kashmir)
GSC 7 (GSC 2015 154 Punjab Agricultural 40.5 22.20 Punjab, Haryana, Timely sown irrigated
101) University, Ludhiana Himachal Pradesh, conditions, canola
(Punjab) Jammu and Kashmir, and quality variety (<2%
Rajasthan erucic and <30 ppm
glucosinolate)
D. K. Yadava et al.
 15

PGHS 1699 2021 168 Punjab Agricultural 41.9 15.81 Punjab, Himachal Timely sown irrigated
(GSH 1699) University, Ludhiana Pradesh, Jammu and conditions, canola
(Punjab) Kashmir quality variety (<2%
erucic and <30 ppm
glucosinolate)
Him 2021 168 CSK Himachal Pradesh 40.4 15.60 Himachal Pradesh, Irrigated, timely sown
Brassica Breeding

Palampur Krishi Visvavidyalay, Punjab, Jammu and variety having resistance

Gobhi Sarson Palampur (Himachal Kashmir to white rust
1 (AKMS Pradesh)
8141)
825
826 D. K. Yadava et al.

• Use of genomics and gene editing tools as precision breeding methods for the
development of improved quality and climate-resilient varieties.

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Groundnut Breeding
16
T. Radhakrishnan, Praveen Kona, B. C. Ajay, and Narendra Kumar

Abstract

Considerable progress has been made in groundnut breeding programmes where

233 varieties were released from the past 25 years. The chapter will throw insights
on the heritability, gene action of different traits and their improvement using
conventional and modern non-conventional approaches with an aim to reach the
ultimate goal of farmers or breeders, i.e. yield. Approaches to overcome problems
encountered in resistance breeding are discussed, with particular reference to
foliar fungal diseases, aflatoxins, viruses, bacterial wilt, insects, drought, heat,
etc. Progress in breeding for confectionery groundnut and biofortification and
adaptation is also considered. Different techniques were highlighted such as
interspecific hybridization and genetic engineering to transfer useful genes from
wild Arachis species and other sources into A. hypogaea lines.

Keywords
Germplasm · Gene pool · Breeding objectives · Karyotype · Genomics

16.1 Introduction

Groundnut is one of the major oil and protein crops grown globally over more than
100 countries. China is the world leader having the largest production of about
16.6 M tons followed by India (7 M tons) followed by Nigeria (3.4 M tons), while
the crop is grown over a total of more than 26 M ha with a production of about 44 M
tons. Groundnut yield varies considerably across the groundnut-growing countries
with an average of 1655 kg/ha, and the highest average yield of more than 3500 kg/

T. Radhakrishnan (*) · P. Kona · B. C. Ajay · N. Kumar

ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 837
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_16
838 T. Radhakrishnan et al.

ha is realized in the USA. Nearly 60% of the cultivation is Asia followed by Africa
(32%). In semi-arid tropics of Asia and Africa, the crop is grown by small and
marginal under rainfed conditions with limited or no inputs. Groundnut is a rich
source of nutrients like protein (about 25%), oil (45–55%), carbohydrates (10–20%),
dietary fibre, vitamins, minerals and antioxidants. Nearly 60% of the groundnut
produced globally is used for extraction oil for edible and industrial uses, while
about 40% is consumed in food and confectionary uses and as seed for sowing the
next season crop (Birthal et al. 2010; Janila et al. 2013). Groundnut oil has a high
smoking point which makes it a preferred cooking medium in India, China, Vietnam
and Myanmar (Singh and Diwakar 1993).
The de-oiled cake of groundnut is a very rich source of protein, and in India it is
mainly consumed as animal feed and in preparing food for children and the aged and
as soil amendment, while in Europe and North and South America, nearly 75% of
the produce is used directly as raw, boiled or roasted and for culinary purposes. In
the USA, Canada, and Australia peanut butter is the most popular groundnut-based
product. The groundnut shells are used in particle board industry, as a fuel or filler in
fertilizer and feed industry and as a substrate for industrial production of pectinase
(Dey et al. 2001). Haulm of groundnut is a preferred fodder for livestock, which has
a digestibility of around 53%, and it contains carbohydrate (38–45%), minerals
(9–17%), protein (8–15%) and lipids (1–3%). Being a nodulating leguminous crop
groundnut helps in improving soil health and fertility by leaving behind the nitrogen
fixed by the root nodules (Janila et al. 2013).
Significant improvement in the productivity of groundnut globally has taken
place during the last 50 years, and starting from an average productivity of
850 kg/ha, we are now at more than 1655 kg/ha with improved cultivars and the
crop management practices. Now with the availability of the modern methods of
breeding and the genomic resources, the process of cultivar development will be
accelerated further. This chapter summarizes the advances in groundnut breeding
process for enhancing the genetic gain and to improve the productivity.

16.2 Origin, Evolution, and Distribution

The genus Arachis is native to South America, and the species of Arachis are
distributed in the river beds of Amazon in the north, Rio de la Plato in the south,
the Andes to the west and the Atlantic to the east. The centre of diversity of the genus
Arachis is the Mato Grasso, Brazil, from where the majority of the species are
reported and the origin of the cultivated groundnut, Arachis hypogaea, is believed to
be northern Argentina and south Bolivia Krapovickas (1969). The other regions
from where large number of Arachis species were reported are Bolivia, Paraguay,
Argentina and Uruguay. Six gene centres, as indicated in Table 16.1, have been
proposed for the cultivated types.
The first five centres in the list are considered as secondary centre of diversity,
and North-East Brazil and Africa are considered as a tertiary centre. The genetic
variability reported from Africa is resulted from the introduction of cultivated types
16 Groundnut Breeding 839

Table 16.1 Centre of diversity and distribution of cultivated type

Centre of diversity Distribution of cultivated type
Guarani region (Paraguay-Parana) Erect Valencia type, ssp. fastigiata and intermediate type
between var. fastigiata and vulgaris
Goias and mina Gerais region Erect type, ssp. fastigiata var. fastigiata and races of both
(Tocatins, San Frasncisco) var. fastigiata and vulgaris
Rondonia North-West Mato Nambyquarae type of ssp. hypogaea and erect type with
Grosso (Brazil) yellow testa colour
Eastern foothills of the Andes and Subspecies hypogaea var. hypogaea and few races of ssp.
Bolivia fastigiata and intermediate of these two ssp.
Peru (Upper Amazon and West Races of ssp. hypogaea, with constriction, veins and beak,
Coast) similar type of ssp. fastigiata var. fastigiata (var.
peruviana) and ssp. hypogaea var. hirsuta
North-East Brazil All morphological types along with intermediate types
between var. fastigiata and var. hypogaea
ssp subspecies, Source: Singh and Simpson (1994)

from different countries especially from Bolivia, Brazil and China (Smartt 1990;
Singh and Simpson 1994).

16.3 Systematics and Species Relationships

Groundnuts belong to the legume family (Fabaceae), and the members of genus
Arachis are distinctly differentiated by the geocarpic fruit development and are well
defined morphologically as well. The genus Arachis is included in the sub-tribe
Stylosanthinae of the tribe Aeschynumeneae along with Arthrocarpum,
Chapmannia, Pachecoa and Stylosanthes based on their common morphological
characters and floral morphology. The taxonomical hierarchy of the genus is as
follows:

Kingdom Plantae
Division Tracheophyta
Class Magnoliophyta
Order Fabales
Family Fabaceae
Subfamily Faboideae
Tribe Aeschynomeneae
Genus Arachis

Till the sixteenth century, the only species known under the genus Arachis was
A. hypogaea (Von Linnaeus 1753) and later on five more species, A. glabrata,
A. pusilla, A. villosa, A. prostrata and A. tuberosa, were described by Bentham
(1841). Another 11 new species were added by Valls and Simpson (1997), which are
yet to be described formally, totalling the number of species to 80 (Lavia 2000). A
subgeneric classification dividing the genus into sections and series (Table 16.2) was
840 T. Radhakrishnan et al.

Table 16.2 Taxonomic treatment of the genus Arachis (Krapovickas 1969, 1973, 1990; Gregory
et al. 1980) and proposed genomes
Section Series Genome Chromosome no. (2n)
Arachis 1. Annuae A, B, D 20
2. Perennes A 20
3. Amphiploides AB 40
Erectoides 1. Trifoliolatae E1 20
2. Tetrafolilatae E2 20
Procumbensae – P 20
Caulorhizae – C 20
Rhizomatosae 1. Prorhizomatosae R 20
2. Eurhizomatosae 2R 40
Extranervosae – Ex 20
Ambinervosae – AM 20
Triseminalae – T 20

Table 16.3 Most widely adopted classification of groundnut (Arachis hypogaea L.)
Botanical Branching Seed/
Subspecies Varieties type pattern Growth habit pod
Hypogaea hypogaea Virginia Alternate Prostrate to semi- 2–3
erect
hirsuta Peruvian Alternate Prostrate 2–4
runner
Fastigiata fastigiata Valencia Sequential Erect 3–5
vulgaris Spanish Sequential Erect 2

proposed based on morphology, cross-compatibility and pollen fertility of interspe-

cific hybrids (Krapovickas 1973; IBPGR 1990; Gregory et al. 1973, 1980). The
cultivated species have been grouped into two subspecies, with two botanical
varieties each as in Table 16.3 (Krapovickas and Rigonii 1960; Krapovickas 1969)
and further into six botanical varieties (Krapovickas and Gregory 1994)
(Table 16.4). This grouping, which is most frequently used, is on the basis of growth
habit, branching pattern, flowering pattern, pod and seed characters, seed dormancy,
etc. Due to the vide variations and several intermediate forms observed in the
germplasm and breeding populations of cultivated groundnut, mostly the
classifications are restricted to the three botanical types erect, semi-spreading and
spreading for the sake of practical applications.

16.3.1 Gene Pools of Groundnut

The Arachis gene pools have been classified into primary, secondary and tertiary
based on the cross-compatibility relationships. The primary gene pool of Arachis
includes the two tetraploid species, viz. Arachis hypogaea and A. monticola of
16 Groundnut Breeding 841

Table 16.4 Botanical classification of Arachis hypogaea as proposed by Krapovickas and

Gregory (1994)
Market South American location
Varieties type where it is abundant Characteristics
Subspecies hypogaea
No floral axes on main stem; alternating pairs of floral and reproductive axes on branches;
branches short; less hairy
Hypogaea Virginia Bolivia, Amazon Less hairy; large seeded
runner
hirsuta Peruvian Peru More hairy, small seeded
runner
Subspecies fastigiata
Floral axes on main stem; alternating pairs of floral and vegetative axes on branches
Fastigiata Valencia Brazil Less branches, long upright branches,
Guranian hairy leaf
Goias
Minas gerais
Paraguay
Peru
Uruguay
peruviana Peruvian Peru Less hairy; deep pod reticulation
forms N.W. Bolivia
aequatoriana Peruvian Ecuador Very hairy; deep pod reticulation;
forms purple stems; more branched, erect
vulgaris Spanish Brazil More branched; upright branches
bunch Guranian
Goias
Minas Gerais
Paraguay
Uruguay

section Arachis. All the diploid species of section Arachis are grouped under the
secondary gene pool. The species under the sections other than Arachis are grouped
under tertiary.

16.3.2 Evolution of Cultivated Groundnut

The cultivated groundnut, Arachis hypogaea, is an allopolyploid with two different

genomes ‘AABB’ (Stalker 1992; Raina and Mukai 1999). Krapovickas and Rigoni
(1957) proposed the direct amphidiploid origin, while Smartt and Gregory (1967)
suggested its origin from a pre-existing wild allotetraploid. A hybridization between
an annual x perennial species within the section Arachis is considered as the key
event in the evolution of groundnut.
Different species, viz. A. cardenasii, A. chacoense, A. correntina, A. duranensis
nom.nud. and A. villosa, were proposed as putative “A” genome donors and
A. batizocoi as “B” genome donor of A. hypogaea (Stalker and Moss 1987; Singh
842 T. Radhakrishnan et al.

and Smartt 1998). However, Paik-Ro et al. (1992) reported that A. batizocoi is not
closely related to A. hypogaea and hence cannot be considered as the “B” genome
donor. A. ipaensis was proposed as putative “B” genome donor on the basis of
restriction fragment length polymorphism (RFLP) analysis (Kochert et al. 1991).
Fernandez and Krapovikas (1994) supported A. duranensis and A. ipaensis as the
“A” and “B” genome donors, respectively. Based on crossability and molecular data,
scientists at ICRISAT proposed A. hanoei as the “B” genome and A. duranensis as
“A” genome donors of cultivated groundnut (Upadhyaya et al. 2011). However, till
date no cross combinations between “A” and “B” species could recreate
A. hypogaea-like species. Molecular studies (Kochert et al. 1991; Halward et al.
1991a; Stalker 1991) at DNA levels (RFLP, PCR, isozymes, and seed storage
proteins) have indicated that a large amount of genetic differentiation had already
taken place in ‘A’ and ‘B’ genomes as reported earlier by Stalker and Dalmacio
(1981) and Singh and Moss (1982) thus making it difficult to predict either one or
both the putative genome donors of A. hypogaea. More recently, Chen et al. (2019)
analysed the evolution of the cultivated groundnut with the support of genome
sequence information and concluded that asymmetrical evolution involving several
hybridizations A genome progenitor undergoing gene loss and conversions, and
rearrangement, pointing to the possibility of more A genome progenitors other than
A. duranensis or hybridization of A. ipaensis with several varieties of A. duranensis
contributed to the formation of the allotetraploid.

16.4 Karyology of Arachis

16.4.1 Chromosome Numbers

The chromosome number of cultivated groundnut A. hypogaea is of 2n ¼ 40 (Husted

1931, 1933, 1936; Ghimpu 1930; Kawakami 1930). The first chromosome count
reported for a wild species was 2n ¼ 40 for A. glabrata (section: Rhizomatosae)
(Gregory 1946). However, majority of the wild species in the genus Arachis are
diploid (2n ¼ 20). Though the tetraploid species in sections Arachis and
Rhizomatosae have the same chromosome numbers 2n ¼ 40, they are reported to
be cross-incompatible indicating the independent evolution of polyploidy in the two
sections Arachis and Rhizomatosae of this genus.
Lavia (1998) reported a chromosome number of x ¼ 9 for A. palustris and
A. praecox and in A. décora (Penaloza et al. 1996) of the section Arachis. Among
the two series of chromosome numbers that appear to occur in the genus Arachis
(2n ¼ 2x ¼ 20 and 2n ¼ 4x ¼ 40), the diploid forms are more predominant, and
hence the basic chromosome number is believed to be x ¼ 10. The proposed basic
chromosome number of x ¼ 9 in the species A. palustris and A. praecox might have
originated by the selective elimination of a single chromosome from the other
species having x ¼ 10. On the other hand, Bera et al. (2002) proposed that reverse
may be true and species with chromosome number x ¼ 10 might have originated by
selective duplication of a single chromosome. The presence of two basic
16 Groundnut Breeding 843

chromosome number (x ¼ 9 and x ¼ 10) and less existence of polyploid species in

the genus Arachis indicate that aneuploidy has played a key role in the evolution and
speciation of Arachis species rather polyploidization. Therefore, the species diver-
sity of Arachis may be mainly due to structural chromosomal rearrangements and
thus supports the theory that groundnut is segmental polyploidy and that the section
Arachis represents the most advanced traits within the genus.

16.4.2 Karyotype and Pairing Behaviour

The chromosomes of groundnut are small ranging from 1.4 to 3.9 μm in length and
are predominantly metacentric. Several karyotypic analysis have revealed a pair of a
small chromosomes termed as “A” chromosomes and another pair with a secondary
constriction, termed as “B” chromosomes in the somatic cells of Arachis (Husted
1933, 1936; Stalker and Dalmacio 1981; Singh and Moss 1982; Stalker 1991).
However, the “A” chromosome was absent in the species, A. batizocoi,
A. cruziana, A. magna, A. williamsii and A. ipaensis which had the “B” chromosome
pair (satellite chromosome) (Smartt et al. 1978). Babu (1955) reported several types
of secondary constriction in A. hypogaea, and D’Cruz and Tanskasale (1961) and
Stalker and Dalmacio (1986) proposed that cultivars could be distinguished based on
karyotype differences. On the basis of this, the “A” and “B” genomes designated in
groundnut to describe the two cytological groups. Stalker (1991) designated
A. glandulifera as “D” genome species, and further, the B genome was divided
into B, F and K genomes by Seijo et al. (2004) and Robledo and Seijo (2010).
The meiotic chromosomes of A. hypogaea pair mostly as 20 bivalents, but a few
multivalents occasionally have also been reported (Husted 1936). Husted (1936),
Raman (1976) and Stalker (1980) concluded that structural differences in
chromosomes exist between the two subspecies hypogaea and fastigiata and intra-
specific hybrids mostly have bivalents at metaphase I, though univalents also exist at
a low frequency.

16.5 Plant Genetic Resources

Genetic resources are the reservoir of variability in economically important traits

which are invaluable in crop improvement. The largest collection of germplasm
(15,445 accessions from 93 countries) is held at ICRISAT, India (Pandey et al.
2012). The ICAR-NBPGR, India, has 14,585 accessions in their gene bank, while
the ICAR-Directorate of Groundnut Research, India, holds 9024 accessions. The US
Department of Agriculture (USDA) stores 9917 accessions, and the Oil Crops
Research Institute (OCRI) of China has 8083 accessions, while the Crops Research
Institute of the Guangdong Academy of Agricultural Sciences in China conserves
4210 accessions. In addition to this, small to medium collections are held at the
different research organizations across the world.
844 T. Radhakrishnan et al.

Though the number of wild species available in the gene banks prior to the 1980s
were very few, the explorations in Bolivia, Brazil, Paraguay and northern Argentina
have enriched the collection (Stalker 2012). So far, 83 species of Arachis have been
described, and more than 3400 accessions of Arachis species have been documented
of which nearly 1300 are available in field gene banks or storages (Stalker et al.
2002). The largest collection of Arachis species are with Brazilian Agricultural
Research Corporation (EMBRAPA), Brazil and Texas A & M University (1200
accessions each). The USDA holds 607 accessions, and the ICRISAT has 477. More
than 400 accessions are being held at the Instituto de Botánica del Nordeste (IBONE)
in Argentina and at North Carolina State University (Singh and Simpson 1994;
Pandey et al. 2012). About 50% of wild species accessions have <50 seeds in
storage, and several are propagated in greenhouses or in field as vegetatively (Stalker
2012).
In order to facilitate the utilization of the large number of germplasm, a represen-
tative collection of about 10% of the entire germplasm collection has been identified
so as to have a manageable and cost-effective starting point in identifying candidate
genotypes with new sources of disease and pest resistance or abiotic stress tolerance
(Brown 1989). Such representative collections have been designated as core collec-
tion comprising 1704 A. hypogaea accessions was developed at ICRISAT, which is
similar to the USA. With the increasing number of the accessions, the size of these
core collections also has become too large for easy exploitation by breeders.
Therefore, “mini-core collections” (i.e. 10% of the core collections and 1% of entire
germplasm collection).
In addition to germplasm collections, amphiploids and autotetraploids
(Mallikarjuna et al. 2011), chromosome segment substitution (CSSL) lines (Fonceka
et al. 2012) and multiparent advanced generation intercross (MAGIC) populations
(Janila et al. 2016a) have also been developed to facilitate groundnut breeding.

16.6 Floral Biology: Emasculation—Pollination Techniques

16.6.1 Plant Morphology and Floral Biology

The groundnut seed is dicotyledonous with a stem axis, leaf primordia, hypocotyl
and primary root. It is interesting to note that all primordial leaves and above-ground
structures appearing within the first few weeks after germination are already present
in the seed. Germination is epigeal; hypocotyl is white and very prominent in the
early stages of growth but becomes indistinguishable from the roots as the plant
matures. The primary root system is tap rooted, but many lateral roots develop about
3 days after germination. Even though roots can reach 135 cm deep, generally they
are restricted to 5–35 cm below the soil surface (Intorzato and Tella 1960). Roots do
not have typical root hairs, but tuffs of hairs emerge in the axils of lateral roots (Moss
and Ramanatha Rao 1995). Although groundnut has a symbiotic relationship with
Bradyrhizobium, root hairs are not the site of infection as observed in many legumes
(Elkan 1995).
16 Groundnut Breeding 845

Fig. 16.1 Parts of a groundnut flower

Stems are solid, but become slightly hallow when the plant matures. The main
stem develops from a terminal bud of the epicotyl, and two cotyledonary laterals
develop and grow on the opposite sides near the soil level. The main stem can be
upright or prostrate depending on the botanical type. The shape of the leaflets on the
main stem and lateral branches may vary. Branching pattern of reproductive to
vegetative nodes on the cotyledonary laterals is one of the prime criteria for grouping
of the two subspecies.
Groundnut inflorescence is unique among domesticated plants in that it flowers
above ground but produces seeds below the soil surface. Flowers are borne on axils
of leaves on primary or secondary branches, spike-like, simple or compound
monopodia, and each node has up to five flowers. However, three flowers per
inflorescence are most common. Only one flower per inflorescence opens at any
given time. The flowers are modified sessile and papilionaceous that appear to be
stalked due to the presence of a tubular hypanthium or “calyx tube”. The flower is
subtended by a bract, with a second bract on the inflorescence branch. There are two
calyx lobes, an awn-like one opposite the keel (includes one sepal) and a broad one
opposite to the back of the standard (includes four sepals-fused). The corolla consists
of five petals (one standard, two wing, two keel), and the calyx has five sepals both
are borne at distal end of the calyx tube. The colour of the standard petal varies from
light yellow to deep orange or rarely white. A central crescent area exists on the face
of the standard petal which can be deeper in colour as that of standard or even
express a different colour. The colour of the standard and wing is usually the same
though there are varietal differences.
The style is enclosed within the calyx tube, and both calyx tube and style elongate
rapidly up to 5–7 cm in 24 h prior to anthesis. The androecium is a monoadelphous
structure with the staminal tube bearing five oblong and five globular anthers
(Fig. 16.1). The filaments are fused for two-thirds of their length. Among the
globular anthers, two are sterile. This number usually varies in different varieties.
In erect types, the sterile anthers are more common, while it may be absent in
spreading types.
The eight fertile normally developed anthers consist of four globose, dorsifixed,
uniloculate anthers alternating with four adnate, introse, oblong anthers. Ovary is
superior, small and conical with a beak-shaped point at the tip and contains a single
846 T. Radhakrishnan et al.

sessile carpel with 1 to 6 ovules; style is glabrous throughout its length and covered
with bristles near the club-shaped stigma and is enclosed in a filiform hypanthium.

16.6.2 Flower Emergence and Opening

Groundnut produces a large flush of flowers of which nearly 40% of flowers fail to
develop pegs or pegs do to produce mature pods and nearly 20% of flowers produce
mature fruits. Genotypes which flower early and produce most of the flowers during
first 2 weeks of the flowering period produce greater number of pods. Depending on
photoperiod, temperature and genotype, flowering starts at about 25 days after
emergence. The number of days required to first flowering increases from 24 to
38 days when the daily mean temperature rises to 20–30  C in spreading and semi-
spreading types, while it drops from 35 to 24 days in Spanish and Valencia types.
The most prolific flowering occurs between 5 and 11 weeks after sowing depending
on the duration of cultivar and the season with a high degree of first formed flowers
producing mature fruits.
Usually four to flushes of flowering can be observed in a groundnut plant. Very
few flowers are produced in the initial flush which is followed by a large number of
flowers in the second flush. After reaching a peak in the second flush, there will be a
gradual decline in the number of flowers in the subsequent flushes. In some
genotypes, there may be only two flushes of flowering, and generally the fruits
developed from the flowers of the later flushes may not reach maturity at the time of
harvest.

16.6.3 Anthesis and Pollination

Anthesis takes place when the flower bud is 50–70 mm long. Flower buds generally
open at the beginning of the light period; it may be delayed in cold or wet weather.
The pollen matures 6–8 h before anthesis and has two generative nuclei at the time of
anthesis. The self-pollination occurs because the stigma and anthers are enclosed by
the keel. Cross-pollination (ranging from 0 to 6.16%) also occurs through bees to a
very limited extent. The stigma is at the same level or protrudes beyond anthers,
papillate type without surrounding hairs (surrounded by many papillae), elongated
and strongly curved. Stigma is receptive before anthesis. Pollination takes place at or
near the time of anthesis (flower opening). Enzymes associated with pollen germi-
nation are produced on the stigmatic surface from 48 h before to 8 h after anthesis.
The ovary is unilocular and has 1–3 ovules, superior with the calyx tube attached
to the base of the ovary. Fertilization is complete within 6 h after pollination or
before midday. After fertilization, the flower drops, and the hypanthium and the style
may remain attached to the base of the ovary for 4–5 days. The ovary at the base of
the calyx tube starts growing actively within a week by the activation of the
intercalary meristem located below the ovary. The green ovary becomes purplish
at its tip, and the developing ovary pierces through the floral parts to produce
ageotropically elongating peg (botanically a “carpophore” or “gynophore”) which
16 Groundnut Breeding 847

carries the ovule at its tip. The pegs stop growing after penetrating the soil. The
normal pod-forming zone is 4–7 cm below soil surface, and the optimum tempera-
ture in zone is about 31–33  C. Lower soil temperature around 23  C increases
number of pods and pod weight but increases filling duration thus increasing
maturity. It takes about 60 days from the time of fertilization to full maturity.
Pods are elongated with varying degrees of reticulation on the surface. They
contain two to five seeds although differences exist among members of the subsp.
hypogaea and fastigiata. Seeds (kernels) may be oval, round or elliptical, have
pointed or flattened ends, vary in seed coat colour from off-white to deep purple
and may be monochrome or variegated. Seed size ranges from 0.15 to more than
1.3 g/seed, while the seeds of the wild species weigh as low as 0.047 g/seed (Stalker
1997). For further understanding on morphological variations in groundnut readers
may refer to IBPGR/ICRISAT (1992); Krapovickas and Gregory (1994); IBPGR
(1990); Rao and Murty (1994), and Stalker and Simpson (1995).

16.6.4 Emasculation and Pollination Techniques

Flower buds of appropriate size, which may open the next day, are emasculated in
the evening. Different methods are employed for emasculation.

16.6.4.1 Ring Cut Method

Described by Kale and Mouli (1984) where bud was hold between the thumb and the
index finger of the left hand, and with the help of a razor blade in the right hand, a
superficial circular incision was made with a razor blade in the bud at about
two-thirds down from the top or 2 mm above the base. Using a forceps the standard
petala and calyx are removed exposing the wing petals. The wing petals are forced
back using the forces to expose the keel so as to remove the anthers without
damaging the style and stigma.

16.6.4.2 Straw Tube Insertion Method

Described by Reddy et al. (1970), a razor blade is used to make a cut on the
depressed side of the bud at two-thirds of its length below the tip so as to cut the
standard and a portion of the wing petals. The sepals and petals, except the keel, are
removed. Emasculation is carried out with forceps after separating the stamens and
the pistil from the keel. Verify with the help of a magnifying glass that all the anthers
are removed. A 4–5 cm straw (used for sipping drinks) is then inserved over the
calyx tube and close the upper open end with the help of the forceps. The straw has to
be removed at the time of pollination and re-instated after pollination.

16.6.4.3 Paper Towel Use Method

Norden and Rodriguez (1971) described a Paper Towel method where the flower
bud is emasculated by first removing the lower lip of the calyx and then the wing and
keel petals. The standard, which is retained, is held out of the way, while the anthers
are removed. The standard returns to its original position and curls over the stigma
after emasculation. A paper towel, approximately 12 cm  12 cm, is dampened with
848 T. Radhakrishnan et al.

water and placed around the flower immediately after pollination. A slit is made in
the towel on one edge to slide it in between the stem and leaf axil. The wet paper
towel provides shade and a favourable environment for the germination and
subsequent growth of pollen on the stigma.
The emasculated buds are marked by coloured nylon threads which are date
coded. Pollinations are to be done in the early morning hours of the subsequent day
of emasculation. Pollens can be dusted directly on the stigma from the detached
flowers of the pollen parent of by using a forceps or brush. Pegs will start generally
5–7 days after pollination.

16.7 Genetic Studies of Qualitative and Quantitative Traits

Majority of the traits of agronomic importance in groundnut follow quantitative

inheritance and, hence, highly have a high G  E interaction. Additive inheritance
was observed as principal component of variance when the parental genotypes are
from the same botanical varieties while when crosses involve different botanical
varieties non-additive variance also reported (Table 16.5).

16.7.1 Heritability of Various Traits

The heritability estimates reported were dependent on the experimental design,

genotypes used and the traits studied, method used to estimate, environmental
conditions and the controls used (Table 16.6).

16.8 Breeding Objectives

16.8.1 Breeding for Yield and Yield-Related Traits

Most extensively targeted traits of groundnut are the yield and yield contributing traits
in the crop improvement programmes worldwide. High yields in terms of pod and seed
are the main goals of a groundnut breeder. Due to large G  E interactions selection
for yield per se was low and slow (Nigam et al. 1991a) even though it is a major basis
for improving groundnut productivity in the world. The pod yield is a function of crop
growth rate, fraction of crop growth rate and the duration of reproductive growth
partitioned towards pod yield. Therefore, better understanding physiology of yield is
also necessary to better target yield increase. Number of pods per plant, pod yield per
plant, 100-seed mass and shelling outturn are the important yield contributing
parameters. There exists a wide gap between the realized and potential yields mainly
due to rainfed cultivation of the crop with little or no inputs, and recurrent drought
coupled with biotic factors reduces yield of groundnut in Kharif season. Developing
Kharif groundnut varieties with stress tolerance along with low inputs response and
rabi-summer cultivation varieties with response to high nutrient and water manage-
ment conditions will be fruitful and increase the productivity.
16 Groundnut Breeding 849

Table 16.5 Genetics/inheritance of various traits in groundnut

S. no. Trait Reported inheritance in literature
1. Plant type and associated traits
Growth habit—erect/bunch (Valencia and Complex inheritance—monogenic,
Spanish types), semi-spreading/ digenic, trigenic, tetragenic, gene
spreading/runner (Virginia type) cytoplasmic and maternal inheritance for
growth habit; generally spreading habit
dominant over bunch habit but in some
cases, the opposite also found; semi
spreading habit monogenic dominant to
bunch and spreading forms; spreading
dominant to bunch with complementary
and duplicate effects of two genes
Plant height Both additive and on-additive gene effects
Dwarf plant stature Different forms of dwarfism are observed:
sterile brachytic, fertile dwarf, etc. Sterile
brachytic—monogenic recessive in
natural and induced mutants; two
recessive complementary factors; trigenic
complementary; tetragenic inheritance
with two sets of factors with
complementary-duplicate action; fertile
dwarf—normal monogenic dominant over
dwarf with cytoplasmic modifiers; more
than one gene involved in plant height
determination; dominant with variable
expressivity and penetrance
Canopy breadth Additive gene effects; partial dominance
Branching vs. non-branching Branching in Virginia type monogenic
dominant over non-branching Valencia
type; monogenically recessive/double
recessive for suppressed primary branches
in induced mutants; quantitative
inheritance
Number of primary branches Both additive and non-additive gene
effects
Number of secondary branches Both additive and non-additive gene
effects
Length of primary branches Both additive and non-additive gene
effects
Reproductive branches on main stem Absence is dominant to the presence; two
sets of duplicate loci with epistatic control,
when both loci of each set or all four loci
are recessive flowering occurs; two, three
or four sets of homozygous recessive loci
or modifying factors
Stem pigmentation Purple or red pigmentation monogenic
dominant/incompletely dominant over
light or green colour; monogenic, digenic
duplicate and digenic complementary
inheritance for purple colour; two sets of
(continued)
850 T. Radhakrishnan et al.

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
genes of which one responsible for purple
and the second for green pigmentation,
extra nuclear factors; duplicate recessive
for white stem
Stem pubescence Stem pubescence monogenic dominant/
incompletely dominant over absence of
pubescence; monogenic inheritance with
overdominance of hairiness
2. Leaf traits
Elliptical shape Elliptical leaflet shape on the main axis
monogenic recessive to elliptical-oblong
shape
Krinkle leaf Both monogenic dominant and recessive
in different krinkle mutants
Mottled leaf Monogenic dominant to normal leaf in
natural mutants
Narrow leaf TMV 2 narrow leaf mutant and Gujarat
narrow leaf mutant are genetically
different; partial dominant monogenic;
monogenic dominant in induced mutant
Cup leaf Monogenic recessive in induced mutant
Flop leaf Monogenic recessive and digenic
recessive in induced mutants
Curly leaf Monogenic recessive in a natural mutant
Corduroy leaf Duplicate recessive in induced mutant
Puckered leaf Recessive with 13 normal: 3 puckered leaf
ratio
Dark green leaf colour Dark green colour monogenic dominant/
incomplete dominant over light green
colour; dark green colour duplicate
recessive in radiation-induced mutant;
light green colour dominant over dark
green colour in crosses involving Chico
variety with at least two dominant alleles
of one of the two loci or one dominant
allele each at both loci necessary for
regulation of chlorophyll synthesis
Lutescent leaf colour Two duplicate recessive genes
Golden yellow colour Two duplicate recessive genes
Albinism Duplicate recessive, triplicate recessive,
trigenic model in which duplicate loci
controlling chlorophyll development
epistatic to a third locus governing a
zygotic lethal; cytoplasmic factors
influencing expression of nuclear genes
governing albinism
(continued)
16 Groundnut Breeding 851

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Variegated leaf Monogenic dominant in induced mutant,
maternally inherited
Leaflet size/leaf area Intra-plant variation in leaflet size
common in groundnut. Large leaflet size
incompletely/completely dominant over
small size; monogenic/duplicate recessive
in induced and natural mutants;
predominant additive gene effects for leaf
length and both additive and non-additive
gene effects for leaf width; predominantly
non-additive gene effects and reciprocal
effects for leaf area
Petiole length Both additive and non-additive gene
effects important; three recessive genes for
short petiole
Number of stomata Low number monogenic recessive and
digenic recessive
Number of leaves on main stem Both additive and non-additive gene
effects
Number of leaves on cotyledonary Predominantly additive gene effects
branches
3. Inflorescence
Inflorescence length Elongated inflorescence dominant over
condensed inflorescence with two genes
with complementary interaction
Type of inflorescence Two complementary genes with 9 simple:
7 compound inflorescences in Valencia
(simple)  Virginia (simple)crosses,
however, a ratio of 13 compound—3
simple inflorescences observed in
Valencia (simple)  Spanish(compound)
crosses suggesting presence of two genes
inhibiting expression of simple
inflorescence in Spanish type
Colour of standard petal Five different intensities of standard petal
colour observed; in general deep colour
dominant over light colours; orange
monogenic dominant/incomplete
dominant/co-dominant over white; faint
orange monogenic recessive to orange;
duplicate recessive control of white flower
when crossed with lines having yellow
flowers; incomplete monogenic
dominance of yellow flower over white
flower; additive effects of two different
genes for yellow colour; lemon yellow
dominant to orange flower with presence
of transposable elements; two
complementary genes for garnet colour
which is dominant over orange colour;
trigenic control
(continued)
852 T. Radhakrishnan et al.

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Presence vs. absence of standard crescent Purple crescent dominant to no crescent
governed by duplicate genes; single
dominant gene for purple crescent
Number of pegs Both additive and non-additive gene
effects
Peg strength Significant SCA
Peg pigmentation Monogenic dominant/digenic inheritance
for purple pigmentation of pegs
Brachytic sterility One, two, three or more recessive genes;
two sets of factors with complementary
duplicate action condition brachytic
character
Female sterility Monogenic and trigenic recessive
inheritance
Male sterility Two recessive genes
4. Pod traits
Pod size Large size dominant over small size and
monogenic, digenic, trigenic and
multigenic control reported; small size
dominant over large size with duplicate
gene interaction; predominantly additive
gene effects
Pod length Normal length dominant over long length
with duplicate genes; both additive and
non-additive gene effects, maternal effects
Pod width Both additive and dominance gene effects,
maternal effects
Pod constriction Absence of constriction or shallow
constriction dominant over deep
constriction and controlled by two
independent dominant genes; trigenic
complementary inheritance for shallow
constriction; three unlinked loci and
cytoplasmic factor
Pod reticulation Monogenic dominant for strong
reticulation over shallow or absence of
reticulation; at least four factors for deep
reticulation; smooth pods dominant over
reticulated pods with digenic inhibitory
gene action (13 smooth: 3 reticulated
types)
Pod pubescence Two loci with additive gene action
Pericarp thickness Monogenic dominant thin pericarp over
thick pericarp; five factors with thin
pericarp dominant over thick pericarp;
three complementary genes for
moderately thick pericarp
(continued)
16 Groundnut Breeding 853

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Pod beak Non-beaked pods monogenic dominant
over beaked pods; prominent beak
monogenic dominant over non-beaked
pods
Aerial podding Aerial podding monogenic dominant over
normal podding and the opposite also true
depending upon the genetic backgrounds
of the parents
One-seed pod Any two of three duplicate recessive genes
control one-seed pod
5. Seed characters
Number of seeds per pod Three or more seeds dominant over fewer
seeds with trigenic/monogenic control;
fewer than three seeds dominant over three
or more seeds with monogenic control
Seed size Large seed size monogenic dominant over
small size with possible modifiers; five
pairs of genes with four having
isodirectional effects
Shrivelled seeds Single recessive gene
Seed shape Round shape monogenic/duplicate genes
recessive to elongated seeds; seed length
maternally controlled; button type seeds
dominant over normal seeds (round or
elongated) with digenic ratio of 13:3
indicating influence of inhibitory genes on
seed shape
Seed ends Flat ends of seed monogenic dominant
over smooth ends
Seed length Mainly additive gene effects and
significant reciprocal/maternal effects;
both additive and dominance gene effects
Seed width Mainly additive gene effects and
significant reciprocal/maternal effects;
both additive and dominance gene effects
Seed length and width ratio Mainly additive gene effects and
significant reciprocal/maternal effects
Hard seed Paternal inheritance, both hard and soft
seeds are allelic and follow monogenic
inheritance in induced mutant; the gene for
hard seed has pleiotropic effect
Rough testa Duplicate genes with recessive epistasis
with 9 rough:7 smooth testa
Testa colour Inheritance of testa colour varies from
simple to very complex. Seven gene pairs/
nine loci interacting in several ways to
produce different testa colour
(continued)
854 T. Radhakrishnan et al.

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
(a) Flesh (rose/pink/russet or tan) testa Duplicate dominant loci
(b) White testa Recessive to coloured tests; two different
dominant genes epistatic to red and flesh
testa colour in specific genotypes
(c) Red testa One dominant gene/partial dominance/
single recessive gene/two duplicate
recessive genes/two complementary
recessive genes/polygenic control
responsible for red testa colour
(d) Purple testa Partial/complete dominance over all other
colours with inheritance monogenic/
digenic epistatic, duplicate, digenic
cumulative, trigenic and tetragenic with
complex interactions; duplicate recessive
(e) Wine testa Monogenic recessive
(f) Chocolate testa Monogenic/digenic recessive in an
induced mutant
(g) Variegated testa Dominant/partially dominant and
recessive to non-variegated testa;
monogenic/digenic/two genes with
cumulative effects; trigenic inheritance
with epistatic effect of purple over red
Seed coat splitting Monogenic inheritance with additive
effects, duplicate additive and digenic
complementary
6. Yield and related traits
Pod yield Both additive and non-additive gene
effects
Number of mature pods per plant Both additive and non-additive gene
effects
Number of immature pods per plant Both additive and non-additive gene
effects
Shelling outturn Governed by a pair of genes without
dominance; both additive and
non-additive gene effects
Weight of seed per plant Both additive and non-additive gene
effects
Seed number per kg Predominantly additive gene effects
% sound mature kernels Predominantly on-additive gene effects
100-pod weight Both additive and non-additive gene
effects
100-seed weight Both additive and non-additive gene
effects; mainly additive gene effects and
significant reciprocal/maternal effects
7. Haulm yield and quality
Green weight/haulm yield Both additive and non-additive gene
effects; both GCA and SCA for biomass
(continued)
16 Groundnut Breeding 855

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
8. Life cycle
Annual vs. perennial Perennial growth habit dominant over
annual habit
9. Crop duration
Early maturity and its components Late maturity monogenic dominant/
incompletely dominant over earliness;
four or five genes with complete
dominance of lateness over earliness and
absence of reciprocal differences; single
gene with additive effect/predominantly
additive gene effects for days to flower,
three genes with two types of epistasis
(dominant recessive, 13 late: 3 early and
duplicate dominant, 1 late: 15 early) for
days to accumulation of first 25 flowers
and absence of reciprocal differences; two
recessive genes acting in an additive
manner for days from seedling emergence
to first flower; significantly higher GCA
variance than SCA variance for time of
emergence (in h), time to first leaf opening
on cotyledonary branch (in h), time to first
leaf opening on main stem (in h), days to
first flower and number flowers per plant
(at 32 days) under controlled environment
conditions; significantly higher GCA
variance than SCA variance for days to
first flower under field conditions;
significant additive genetic variance with
bidirectional dominance/non-additive
gene effects for days to first flower;
significant additive genetic variance for
pod and seed maturity indices; both
additive and dominance genetic effects for
maturity index; highly significant additive
and significant dominance,
additive  additive and
dominance  dominance effects with
duplicate digenic interaction for days from
emergence to first flower, more than two
genes or linkage effects between the genes
for number of flowers produced during
first 4 days of flowering, highly significant
additive and significant dominance effects
for percentage of ripe pods at 80 days after
sowing; predominantly non-additive gene
effects for days to maturity
10. Biochemical/nutritional traits
Oil content Both additive and non-additive gene
effects; epistatic interaction
(continued)
856 T. Radhakrishnan et al.

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Protein content Both additive and non-additive gene
effects; epistatic interaction
Oleic acid content One/two recessive genes for high oleic
acid
Fatty acids (palmitic, stearic, oleic, Additive gene effects and
linoleic, arachidic, eicosenioic, behenic additive  additive interaction
and lignoceric fatty acids, total saturated
fatty acids and long chain saturated fatty
acids)
Oleic/linoleic fatty acid (O/L) ratio Single recessive or two recessive genes
and some possible modifiers depending
upon the parents involved in the crosses;
additive gene effects and
additive  additive interactions
Polyunsaturated/saturated fatty acid Both additive and dominance gene effects
(PS) ratio and additive  additive and
additive  dominance interactions
Arginine content Two major genes with partial dominance
for low arginine
Iodine value Both additive and dominance gene effects
and additive  additive and
additive  dominance interactions
Soluble sugars Predominantly additive gene effects
11. Physiological traits
Iron chlorosis One basic gene and two or four inhibitory
complementary genes for expression of
iron chlorosis
Harvest index Both GCA and SCA; predominantly
GCA; predominantly additive gene effects
with additive  additive epistasis
Leaf chlorophyll content Quasi-quantitative with modifiers either in
positive or negative direction in different
genetic backgrounds
Chlorophyll a, chlorophyll b and total Non-additive gene effects with significant
chlorophyll additive  dominant epistatic interaction
Carotenoid content Dominant gene effects with significant
additive  dominance and
dominance  dominance interactions
SPAD chlorophyll meter reading Both additive gene effects and dominance
(SCMR) gene effects with duplicate and
complementary epistatic and
additive  additive interactions
Specific leaf area (SLA) Predominantly additive gene effects and
additive  additive interactions;
predominantly dominance gene effects
with duplicate epistasis
(continued)
16 Groundnut Breeding 857

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Specific leaf weight Predominantly non-additive gene effects
Fresh seed dormancy Complete/incomplete monogenic
dominance for dormancy over
nondormancy; multigenic control.
Apparent photosynthesis Dominance and overdominance effects
Response to photoperiod Mainly GCA, additive gene effects in
some cases and partial dominance to
dominance in others. Maternal effects
12. Nitrogen fixation
Nodulation and nitrogen fixation Nodulation dominant to non-nodulation;
monogenic, digenic and trigenic
inheritance; a trigenic model proposed—
the first two genes produce nodulation,
while the third one inhibits nodulation
when dominant and the former two in
homozygous recessive condition.
Although the presence or absence of
nodulation is governed by a few major
genes, the intensity of nodulation appears
to be controlled quantitatively;
predominantly additive gene effects for
nitrogen fixation; both additive and
non-additive gene effects and additive x
additive, additive x dominance and
dominance x dominance interactions for
nodule number and nodule mass per plant,
nitrogenase activity and acetylene
reduction; non-additive gene action and
reciprocal effects for nitrogenase activity,
nodule number, nodule mass and total
nitrogen; predominantly SCA for nodule
number and weight, specific nitrogenase
activity, shoot weight and total plant
nitrogen, maternal effects also important
13. Disease resistance
Rust Sexual stage and races in groundnut rust
pathogen not yet observed. Monogenic/
digenic/trigenic inheritance with
resistance being recessive; preponderance
of non-additive gene action; greater
dominance variance; dominant, partial
dominant or additive gene action for
resistance; both additive and non-additive
gene effects and additive  additive and
additive  dominance interactions;
significant GCA and SCA for rust
resistance; resistance dominant/partial
dominant in wild Arachis species. The
resistance is stable overs years and
locations
(continued)
858 T. Radhakrishnan et al.

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Late leaf spot (LLS) LLS and ELS inherited independently;
duplicate complementary recessive in
induced mutants; resistance recessive and
level of resistance controlled by presence
of recessive gene(s) at any or all of the five
loci; 4–5 duplicate recessive genes; both
additive and non-additive gene effects and
additive  dominance epistatic, maternal
effect; additive gene effects for
components of resistance (lesion number,
lesion area, defoliation, latent period and
spore production)
Early leaf spot (ELS) Chemical-induced physiological races
observed which may give differential
reaction to resistant sources. Additive and
non-additive gene effects and
additive  additive gene interaction for
resistance with involvement of
cytoplasmic factors; duplicate recessive in
induced mutants
Sclerotinia blight At least two genes involved; quantitative
inheritance with involvement of
dominance, epistatic and cytoplasmic
factors
Cylindrocladium black rot Predominant additive gene effects;
complex inheritance with resistance
delaying the onset of disease
Aspergillus flavus/A. parasiticus and No correlation between aflatoxin content
aflatoxin production and in vitro seed colonization and the
population density of A. flavus in the soil;
three resistance mechanisms—preharvest
resistance, seed coat resistance (in vitro
seed colonization and cotyledon resistance
(aflatoxin production)), all inherited
independently; predominance of additive
gene effects for seed coat resistance,
reciprocal differences observed;
predominantly non-additive gene effects
for aflatoxin production
Groundnut rosette disease(GRD)— Three agents responsible for expression of
chlorotic rosette and green rosette disease symptoms – groundnut rosette
virus (GRV), groundnut rosette assistor
virus (GRAV) and satellite RNA
(SatRNA); two independent recessive
genes for resistance to GRD (effective
against GRV and SatRNA but not against
GRAV)
(continued)
16 Groundnut Breeding 859

Table 16.5 (continued)

S. no. Trait Reported inheritance in literature
Peanut bud necrosis disease(PBND) Three resistance factors inherited
additively for reduced disease incidence;
highly significant GCA and significant
SCA and reciprocal effects; non-additive/
additive/dominance/epistatic and additive
x additive gene effects in different crosses
Tomato spotted wilt virus disease Significant GCA and SCA; transgressive
(TSWV) segregation for resistance observed
Peanut stripe virus disease (PStV) Significant GCA and SCA
Bacterial wilt Partially dominant involving three pairs of
major genes and some minor genes;
recessive resistance; nucleo-cytoplasmic
interaction and both additive and
dominant gene actions
14. Resistance to nematodes
Meloidogyne arenaria (root-knot Resistance conferred by single/two
nematode) race 1 dominant genes (one inhibits root galling
and the other inhibits egg production)
15. Insect pest resistance
Leaf hopper Resistance controlled by three recessive
genes with additive effects; predominant
additive gene effects for long trichomes on
mid-rib and petiole and jassid damage;
predominant non-additive gene effects for
short, medium or long trichomes on
adaxial leaf surface, margins, mid-rib and
petiole
Aphids Single recessive gene for resistance
Leaf miner Significant GCA and SCA
Adapted from Nigam (2014)

Recently, physiological traits like harvest index, transpiration-use-efficiency, etc.

which are associated with yield are also gaining attention in breeding programmes
where necessary infrastructure and resources are available. High peg-strength to
reduce harvest losses, ease in shelling, more number of seeds per pod, pod characters
like constriction, beak and reticulation, kernel shape and uniformity, testa colour and
blachability have also emerged as traits being sought after by farmers and industry.
Haulm yield coupled with pod yield is an important consideration for development
of dual-purpose varieties. For improved quality of haulm, the traits to be targeted are
digestibility and nitrogen content. To tide over the problem of viviparity in Spanish
varieties resulting from unseasonal rain, fresh-seed dormancy and short duration
(maturing in nearly 90 days) are traits or relevance. Early maturity makes crop suited
for multiple cropping systems by evading the drought and frost stress conditions.
Lack of fresh seed dormancy results in in situ germination and leads to loss in pod
yield and quality in rainfed environments when rain coincide with the maturity stage
of the crop. Globally released most of the high-yielding varieties of groundnut were
860 T. Radhakrishnan et al.

Table 16.6 Heritability of various traits reported from different studies in literature
Narrow sense
heritability
S. no. Trait Broad sense heritability (H) (h2)
1. Height of main axis 33.7–97.2 71.0
2. Branching pattern 90.4 55.3
3. No. of primary branches 33.5–94.5 23.2–59.0
4. No. of secondary branches 12.0–98.9 –
5. Length of primary branch 28.0 64.5
6. Length of secondary branch 38.0 36.2
7. Shoot dry weight 37.0–100.0 –
8. Plant fresh weight 1.0 –
9. Total dry matter 38.8–98.0 –
10. No. of nodules per plant 44.3 –
11. Single nodule weight 42.9 –
12. Nodule weight per plant 33.0–100.0 –
13. Nitrogenase activity 60.8 –
14. Acetylene reduction 31.0 –
15. Days to emergence 48.0–83.0 51
16. Days from emergence to first flower 11.9–96.9 23.0–39.0
17. Days to 50% flowering 66.5–96.3 60.0
18. Days from emergence to 17.0–61.0 –
accumulation of 25 flowers
19. Number of flowers produced during 16.0–44.0 9.0–38.0
first 4 days of flowering
20. Peg number 54.2–56.2 11.7–45.7
21. Peg strength 74.1 –
22. Peg length 74.0 37.7
23. Peg diameter 75.0 –
24. Pod-peg ratio 48.8 –
25. Days to maturity 91.7–98.6 –
26. Fruit maturity based on oil 69.0–95.0
pigmentation
27. Maturity based on hull scrap 71.0
method
28. Percentage of ripe pods 80 days 13.0–41.0 24.0
after sowing
29. No. of immature pods per plant 3.7–92.7 1.4–5.1
30. Pod size – 42.0–50.0
31. No. of mature pods per plant 26.1–100.0 31.7–32.0
32. Pod weight 42.0–80.0 –
33. Pod length 54.0–92.0 –
34. Pod yield per plant 13.2–98.0 59.8
35. 100-pod weight 75.0–100.0 –
36. Seed yield 38.3–83.9 31.5
37. 100-seed weight 28.6–100.0 57.3–66.8
38. Harvest index 27.7–100.0 –
(continued)
16 Groundnut Breeding 861

Table 16.6 (continued)

Narrow sense
heritability
S. no. Trait Broad sense heritability (H) (h2)
39. Shelling outturn 33.3–100.0 10.5–42.0
40. Oil content in seed 22.0–94.4 29.0
41. Protein content in seed 43.0–64.0 14.0
42. Zn content in seed 92.0 –
43. Fe content in seed 81.0 –
44. Carbon isotope discrimination 53.0 –
(Lab)
45. Carbon isotope discrimination 75.0–89.0 –
(Field)
46. Transpiration efficiency 34.0–86.0 –
47. Total transpiration 12.0–70.0 –
48. SPAD chlorophyll meter reading 9.0–98.0 –
49. Specific leaf area 5.0–98.0 –
50. Drought tolerance index 54.0–98.0 –
51. LLS disease index – 22.0–27.0
52. LLS resistance – 0–13.0
53. ELS resistance 51.7 –
54. Resistance to CBR 48.0–65.0 51.7
55. Resistance to S. miner# of days 41.5–50.314-23 1.0-11.0
until plants wilted Disease rating
56. Seed coat resistance to A. flavus 78.5 –
57. Resistance to A. parasiticus. Dry 30.0–65.020.0–65.027.0–33.0 –
seed resistance. ii. Aflatoxin
production. iii. Pre-harvest
resistance
58. Fodder quality traits. (1) Nitrogen 0.720.720.670.91 –
content. (2) In vitro organic matter
digestibility (OMD)
(3) Metabolizable energy content
(ME) (4) Digestible haulm yield
Adapted from Murthy and Reddy (1993), Nigam (2014), and others

resulted from the higher harvest index brought about by reduction in the total
biomass. Breeding for high harvest index coupled with high biomass can be one
of the strategies to further increase groundnut yield.

16.8.2 Breeding for Abiotic Stress Resistance Including Climate

Change

In India, 106 million ha of area is completely unirrigated and is under dryland

agriculture generating nearly half of total value of agricultural output. In these
862 T. Radhakrishnan et al.

regions, around 300 million people depend for their sustenance on dryland agricul-
ture, of whom 30–40% can be classified as poor (Ryan and Spencer 2001). Peanut is
an important crop of dryland agriculture wherein it is valued both for its seed and
fodder. Groundnut fodder is highly nutritive and forms an important component of
cattle feed. Nearly, 85% area under peanut remains rainfed of which approximately
80% comes under dryland where irrigation facilities do not exist at all (Roy and
Shiyani 2000). Water stress in dryland is intermittent and unpredictable (Vorasoot
et al. 1985) and can occur at any stage of the crop starting from pre-flowering,
flowering, pegging and pod development (Jogloy et al. 1996) and causes significant
yield loss. Yield losses due to water stress are dependent on crop growth stage,
intensity and duration of its occurrence (Nigam et al. 2005). Drought stress at
pre-flowering stage increased the yield by 13–19% (Nageswara Rao et al. 1985a),
whereas at pod setting stage it caused yield losses up to 88% (Vorasoot et al. 2003).
Not only the yield but also the quality of products decreases under drought stress
(Rucker et al. 1995; Stansell and Pallas 1985), and the latter was aggravated by the
contamination of aflatoxin under drought environment (Sanders et al. 1993).
Drought in rain-dependent cropping system is always associated with heat stress
(Nautiyal et al. 2004). In the last few decades, there has been constant increase in
global air temperature (Nautiyal et al. 2004) and in the twenty-first century, it is
predicted to increase further and associated with frequent warm spells, heat waves
and heavy rainfall and a likely increase in the frequency of droughts (Qin et al.
2007). In India, temperature increase is predicted to be 3.5 and 5.5  C by 2080 (Lal
2001). Studies made by the CGIAR have reported that the high temperature stress
(above 30  C) will be widespread in East and Southern Africa, India, South East
Asia and Northern Latin America which are important groundnut-growing areas.
Thus, efforts to breed varieties that can thrive and yield under both drought and heat
stress need to be intensified (Janila et al. 2013).
Climate change being projected for India will increase the problem of heat and
drought stress in groundnut, thus further limiting the production potential (Singh
et al. 2014). Temperatures during the crop growing seasons in certain areas of India
are already above the upper limit of optimum temperature range (20–30  C). When
climate changes are small, agronomic practices can help farmers to adopt, but when
changes are intensive then we need extensive changes like genetic improvement of
crop for greater tolerance to high temperature and drought, improved response to
rising CO2 and development of new agronomic practices (Boote et al. 2011). The
critical stages to heat stress in groundnut are at the flowering (3–6 days before
flowering) and pod formation (Craufurd et al. 2002, 2003).
Apart from low unpredictable water supply and increased temperatures, arid
regions are also known for low soil fertility (Peek and Forseth 2003). Due to
capillarity in the in drought-affected soils, the nutrient uptake will be low as
air-filled capillaries block water diffusion into roots (Baligar et al. 2001; Fageria
et al. 2002; Gunes et al. 2006; Ghanbari et al. 2011). Like other agricultural crops,
peanut requires essential nutrients during its life cycle. This may further lead to the
impaired active transport and membrane permeability (Tanguilig et al. 1987). In
peanut water deficit during pod filling stages (Kulkarni et al. 1988) and a long-term
16 Groundnut Breeding 863

drought period from 14 days after emergence until harvest (Arunyanark et al. 2008)
reduced uptakes of N. Likewise, reductions of K, P, Ca and Mg uptake as a result of
drought at flowering pegging, pod formation and development stages were also
observed (Kolay 2008). Htoon et al. (2014) and Dinh et al. (2014) have proposed
nutrient uptake under drought stress as a surrogate trait for drought tolerance.
Though 235 varieties have been developed in groundnut, none of those have been
bred with specific objectives to suit them of typical dryland conditions. It has been an
ever-increasing challenge for the plant breeders to evolve efficient varieties for
dryland conditions because of extreme variability in the agro-climatic conditions
of such stress areas. Hence, for groundnut to sustain its yield in the future, it should
possess tolerance to drought, heat stress and ability of high nutrient use efficiency
under drought conditions. In order to make significant progress in breeding
programmes for these stresses, we need to identify sources of resistance/tolerance.
Few sources of tolerance to drought, heat and nutrient stresses are available in
literature. Genetic variability for thermotolerance of selected peanut genotypes was
studied (Nautiyal et al. 2004) using leaf cell membrane thermostability and identified
ICGS 44 and ICGV 86031 as tolerant to high temperature and water deficit stress.
Calcium enrichment in peanut tissues has shown to improve drought tolerance in
peanut (Chari et al. 1986), and genetic variability for Ca uptake was established the
genotypes ICGHNG88448, NRCG 7085-1 and NRCG 6155 (Singh et al. 2004). As
moisture availability is low under drought conditions, absorption and mobility of
nutrients such as phosphorus is also affected.
Singh and Basu (2005) screened peanut genotypes under low P availability and
identified genotypes GG 5, NRCG 7085-1, NRCG 6919, NRCG 1308, NRCG 3498
and SP250A as P efficient. Rajgopal and Bandyopadhyaya (1999) screened available
germplasms and identified genotypes NRCG 3787, 3778, 1116, 5150, 7627, 5311,
3920, 4481 and 7706 as drought and heat stress tolerant. Vasanthi et al. (2006) have
identified genotypes ICGV 8603, CSMG 84-1, ICGS 76 and TAG 24 with most
useful traits for drought tolerance. Likewise, several promising genotypes have been
identified for drought tolerance such as Dh 3–30, JGN 2, ICGS 1, ICGS 37, JGN
3, GG 5, Kadiri 5, Abhaya, Kadiri 9, BG 3 and ICGS 5 (Rathnakumar et al. 2013).
Transgenic approach has been used to develop drought-tolerant genotypes using
AtDREB1A (Sarkar et al. 2014, 2016, 2019; Bhalani et al. 2019) and mtlD genes
(Bhauso et al. 2014; Patel et al. 2017). Salinity-tolerant genotypes have also been
developed using transgenic approaches in peanut by deploying the AtDREB1A
(Sarkar et al. 2014) and mtlD (Bhauso et al. 2014; Patel et al. 2016) genes. Breeding
programmes are underway to develop either heat stress-tolerant, drought-tolerant or
nutrient use-efficient genotypes. But in actual field conditions drought stress, heat
stress, nutrient use efficiency and other abiotic stresses are interrelated. Hence, to
increase productivity under dryland conditions, it is important to develop a cultivar
which is drought and heat stress tolerant and also take up and utilize nutrients
efficiently.
864 T. Radhakrishnan et al.

16.8.3 Breeding for Quality Characters

Quality traits vary from the consumer demand in groundnut. Different end users
have different prerequisites in terms of quality traits. Groundnut is categorized as oil
types and confectionary types according to its utilization pattern.

16.8.3.1 Breeding for High Oil Content and Quality

Wide variation exists for oil content in groundnut germplasm. It ranged from 46.5 to
63.1% in cultivated types, while the range observed in wild species was from 43.6 to
55.5% (Nordan et al. 1982). In few wild Arachis species, oil content up to 60% has
also been reported by the Directorate of Groundnut Research, Junagadh, Gujarat.
Few promising high oil lines (>52%) have also been reported by Directorate of
Groundnut Research, Junagadh, Gujarat and ICRISAT. Oil content and yield have
been reported to be independent thus suggesting possibilities of breeding varieties
with high yield and oil content. Narrow-sense heritability has been worked out to be
high (Martin 1967) for oil content. Inheritance of oil is governed by two pair of
alleles with non-additive genetic component being predominant (Basu et al. 1988).
Selection should be postponed to later generations to eliminate the undesirable
recombinants.
The oil content, fatty acid composition, iodine value, ratio of oleic to linoleic acid
(O/L) and stability or shelf life are factors to be considered in oil quality of
groundnut. Genetic manipulation of fatty acid composition has been reported by
few workers. The Virginia types generally have higher oleic acid content, while
Spanish-Valencias have higher linoleic acid. This results in a lower iodine value for
oil of Virginia types and indicates that these types will become rancid through auto-
oxidation more slowly than the Spanish-Valencias. The groundnut breeder is faced
with a paradox when breeding for oil quality. Consumers prefer to have oils both
with low iodine (long shelf-life) and high iodine value (to have high level of
unsaturation from the health point of view). Crosses between all the four habit
groups have shown that a wide range of iodine values can be obtained through
recombination of genes from different parents and that the iodine value in
groundnuts is highly heritable (Bovi 1982).
High oleic acid groundnut is one of the most sought types by the processing
industry especially the confectionaries. High oleic groundnut has better keeping
quality (O’Keefe et al. 1993; Braddock et al. 1995), nutritional quality and better
flavour. It is reported to have a gain of tenfold in shelf life. High oleic groundnut has
a mutation in the fatty acid dehydrogenase (FAD) gene which is responsible for
adding the second double bond to oleic acid resulting in linoleic acid. By preventing
this conversion, the oleic acid content can go up to 80% while keeping linoleic acid
content around 2–5%. Since cultivated groundnut is an allotetraploid, there are two
homeologous gene sequences, FAD2A and FAD2B, believed to have originated
from the two progenitor species genomes, Arachis duranensis and Arachis ipaensis
(Bertioli et al. 2019; Chen et al. 2019; Zhuang et al. 2019), and a mutation in either
one of these genes result in an enhanced oleic acid content (Nawade et al. 2016;
Nawade et al. 2018). However, to achieve more than 75% of oleic acid, mutations in
16 Groundnut Breeding 865

both alleles are essential (Pandey et al. 2014a, b) which is further confirmed by Janila
et al. (2016a, b) in introgression line developed using allele-specific markers and
also by Nawade et al. (2019). At ICAR-DGR using marker-assisted introgression,
two new varieties were developed, Girnar 4 and Girnar 5, with having >78% of oleic
acid content.

16.8.3.2 Breeding for Confectionery Groundnut

There are important trade attributes for confectionary-type groundnut, and the
groundnut cultivars should possess certain physical attributes and chemical compo-
sition and maintain some definite processing and end-use characteristics to be
acceptable to traders, manufacturers and ultimate consumers. Among the physical
quality requirements for confectionery groundnuts, size, shape and high sound
mature kernel (SMK) are important. High SMK of >80%, 100-seedmass (HSM),
kernels with elongated shape, tapering ends and pink to light brown testa colour and
large seed size are desirable traits (Nigam et al. 1989). Though no parameter has
been fixed for chemical properties, low (<1%) free fatty acid (FFA), high sugars
(>6%) and high protein (>30%) along with nutritional qualities like high O/L and
low oil (<45%) are preferred traits for confectionery groundnuts (Kona et al. 2019,
2020).
Indian Hand Picked Select (HPS) peanuts have a strong demand in Southeast
Asia and countries neighbouring India. The Agricultural and Processed Food
Products Export Development Authority (APEDA) and the Indian Oilseeds and
Produce Export Promotion Council (IOPEPC) are jointly working towards the
increase of international awareness of Indian groundnut offer and addressing
quality-related concerns. APEDA has issued export guidelines for groundnuts and
groundnut products and provides information on registration of groundnut
processing units and/or warehouse, as well as on the issuance of export certificates
by IOPEPC.
In the past, for confection, protein content of 20%, >55 g of HKW and low oil
content (42%) were preferred (Ramanathan 2004). With the evolving market and
industry requirement, the traits for confectionary uses now are greater proportion of
sound mature kernels (SMK), free from aflatoxin contamination, attractive seed size
and shape, pink or tan seed colour, flavour, 100-seed weight exceeding 55 g, >6% of
sugar content, >24% of protein content, blanchability (>60%), low oil content
(<45%) and high oleic/linoleic (O/L) ratio (Nigam et al. 1989; Dwivedi and
Nigam 1995; Kona et al. 2019, 2020) (Table 16.7). Seed mass is an important
attribute to confectionary quality; however, like yield and yield parameters, it is
highly influenced by environment. The carbohydrate components of the kernel
determine the taste and sensory attributes of roasted groundnuts (Pattee et al.
2000). Seed colour and shape and flavour are the other important confectionary
attributes. Blanchability is removal of testa or seed coat (skin) from raw or roasted
groundnuts, and this attribute is of economic importance in processed groundnut
food products, which include peanut butter, salted groundnuts, candies and bakery
products and groundnut flour. Breeding programme for confectionery quality trait
improvement especially for protein and sugar requires non-destructive estimation
866 T. Radhakrishnan et al.

Table 16.7 Standards for confectionery groundnut

Traits Desirable aspects
Seed size 155–170 seed/100 g
>55 g 100 seed mass
Seed shape Round or elongated with tapering ends
Colour Pods; light golden-yellow
Kernels, with tan rose and pink testa
Flavour (roasted) Almond, coffee, nutty popcorn, smoky and sweet
Texture (roasted) Firm and crispy
Biochemical and Low oil content (<45%), high protein content (>24%), high O/L ratio
nutritional (>60% oleic acid), high vitamins B1, B2, E, high in minerals like Ca,
Mg, Fe, low in anti-nutritional compounds like oxalic and phytic acid,
blanchability (>60%), high sugar content (>6%)
Aflatoxin Free from aflatoxin
Nigam et al. 1989; Dwivedi and Nigam 1995; Basu et al. 2003; Kona et al. 2019, 2020; Aman et al.
2020; Sushmita et al. 2020

procedures and molecular markers linked to them so that selection in segregating

generations will be easy and reduces the cumbersome process. Both nutritional and
food processing quality traits are gaining importance in the breeding programmes to
meet various uses as well as consumer preference.
Many varieties having large seed size were developed in India (Table 16.8) of
which very few genotypes have export potential (GAUG 10, M 13, TMV 10, ICGS
76, GG 20, BAU 13, B 95, HNG 10, Girnar 2, Mallika (ICHG-00440), GJG 22, RG
559–3 (Raj Mungfali 3)).
The cultivation of specifically developed confectionery groundnut cultivars to
meeting the international standards using their production technologies are most
vital to increase the export. Some of the regions in India are suited for the cultivation
of confectionery groundnut; however, it cannot be grown on all soils with full
potential. Most of the production of export quality groundnut is obtained from
Gujarat and Tamil Nadu and now from Rajasthan. Bold-type groundnut is mostly
obtained from Rajasthan, Gujarat, Madhya Pradesh, Punjab and Haryana states
which are grown from light textured to heavy soil with FYM. The other states
mostly produce Java-type groundnut. Indian groundnuts in the Far East are preferred
over others origins such as China because of the high oil content. The Saurashtra
region of Gujarat and other part of Gujarat produce both Java and bold type of export
quality. Raising of good-quality groundnut requires a high standard of crop hus-
bandry which should not suffer from diseases, insect pests and moisture and
nutritional stresses. Further, in the context of India, the crop duration should be
short as in long duration crop the management becomes difficult. Therefore, cultiva-
tion of large seeded and confectionery groundnut for export promotion should
preferably be entrusted to resource-rich farmers capable of affording good manage-
ment practices.
16 Groundnut Breeding 867

Table 16.8 Varieties released in India having combination of traits suitable for confection or table
purpose
Pod yield Duration
S. no. Variety Season Area of adoption (kg ha1) (days)
Spanish bunch
1 TKG-19A Rabi- Konkan region of 2260 107
(TG-19A) summer Maharashtra
2 TPG-41 Rabi- All India 2088 122
summer
3 TLG-45 (Trombay- Kharif Maharashtra 1506–2000 115
Latur Groundnut-
45)
4 RARS-T-1 Kharif, Andhra Pradesh 2500–4000 115
Rabi-
summer
Valencia
1 Gangapuri Kharif Madhya Pradesh 2000 95–105
Virginia bunch
1 Vikram (TG-1) Kharif Maharashtra 2695 120
2 Kadiri-2 Kharif Andhra Pradesh 1800 115–120
3 BG-1 (Birsa Kharif Bihar 2200 120–125
Groundnut-1)
4 BG-2 (Birsa Kharif Bihar 2200 120–125
Groundnut-2)
5 BAU-13 (Birsa Kharif Bihar 2191 125–135
bold-1)
6 ICGS-76 Kharif Southern 1300 115–125
Maharashtra,
Karnataka
7 GG20 Kharif Gujarat 1960 109
8 Koyana (B-95) Kharif, Southern 3345 115–125
Rabi- Maharashtra
summer
9 M-522 Kharif Punjab 2525 110–120
10 Ak-303 Kharif Maharashtra 2100 125
11 TBG-39 (TG-39) Kharif Rajasthan 3154 118
12 Girnar-2 Kharif Uttar Pradesh, 2907 130
Punjab, northern
Rajasthan
13 Kadiri-7 (K-7) Kharif Andhra Pradesh 1643 120–125
14 Kadiri-8 (K-8) Kharif Andhra Pradesh 1523 120–125
15 Mallika (ICHG- Kharif All India 2579 125–130
00440)
16 TGLPS-3 (TDG-39) Kharif Karnataka 2500–3000 115–120
17 Gujarat Groundnut Kharif Gujarat 2835 121
HPS 2 (GG HPS 2)
GJG 22 Kharif Tamil Nadu 1914 125–130
(continued)
868 T. Radhakrishnan et al.

Table 16.8 (continued)

Pod yield Duration
S. no. Variety Season Area of adoption (kg ha1) (days)
Virginia runner
1 M-13 (Moongphali Kharif All India 2750 135
No.13)
2 Chandra (Ah-114) Kharif Uttar Pradesh 2500 130
M-335 Kharif Sandy soil areas of 2300 120–125
Punjab
4 Somnath (TGS-1) Kharif Gujarat and 1900 110–125
Rajasthan
5 GJG-HPS-1 Kharif Gujarat 2125 110–120
(JSP-HPS-44)
6 Raj Mungfali 1 Kharif Rajasthan and 2558 112–138
(RG 510) Punjab
7 RG 559–3 (Raj Kharif Rajasthan, Uttar 3173 120–125
Mungfali 3) Pradesh and Punjab

Zinc and Iron Biofortification

Micronutrient deficiencies have increased over recent decades due to a generalized
decrease in the quality of poor people’s diets both in developed and developing
countries and even in areas where food is not a limiting factor (Welch and Graham
1999; Graham et al. 2001). Micronutrient malnutrition affects more than one-half of
the world’s population, especially women and pre-school children (UNSCN 2004).
Furthermore, micronutrient deficiencies are more widespread than deficiencies
caused by inadequate consumption of energy or protein. Breeding crop plants for
higher micronutrient concentration, an approach termed as biofortification, has
become an active goal of plant breeding programmes in the developing world at
both the international and national agricultural research centres (Welch 2002; Bouis
2003). It aims on the development of micronutrient-dense staple crops using the best
traditional breeding practices and modern biotechnology.
Staple diet is the prime sources of the total intake of zinc for the people in
developing countries. Biofortification, wherever possible, is a cost-effective and
sustainable solution for tackling the micronutrient deficiencies as the intake of
micronutrients is on a continuing basis with no additional costs to the consumer in
the developing countries (Kumar et al. 2011). It has the potential to help to alleviate
the suffering, death, disability and failures to achieve human potential, which results
from micronutrient deficiency-related diseases. In comparison to other strategies, it
provides a truly feasible means of reaching out to remote and rural areas where
people has limited access to diverse diets, commercially fortified foods and
supplements, to deliver naturally fortified foods (Bouis et al. 2011). Results from
germplasm screening suggest that the iron and zinc concentration of staple foods can
be doubled through conventional breeding. This result, in turn, implies that iron and
zinc intakes in poor people’s diets can be increased by 50 per cent. This should result
in an appreciable improvement in nutrition and health even for those whose intakes
remain below recommended daily intakes.
16 Groundnut Breeding 869

Groundnut is valued as a rich source of energy contributed by oil (48–50%) and

protein (25–28%) in the kernels. In addition, groundnut kernels also contain
antioxidants and vitamins and are rich in mono-unsaturated fatty acids (Janila
et al. 2013). Those contain vitamin E and many important B-complex group of
vitamins like thiamin, pantothenic acid, vitamin B-6 and niacin. Of the 20 minerals
necessary for normal body growth and maintenance, seven, including iron and zinc,
are present in peanut. Groundnut is a dietary source of biologically active
polyphenols, flavonoids and isoflavones but lacks completely in vitamin A (Misra
2006). Developing countries, where micronutrient deficiencies are widespread,
contribute world’s maximum peanut area and production (FAOSTAT 2011).
Thus, peanut can contribute significantly towards reduction of protein-energy and
micronutrient malnutrition (Janila et al. 2014). If there is sufficient genetic variation
for the density of micronutrients in edible parts of the crop, biofortification can be
achieved through plant breeding (Mayer et al. 2008). In groundnut genetic
variability was reported for iron and zinc concentration (Upadhyaya et al. 2012;
Janila et al. 2014), and thus biofortification is possible.

16.9 Breeding for Major Biotic Stresses

Groundnut is a mainly grown as a rainfed crop in India which accounts about 84% of
the total area. Many biotic stresses are known to limit groundnut productivity during
Kharif and rabi-summer season, but their severity and distribution vary with
prevailing environmental conditions. These biotic stresses reduce the quality
(nutritional, appearance, sensory attributes) and quantity in terms of pod and
haulm yield of groundnut. Groundnut is attacked by several diseases caused by
fungi, virus, nematodes and insects and pests. Early leaf spot (ELS) caused by
Cercospora arachidicola Hori, late leaf spot (LLS) caused by Phaeoisariopsis
personata (Berk. & Curt.) Van Arx and rust caused by Puccinia arachidic
Spegazzini are among the major foliar fungal diseases worldwide (Gajjar et al.
2014; Bala et al. 2016). Stem and podrot, caused by Sclerotium rolfsii, collar rot
caused by Aspergillus niger van Tiegham and dry root rot caused by Macrophomina
phaseolina are major soilborne diseases of groundnut production in many warm,
humid and dry areas (Thirumalaisamy et al. 2014; Bosamia et al. 2020). Aflatoxins
are carcinogenic substances produced by the fungi Aspergillus flavus and
A. parasiticus, and the contamination of export consignments by this toxin had
forced several importing countries to impose strict regimes in place on permissible
levels of aflatoxins (Dodia et al. 2014; Singh et al. 2015a, b). The major viral
diseases of groundnut are peanut bud necrosis disease (PBND) in India and peanut,
groundnut rosette disease (GRD) in Africa, tomato spotted wilt virus (TSWV) in the
USA, peanut stripe potyvirus (PStV) in East and Southeast Asia, peanut stem
necrosis disease (PSND) in pockets in Southern India and peanut clump virus
disease (PCVD) in West Africa and some parts of India (Nigam et al. 2012).
Bacterial wilt of groundnut caused by Pseudomonas solanacearum is prevalent in
Southeast Asia, the Far East and Uganda (Hayward 1991).
870 T. Radhakrishnan et al.

Aphids (Aphis craccivora Koch), several species of thrips (Frankliniella

schultzei, Thrips palmi and F. fusca), leaf miner (Aproaerema modicella), red
hairy caterpillar (Amsacta albistriga), jassids (Empoasca kerri and E. fabae) and
Spodoptera are the major insect pests in groundnut, among which aphids, thrips and
Spodoptera have worldwide distribution and cause serious damage (Wightman and
Amin 1988). Termites and white grubs are major soil arthropods causing damage to
groundnuts. Groundnut bruchid beetle (Caryedon serratus (Olivier)) are the major
storage insect pests in groundnut. Breeding for resistance to insect pest has been
limited as only moderate degrees of resistance to the sucking insects like aphids,
jassids and thrips and leaf miner are available in the cultivated germplasm, and the
transfer of these into high yielding backgrounds has not been very successful.
Root-knot diseases caused by Meloidogyne species of nematode are widely
distributed in Asia, Australia and North America (Sharma et al. 1990). Globally,
nematodes cause nearly 11.8% yield loss in groundnut. The root-knot nematodes,
Meloidogyne spp., and the lesion nematodes, Pratylenchus spp., are important
(Sharma and McDonald 1990a), while Meloidogyne arenaria and M. javanica are
predominant species causing economic loss of nearly 21.6% in India (Khan et al.
2010).

16.9.1 Breeding for Foliar Diseases Resistance

Among foliar fungal diseases, early leaf spot (Cercospora arachidicola Hori), late
leaf spot [Phaeoisariopsis personata (Berk. & Curt.)Van.Arx.] and rust (Puccinia
arachidic Speg.) are widely distributed and economically important worldwide.
These diseases together can cause more than 70% loss in yield besides adversely
affecting the quality of the produce (pods, seeds and haulm) (Aruna et al. 2005). Late
leaf spot is the major and widely distributed disease, which can cause defoliation and
reduce pod and fodder yields about 50% and adversely affect quality of produce
(Subrahmanyam et al. 1984). Rust is also economically important causing yield
losses ranging from 10 to 52% and affecting seed and fodder quality
(Subrahmanyam et al. 1995). Foliar diseases can be controlled by chemical
measures, but they increase costs of production thus beyond the reach of small and
marginal farmers and also pollute the environment. Therefore, development and
growing of resistant cultivars are the best viable option to minimize economic losses
of farmer and to maintain the quality of the produce.
Foliar disease resistance breeding has started in the early 1970s, and high levels of
resistance or immunity in wild Arachis species for early leaf spot in A. chacoense
and late leaf spot in A. cardenasii were reported by Abdou et al. (1974). However,
foliar disease resistance was found to be liked to undesirable pod and seed
characters, low shelling outturn and long duration. By utilizing resistant source
NCAc-17,090, first-generation foliar disease-resistant varieties, viz. ICGS (FDRS)
10 and Girnar 1, were released in India. Later on, advanced resistant breeding lines
were used to develop new resistant cultivars with desirable agronomic characters,
and the resistant cultivars ICGV 86590 and ALR 2 were released in India. These
16 Groundnut Breeding 871

cultivars also suffered the drawbacks associated with the linkage drag of traits like
long duration and lower partitioning and with undesirable pod (highly reticulated,
constricted, prominently ridged and conspicuously beaked pods with thick shells)
and seed (purple or blotched seed colour) characteristics (Wynne et al. 1991; Singh
et al. 1997). An interspecific derivative, GPBD-4 (KRG 1 x ICGV 86855), which
combined early maturity, high yield potential and high shelling outturns with
minimum reduction in yield due to high level of resistance to rust and late leaf
spot (Gowda et al. 2002). Many high-yielding groundnut varieties with resistance of
multiple foliar diseases (leaf spot and rust) have been released for commercial
cultivation to groundnut farmers in India, viz. AK 265, PhuleBharti (JL 776),
PhuleMorna (KDG 123), PhuleWarna (KDG 128), GJG 32 (ICGV 03043),
PhuleUnnati (RHRG-6083).
Modern crop breeding approaches like marker-assisted selection improve the
precision of or targeted breeding (Bosamia et al. 2015). Development of tightly
linked markers for LLS and rust resistance would make breeding programmes more
efficient in production of resistant cultivars in shorter time. Recently, many DNA
markers have been found to be putatively linked to rust and LLS resistance genes,
and many markers were recently found to be associated with QTLs for rust and late
leaf spot (Mondal and Badigannavar 2010, 2018; Sujay et al. 2012; Mishra et al.
2015; Zhou et al. 2016; Ahmad et al. 2020). The molecular markers validated for
LLS and rust resistance (Sukruth et al. 2015; Yeri and Bhat 2016) were used to
improve LLS and rust-resistance of the cultivars TAG 24, ICGV 91114 and JL
24 through MABC (Varshney et al. 2014). In the same lines, the cultivars GJG 9, GG
20 and GJG-HPS 1 have also been improved for their resistance to foliar disease
resistance along with high oleic acid (Shasidhar et al. 2020).
Alternaria leaf blight is a minor disease but becoming a severe in rabi-summer
season as compared to Kharif season groundnut-growing states of India. Therefore,
very little breeding work has been done to identify resistance sources and to develop
resistant varieties. The genotypes PI 405132, PI 259747, PI 215696, NcAc 17,132,
NcAc 17,133 RF and NcAc 17,135 were reported to be resistant to A. alternata
(Muthuswamy et al. 1991). Five multiple disease-resistant germplasm accessions,
viz. NCAc17149, NCAc927, NCAc17133 (RF), PI 393646 and PI 341879 have
been identified resistant to early leaf spot, rust and Alternaria leaf spot (Ghewande
et al. 1992).
Bera et al. (2011a, b, c, d, e, f, g, h) reported eight groundnut germplasm, viz.
NRCGCS 77, NRCGCS 83, NRCGCS 85, NRCGCS 86, NRCGCS 21, NRCGCS
124, NRCGCS 180 and NRCGCS 222 having multiple disease resistance to PBND,
stem rot, late leaf spot, early leaf spot, rust and Alternaria leaf blight. It has been
observed that cultivars TG-37A, ICGS-37, JL-24, AK-159, DRG-12 and TPG-41
were susceptible to Alternaria leaf blight (Kumar et al. 2012). Three cultivars, viz.
Kaidiri 9, KadiriHaritandra and ICGV 00348; four advanced breeding lines, viz.
PBS 12190, PBS 22131, PBS 22132 and PBS 22133; and four interspecific
derivatives, viz. NRCGCS 176, NRCGCS 180, NRCGCS 196 and NRCGCS
298 found resistant to Alternaria leaf blight. Therefore, these varieties may be
used directly in rabi-summer groundnut areas of India (Anonymous 2019).
872 T. Radhakrishnan et al.

16.9.2 Breeding for Soilborne Diseases

Stem rot caused by Sclerotium rolfsii Sacc. and collar rot caused by Aspergillus
niger van Tieghem are prevalent in almost all groundnut-growing areas of India
especially in medium black and sandy loam soils, respectively. Stem rot pathogen is
prevalent in warm temperate and sub-tropical regions of the world and has a host
range of over 500 plant species (Harlton et al. 1995; Dodia et al. 2016, 2019). It is
reported from India, Thailand, Indonesia, Taiwan and the Philippines where yield
losses were ranging from 10 to 25% (Mayee and Datar 1988). In India, it is
widespread in Gujarat, Maharashtra, Karnataka, Tamil Nadu and Andhra Pradesh
causing 10 to 40% yield losses (Akgul et al. 2011; Bera et al. 2014).
Several germplasm accessions and breeding lines were screened for their resis-
tance to stem rot. Among them, nine breeding lines (ICGV 86034, 86,124, 86,252,
86,388, 86,590, 86,606, 86,635, 87,160 and 87,359) showed low susceptibility to
stem and/or pod rot (Mehan et al. 1995). The disease can be managed through
cultural practices together with resistant cultivars (Shew et al. 1984). Most sources of
resistance to soilborne fungi reported in groundnut show low levels of resistance or
tolerance. Such partial resistance is presumably governed by polygenes and is
assumed to be similar to horizontal resistance (Fry 1982). There are practical
difficulties in incorporating this type of resistance from germplasm with desired
agronomic traits. The strategy has been to breed for a low level of host pathogen
coexistence that is stable, environmentally balanced and economically useful
(Wynne et al. 1991).
Although several advanced breeding lines, cultivars and wild species have been
screened for resistance against stem rot by several workers, absolute resistance for
stem and collar rot is not present in available groundnut germplasm, only partial
resistance has been identified in groundnut which is being utilized currently for
cultivar development. Currently interspecific derivatives, viz. NRCGCS 19 and
NRCGCS 319, and one breeding line PBS 18037 have resistance to stem rot and
are being utilized breeding programme widely.
With the advancement of molecular marker technology, various genomic tools
have been utilized to identify specific DNA regions tightly linked to stem rot
resistance in groundnut. Bera et al. (2016) developed SSR-based genetic map and
identified 12 SSR polymorphic marker loci with one major QTL (QTL qstga01.1)
for stem rot disease resistance in groundnut. Dodia et al. (2019) reported develop-
ment of high-quality genetic map with 585 SNP loci with spanning the distance of
2430 cM with an average inter-marker distance of 4.1 cM. She identified 44 major
epistatic QTLs with phenotypic variation explained ranging from 14.32 to 67.95%.
Collar rot is an important disease caused by Aspergillus niger van Tieghem and is
a filamentous fungus growing aerobically on organic matter. Collar rot can be rotting
of seed, pre-emergence soft rot of hypocotyls and post-emergence collar rot of
seedlings (Mehan et al. 1995). Collar rot is prevalent in almost all groundnut-
growing states of India, viz. Rajasthan, Gujarat, Punjab, Andhra Pradesh, Tamil
Nadu, Uttar Pradesh, Maharashtra, Orissa, Karnataka and Madhya Pradesh particu-
larly in sandy loam and medium black soils. In Gujarat the losses in terms of
16 Groundnut Breeding 873

mortality of plants due to collar rot range from 28 to 50 per cent (Ghewande et al.
2002). In India, the breeding work on resistance of collar rot was not much due to
non-availability of stable source of resistance to collar rot. The cultivars J11, JCG
88 and OG 52-1 were reported to be moderately tolerant to collar rot (Ghewande
et al. 2002). Palaiah et al. (2019) found 37 germplasm lines were resistance and
cultivars, viz. KRG-1, R-2001-3, Kadiri-9, ICGV-00350, ICGV-00351, TG-37A,
GPBD-4, GPBD-5, KDD-128, Dh-101, Dh-216, G2–52, Ch-2, TDG-51, S-230,
DSG-1, Chintamani-2 and J-11, were moderately resistant to collar rot. Divya
Rani et al. (2018) reported following breeding lines having less than 15% disease
incidence, viz. ICGV 00202, ICGV 00211, ICGV 86590, ICGV 91114, ICGV
05155, ICGV 00350, ICGV 93261, ICGV 92195, ICGV 92035 and ICR 48. Most
of resistant sources are from the wild species which are generally cross-incompatible
with cultivated genotypes and linked with undesirable agronomic traits. While
selecting for better agronomic traits, the levels of resistance often diluted. Therefore,
breeding strategy should be developing cultivars with low level of host pathogen
interaction for durable resistance.

16.9.3 Breeding for Reduced Aflatoxin Contamination

Aflatoxins are one of the most potent toxic and extremely carcinogenic secondary
metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus.
There are four major aflatoxins that occur in crops, including B1, B2, G1 and G2,
and sum of these four is referred to as the total aflatoxin. The dominant aflatoxins
produced by A. flavus are B1 and B2, whereas A. parasiticus produces two additional
aflatoxins, G1 and G2 (Payne 1998). Aflatoxin B1 is considered to be the most
important of the four because it is the most toxic and has been classified by the
International Agency for Research on Cancer as a probable human carcinogen
(IARC 1987).
In groundnut, based on the site of action of the aflatoxin-producing fungi, there
are three types of host-pathogen resistance mechanisms: pre-harvest aflatoxin con-
tamination (PAC) at pod wall; in vitroseed colonization (IVSC) at seed coat; and
resistance to aflatoxin production (AP) at cotyledons level (Nigam et al. 2009).
Mixon and Rogers (1973) were the first to suggest the use of resistant cultivars to
contain the problem of aflatoxin contamination in peanut. They reported two
Valencia genotypes, PI 337394 F and PI 337409, as having high levels of resistance
to in vitro seed colonization (IVSC) by both pathogens (A. flavus and A. parasiticus).
Genotypes PI 337409, PI 337394F and UF 71513 were reported to be resistant to
seed invasion and colonization, the cultivars Doran and Shulamit to be resistant to
pod infection and U-4-477, 55–437, 73–30 and J 11 resistant to seed infection in the
field and U 4–7-5 and VRR 245 with low production of aflatoxin B1 (Mehan 1989).
However, the aflatoxin content and seed colonization could not be correlated with
the population of A. flavus in the soil (Will et al. 1994). Nigam (2002) has reported
that preharvest seed infection and aflatoxin production are influenced significantly
by the G  E interactions. Relationships between in vitro seed colonization (IVSC)
874 T. Radhakrishnan et al.

and natural seed infection and aflatoxin production in the field and their contribution
in reducing aflatoxin contamination are not understood clearly (Xue et al. 2004). The
resistance breeding programme requires stable resistance source and a reliable,
efficient and reproducible screening technique. Lack of high levels of resistance
and limitations of screening techniques place severe constraints on the progress in
resistance breeding to eliminate aflatoxin (Nigam et al. 2009). Further, it is suggested
that genetic resistance alone cannot solve the problem of aflatoxin contamination in
groundnut until unless other cultural management practices such as soil and water
management, bio-control, soil pest management and postharvest management
practices should be followed for managing this disease.
However, the advancement of genomic tools may provide an opportunity to
achieve stable genetic resistance by combining the three mechanisms of aflatoxin
resistance. Currently resistant genotypes are being deployed for breeding aflatoxin-
resistant lines and to develop different types of genetic populations such as associa-
tion mapping panels, bi-parental and multi-parent populations (Pandey et al. 2016).
ICRISAT, together with its NARS partners, are working on such an integrated
approach wherein a MAGIC population and bi-parental populations are planned to
be used for genetic mapping and QTL discovery, while a mini core collection will be
used for association analysis to discover marker-trait associations (MTAs). These
studies are likely to facilitate the identification of genomic regions controlling
aflatoxin resistance. At the same time, a transcriptomic approach has been deployed
to study the functional genomics of resistance mechanisms IVSC, PAC and AP by
conducting separate RNAseq experiments. These integrated approaches comprising
genetics, structural genomics and functional genomics together with next-generation
sequencing and comprehensive analysis will provide precise information on candi-
date genes to facilitate the development and validation of genetic markers for use in
molecular breeding (Pandey et al. 2019).

16.9.4 Breeding for Virus Diseases

About 31 viruses representing 14 genera are reported to naturally infect groundnut

worldwide, although only few are economic importance. Viral diseases are very
difficult to manage because most of those are transmitted through vectors, and there
are no viricides available in the market for control of viruses within plants. Most of
the chemicals are used for controlling virus vectors. Therefore, integrated approach
including growing resistant cultivars with suitable cultural practices is the most
effective approaches to reduce yield losses due to viral diseases.
Peanut bud necrosis disease (PBND) was first noticed in farmers’ fields in Punjab
during 1958–1959 and is one of the deadliest diseases of peanut (Patil et al. 2017).
Reddy et al. (2000) found that two cross compatible wild species of three accessions
of A. cardenasii, viz. ICG 11564, 13,164 and 13,165; and the two accessions of
A. villosa ICG 8144 and 13,168 are free from virus in the field. Dwivedi et al. (1995)
reported that several breeding lines with vector resistance, ICGV 86031 and 86,388,
showed resistance to PBNV. Gururaj et al. (2002) screened 172 genotypes of
16 Groundnut Breeding 875

cultivated groundnut for 3 years. Among them seven genotypes, DRG 18, ICG 7812,
ICG(FDRS) 10, ICGV 80325, JSSP 3, KNG 22 and PI 393516 were highly resistant
to PBND (up to 1% disease incidence). Several high-yielding cultivars with field
resistance to PBND have been released in India. These are CO 3, ICGS 11, ICGS
44 (ICGV 87128), ICGS 37 (ICGV 87187), R 8808 (KRG 2), R 9251, K 134, DRG
12, RSHY 1, Kadiri 4, JCC 88, GG 7 and DRG 17 (Basu et al. 2002). Other cultivars
reported with field resistance to PBND in India are Kadiri 3, ICGS 5, RS 138, CSMG
881, CSMG 888 and CSMG 892 (Singh et al. 1994); ICGS 1 (Nigam et al. 1991b);
ICGV 87141 (ICGS 76) (Nigam et al. 1991c); ICGV 86699 (Reddy et al. 1996);
ICGV 86325 (Dwivedi et al. 1996); GPBD 4, JSSP 9 and Dh 53 (Nagaraja et al.
2005); PratapMungphali 1 (Nagda and Joshi 2004); and PratapMungphali 2 (Nagda
and Dashora 2005). The breeding approach for resistance to PBND should be
improving the levels of resistance to the vector and the virus into superior agronomic
backgrounds.
Peanut stem necrosis disease (PSND) caused by tobacco streak virus (TSV) has
been epidemic in Anantapur district in Andhra Pradesh in 2000, affecting
2,25,000 ha and causing an economic loss of US$ 65 million (Reddy et al. 2002).
PSND has been reported from parts of Andhra Pradesh (Anantapur, Kurnool,
Cuddapah and Chittoor or districts) and adjoining areas in Karnataka (Raichur
district). It remains a potential threat to peanut in southern states in India (Nigam
et al. 2012). Kalyani et al. (2007) screened 56 germplasm accessions from 20 wild
Arachis species belonging to Arachis, Erectoides, Procumbente and Rhizomatosae
sections. Among them, eight accessions, ICG 8139, 8195, 8200, 8203, 8205 and
11,550, belonging to A. duranensis, ICG 8144 belonging to A. villosa and ICG
13210 belonging to A. stenosperma were found to be free from virus on mechanical
inoculation. As the level of resistance to TSV is not available in the cultivated
germplasm, interspecific hybridization programme utilizing available Arachis
accessions should be started to transfer in cultivated groundnut genotypes in superior
agronomic background. Besides this, high levels of resistance for thrips vectors are
available in cultivated germplasm and should also be utilized in breeding
programmes. Marker-assisted backcrossing has been reported to be successful in
improving resistance to tomato spotted wilt virus (TSWV) (Holbrook et al. 2017).

16.9.5 Breeding for Insect Pest Resistance

More than 360 soil and foliage inhabiting arthropod pests of groundnut have been
reported in the literature. However, only a few are economically important to the
crop either because they cause significant direct yield loss or acting as vectors of
virus diseases. These include aphids, thrips, jassids, leaf miner, Spodoptera and
white grub in Asia and aphids, jassids, Spodoptera, Hilda, millipedes, termites and
white grub in Africa (Nigam et al. 1991a). Aphids (Aphis craccivora Koch), some
species of thrips (Frankliniella schultzei, Thrips palmi and F. fusca), leaf miner
(Aproaerema modicella), red hairy caterpillar (Amsacta albistriga), jassids
(Empoasca kerri and E. fabae) and Spodoptera are the major insect pests in
876 T. Radhakrishnan et al.

groundnut. Aphids, thrips and Spodoptera have worldwide distribution and cause
serious damage (Wightman and Amin 1988). Patel and Vora (1981) reported jassids
as serious pests of groundnut in India. They can cause about 9% reduction in pod
yield and 18% reduction in haulm weight.
Chemical control of insects is possible in groundnut. But development of insecti-
cide resistance in the insects, insecticide residues in the food products and adverse
effects of insecticide use on the environment have received considerable attention.
Host plant resistance is one of the most economical and eco-friendly approach to
manage pest populations in groundnut. Several sources of resistance to insect pests,
particularly thrips, jassids and termites have been identified in groundnut
germplasm.
A Spanish-type groundnut variety ICGV 86031 (PI 561917) was released in 1991
as a source of resistance to S. litura, Thrips palmi, Empoasca kerri, Aproaerema
modicella and bud necrosis virus (Dwivedi et al. 1993). Several groundnut
genotypes were screened for Helicoverpa armigera and S. litura. Only BG 2, a
Virginia bunch groundnut variety, was found resistant to both pests (Singh et al.
1993).
Bruchid beetle (Caryedon serrate Olivier) is the only primary pest of stored
groundnut causing both quantitative and qualitative losses. The pod damages in
groundnut varied according to the storage period, and it may vary from 19 to 60%,
when the groundnut was stored for 5 months (Matokot et al. 1987). If the groundnut
is stored about 90 days, the damage of seven groundnut varieties ranged from 64 to
93% (Ghorpade et al. 1998). Prasad et al. (2012) screened cultivars for resistant to
bruchid beetle. The cultivar CO-2 recorded least susceptible with growth index value
of 0.079 followed by VRI 3, R 8808 and GG4 indicating their resistance to
C. serratus infestation. Most of the germplasm accessions of A. hypogaea are
susceptible to lepidopterous pests (Wightman et al. 1990), and wild relatives possess
high levels of resistance to insects feeding on groundnut (Sharma et al. 2003).
Stevenson et al. (1993) reported that more than 90% mortality of larvae of
S. litura fed on the excised leaves of A. batizogaea (ICG 8901), A. kempff-mercadoi
(ICG 8959 and ICG 13159), A. appressipila (PI 2261877), A. paraguariensis (ICG
8964) and A. villosa (ICG13169) compared with less than 20% mortality on the
cultivar TMV 2. He reported that accessions belong to A. cardenasii (ICG 8216),
A. duranensis (ICG 13242, except for leaf feeding), A. ipaensis (ICG 8206),
A. paraguariensis (ICG 8130) and A. appressipila (ICG 8946) showing resistance
to leaf feeding and antibiosis to S. litura under no-choice tests in the greenhouse
conditions. Lack of a high level of resistance to S. litura, Helicoverpa armigera and
sucking pests in cultivated groundnut and reliable screening technique under field
conditions are the main reasons for the slow progress of breeding for resistance to
insect pest in groundnut.
16 Groundnut Breeding 877

16.9.6 Breeding for Nematode Resistance

The root-knot nematodes, Meloidogyne spp., and the lesion nematodes,

Pratylenchus spp., are important in groundnut (Sharma and McDonald 1990a).
Based on the worldwide survey of nematologists, annual losses caused by all the
nematodes to groundnut were estimated at 12% (Sasser and Freckman 1987). Root-
knot disease is a serious problem in groundnut-growing areas of the world and also
economic important in India. Estimated crop losses due to Meloidogyne spp. range
from 5 to 43% (Sasser 1980). In India, the estimated yield loss of groundnut was
reported 21.60% due to M. arenaria and M. javanica. In Gujarat, M. arenaria in
Saurashtra and M. javanica in middle Gujarat infect groundnut and cause yield
losses up to 31–38% in groundnut (Khan et al. 2010).
The cultivated groundnut has no resistance to M. arenaria, but resistance has
been reported from several wild Arachis spp. (Baltensperger et al. 1986; Holbrook
and Noe 1990; Nelson et al. 1989). Nelson et al. (1990) reported that resistance to
M. arenaria in A. cardenasii. Stalker et al. (1995) identified M. arenaria-resistant
genotypes (TxAG-6, TxAG-7) where resistance was introgressed into A. hypogaea
from A. cardenasii using a hexaploid pathway. TxAG-6 was developed from a
complex cross of Arachis batizocoi  (A. cardenasii  A. diogoi) (Nelson et al.
1989; Starr et al. 1995). Second germplasm line TxAG-7 which is resistant to
M. arenaria, M. javanica and an undescribed Meloidogyne sp. from Texas was
developed from a backcross of A. hypogaea (‘Florunner’)  TxAG-6 (Simpson et al.
1993).
The root-knot nematode resistance from TxAG-7 was introgressed in to breeding
populations through backcross breeding (Starr et al. 1995). The first root-knot
nematode (M. arenaria)-resistant peanut cultivar “COAN” with the resistance gene
introgressed from A. cardenasii was released in the USA (Simpson and Starr 2001).
Another groundnut variety “Tifguard”, bred for resistance to both root-knot nema-
tode and TSWV (Holbrook et al. 2008). Currently, there are six registered interspe-
cific germplasm lines with resistance to M. arenaria: TxAG-6 and TxAG-7
(Simpson et al. 1993), GP-NC WS 5 and GP-NC WS 6 (Stalker et al. 2002) and
NR 0812 and NR 0817 (Anderson et al. 2006). Ravindra et al. (2013) screened
71 groundnut genotypes for resistance to M. arenaria and M. javanica, and the
cultivar TAG 24 was found to be highly resistant. The other cultivars ICGV 86590,
JL 24, Dh- 2000-1 and TMV 2 were resistant, while Dh-3-30, Dh 86, JSP 39, GPBD
4 and Dh 101 were moderately resistant to root-knot nematodes.
In Kalahasti and Nellore district of Andhra Pradesh in India, a severe nematode
disease caused by Tylenchorhynchus brevilineatus of groundnut reported in 1976
which has been later known as “Kalahasti malady”. The reduction in the yield due to
this disease was up to 50% (Vasanthi et al. 2003). Mehan et al. (1993) screened 1599
groundnut germplasm accessions and breeding lines for resistance to the nematode
disease “Kalahasti malady”. Of those TCG 1518 (Tirupti 3), a high-yielding breed-
ing Virginia bunch line was found resistant to Kalahasti malady and released for
disease-affected areas of Andhra Pradesh. But it was less popular among the farmers
due to long duration (125–130 days). Therefore, a breeding programme was initiated
878 T. Radhakrishnan et al.

Table 16.9 Resistant/tolerant germplasm lines of groundnut for various biotic factors
Biotic factors Genotypes
Diseases
Early leaf spot ICGs 6902, 11,476, 8298, 6284, 6902, 7878, NRCG Nos. 5201, 6900, 6935,
6947, 6985, 7020, 7066, 7216, 7326, 7345
Late leaf spot ICGs 2716, 6330, 7888, 10,035, NRCG Nos. 10,121, 10,123, 10,125, 10,183,
10,427, 11,108, 11,616, 12,488, 12,338, 12,565, 12,652, 12,900, 12,925,
12,929, 2375, 2392, 5292, 7041, 7353
Rust ICGs 1697, 2716, 4746, 7296, 7893, 7899, NRCG Nos. 10,121, 10,123,
10,950, 11,072, 11,108, 11,597, 12,487, 12,510, 12,565, 12,566, 12,652,
12,718, 12,889, 12,900, 12,912, 12,915, 12,925
Stem rot NRCG Nos. 10,181, 10,527, 10,733, 10,751, 10,965, 11,073, 11,494, 12,488
Limb rot NRCG Nos. 7065, 7170, 7247, 7410, 7480, 7548, 7587, 7597
PBND NRCG Nos. 10,121, 10,123, 10,125, 10,143, 10,181, 10,233, 10,427, 10,950,
11,001, 11,069, 11,108, 6508, 7162
PSND NRCG Nos. 12,283, 12,295, 12,316, 12,392, 12,394, 12,406, 12,408, 12,527,
12,706, 12,878
Insect pests
Leaf miner ICGVs 87,237, 86,709, 87,157, 87,160, 85,011, 86,162, 86,031, 87,194,
87,242, 86,601, 87,326, 87,327, 87,339, 87,341, 87,165, 86,598, 86,027,
NRCG 5001, 6701, 6704
Leaf hoppers NRCG 9773, 9767, 6688
Spodoptera ICGVs 86,029, 86,030, 86,031, 86,590, NRCG 5724, 2615, 9773, 8313, 8673
litura
Ash-weevil NRCG 5014, 9465, 8938
Jassids ICGs 2271, 2036, 2307, 5040, 5041, 5043
Thrips ICGs 2271, 2307, 5037, 5040, 5041, 5042, 5043, 5044, 5045, 799
Aphids ICG 5240
Source: ICRISAT Information Bulletin Nos. 47 and 50; Basu 2003

during 1988–1889 utilizing TCGS 1518 as source of resistance to Kalahasti malady.

A breeding line TCGS 320 was released in 2002 as “Kalahasti” is a short-duration
(105–110 days), high-yielding, Spanish bunch variety resistant to Kalahasti malady.
The source of resistance to Kalahasti malady is available in the cultivated groundnut
germplasm as well as cultivars which can be easily utilized breeding programme to
develop superior cultivars for disease-prone areas. However, the sources of resis-
tance are available, but levels of resistance to root-knot nematode in cultivated
groundnut germplasm are quite low, and wild species possess high levels of resis-
tance to root-knot nematodes.
Many resistance sources for various biotic stresses were identified (Table 16.9),
and at ICAR-DGR, Junagadh, many advanced breeding cultures were developed
which possess resistance/tolerance to one or more stresses (Table 16.10). So many
varieties with disease resistance/tolerance have been reported (Table 16.11).
16 Groundnut Breeding 879

Table 16.10 Advanced breeding cultures developed at ICAR-DGR possessing resistance/toler-

ance to one or more stresses
Stress component Genotypes
ELS and LLS PBS 12,024, 12,031, 12,144, 12,032, 12,034, 12,038, 12,127,
12,048, 12,050, 12,056, 12,059, 12,077, 12,079, 12,080, 12,081
ELS PBS 12,060, 12,038, 22,020
LLS PBS 22,012, 22,017, 22,018, 12,097, 12,137
Alternaria blight PBS 23,017, 13,013
Aspergillus flavus PBS 19,003, 21,076, 23,017, 23,007, 23,019, 29,027, 29,031
Helicoverpa PBS 23,007, 23,010 (moderately resistant)
Spodoptera I instar PBS 13,010, 23,010, 23,011, 23,017, 23,018, 21,062, 11,050 (all
highly resistant)
Spodoptera III instar PBS 23,007, 23,010, 23,017, 23,018, 23,019, 21,062, 11,050 (all
moderately resistant)
Spodoptera V instar PBS 12,025, 12,144, 12,034, 12,039, 12,047, 12,048, 12,066,
12,067, 12,085, 22,011, 22,013, 22,020, 22,025, 22,035 (moderately
resistant)
Thrips PBS 13,010, 23,003, 24,005, 24,006, 24,030, 24,040
Leaf miner PBS 11,050, 21,062
Alternaria, leaf hoppers PBS 12,026, 12,039, 12,069, 12,086, 23,009
and thrips
Source: Basu 2003

Table 16.11 Disease-resistant/disease-tolerant groundnut cultivars

Disease Resistant/tolerant cultivars
Early leaf spot, late leaf ALR 1, ALR 2, ALR 3, Girnar 1, ICGV 86590, ICGV 87160, ICGV
spot, rust 86325, CSMG 84–1, OG 52–1, RSHY 1, DRG 12, DRG 17, TAG
24, BSR 1, VRI 5, Co4
Collar rot and aflaroot OG 52–1, JCG 88, and J 11
Stem rot OG 52–1, Dh 8 and ICGV 86590
Peanut bud necrosis ICGS 11, ICGS 44, ICGS 37, Kadiri 3, ICGV 86325, K 134, DRG
disease (PBND) 12, R 8808, JCG 88, CSMG 884, Chandra
Source: Ghewande et al. (2002)

16.10 Breeding Approaches-Conventional

and Non-Conventional

The breeding methods employed in self-pollinated crops such as mass selection,

pedigree, bulk, single seed descent and backcross methods are used in groundnut
breeding. Introduction and mass selections played a pivotal role in the beginning, but
later, hybridization followed by selection in segregating generations adopting differ-
ent methods was predominantly practiced in breeding improved groundnut varieties.
Cumbersome process of emasculation and pollination procedures with low success
880 T. Radhakrishnan et al.

rate of making crosses and huge time lag (8 years or more) for release as variety are
the major limitations in breeding programmes of groundnut.
In most of the crossing programmes in groundnut, only two parents were used,
whereas double or convergent crosses which could create form variability for
selection are sparingly used. Pedigree method has been the most used one for highly
heritable traits like plant type, pod size, seed shape and size, test colour, etc. and for
quantitative trails like yield and seed quality pedigree method with delayed selection.
For traits with low heritability, bulk-pedigree is the most used approach. When
resources and space are a constraint, single seed decent method also is being resorted
to (Isleib et al. 1994). Though limited use has been made of the recurrent selection
procedures (Wynne and Gregory 1981), owing to space and hybridization
requirements, it has been used for continued genetic enhancement in groundnut
(Guok et al. 1986; Halward et al. 1991b).
Backcross breeding methods have not been used extensively as most of the
economically important traits in groundnut are quantitatively inherited (Wynne
and Gregory 1981; Knauft and Wynne 1995). With the increased emphasis on
multiple resistance breeding, emphasis is now focused on complex crosses followed
by inter-crossing of segregants to bring the desired improvement into breeding
populations. While selection for resistance to insect pests and diseases is practiced
in early generations, selection for yield and yield component traits is delayed to later
generations (Dwivedi et al. 2003). Mutation breeding in groundnut has led to the
development of several improved varieties (Janila et al. 2013). With the advent of
molecular markers linked to the target trait and quantitative trait locus (QTL), marker
assisted backcross breeding is now being used frequently in breeding programmes
aimed at trait based crop improvement.
Groundnut is not native to India, and it was introduced in the sixteenth century;
the systematic attempts for its improvement were initiated in twentieth century. In
1884, the’ Mauritius’ variety was introduced to Pondicherry and Madras from
Mauritius, ‘Spanish’ and ‘Virginia’ from the USA and ‘Small Japan’ and ‘Large
Japan’ from Japan in 1901–1902. Pedigree followed by mass selection, pureline
selection, bulk-pedigree, modified bulk-pedigree, mutation and introduction are the
breeding methods which are frequently used in groundnut breeding (Table 16.12).
Currently, 233 groundnut cultivars have been released till 2021 for commercial
cultivation in India. Groundnut varieties released for commercial cultivation in
India during the last 10 years was given in Table 16.13. New breeding programme
like ‘Speed breeding’ especially uses single seed descent method by rapidly advanc-
ing the generations by altering photoperiod, and temperature during the growth of
the crop is also now being resorted.
By the enhanced availability of genomic resources, use of genomic tools also has
been employed in groundnut breeding, which could accelerate the process and
enhance the efficiency. Diagnostic molecular markers linked to the major effect of
QTLs or other traits of breeding interest like disease resistance reported. Markers
linked with root-knot nematode (Choi et al. 1999; Chu et al. 2007; Church et al.
2000; Garcia et al. 1996; Simpson and Starr 2001), rust (Khedikar et al. 2010;
Mondal et al. 2012a, b), and LLS (Kolekar et al. 2016; Sujay et al. 2012), nutritional
16 Groundnut Breeding 881

Table 16.12 Breeding methods employed for developing groundnut varieties in India
S. no. Breeding method Varieties developed (no.)
1 Introduction 3
2 Mass selection 32
3 Pureline selection 23
4 Pedigree 130
5 Bulk-pedigree 20
6 Modified bulk-pedigree 14
7 Single seed descent 1
8 Mutation 8
9 Marker assisted backcrossing 2
Total 233

quality traits (Chen et al. 2010; Chu et al. 2009; Sarvamangala et al. 2011; Wilson
et al. 2017), TSWV (Tseng et al. 2016) and growth habit (Li et al. 2017). Such
validated molecular makers were deployed in marker assigned breeding
programmes, and the approach was successful in pyramiding nematode resistance
and high oleic acid (Chu et al. 2011).
The validated markers from the rust-resistant cultivar GPBD were used to
improve the disease resistance of the popular cultivars ICGV 91114, JL 24 and
TAG 24 (Varshney et al. 2014). Besides, MAS and MABC were used to improve the
oil quality traits in three groundnut varieties ICGV 06110, ICGV 06142 and ICGV
06420 by transferring FAD2 mutant alleles from SunOleic 95R. A large number of
lines with increased oleic acid in the range of 62%–83% were identified (Shasidhar
et al. 2017). At Dharwad University of Agricultural Sciences in India, MABC was
used to improve JL 24 with GPBD 4 as donor parent (Yeri and Bhat 2016).
Similarly, MABC was employed to improve TMV 2 for LLS and rust using
GPBD 4 where two backcross lines showed enhanced resistance to LLS and rust
along with 71.0% and 62.7% increase of pod yield over TMV 2 (Kolekar et al.
2017). A genome-wide association study reported by Pandey et al. (2014a, b) on
50 agronomic traits involving 300 genotypes of a “reference set” could identify
524 highly significant MTAs for 36 traits pointing to the complex genetic control.
Though marker-assisted recurrent selection and genomic selection are the preferred
approaches for introgression of a larger number, small-effect QTLs of such
approaches have not yet been widely used in groundnut.

16.10.1 Precise and High-Throughput Phenotyping Protocols

for Key Traits

The conventional phenotyping methods are laborious, time-consuming and less

efficient, when a large number of genotypes are to be handled. Hence, it is time to
resort to novel methodologies of high-throughput phenotyping that connects exten-
sive genotypic data to phenotypic characteristics in a field context (Furbank and
Table 16.13 Groundnut varieties released for commercial cultivation in India during last 10 years
882

Habit Production
Cultivar group Year Area of adoption system Pedigree Special characters
JL 501 SB 2010 Gujarat and southern Kharif Selection from TAG 24 Comparatively lowest intensity of
Rajasthan LLS was observed in case of
JL-501 as against higher in variety
JL-24; suitable for early as well as
late sown conditions
Vijetha SB 2010 W.B., Orissa, Jharkhand, Kharif ICGS 11  ICG 4728 Resistant to PBND
(R 2001–2) Assam, Maharashtra,
Karnataka, A.P. and, T.N.
GPBD-5 SB 2010 Jharkhand and Manipur Kharif TG-49  GPBD-4 Resistant to LLS and rust
Girnar 3 (PBS SB 2010 W.B, Orissa, Manipur Kharif Girnar 1  ICGS 11 Tolerant of leaf miner and thrips
12160)
Kadiri SB 2010 Karnataka and Maharashtra Rabi- 91/57–2 X PI 476177 Multiple diseases (rust, ELS, LLs,
Haritandhra summer stem rot, PBND) and insect pests
(K 1319) (thrips, Spodoptera litura, jassid,
Helicoverpa) resistant
HNG 69 VB 2010 U.P., Punjab and northern Kharif CSMG 84-1 X PG 1 Tolerant to collar rot, stem rot and
Rajasthan ELS
GJG-HPS-1 VR 2010 Gujarat Kharif JSP 21 X VG 5 Tolerant to PBND
(JSP-HPS-44)
Divya (CSMG VR 2011 UP and Rajasthan Kharif Amber  ICG-1697 Tolerant to PBND
2003–19)
RARS-T-1 SB 2011 Andhra Pradesh Kharif and TAG-24 X TG-19 Tolerant to leaf spots and rust,
rabi- sucking pests (thrips and jassids)
summer
RARS-T-2 SB 2011 Andhra Pradesh Kharif and Tirupati-4 X TIR-45 Moderately tolerant to Spodoptera
rabi- litura and leaf hoppers
summer
T. Radhakrishnan et al.
 16

Pratap Raj SB 2011 Rajasthan Kharif and Selection from ICGV-98223 Tolerant to ELS, LLS, PBND,
Mungphali summer jassids, thrips and leaf miner and
Spodoptera litura; early maturity
RG 425 VB 2011 Rajasthan Kharif ICG 5013 X RG 340 UP, RJ under timely sown irritated
condition
ICGV 00350 SB 2012 TN and AP Rabi- ICGV 87290 X ICGV 87846 Resistant to LLS and rust, tolerant
summer of stem rot
Groundnut Breeding

HNG 123 VB 2012 Rajasthan, UP and Punjab Kharif Chandra X RSB-87 Tolerant to collar rot, stem rot,
LLS, Spodoptera litura and leaf
miner
Raj Mungfali-1 VR 2012 Rajasthan and Punjab Kharif RG 318 X RG 340 Tolerant to collar rot, stem rot,
(RG 510) LLS, peanut stem necrosis
diseases, thrips, jassids and grass
hopper
GJG 31 (J 71) SB 2012 Gujarat Kharif GG 5 X ICGV 90116 Tolerant to stem rot
GJG 9 (J 69) SB 2012 Gujarat Summer GG 2 X PBS 21065 GJ under rabi-summer irrigated
condition
CO 6 VB 2012 Tamil Nadu Kharif CS-9 X ICGS-5 Resistant to LLS and rust
Dharani (TCGS SB 2013 Andhra Pradesh Kharif and VRI 2  TCGP 6 Tolerant to stem rot, dry root rot
1043) summer and drought tolerant
GJG-22 (JSSP VB 2013 Gujarat Kharif JSSP 17 X GG 20 Tolerant to collar rot
36)
GJG-17 VR 2013 Gujarat Kharif JSSP 11 X GG 6 Tolerant to stem rot
(JSP-48)
Phule Bharti SB 2015 Maharashtra and Madhya Kharif Selection from (ICGV Resistant to S. litura and rust in
(JL 776) Pradesh 92069  ICGV 93184)  ICGV field condition
98300
Raj Mungfali- VB 2015 Odisha, WB and Manipur Kharif ICG 5013  RG 141 Resistant to LLS, dry root rot,
2 (RG 578) ELS and rust; tolerant to S. litura,
thrips, jassids. Leaf miner
883

(continued)
Table 16.13 (continued)
884

Habit Production
Cultivar group Year Area of adoption system Pedigree Special characters
GJG 18 (JSP VR 2015 Odisha, WB, Jharkhand and Kharif JSSP 12  LGN 2 OD, WB, JH, MN in timely sown
49) Manipur rainfed condition
Groundnut Co SB 2015 Tamil Nadu Kharif and Cross derivative from ICGV Resistant to rust
7 summer 87290  ICGV 87846
Birsa VB 2015 Jharkhand Kharif Robut  M-13 Resistant to LLS
Groundnut
4 (BAU 25)
Raj Mungfali VB 2016 Rajasthan, UP and Punjab Kharif (TKG 19A  Kadiri 3)  TKG Tolerant to S. litura, leaf miner
3 (RG 559–3) 19A and thrips
Phule Warna VB 2016 Tamil Nadu, Andhra Kharif Selection from ICGV-020059- Moderately resistance to rust and
(KDG 128) Pradesh, Karnataka and SSU-SSD-P 37-B; (ICGV leaf spot
southern Maharashtra 87121  ICGV
87853)  92023)  ICGV 98300)
Phule Moma VB 2016 Gujarat and Rajasthan Kharif Secondary selection from line Moderately resistance to rust and
(KDG 123) ICGV-04168; (ICGV leaf spot
96050  ICGV 96239)
GJG 19 (JSP VR 2016 Odisha, West Bengal, Kharif JSSP-12  LGN-2; K-99-13-B-1- Tolerant to stem rot, dry root rot
51) Jharkhand and Manipur 2-B-B and rust as compared to check
(KDG 123)
G 2–52 SB 2016 Karnataka Kharif Gamma rays (200 Gy) induced Foliar disease resistant
mutant of GPBD 4
KCG 6 (CTMG SB 2016 Karnataka Rabi- (BPI PnG  ICGV Moderately resistance to rust and
6) summer 95172)  ICGV 96234 late leaf spot
GKVK 5 2016 Southern Karnataka Kharif and NRCG 11915  NRCG 12326 Tolerant to rust and LLS
Summer
Central SB 2017 Tamil Nadu and Andhra Rabi- (J 11  CG 52)  ICGV 86015 Tolerant to rust, LLS and peanut
Groundnut Pradesh summer bud necrosis disease (PBND),
T. Radhakrishnan et al.

ALG 06-320 S. litura, leaf miner and thrips

 16

VRI SB 2017 Tamil Nadu Kharif and R 3  AK 303 Moderately resistant to sucking
8 (VG 09220) Summer pest (jassids and thrips),
moderately resistant to LLS and
rust
Kadiri 2017 Andhra Pradesh Kadiri 6  NCAc 2242 Field tolerance to PBND
Amaravathi
(K 1535)
GJG 32 (ICGV SB 2018 Tamil Nadu, Andhra Kharif [(F 334 A-B-14  NCAc Tolerant to stem rot, colour rot
Groundnut Breeding

03043) Pradesh, Karnataka, 2214)  ICG 2241)  (ICGMS and rust

southern Maharashtra and 42  Kadiri 3)  ICGMS
Telangana 28  (F 334 A-B-14  NCAc
2214)]  LI  (Robut 33–1–1-5)
GJG 33 (ICGV SB 2018 Tamil Nadu, Andhra Rabi- [(ICGV-92069  ICGV-93184) Tolerant to colour rot and rust
07222) Pradesh and Telangana summer SIL-4  (ICGS 44  ICGS 76)]
VRI SB 2017 Tamil Nadu Kharif and ALR 3  AK 303 Moderately resistant to sucking
8 (VG 09220) Summer pest (jassids and thrips),
moderately resistant to LLS and
rust
DH-232 SB 2018 Karnataka Kharif GPBD 4  TG 37A Resistance to foliar diseases,
‘High Shelling (78.7%)
DH-245 SB 2018 Karnataka Kharif Mutation of GPBD 4 Resistance to foliar diseases,
‘High oleic acid (>70%)
Avtar (ICGV SB 2018 Uttar Pradesh Rabi- ICGV 86015  ICGV 86155 Tolerant to BND, fungal diseases,
93468) summer jassid and pod borer, ‘Early
maturity
TMV 14 SB 2019 Tamil Nadu Kharif VRI Gn. 6  R2001–2 Tolerant to S. litura, thrips, leaf
minor; moderately resistance to
LLS and rust, ‘Early maturity
Phule SB 2019 Tamil Nadu, Telangana and Rabi- Selection from [(ICGV 92069  Moderately resistance to stem rot
Chaitanya Andhra Pradesh summer ICGV 93184)  (ICGV 87121  and LLS, ‘High Oil content
(Central- KDG ICGV 87853)  ICGV 92023] (51.6%)
885

160)
(continued)
Table 16.13 (continued)
886

Habit Production
Cultivar group Year Area of adoption system Pedigree Special characters
Konkan VB 2019 Maharashtra Kharif PBS 24030  GPBD 4 Resistance to ELS, LLS, rust,
Bhuratna PBND, thrips, jassids and leaf
(RTNG-29) miner, ‘High Oil content (50.1%)
Gujarat VB 2019 Gujarat Kharif JVB HPS 2  GG 20 Large seeded
Groundnut
HPS
2 (GG HPS 2)
AK SB 2019 Maharashtra Kharif Selection from TG 36B Moderately resistance to tikka,
335 (PDKVG- collar rot, stem rot, jassid, thrips
335) and aphids
Phule Unnati SB 2019 Maharashtra Kharif and (ICGV 92069  ICGV 93184)  Resistance to LLS, stem rot, rust,
(RHRG 6083) Rabi- (ICGS 44  ICGS 76) S. litura, and thrips, ‘High Oil
summer content (52%)
Phule Dhani SB 2019 Tamil Nadu, Andhra Kharif JL 24  ICGV 03061 Resistance to LLS and rust
(JL 1085) Pradesh and Karnataka
Gujarat SB 2019 Gujarat Summer TG 26  ICGV 00380 High oil content (52.8%)
Groundnut-34
(GG 34)
(AG-2012-06)
Dheeraj (TCGS SB 2019 Andhra Pradesh Kharif and JAL 30  Narayani Possesses heat tolerance and high
1073) Summer water use efficiency
BSR 2 (BSG SB 2019 Tamil Nadu Kharif and VRI 2  TVG 0004 Moderately resistant to rust, LLS,
0912) Rabi- jassid, thrips and aphids
summer
Central-Pragati SB 2019 Tamil Nadu, Telangana and Rabi- Selection from sp. Mutant 1
(TCGS 894) Andhra Pradesh summer
Dh 256 SB 2019 Tamil Nadu, Andhra Kharif R 2001–2  GM 4–3-12 Tolerant to S. litura, thrips and
Pradesh, Karnataka and leaf miner and leaf hopper,
T. Radhakrishnan et al.

Telangana tolerant to mid-season drought

 16

Girnar 4 (ICGV VB 2020 Rajasthan, Gujarat, Kharif [ICGV 06420  (ICGV Recorded 78.5% oleic acid and
15083) Karnataka, Tamil Nadu and 06420  Sun Oleic 95R)] 4.8% linoleic acid. Tolerant to late
Andhra Pradesh leaf spot, rust, stem rot and peanut
bud necrosis disease, leaf hopper,
leaf miner, thrips and Spodoptera
litura
Girnar 5 (ICGV VB 2020 Rajasthan, Gujarat, Kharif [ICGV 06420  (ICGV Recorded 78.4% oleic acid and
Groundnut Breeding

15090) Karnataka, Tamil Nadu and 06420  Sun Oleic 95R)] 4.6% linoleic acid. Tolerant to late
Andhra Pradesh leaf spot, rust, stem rot and collar
rot, leaf hopper, leaf miner, thrips
and Spodoptera litura
Pratap SB 2020 Rajasthan Kharif and Selection from ICGV 03063 Moderately tolerant to early leaf
Mungphali Summer spot (ELS), late leaf spot (LLS),
3 (UG 116) rust, collar rot and dry root rot;
moderately resistant to
Spodoptera litura, leaf miner,
defoliators, jassids, thrips and
leafhopper
K 1719 (Kadiri SB 2020 Andhra Pradesh, Telangana Rabi- Kadiri 7 Bold  TAG 24 Large seeded. Moderately
Chithravati) and Tamil Nadu summer resistant to thrips; collar rot and
PBND
K 1812 (Kadiri SB 2020 Tamil Nadu, Andhra Kharif ((ICGV 92069  ICGV 93184) Tolerance to leaf miner, PBND,
Lepakshi) Pradesh Karnataka and SIL4  ICGV 98300) ELS
Telangana
J 87 SB 2020 Uttar Pradesh and Punjab Rabi- JVR- 244  JB-866 Moderately resistant to leaf miner
summer and ELS
Dh 257 SB 2020 Karnataka and Maharashtra Rabi- ICGV 07211  ICG 2381 Tolerant to mid-season drought.
summer Tolerance to Spodoptera litura
887
888 T. Radhakrishnan et al.

Tester 2011) and overcomes the defects of manual techniques and provides a multi-
trait assessment. This approach using the automated readings and data recording
reduces considerably the time required and gives the advantage of precision in
readings, non-destructive samplings, high throughput with large number of data
points and direct storage of the data.
It provides quantitative and non-destructive analysis of crops, automated plant
handling, image-based characterization of plant growth, structure and composition,
daily data acquisition and analysis for pipeline screening, gathers many data points
on a large number of plants in relatively short times and acquisition of high-quality
digital phenotypic data with explicit metadata and has high computing capacity for
image analysis. Automation enables flexible growth conditions to elicit and measure
stress responses, enables automated statistical analysis and reports integration with
corporate data systems.
Ground-based camera has been used to measure the leaf water potential in
groundnut effectively where random plants were selected in plots to classify and
differentiate young and old leaves and subjecting the images to principal component
analysis (Zakaluk and Sri Ranjan 2008). The other important trait is stomatal
conductance, chlorophyll content, etc. which also have been estimated through
automated setup. Chlorophyll estimates using SPAD have been widely used as
rapid tool for rapid assessment of relative chlorophyll status especially under stress
conditions (Arunyanark et al. 2009). Hyperspectral sensing technologies involving
point spectroscopy and thermal imaging can profitably be used in estimating the
incidence foliar diseases in endemic areas (Omran 2017). A basic parameter for the
interpretation of remotely sensed data is the spectral reflection of the disease.
Reflectance data helps in detecting changes in the biophysical properties of plant
canopy and leaf associated with pathogens. The spectral reflectance factors differ
significantly according to the health condition of the plant. The leaves of the healthy
peanut show a decreasing reflection in 1015 nm, whereas the heavily diseased leaves
show an increasing reflection. In the thermal infrared range, diseased plants show
higher temperature than healthy ones. The temperature difference allows the dis-
crimination between the infected and healthy leaves before the appearance of visible
necrosis on leaves. Two simple indices, early leaf spot index (ELSI) and late leaf
spot index (LLSI), allows early prediction of the peanut disease severity. The disease
severity estimation using ELSI and LLSI have an overall accuracy of 78% and 89%,
respectively.
Screening a large set of germplasm at early stages of growth will reduce the load
of field evaluation for plant breeders and plant genetic resource managers. Precise
phenotyping of germplasm enables breeders to use these readily in their breeding
activity. In the present situation, it is necessary for the breeders to be equipped with
the emerging technologies to develop crop varieties to suit changing climate and
cropping patterns.
16 Groundnut Breeding 889

16.11 Modernization of Crop Improvement Programme

in Groundnut

Though significant contributions have been made by the conventional breeding

approaches, to break the existing yield barriers to exploit the targeted approaches
for breeding the use of genomic tools is profitable and will accelerate the cultivar
development. Technologies such as next-generation sequencing (NGS) and
genotyping have facilitated the discovery of functional genes and functional markers
that would enhance the momentum of cultivar development (Varshney 2016). Most
of the progress in the generation of genetic information of groundnut has now been
made possible in recent advancements, whereby new molecular markers have been
developed, refined expressed sequence tags (EST) identified, genetic and physical
maps that are dense generated, important genes discovered and chromosomal
regions (QTL) linked to stresses of economic importance identified (Table 16.14).
This has further led to the application of molecular markers in breeding (MAB) to
complement conventional methods, culminating into the release of superior ground-
nut varieties.

16.12 Future Thrusts

Considerable improvement has been made in the cultivar development globally

leading to the release of a good number of varieties with improved productivity
and quality. Several sources of variability for economically important traits in
groundnut were identified or developed. A good number of new germplasms also
has been registered with the national repositories. Though there was an initial lag, a
large volume of genomic resources was added during the last decade, and genomic
tools like MAS, MABC, etc. have been applied in groundnut breeding. Further
advancement resulted from the availability of the genome sequence of cultivated
groundnut, and its progenitors have facilitated more precise approaches of genome-
assisted breeding. The methodologies of high-throughput genotyping and
phenotyping also have accelerated the process or trait-oriented breeding. The
low-cost genotyping services have added an additional impetus to the progress
accelerated breeding. Thus, with these emerging technologies and developments,
we look forward for more improved cultivars with higher productivity and quality.
890 T. Radhakrishnan et al.

Table 16.14 The QTLs reported in groundnut

QTL for the trait Number References
Leaf spot resistance 28 Wang et al. (2013) and Liang et al. (2017)
Late leaf spot resistance 45 Agarwal et al. (2018) and Kolekar et al. (2016)
Thrips resistance 3 Wang et al. (2013)
Total number of holes on 3 Mondal et al. (2014a)
pods (bruchid)
Per cent pod weight loss 1 Mondal et al. (2014a)
(bruchid)
Total development period 4 Mondal et al. (2014a)
(bruchid)
Per cent adult emergence 4 Mondal et al. (2014a)
(bruchid)
Susceptibility index 4 Leal-Bertioli et al. (2015)
Rust resistance 51 Kolekar et al. (2016), Leal-Bertioli et al. (2015) and
Mondal et al. (2014b)
Total number of lesions/ 3 Leal-Bertioli et al. (2015)
leaf area
Log incubation period 3 Leal-Bertioli et al. (2015)
Number of sporulated 2 Leal-Bertioli et al. (2015)
lesions/leaf area
Lateral branch length 5 Leal-Bertioli et al. (2016) and Wang et al. (2018)
Number of lateral branches 2 Leal-Bertioli et al. (2016)
Specific leaf area_40 days 5 Leal-Bertioli et al. (2016)
Root galling index 5 Leal-Bertioli et al. (2016)
Eggs per gram of 3 Leal-Bertioli et al. (2016)
root_2011
Root-knot nematode 17 Burow et al. (2014) and Leal-Bertioli et al. (2016)
resistance
Linoleic acid 52 Sarvamangala et al. (2011), Hu et al. (2018) and
Pandey et al. (2014a, b)
Palmitic acid 31 Wang et al. (2015)
Oil content 27 Selvaraj et al. (2009), Sarvamangala et al. (2011),
Huang et al. (2015) and Pandey et al. (2014b)
Oleic acid 27 Sarvamangala et al. (2011) and Hu et al. (2018)
SPAD chlorophyll meter 12 Faye et al. (2015)
reading
SPAD chlorophyll meter 7 Leal-Bertioli et al. (2016)
reading_40 days
Peg length 11 Fonceka et al. (2012)
Pod beak 10 Fonceka et al. (2012)
Pod constriction 14 Fonceka et al. (2012)
Leal-Bertioli et al. (2015)
Hundred pod weight 6 Fonceka et al. (2012) and Wang et al. (2018)
Pod width 21 Fonceka et al. (2012), Wang et al. (2018) and Chavarro
et al. (2020)
Pod length width ratio 4 Wang et al. (2018)
(continued)
16 Groundnut Breeding 891

Table 16.14 (continued)

QTL for the trait Number References
Protein content 8 Sarvamangala et al. (2011)
Log root dry weight 2 Leal-Bertioli et al. (2016)
Seed length 18 Selvaraj et al. (2009), Fonceka et al. (2012) and Wang
et al. (2018)
100-seed weight 5 Selvaraj et al. (2009) and Fonceka et al. (2012)
Seed size index 3 Chavarro et al. (2020)
Kernel percentage 3 Chavarro et al. (2020)
Single kernel pod 4 Chavarro et al. (2020)
Double kernel pod 2 Chavarro et al. (2020)
Pod area 3 Chavarro et al. (2020)
Pod density 3 Chavarro et al. (2020)
Weight of 10 seeds 2 Leal-Bertioli et al. (2015)
Log weight of 10 seeds 4 Leal-Bertioli et al. (2016)
Seed width 13 Fonceka et al. (2012) and Chavarro et al. (2020)
Stress tolerance index, 2 Fonceka et al. (2012)
hundred pod weight
Stress tolerance index, 2 Fonceka et al. (2012)
seed number
Stress tolerance index, 2 Fonceka et al. (2012)
total biomass
Stress tolerance index, 2 Fonceka et al. (2012)
hundred seed weight
Stress tolerance index, 2 Fonceka et al. (2012)
haulm weight
Stress tolerance index, pod 3 Fonceka et al. (2012)
number
Resistance to tomato 18 Qin et al. (2012) and Wang et al. (2013)
spotted wilt virus (TSWV)
Tomato spotted wilt virus 12 Agarwal et al. (2018)
resistance
Total biomass 5 Fonceka et al. (2012) and Leal-Bertioli et al. (2016)
Haulm weight 16 Fonceka et al. (2012), Leal-Bertioli et al. (2016) and
Faye et al. (2015)
Main stem height 11 Fonceka et al. (2012) and Leal-Bertioli et al. (2015)
Log_Main stem height 3 Leal-Bertioli et al. (2015)
Plant weight 1 Selvaraj et al. (2009)
Log weight ratio root/ 3 Leal-Bertioli et al. (2016)
aerial part
Growth habit 6 Fonceka et al. (2012)
Harvest index 2 Fonceka et al. (2012) and Faye et al. (2015)
Shell weight 1 Fonceka et al. (2012)
Pod weight 7 Fonceka et al. (2012) and Faye et al. (2015)
Number of pods per plant 6 Selvaraj et al. (2009) and Chen et al. (2019)
Pod number 2 Fonceka et al. (2012)
(continued)
892 T. Radhakrishnan et al.

Table 16.14 (continued)

QTL for the trait Number References
Seed weight 6 Fonceka et al. (2012), Dodia et al. (2019) and Chavarro
et al. (2020)
Seed number 8 Fonceka et al. (2012), Leal-Bertioli et al. (2016) and
Chen et al. (2019)
Log seed number 3 Leal-Bertioli et al. (2015)
Fruiting branches 5 Wang et al. (2018)
Total number of branches 4 Wang et al. (2018)
Internode number 4 Wang et al. (2018)
Stem rot resistance 43 Bera et al. (2016), Dodia et al. (2019) and Luo et al.
(2020)
Root hairiness 3 Dodia et al. (2019)
Leaf shape 2 Dodia et al. (2019)
No of primary branches 1 Dodia et al. (2019)
No of secondary branches 1 Dodia et al. (2019)
Plant height 11 Dodia et al. (2019), Wang et al. (2018) and Faye et al.
(2015)
Pod length 4 Dodia et al. (2019) and Wang et al. (2018)
Shelling percentage 5 Dodia et al. (2019), Faye et al. (2015) and Huang et al.
(2015)
Per cent seed infection 2 Yu et al. (2019)
index (aflatoxin)
Aflatoxin B1 content 7 Yu et al. (2019)
Aflatoxin B2 content 5 Yu et al. (2019)
Aflatoxin resistance 3 Pandey et al. (2014a, b) and Zuang (cited from Soni
et al. 2020)

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Soybean Breeding
17
Anita Rani and Vineet Kumar

Abstract

Unique confluence of oilseed, leguminous and nutraceutical properties in soy-

bean seed has made this crop the leading oilseed, the major animal feed and a
much sought-after health food of this century. Undoubtedly, sustained effort to
breed soybean varieties to enhance the yield is the major objective; however,
there is a tremendous scope for genetic improvement to meet the requirement of
each segment of the soy industry. To begin with, the chapter briefs about the
historical account of soybean across the world and the morphological phenotypes
important from the point of view of soybean breeder. Subsequently, the major
breeding methods employed in soybean, the genetics of the important qualitative
and quantitative traits and the interventions required on the improvement of the
yield components, resistance against major diseases, enhancement of oil and
protein, improvement of oil quality, elimination/reduction of anti-nutritional
and undesirable factors such as Kunitz trypsin inhibitor and off-flavour
generating lipoxygenases are discussed. Conventional, molecular and transgenic
approaches employed for achieving the breeding objectives are highlighted.

Keywords
Glycine max · Breeding methods · Maturity · Disease resistance · Speed breeding ·
Yield components · Kunitz trypsin inhibitor · Off-flavour · Marker-assisted
breeding · Oleic acid and phytic acid · Transgenic

A. Rani (*) · V. Kumar

ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, India
e-mail: anita.rani@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 907
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_17
908 A. Rani and V. Kumar

17.1 Introduction

Globally, soybean [Glycine max (L.) Merr.] is the leading oilseed crop with a
production of 363.27 million tonnes, accounting for 60.43% of the world oilseed
production (601.14 million tonnes) (United States Department of Agriculture 2021).
Brazil is the leading country in soybean production with a share of 37.71% in the
world’s soybean production, followed by the United States of America (30.97%),
Argentina (12.66%), China (5.39%), India (2.87%), Paraguay (2.72%) and Canada
(1.74%) (United States Department of Agriculture 2021). India ranks fifth position in
the world soybean production. Soybean oil is the most consumed vegetable oil
worldwide after palm oil. The global soybean oil production in 2020–2021 was
59.74 million tonnes, which accounted for 28.85% of total vegetable oil (207.01
million tonnes) produced worldwide (United State Department of Agriculture 2019).
China is the leading soybean oil-producing country with a share of 28.20% followed
by the United States of America (18.97%), Brazil (15.06%), Argentina (13.55%), the
European Union (5.12%) and India (2.82%). Deoiled cake obtained after crushing
soybean for extraction of oil fraction is termed soymeal and is a protein-rich
commodity animal feed and processing soy products for human consumption. A
total of 249.75 million tonnes soybean meal is produced worldwide in 2020–2021,
which is 71.24% of total protein meal (350.55 million tonnes) produced.
China is the leading soybean meal-producing country with a share of 29.80%,
followed by the United States of America (18.40%), Brazil (14.51%), Argentina
(12.59%), the European Union (5.09%) and India (3.01%). Besides being a rich
source of oil (average 18–20%) and protein (about 40%) which determine the market
value of soybean crop, soybean is a rich source of several nutraceutical molecules
such as isoflavones, tocopherols, essential fatty acids, and phosphatidylcholine
(lecithin) which provide special health benefits to the consumers (Messina et al.
1994; Potter et al. 1998; Nordentoft et al. 2008; Kumar et al. 2010c). Besides, low
glycemic index of soybean makes it an ideal food ingredient for diabetic patients.
Utilization of this golden bean in food uses is by and large confined to southeast
nations where soybean constitutes the staple diet of the masses. In the wake of
expanding awareness about the special health benefits soybean provides the con-
sumer, apart from a rich source of plant-based protein, efforts are being made to
incorporate soybean in a regular diet in the countries beyond its traditional bastion of
Southeast Asia. This has necessitated the development of specialty soybean suiting
the local mode of incorporation of soybean in regular diet.

17.2 Historical Account (Origin, Evolution and Expansion

of Soybean)

There is a common concurrence that soybean cultivation originated in China about

3000–3700 years ago based upon the carbon dating of the soybean seed remains
obtained in excavation. Theories do exist that the crop originated in northeast,
Huang-Huai Valley (HHV) and southern region of China. However, Lu (1978)
17 Soybean Breeding 909

opined that soybean originated from several regions of China as indicated by the
geographical distribution of short-day character of wild soybean. During the rule of
Zhou dynasty in China (1050 BC–250 BC), it was one of the five sacred grains along
with wheat, barley, rice and millet, and used to be known by the name shu. Modern
cultivated soybean was domesticated from wild soybean (Glycine soja) about
6000–9000 years before. Han et al. (2016) sequenced more than 50,000 targeted
genomic regions of 404 accessions of Glycine max, 72 accessions of Glycine soja
and 36 accessions of Glycine gracilis and land races. Glycine gracilis is considered
as an evolutionary product of domestication of soybean. The authors reported that
there was no gene flow from Glycine max to Glycine gracilis or Glycine soja, but
significant gene flow was observed from Glycine soja to Glycine gracilis and from
Glycine gracilis to Glycine max. A moderate gene flow from Glycine soja to Glycine
max was also observed.
This substantiated the theory that Glycine soja is the progenitor of both Glycine
max and Glycine gracilis. Far greater genetic introgression from Glycine soja in
Glycine max accession from the Huang-Huai Valley (HHV) region of China than
from the accessions from other geographical regions of China also substantiated that
HHV of China is the most likely centre of domestication of soybean (Sedivy et al.
2017). During the period between 200 BC and 200 AD, soybeans from North China
came to Japan via Korea. In the third century, there is a mention of soybean varieties
in Korean literature. Further, soya sauce and meso as soya food are mentioned in
Korean literature in 638 AD. The earliest Japanese reference to soybean is in the
classic Kojiki in 712 AD. In the early eighteenth century, Europeans started raising
soybean in their botanical gardens; however, commercial cultivation of the crop in
this continent commenced in 1875. In 1829, US farmers raised the soybean variety
for soy sauce. The earliest known reference of soybean in India was in 1832 by
Roxburgh who described a soybean variety grown in Calcutta Botanic Garden;
however commercial cultivation of soybean in the country commenced in the late
1960s as an economical source of plant-based protein to combat malnutrition.
However, it transformed as a major oilseed crop of the country. In Brazil, soybean
arrived around 1882 to the state of Bahia where Gustavo Duttra evaluated soybean
cultivars (Gavioli 2013). In Brazil, immigration of Japanese people in the first
decade of the twentieth century led to the promotion of soybean in this country as
soybean was in the staple diet of the immigrants. Presently, Brazil is the leading
producer which grows soybean in 38 million ha, followed by the United States of
America (33.6 million ha), Argentina (16.4 million ha), China (9.3 million ha) and
India (12 million ha).

17.3 Taxonomy, Floral Biology and Hybridization

Soybean falls in the order Fabales, family Fabaceae, tribe Phaseoleae, subfamily
Papilionoideae, genus Glycine and subgenus Soja. Cultivated soybean Glycine max
is considered to be domesticated from its wild annual soybean Glycine soja
(2n ¼ 40) and on crossing with the latter produce fertile F1 hybrids. Besides, the
910 A. Rani and V. Kumar

subgenus Glycine consists of 26 wild perennial species, which are native to Australia
and replete with genes for resistance against insect-pests and developing climate-
smart genotypes.
Both the main stem and the branches bear axillary buds which blossom into
racemes, containing 8–16 or more number of flowers depending upon the genotype.
Soybean has a typical papilionaceous flower, with tubular calyx of five unequal
sepals, corolla of five petals, androecium of ten stamens and a gynoecium. The
flower is white or purple. Five petals are arranged in one large petal in the posterior
region, two lateral wing petals and two anterior keel petals. The keel surrounds the
androecium, which has nine fused and one free posterior stamen filament. Gynoe-
cium has one ovary with four ovules and one style which terminates into a capitate
stigma tilting towards the free stamen filament. Growth of the style and stamens is
synchronous which facilitates shedding of the pollens at maturity directly on the
stigma. As a result, the floral biology of the soybean flower makes soybean largely a
self-pollinated crop. This necessitates the removal of anthers for crossing between
the desired parents. For crossing, if the days-to-flowering information of the parents
is not known, the parents are planted on staggered dates to synchronize the appear-
ance of buds of the female parent with the opening of flowers for the availability of
pollens from the male parent to affect the hybridization. In general, both emascula-
tion and pollination are done in the morning hours using forceps and needles, and in
1 h, a skilled person can affect 25 crossing events, comprising of both emasculation
and pollination procedures. True F1 plants can be identified by dominant morpho-
logical markers such as hypocotyl pigmentation, flower colour, glabrous nature of
the pod and stem and pubescence colour on the stem and pods. The absence of these
contrasting morphological features in female and male parent, necessitates the
deployment of co-dominant molecular markers or trait gene-specific markers for
the identification of the true F1 plants (Fig. 17.1).

17.4 Breeding Methods

Soybean breeding, like the breeding of other self-pollinated crops, involves devel-
opment of variability for desired traits, generation advancement for achieving
homozygosity and identification of superior genotypes. To achieve sufficient
variability selection of parents is a very important step. Parents are selected on the
basis of their genotypic diversity and the traits desired in the final variety. Progenies
of these crosses segregate genetically during generation advancement; most of the
loci get fixed after six to seven generations of selfing, and new recombinants are thus
formed. The selection methods used for identification of genotypes with most useful
combinations of the desired traits are pedigree method, single-seed descent method,
backcross method, recurrent method and bulk method.
Pedigree selection involves visual selection of the families with high-yielding
capacity in each generation followed by within-family selection of one or more
plants to advance to the next generation. This increases the frequency of lines with
desirable traits. Single-seed descent (SSD) method involves advancing one seed
17 Soybean Breeding 911

Fig. 17.1 Confirmation of true F1 plants using null KTI allele-specific marker (a) and KTI-linked
SSR marker, Satt228 (b), in NRC7-derived KTI-free lineNRC109. Lane nos. 2, 4, 5 and 8 corre-
spond to true F1 plants. P1 and P2 correspond to NRC7 and PI542044 (donor of null KTI allele),
respectively. Lane L corresponds to 50 bp DNA ladder

from each progeny plant to the next generation to develop nearly homozygous lines
that still preserve most of the original genetic variation in a population. Single-pod
method is also used instead of single-seed descent method, for the added conve-
nience of collecting pod from each plant and maintaining the variability during
generation advancement in case one seed from the pod fails to establish a plant due
to any unfavourable condition. SSD method of selection in combination with speed-
breeding method of multiple generations in a single year is a very effective method
of breeding soybean varieties with desirable trait. But there are certain shortcomings
as a large number of progenies have to be maintained until the production of a
generation in which uniform lines are selected for yield testing.
In bulk method of breeding, the population is advanced in bulk with no artificial
selection until later generations, when nearly homozygous lines are selected for yield
testing (Orf et al. 2004). Bulk method is simple method, but there are certain
shortcomings like a steady reduction of genetic variability in each generation due
to inadequate sample size and the natural selection within the population moving in
an undesirable direction. However, the population exhibited a higher genetic gain
from selection and higher mean values than populations developed by the other two
methods (pedigree and single-seed descent), when natural selection within the
population favoured high-yielding genotypes. Backcross breeding method is mainly
used to introgress disease resistance or quality trait governed by major genes in
popular and adapted varieties lacking few desirable traits. Molecular markers are
912 A. Rani and V. Kumar

very helpful in introgression of desirable trait in adapted varieties. In India, resis-

tance to yellow mosaic disease was introgressed in the most popular soybean variety
JS335 to make it resistant to the disease, and null allele of Kunitz trypsin inhibitor
(KTI) was introgressed in soybean cultivar with multiple disease resistance variety
JS97-52 using marker-assisted backcross selection. Mass selection (Burton and Brim
1981; Tinius et al. 1991), selection among half-sib families (Burton and Carver
1993), selection within half-sib families (Burton et al. 1983) and the selection from
S1 (or S2) families (Brim and Burton 1979; Kenworthy and Brim 1979; Sumarno
and Fehr 1982; Rose et al. 1992) are other alternate breeding methods used in
soybean cultivar development. The traditional pedigree method and the single-
seed descent method (SSD) are most often used in soybean breeding (Goulden
1939; Grafus 1965; Cooper 1990). The selection of breeding method depends on
the breeding objective, available variability and availability of resources. Breeding
objectives depend on the local ecological conditions, diseases and insect-pest pres-
sure and the market demand. The efficiency of various methods of selection failed to
show significant differences among them (Raeber and Weber 1953; Torrie 1958;
Luedders et al. 1973; Boerma and Cooper 1975; Degago and Caviness 1987; Byron
and Orf 1991; Bravo et al. 1999; Cober and Voldeng 2000). The highest genetic
gains in seed yield from selection were most frequently found in populations
developed by the pedigree method, while the highest mean values were found in
populations developed by the SSD method.

17.5 Speed Breeding

Cross breeding in soybean is time-consuming as the crop life cycle takes 3–4 months
for completion. Therefore, genetic improvement rate in soybean is slow. Shuttle
breeding is the regular strategy to increase the generation turnover to accelerate the
breeding programmes in soybean. Ghosh et al. (2018) reported the speed-breeding
platform developed by scientists at the John Innes Centre, University of Queensland
and University of Sydney. This uses a glasshouse or an artificial environment with
enhanced lighting to create intense day-long regimes to speed up the breeding
programmes, which greatly shortens generation time and accelerates breeding and
research programmes. An economical method of speed breeding has also been lately
suggested by Rani et al. (2020), which comprises of simple net house instead of
compact growth chamber, and does not deploy fluorescent lamps or carbon dioxide
(CO2) supplementation.
The authors shortened the generation time by combining two approaches. The
first approach was to shorten the photoperiod by covering the pots with black bags in
the evening and their removal in the morning. Soybean is a short-day plant, and
shortening of the photoperiod accelerates the flowering and reproductive growth.
This is attributed to the fact that short inductive period causes initiation of flowering
10–15 days earlier than in the normal/longer photoperiod. Shortening of photoperiod
also reduces the lag phase of around 10 days between the flower-opening and the pod
initiation. A number of flowers and pods decrease due to acceleration of the growth
17 Soybean Breeding 913

induced by short photoperiod; however, fewer flowers or pods produced under short
photoperiod do not matter as single-seed descent (SSD) method is the most common
breeding approach in soybean. The second approach was to harvest immature pods
(30 days after flowering), air-dry them for 7–8 days and sow them. The generation
time combining these two approaches was reduced to 70 days which is significantly
lower than 90–130 days taken under longer photoperiod. Using these approaches,
the authors could advance F2 generation of a cross to F6 generation within a time
span of 1 year. The authors took four generations in a year instead of five possible
generations due to the low temperature experienced during December–January
months, which delayed the flowering and extended the life cycle as the experiment
was performed under ambient conditions. The authors suggested that the use of
temperature-controlled glasshouse with openable roof to control the photoperiod
would allow rapid generation cycling through single-seed descent (SSD) for large
crop improvement programmes.

17.6 Genetics and Breeding for Qualitative

and Quantitative Trait

17.6.1 Qualitative Traits

17.6.1.1 Plant Growth Habit

Soybean crop plant may be determinate, semi-determinate and indeterminate in
terms of plant growth habit. In determinate type, plant vegetative growth terminates
with the completion of flowering, while in indeterminate type, vegetative growth and
flowering occur simultaneously. In semi-determinate, plant growth does occur for a
limited duration after flowering. Two loci Dt1 and Dt2 govern these growth pattern
determinates (Bernard 1972). Determinate type is governed by recessive allele dt1,
while the indeterminate type by Dt1. Dt2 controls semi-determinate type growth, as
the locus reduces the effect of Dt1.

17.6.1.2 Seed Coat Colour

Soybean can be in yellow, green, black, brown and red in its seed coat colour
(Fig. 17.2). It is an important seed attribute that determines that end use of soybean.
It is the yellow seed coat colour soybean which is used as raw material for extraction
of oil. Green, brown, black or any bicolour soybean is primarily used for processing
food products or in soy-based food recipes. They vary in their antioxidative and
nutraceutical properties, with black soybean possessing the highest antioxidative and
nutritional value (Kumar et al. 2010b). Classic genetic studies revealed primarily
five loci I, R, T, W1 and O that determine the seed coat colour appearance (Yang
et al. 2010). I locus has four alleles, namely, I, ii, ik and i. Dominant I allele produces
complete colourless soybean, while i produces coloured seed coat (Senda et al.
2004), and ii and ik determine pigmentation on the hilum and saddle regions of the
seed coat. R and T determine the type and extent of seed coat colour. R, T and i result
in complete black; I, R and t generate imperfect black; i, r and T produces brown; and
914 A. Rani and V. Kumar

Fig. 17.2 Soybean of

varying seed coat colour

i, r and t cause buff seed coat colour. Genetic background of irT (brown colour) is
affected by O locus, as recessive o allele produces red-brown colour, while I,R,
t background is affected by W1 locus, as recessive w1 allele generates buff colour.
Green cotyledon phenotype has been reported to be governed by the nuclear as well
as cytoplasmic genes (Terao 1918). D1 (Glyma.01 g214600 in W82.a2.v1 assembly)
and D2 (Glyma.11 g027400) are two unlinked, paralogous nuclear genes, whose
double-recessive mutant (d1d1d2d2) results in chlorophyll retention, called ‘stay-
green’ (Fang et al. 2014). D1 and D2 are homologs of the STAY-GREEN (SGR)
genes from other plant species and were duplicated as a result of the most recent
whole genome duplication in soybean. Transcriptional analysis by Fang et al. (2014)
showed that both D1 and D2 were more highly expressed in older tissues, and
chlorophyll degradation and programmed cell death-related genes were suppressed
in a d1d2 double mutant, indicating that these genes are probably involved in the
early stages of tissue senescence. Double variants of the D1 and D2 gene result in the
stay-green phenotype, including delayed yellowing of leaves during senescence,
with green seed cotyledons (Guiamet et al. 1991; Fang et al. 2014). Cytoplasmic
inheritance of green cotyledon is governed by 5-bp insertion in the soybean chloro-
plast genome resulting in a frameshift in PsbM, which encodes one of the small
subunits of photosystem II (Kohzuma et al. 2017). The genotyping of D1, D2 and
PsbM from 212 soybeans with green cotyledons revealed that all lines carry either
d1d2 or PsbM with the known mutations (Kohzuma et al. 2017).
17 Soybean Breeding 915

17.6.1.3 Maturity Gene(s)

Soybean is a typical short-day (SD) plant, i.e. the plant enters the reproductive phase
once the day length becomes shorter than the critical length. Soybean plant flowering
under short-day conditions would revert back into vegetative phase if shifted to long-
day (LD) conditions (Washburn and Thomas 2000; Wu et al. 2006). GmFT2a and
GmFT5a genes have been reported to promote flowering in Arabidopsis and soy-
bean (Kong et al. 2010; Sun et al. 2011; Cai et al. 2018), while GmFT4 gene is
induced by LD conditions and was reported to function in delaying flowering when
transformed and expressed in Arabidopsis (Zhai et al. 2014; Cao et al. 2016).
Samanfar et al. (2017) reported that GmFT4 is the most likely candidate gene at a
newly identified maturity locus E10.Hitherto, 13 major genes/loci, namely, E1
(Cober and Voldeng 2001; Molnar et al. 2003), E1La and E1Lb (Xia et al. 2012),
E2 (Cregan et al. 1999), E3 (Molnar et al. 2003), E4 (Abe et al. 2003; Molnar et al.
2003), E6 (Li et al. 2017b), E7 (Cober and Voldeng 2001; Molnar et al. 2003), E8
(Cober et al. 2010), E9 (Kong et al. 2014), E10 (Samanfar et al. 2017) and J and
GmAGL1 (Zeng et al. 2018) affecting flowering and maturity period have been
mapped. Barring E6, E9, J and GmAGL1, the dominant allele of all of these genes,
delay flowering.
With regard to maturity, nine loci have been identified as E1–E8 and J, and these
loci are strengthened and weakened by long-day length condition (LD) and short-
day length condition (SD), respectively (Wang et al. 2008). Furthermore, four
maturity loci have been characterized at the molecular level. E1 gene encodes a
transcription factor which functions as a flowering repressor with a putative nuclear
localization signal and a B3-related domain (Xia et al. 2012), while E2 is an
orthologue of Arabidopsis flowering gene GIGANTEA (Watanabe et al. 2011).
Two E1-L genes, E1 La and E1Lb (Glyma04g24640.1/Gm18g22670), have
been reported to have an expression pattern similar to E1 (Xia et al.
2012). E1Lb retards flowering under long-day conditions by repressing the expres-
sion of FT2a and FT5a independently of E1 (Zhu et al. 2018). E3 and E4 are
phytochrome genes GmPhyA3 (Watanabe et al. 2009) and GmPhyA2 (Liu et al.
2008), respectively. Besides, two homologs of soybean flowering locus T (FT)
genes, GmFT2A and GmFT5A, coordinately regulate flowering. Four identified
maturity genes E1, E2, E3 and E4 delay flowering and maturity under LD through
downregulating GmFT2A and GmFT5A (Kong et al. 2010; Watanabe et al. 2011;
Xia et al. 2012).

17.6.1.4 Pod Shattering

Loss of pod shattering function in low humid and high-temperature condition was
one of the key functions during soybean domestication. Two major genes Pdh1 and
SHAT1–5—a NAC gene—govern pod dehiscence in soybean. According to Dong
et al. (2014), NAC gene triggers the deposition of the secondary walls of the lignified
fibre cap cells (FCC) in the pod ventral suture and determines the binding strength of
pods. Conversely, functional product of Pdh1 gene triggers the dehiscence of pods
under low humidity conditions (Funatsuki et al. 2014). Zhang and Singh (2020)
916 A. Rani and V. Kumar

reported a novel locus NST1A, apart from Pdh1 and NAC gene, associated with pod
shattering and its interaction with Pdh in determining the pod shattering.

17.6.1.5 Breeding for Biofortification

Soybean seed possesses a unique seed composition. Besides being rich in protein, it
does suffer from the shortfall of the presence of undesirable components which
affect protein digestibility and generate off-flavour, thereby limiting its bioavailabil-
ity. The concentration of these biomolecules in soybean seeds may vary depending
upon the location and the environment they have been raised (Kumar et al. 2006a, b).
However, the genetic inheritance of some of the undesirable biomolecules is well
established, and these undesirable molecules can be genetically eliminated from
soybean genotypes through conventional and marker-assisted breeding.

Breeding for Improved Protein Digestibility Through Genetic Elimination

of Kunitz Trypsin Inhibitor
Despite being the rich source of quality seed protein, soybean does suffer from the
shortfall of poor protein digestibility due to the presence of trypsin inhibitor present
in its seeds. Trypsin inhibitor activity in soybean is a function of genotype (Kumar
et al. 2001; Kumar et al. 2019), the growing location and environment (Kumar et al.
2003; Kumar et al. 2006a, b). Kunitz trypsin inhibitor (KTI-a 20kDa polypep-
tide), and Bowman-Birk inhibitor (BBI-a smaller 8 kDa polypeptide) both contribute
to trypsin inhibitor activity. The former is primarily responsible for total trypsin
inhibitor activity, and its contribution to trypsin inhibitor activity is genotype-
dependent (Peric et al. 2014; Kumar et al. 2019), present in immature pods also
(Kumar et al. 2006c), and affects human health (Liener 1994). KTI is relatively more
thermolabile due to the presence of only two disulphide linkages compared to the
seven disulphide bonds present in BBI. However, minimum 15–20 min boiling of
soybean seeds is required for its complete inactivation (Chen et al. 2014). Residual
activity of KTI in the soy food and feed products is ascribed to faulty processing
such as insufficient temperature and duration of the heating (Brandon et al. 1991).
Moreover, heat treatment is not only cost-ineffective but also results in approxi-
mately 20% decline in protein solubility (Anderson 1992).
KTI in soybean seed is governed by a single gene and is controlled by multiple
alleles (Hymowitz 1973; Zhao and Wang 1992). The four electrophoretic forms of
soybean KTI are controlled by co-dominant multiple allelic series (Tia, Tib, Tic and
Tid). A fifth form lacking Kunitz trypsin inhibitor activity is controlled by a recessive
allele ti (Orf and Hymowitz 1979). The gene has been located on the linkage group
(LG) A2, corresponding to chromosome 8 of soybean genome of the soybean
molecular linkage map (Cregan et al. 1999). Several studies have shown the tight
linkage of three SSR markers, namely, Satt409, Satt228 and Satt429, with ti locus
(Kim et al. 2006; Rani et al. 2011). A KTI null allele-specific marker has also been
designed from genotype PI157440 (de Moraes et al. 2006) which has been deployed
in identification of plants carrying the null allele of KTI derived from PI542044
(Kumar et al. 2013b). In India, KTI-free genotypes NRC101 and NRC102 have
been developed using PI542044 as the donor of null KTI allele through
17 Soybean Breeding 917

marker-assisted forward breeding (Rani et al. 2010), and both these advanced
breeding lines were commercialized to private soy food industries in India. Further,
KTI was genetically eliminated from elite soybean varieties, viz. NRC7, JS97–52,
MACS450, JS93–05 and S97–12, through marker-assisted breeding (Kumar et al.
2011a, b, 2012, 2015). The country released its first Kunitz trypsin inhibitor-free
soybean variety NRC127 developed through marker-assisted backcrossing (MABC)
for the farmers of Central India for the entire state of Madhya Pradesh, Vidharbha
and Marathwada region of Maharashtra and Bundelkhand region of Rajasthan, Uttar
Pradesh and Gujarat state. In Serbia, two KTI-free soybean genotypes, viz. ‘Laura’
and ‘Launa’, have been developed (Peric et al. 2014).

Breeding for Improved Flavour and Fragrance

Grassy and beany flavour associated with the soy products constrains human
consumption of soybean in the countries where people are not accustomed to
it. This off-flavour in soy food products is generated by the catalytic oxidation of
unsaturated fatty acids by lipoxygenases Lox1, Lox2 and Lox3 present in the
soybean seed (Gerde and White 2008; Wilson 1996; Axelrod et al. 1981). Lox2 is
the principal contributor to the off-flavour developed in soy products (Davies et al.
1987). The absence of each lipoxygenase isozyme in soybean seed is monogenically
controlled by three null alleles, lox1, lox2 and lox3, which are inherited as simple
recessive alleles (Davies and Nielsen 1986; Hildebrand and Hymowitz 1982;
Kitamura et al. 1983, 1985). The Lox1 and Lox2 loci are tightly linked and are
present on chromosome 13 (LG F). Lox3 locus is present on chromosome 15 (LG E),
and its segregation is independent of Lox1 and Lox2 (Kitamura et al. 1985; Davies
and Nielsen 1986; Hajika et al. 1992). Therefore, it was possible to easily breed
double-null lipoxygenases lx1lx3 and lx2lx3 soybean genotypes. However, the
repulsion-phase linkage present between lox1 and lox2 recessive alleles was the
major impediment in development of triple-null lipoxygenase (lx1lx1lx2lx2lx3lx3)
soybean genotypes (Davies and Nielsen 1986; Hildebrand and Hymowitz 1982;
Kitamura et al. 1985). However, the use of irradiation helped in breaking of
repulsion-phase linkage between mutant alleles at Lox1 and Lox2 loci, resulting in
a coupling-phase linkage which made possible to develop a triple-null lipoxygenase
(lx1lx1lx2lx2lx3lx3) genotype (Hajika et al. 1991; Kitamura 1991).
Genetic basis of mutation in Lx1, Lx2 and Lx3 is known. In null lox2 genotype,
T2849A is the missense mutation, which caused the substitution of glutamine for
histidine in a highly conserved histidine-rich motif (Wang et al. 1994), thereby
causing loss of function of Lox2. Reinprecht et al. (2011) and Shin et al. (2012)
also reported missense mutation (single point mutation T-A) causing conversion of
histidine codon to glutamine codon leading to loss of function of Lox2 in OX948
and Jinpumkong. Lenis et al. (2010) reported a 74 bp deletion in exon 8 in PI 408251
while Reinprecht et al. (2011) reported this deletion in OX948, responsible for the
premature truncation of the Lox1 protein. In PI 133226, a nonsense mutation
C2880A relative to the start codon was observed in lox1 allele (Lenis et al.
2010). For the loss of Lox3 function in PI 20585 and PI 417458, Lenis at al
(2010) attributed loss of function of Lox3 to a single base deletion of a guanine in
918 A. Rani and V. Kumar

a run of five guanine nucleotides, within exon 1, from position 97 to 101 relative to
start codon. Gene specific and simple sequence repeat (SSR) markers linked to Lx1,
Lx2 and Lx3 have been developed through mapping and characterization of Lx1,
Lx2 and Lx3, which have been deployed in development of lipoxygenase-free
soybean varieties in several countries (Lenis et al. 2010; Reinprecht et al. 2011;
Kumar et al. 2012; Rani et al. 2013). In India, ICAR-Indian Institute of Soybean
Research has developed lipoxygenases free advanced breeding lines through marker
assisted breeding (Rawal et al. 2020; Kumar et al. 2013a) and commercialized
lipoxygenase-2-free soybean advanced breeding line NRC109 to private soy food
industries using these markers (Kumar et al. 2013a). Recently, the country released
its first ipoxygenase-2-free soybean variety NRC132 developed through marker
asssisted breeding for the southern zone. In the United States of America, there are
seven lipoxygenase-free soybean varieties, viz. IA1008LF, IA2053LF, IA2076LF,
IA2104LF, IA3027LF, IA3045LF and IA3051LF, for commercial cultivation. In
Canada, Agriculture and Agri-Food Canada (AAFC), Greenhouse and Processing
Crops Research Centre (GPCRC) at Harrow, Ontario, has developed and released
lipoxygenase-free food-grade soybean germplasm line, HS-151, in 2015 (Yu et al.
2016).
Further, immature pods of a special kind of genetic stock of soybean is harvested
at R6 stage (when the pod cavity is completely filled, but has not started turning
yellow) of soybean consumed as snack or vegetable (Shanmugasundaram et al.
1991). These special genotypes which are ‘vegetable or edamame or green soybean’
produce highly sweet and organoleptically good-flavour immature seeds, which is
largely due to higher accumulation of sucrose and sweetness-imparting amino acids,
and bear larger pods with bold size compared to the grain-type soybean (Kumar et al.
2006, 2011a, b). The distinct fragrance in the seeds of vegetable soybean emanates
from volatile compound 2-acetyl-1-pyrroline (2AP) (Fushimi and Masuda 2001),
which is also present in basmati rice. A single recessive gene controls the fragrance
in vegetable soybean. This recessive mutation causes elevated 2AP biosynthesis that
results in a fragrant aroma (Niu et al. 2008). Juwattanasomran et al. (2011) reported a
major QTL contributing to fragrance which is in the proximity of betaine aldehyde
dehydrogenase 2 (GmBADH2). Sequence of gene coding this enzyme in fragrant
and non-fragrant soybean genotypes revealed a non-synonymous SNP in exon
10, resulting in the change of glycine to aspartic acid. The authors developed
PCR-based allele-specific SNP markers for marker-assisted breeding of fragrance
trait in soybean. Juwattanasomran et al. (2012) discovered a new fragrance allele,
which has a 2-bp (TT) deletion in exon 10 of GmBADH2 in another fragrant
soybean cultivar Chamame.

Breeding for Improved Shelf Life of Oil Fraction by Genetically Elevating

Monounsaturated Fatty Acid (Oleic Acid) and Reducing α-Linolenic Acid
Oil fraction of soybean seed which constitutes about 20% of the total mass is
composed of five major fatty acids, palmitic (10–13%), stearic (2–4%), oleic
(20–25%), linoleic (50–55%) and α-linolenic acid (7–8%). Palmitic and stearic
acids are saturated fatty acids, while oleic, linoleic and α-linolenic acids are
17 Soybean Breeding 919

unsaturated fatty acids. Based upon the unsaturation in hydrocarbon chain, fatty
acids have been categorized as monounsaturated or polyunsaturated. Oleic acid
(C18:1) is a monounsaturated fatty acid (MUFA) with single unsaturation. Linoleic
(C18:2/omega 6) and α-linolenic acid (C18:3/omega3), the polyunsaturated fatty
acids (PUFA), have two and three unsaturation, respectively, across the fatty acid
hydrocarbon chain. The higher unsaturation level in linoleic and α-linolenic acid
results in 10.0- and 21.2-fold faster oxidation in these polyunsaturated fatty acids
(PUFA) than oleic acid, respectively. Susceptibility to fast oxidation and develop-
ment of fishy smell in the stored soybean oil is attributed to the high PUFA. To
improve shelf life of soya oil, industries employ partial hydrogenation leading to
generation of trans fats, which trigger diabetes, atherosclerosis and cancer (De Souza
et al. 2015). In several countries, food safety regulatory bodies have made it
mandatory to declare the level of trans fats on the nutrition facts label in commercial
edible oils and the processed food products containing edible oil as the major
ingredient (Food and Drug Administration 2003; Food Safety and Standards Author-
ity of India 2018; Ratnayake et al. 2014). Soybean oil with high oleic acid and low
α-linolenic acid possesses improved oxidative stability, flavour and storability,
thereby obviating the need of partial hydrogenation which incurs cost and generate
health hazardous trans fats. Therefore, development of high oleic acid and low
α-linolenic acid soybean genotypes is one of the most important breeding objectives
for soybean-growing and soybean oil-consuming countries (Kumar et al. 2004;
Kumar et al. 2010a).
During soybean seed development, oleate fatty acid desaturase catalyses the
conversion of oleic acid (C18:1) into linoleic acid (C18:2) by inserting a double
bond at the twelfth carbon from the carboxyl end of fatty acid hydrocarbon chain,
while linoleate desaturase acts upon linoleic acid to produce α-linolenic acid. Omega
6 fatty acid desaturase activity, which is governed by two candidate genes, namely,
FAD2-1A (Glyma10g42470) and FAD2-1B (Glyma20g24530) (Schlueter et al.
2007), determines the accumulation of oleic acid in soybean. Pham et al. (2011)
reported 82–86% oleic acid in soybean genotypes carrying mutated alleles of both
FAD2-1A and FAD2-1B. Recently, Rani et al. (2019) reported genomic regions
associated with other than candidate genes for the biosynthesis of oleic acid. Low
α-linolenic acid soybean genotypes can be developed by modulating the activity of
desaturase which inserts a double bond at the fifteenth carbon from carboxyl end,
thereby converting linoleic to α-linolenic acid. The activity of this desaturase is
determined by at least three loci, namely, FAD3A/fan1 (Glyma.14 g194300),
FAD3B/fan2 (Glyma.02 g227200) and FAD3C/fan3 (Glyma.18 g062000) present
on LGp B2/chr14, LGp G/chr18 and LGp D1b/Chr2, respectively (www.soybase.
org). Deletions, insertions and nonsense mutation in FAD3A (Bilyeu et al. 2005),
FAD3B (Reinprecht et al. 2009) and FAD3C (Bilyeu et al. 2005) have been reported
to reduce α-linolenic acid content. Besides, Thapa et al. (2018) reported three novel
point mutations in FAD3A gene responsible for low α-linolenic acid content. Bilyeu
et al. (2018) successfully combined mutations in FAD2 and FAD3 genes to produce
soybean genotypes with high oleic and low α-linolenic acid soybean using func-
tional markers. Haun et al. (2014) developed transgenic plants homozygous for the
920 A. Rani and V. Kumar

cleaved conserved sequences in FAD2-1A and FAD2-1B with elevated levels of

oleic acid.

Breeding for Improved Bioavailability of Minerals

Phytic acid, 1,2,3,4,5,6-inositol hexaphosphoric acid, is a heat-stable anti-nutritional
factor present in soybean seeds. It is the principal source of phosphorus in soybean
seeds and is present in much higher concentration in soybean seeds compared to
other legumes (Chitra et al. 1995). It binds with nutritionally important metals,
especially zinc, calcium and magnesium, forming phytic acid-metal complexes
(phytin), that are not absorbed readily in the intestine and hence largely excreted
by humans and non-ruminant animals that have either no or limited phytase activity
(O’Dell 1982; Forbes et al. 1983; Solomon 1982). This may cause deficiency of
important nutrients. Being heat stable in nature, phytic acid remains active even after
cooking. At alkaline pH, phytic acid binds with negatively charged protein
molecules, and at pH values below isoelectric point, it binds with positively charged
protein molecules. Therefore, phytic acid not only inhibits the action of a number of
enzymes involved in digestion (Vaintraub and Bulmaga 1991) but also affects the
isoelectric point, solubility and functionality of soy proteins (Chen and Pan 1985)
which are vital in processing quality soy products. In tofu manufacturing, a relatively
large amount of coagulants, namely, CaSO4 and MgCl2, is required to offset the
effect of phytic acid on tofu quality (Schaefer and Love 1992). Further, hard-to-cook
phenomenon of soybean and legumes has also been associated with phytic acid
(Bernal-Lugo et al. 1991; Jones and Boulter 1983). Further, the undigested phytin
excreted through non-ruminants pollute soil and water causing eutrophication
(Raboy 2001).
Myoinositol-1-phosphate synthase (MIPS) is the key enzyme which catalyses the
conversion of Glc-6-P to myoinositol-1-phosphate (MIP), which is in turn converted
to 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (phytic acid) by subsequent
phosphorylations in phytic acid biosynthesis during soybean seed development.
Hitz et al. (2002) discovered a missense mutation in soybean (Glycine max) MIPS
structural gene (GmMIPS1) responsible for 50% reduction in seed phytic acid, while
Wilcox et al. (2000) identified a mutant soybean line CX1834 with reduced phytic
acid content without any change in total seed phosphorus. Walker et al. (2006)
identified recessive mutations at two interacting unlinked loci responsible for low
phytic acid trait of CX1834. Maroof et al. (2009) identified a nonsense mutation
within a candidate lpa1 homolog present on chr 3, Glyma03g32500, for the low
phytic acid phenotype in soybean. Gillman et al. (2009) identified a novel missense
mutation in a conserved portion of the other lpa1 homolog, Glyma19g35230, in
CX1834 and developed high-throughput molecular marker assays to directly select
for the alleles that control the soybean low phytic acid phenotype.
The authors also reported a novel lpa2-b allele in low phytic acid soybean line
M766. Gillman et al. (2009) developed molecular markers which would facilitate in
combining nonsense lpa2-b allele from M766 with the nonsense lpa1-a allele from
CX1834 to produce soybeans with much lower levels of phytic acid and increased
available phosphate levels. Nunes et al. (2006) tried to reduce phytic acid in soybean
17 Soybean Breeding 921

seed by downregulating MIPS by RNA interference (RNAi) technology; however

complete RNAi knockdown of GmMIPS1 expression resulted in aborted soybean
embryos. Bilyeu et al. (2009) developed a soybean line CAPPA, in which an
Escherichia coli periplasmic phytase, the product of the appA gene, was expressed
resulting in 90% reduction in seed PA with concomitant increase in total free
phosphate.

Pyramiding the Desirable Quality Traits

As mentioned in Sects. 17.6.1.5.1 and 17.6.1.5.2, specialty soybean genotypes
genetically free from Kunitz trypsin inhibitor and off-flavour generating
lipoxygenase isozymes have been developed in several countries. However, soybean
breeders felt the need of bringing the null allele of Kunitz trypsin inhibitor and
lipoxygenases in the same genetic background which would be the most ideal raw
material for processing soy products. Kumar et al. (2021) recently stacked null
alleles of Kunitz trypsin inhibitor and lipoxygenase-2 through marker-assisted
backcrossing (Fig. 17.3). In India, soybean genotype NRC142 carrying null alleles
of Kunitz trypsin inhibitor and lipoxygenase-2, which is the principal contributor to
the off-flavour, has been developed through marker-assisted pyramiding of null
alleles of KTI and lipoxygenase-2 by employing null allele-specific markers and

Fig. 17.3 Amplification of null lox2 allele-specific marker (a) and lox2-linked SSR marker,
Satt656 (b), in true F1 plants of NRC7-derived KTI-free line  NRC109. Lanes 1, 2, 3, 6, 7, 9
and 13 correspond to true F1 plants. P1 and P2 correspond to NRC7 and NRC109, respectively; lane
L corresponds to 50 bp ladder
922 A. Rani and V. Kumar

Fig. 17.4 NRC142 double-null (KTI null and off-flavour generating lipoxygenase-2 null) Indian
soybean variety developed through marker-assisted forward breeding
(JS97–52  PI542044  PI596540)

SSR markers linked to both Ti and Lox2 locus (Rani and Kumar 2018) and released
for commercial cultivation for central and southern agroclimatic zones. Average
productivity of this variety is 1999 kg/ha and 2200 kg/ha in central and southern
zone of the country which is significantly higher than the average productivity of
soybean (1300 kg/ha) in the country. A field photograph of NRC142 is presented in
Fig. 17.4. Oliveira et al. (2007) also developed soybean lines pyramided for null
alleles of Kunitz trypsin inhibitor and lipoxygenase-2. Lately, Kumar et al. (2022)
reported improved sprouting and tocopherols contents in introgressed lines for null
Lox2 while improved protein digestibility in introgressed lines for null KTI compared
to the recurrent parent.
17 Soybean Breeding 923

17.6.1.6 Breeding for Disease Resistance

Resistance to Rust
Soybean rust (SBR), caused by Phakopsora pachyrhizi Syd. & P. Syd., can impact
the yield losses up to 80% (Li et al. 2012). P. pachyrhizi was first identified in Japan
in 1902 (Hennings 1903) which gradually spread to soybean-growing countries
around the world (Bromfield 1984; Pretorius et al. 2001; Rossi 2003; Wang and
Hartman 1992; Yorinori et al. 2005). Some of P. pachyrhizi races have developed
increased tolerance to the certain fungicides available to control the disease (Godoy
2009). Development of soybean varieties possessing genetic resistance to this
disease is the most effective sustainable measure to control this fungus. Screening
of soybean accessions for resistance or tolerance to rust across the world (Miles et al.
2008; Pham et al. 2010) has led to the identification of five different loci carrying
dominant alleles: Rpp1 identified in PI 200492 (Mclean and Byth 1980), Rpp2 from
(PI 230970) (Bromfield and Melching 1982), Rpp3 (PI 230970) (Bromfield and
Hartwig 1980), Rpp4 (PI 459025) (Hartwig 1986) and Rpp5 (PI 200487 and PI
471904). Calvo et al. (2008) identified recessive genes controlling SBR resistance.
Brogin et al. (2004) identified simple sequence repeat (SSR) markers linked to rust
resistance present in the variety FT-2 in the linkage group (LG)-C2 of the previous
soybean consensus map reported by Cregan et al. (1999)
Monteros et al. (2007) mapped a SBR resistance gene from the variety Hyuuga at
3 cM interval between Satt134 and Satt460 on LG-C2. Hyten et al. (2007) recently
mapped the Rpp3 locus at the same interval as reported by Monteros et al. (2007).
The Rpp1 locus has been mapped to a 1 cM interval on LG-G between Sct_187 and
Sat-064 LG-G. Bhor et al. (2015) identified two genes, namely, Rpp1b-like loci
linked to SSR marker Satt 191 and Rpp2 loci linked to SSR marker Satt 215 in
soybean rust-resistant exotic genotype EC 241780. Khanh et al. (2013) introgressed
Rpp genes into a premium soybean variety HL203 in Vietnam. Yamanaka et al.
(2015) pyramided Rpp genes in lines No6–12-B, Oy49–4 and No6–12-1 containing
two (Rpp4 + Rpp5), three (Rpp2 + Rpp3 + Rpp4) and three (Rpp2 + Rpp4 + Rpp5)
genes using molecular markers for durable resistance against SBR.

Resistance to Soybean Mosaic Virus

Soybean mosaic virus (SMV) is the most prevalent and destructive viral pathogen in
soybean production worldwide (Hill and Whitham 2014). Seven distinct strains
(G1 to G7) in the United States of America (Cho and Goodman 1979) and 21 strains
(SC1–SC21) in China have been classified (Wang et al. 2003; Guo et al. 2005; Li
et al. 2010) based on their differential responses of susceptible and resistant soybean
cultivars. A number of independent loci governing SMV resistance have been
reported. Rsv1 was the first SMV resistance gene identified in the soybean line PI
96983 (Kiihl and Hartwig 1979), which confers extreme resistance to SMV-G1
through G6 (Chen et al. 1991; Hajimorad and Hill 2001). Thereafter, a series of
multiple Rsv1 alleles including Rsv1-y, Rsv1-m, Rsv1-t, Rsv1-k and Rsv1-r have
been identified from different soybean cultivars with differential reactions to SMV
G1–G7 strains (Chen et al. 2001). Rsv1 was mapped on chromosome 13, and 3gG2
924 A. Rani and V. Kumar

was found to be a strong candidate for Rsv1 (Hayes et al. 2004). Rsv3 was identified
in ‘L29’, a ‘Williams’ isoline derived from Hardee (Bernard et al. 1991; Gunduz
et al. 2000). This locus gives resistance to SMV G5 through G7, but not G1 through
G4 (Jeong et al. 2002).
Jeong et al. (2002) mapped Rsv3 between markers A519F/R and M3Satt on
chromosome 14. Fine mapping led to identification of two closely linked SSR
markers, namely, Sat_424 at a distance of 1.5 cM and Satt726 at a distance of
2.0 cM from Rsv3 locus (Shi et al. 2008). NBS_C, NBS_D and NBS_E in this
genomic region may be the functional alleles of the Rsv3 locus that confer resistance
to SMV (Suh et al. 2011; Redekar et al. 2016; Ma et al. 2017). Rsv4 which confers
resistance to all seven SMV strains (Chen et al. 1993; Ma et al. 1995) was identified
in soybean cultivars V94–5152 and mapped to a 0.4 cM interval between the
proximal marker Rat2 and the distal marker S6ac, in a 94-kb haplotype block on
chromosome 2 (Hayes et al. 2000; Saghai Maroof et al. 2010; Ilut et al. 2016). Two
resistance genes Rsc-8 and Rsc-9, which confer resistance to strains SC-8 and SC-
9, respectively, have been mapped to soybean chromosome 2 (Wang et al. 2004).
Wang et al. (2011) reported Glyma02g13310, 13,320, 13,400, 13,460 and 13,470 as
the probable candidate genes for Rsc-8 based on their predicted functions and
expression patterns (Wang et al. 2011). Yang and Gai (2011) mapped resistance
gene Rsc-15 between Sat_213 and Sat_286 on chromosome 6, while Fu et al. (2006)
identified the resistance gene Rsc-7 in the soybean cultivar Kefeng No. 1 and
mapped to a 2.65 mega-base (Mb) region on soybean chromosome 2. Shi et al.
(2011) developed an 11 SNP/InDel multiplex assay to investigate the mode of
inheritance in a SMV-resistant soybean line carrying Rsv1, Rsv3 and/or Rsv4
through a segregating population with phenotypic data and to select a specific
gene or pyramid two or three genes for SMV resistance through MAS in soybean
breeding programme. The assay is a very useful tool in marker-assisted development
of SMV-resistant soybean varieties. Saghai Maroof et al. (2008) and Shi et al. (2009)
successfully pyramided soybean mosaic virus resistance genes using marker-assisted
selection.

Resistance to Yellow Mosaic Disease

Yellow mosaic virus causes yellow mosaic disease (YMD) in soybean (G. max) and
legumes such as blackgram [Vigna mungo (L.) Hepper], mungbean [Vigna radiata
(L.) R. Wilczek] and cowpea [Vigna unguiculata (L.) Walp.] (Varma et al. 1992).
The virus is transmitted by the white fly (Bemisia tabaci Genn.) (Nariani 1960; Nene
1972, 1973). Two distinct begomoviruses, mungbean yellow mosaic India virus
(MYMIV; Mandal et al. 1997) and mungbean yellow mosaic virus (MYMV;
Morinaga et al. 1990) have been suggested to be associated in the aetiology of
YMD in legumes in India and South Asia based on nucleotide sequence data of the
genomic components of yellow mosaic viruses. Mungbean yellow mosaic India
virus has been reported to infect soybean in India, Vietnam and Indonesia (Nene
1972, 1973). YMD resistance genes were reported in PI171443 by Singh and
Mallick (1978) and in G. soja accession PI 393551. Yadav et al. (2009) reported
accumulation of late viral transcripts and DNA replication in a susceptible cultivar
17 Soybean Breeding 925

Fig. 17.5 Map position of MYMIV resistance gene on C2 linkage group in F2 population and
RILs derived from JS335  PI171443 [Source: Rani et al. (2017) Breeding Science 67:95–100

and rapid degradation of early viral RNAs in resistant cultivars. This rapid degrada-
tion of the early viral transcripts, possibly through a small interfering RNA mecha-
nism, could be a mechanism of natural resistance against geminivirus. There are
several reports on the inheritance of MYMIV resistance in these donors.
Rani et al. (2017) reported a single recessive gene, while Singh and Mallick
(1978) reported double-recessive genes controlling MYMIV resistance in PI171443.
A single dominant gene controlling MYMIV resistance in G. soja PI 393551 was
reported by Bhattacharyya et al. (1999). Rani et al. (2017) mapped MYMIV
resistance gene on chr 6 (LG C2) within a 3.5-cM genome region between two
SSR markers GMAC7L and Satt322 whose size was estimated to be 77.115 kb
(position of 12,259,594–12,336,709 bp) in PI171443 (Fig. 17.5). Deploying these
molecular markers, the authors developed NRCSL1, the first MYMIV-resistant
soybean variety for southern agroclimatic zone using marker-assisted forward
breeding and later NRCSL2, essentially derived variety (EDV) of JS335, the most
popular variety of India, through marker-assisted backcross breeding. In the back-
drop of the fact that MYMIV-resistant soybean varieties of India carry resistance
gene from the same donor PI171443, it is important to pyramid resistance gene from
926 A. Rani and V. Kumar

Fig. 17.6 The map positions

of MYMIV resistance genes
on A2 and B2 linkage in F2
population derived from
cultivar JS335 (Glycine
max)  PI 393551 (Glycine
soja) [Source Rani et al.
(2018) Crop Science 58(4):
1566–1567]

other sources for sustained resistance to MYMIV in the event of breakdown of

resistance to single resistance derived from PI171443. Rani et al. (2018) identified
SSR marker BARCSOYSSR_08_0867 (15,434,295 bp) on chromosome 8 and
BARCSOYSSR_14_1416 (47,686,933 bp) and BARCSOYSSR_14_1417
(47,738,940 bp) on chromosome 14 tightly linked to MYMIV resistance genes in
G. soja (Fig. 17.6), which are being used to pyramid resistance genes from both
G. soja and G. max.

Resistance to Charcoal Rot

Charcoal rot caused by Macrophomina phaseolina can cause yield loss to 100%.
The fungus is both soil and seed borne and has a wide host range. Breeding for
charcoal rot resistance is difficult as sufficient information at the genome level
imparting resistance not available. da Silva (2018) genotyped 140 F2 individual
derived from a biparental cross PI567562A x PI567437 (susceptible) with 5403
single nucleotide polymorphism markers and phenotyped for resistance to charcoal
rot resistance through cut-stem inoculation technique in greenhouse and reported
one QTL on chromosome 15 explaining 29.4% of phenotypic variation and two
QTLS on chr 16 explaining 25.4 and 8.4% of phenotypic variation for resistance to
the disease.

17.6.2 Breeding for Quantitative Traits

17.6.2.1 Protein and Oil

Seed oil and protein content are two most valuable quality traits controlled by
multiple genes in soybean. The phenotypic range of protein content of soybean
has been reported to be 34.1–56.8% of seed dry mass, and oil content ranged from
8.3% to 27.9% (Wilson 2004). The genetic variability available in soybean germ-
plasm suggests that there is a great potential for genetic improvement of soybean
seed protein and oil content. It has been reported in various studies that seed protein
content is negatively correlated to seed oil and sucrose content in soybean (Nichols
et al. 2006; Sonah et al. 2015). Breeding soybean varieties with high protein and
high oil are extremely important for value addition. The negative correlation
between protein and oil content makes improvement of both traits simultaneously
17 Soybean Breeding 927

a challenging task using conventional breeding (Hwang et al. 2014; Bandillo et al.
2015; Chung et al. 2003; Kim et al. 2016). Moreover, protein and oil content in
soybean seed are quantitatively inherited and governed by multiple genetic loci
subject to genotype  environment interactions (Akond et al. 2014; Li et al. 2019;
Patil et al. 2017).
As the differences in seed composition are also affected by epigenetic variation,
expression profile of the genes involved in fatty acid biosynthesis, carbon
partitioning, seed development and possibly many other unknown regulators (Kim
et al. 2016; Nichols et al. 2006; Sebolt et al. 2000), the task of improving oil and
protein content simultaneously becomes more challenging. As the protein and oil
components of soybean seed are very valuable trait, many QTLs controlling these
two seed traits have been reported (Chung et al. 2003; Diers et al. 1992; Nichols et al.
2006; Panthee et al. 2005; Pathan et al. 2013; Wang et al. 2015; Warrington et al.
2015). There have been few studies on identification of candidate genes governing
oil and protein content in soybean seed.
Zhang et al. (2020) mapped major soybean protein and oil QTLs on chromosome
15 to a sugar transporter gene (GmSWEET39). The authors reported that a
two-nucleotide CC deletion truncating C-terminus of GmSWEET39 was strongly
associated with high seed oil and low seed protein, suggesting its pleiotropic effect
on protein and oil content. GmSWEET39 was predominantly expressed in paren-
chyma and integument of the seed coat and likely regulates oil and protein accumu-
lation by affecting sugar delivery from maternal seed coat to the filial embryo. The
authors demonstrated that GmSWEET39 has a dual function for both oil and protein
improvement and undergoes two different paths of artificial selection. A CC deletion
(CC-) haplotype H1 has been intensively selected during domestication and exten-
sively used in soybean improvement worldwide (Zhang et al. 2020). The studies on
the molecular basis underlying the major QTL and GmSWEET39 haplotypes
associated with seed quality components would be helpful in designing new
strategies for soybean seed quality improvement using molecular breeding and
biotechnological approaches.

17.6.2.2 Breeding for Yield Contributing Components

Biotic and abiotic factors are known to affect several plant architecture traits such as
plant height, number of branches, number of nodes, pods per node, number of seeds
per pod and seed traits such as seed size (100-seed weight).

Number of Branches
Branch number is one of the important determinants of yield. Branching in soybean
depends upon environmental factors such as plant density and light quality
(Agudamu and Shiraiwa 2016; Board 2000). Lower plant density generally used
to avoid lodging and the incidence of diseases results in increased branch number on
the main stem as the plant compensates for the lower seed rate. However, phenotypic
data from Germplasm Resources Information Network (GRIN) shows genetic
differences for the branch development as indicated by the higher number of
branches in the Japanese/Korean cultivars than the American soybean varieties.
928 A. Rani and V. Kumar

Several studies have shown QTLs associated with the branch number in soybean in
F2 or RIL mapping population. Shim (2019) identified a candidate gene GmBRC1
for branching in soybean.

Pod Numbers and Number of Seeds per Pods

The number of pods per plant is another important parameter that determines the
seed yield of genotype. Keeping in view the importance of the total number of pods
per plant, several studies identified QTLs associated with the total number of pods
with the aim to increase the efficiency of breeding for higher yields (Zhang et al.
2010; Rodrigues et al. 2016; Liu et al. 2017). However, vertical distribution of pods
on soybean is uneven as more number of pods are distributed in the upper and the
central region than in the lower region (Liu et al. 2010). Ning et al. (2018) identified
QTLs associated with one-seeded, two-seeded, three-seeded and four-seeded pods in
the three different regions, i.e. upper, middle and lower region, of the soybean plant
in two associated recombinant inbred lines. Similarly, the number of seed per pod is
equally important determinant of yield of any genotype. In general, soybean plant
bears three, two and one seeded. Four-seeded pods are also not rare, and occasionally
five-seeded pods are also available. The number of seed per plant has been suggested
to be tightly associated with LN gene (Domingo 1945). Weiss (1970) attributed the
greater frequency of four-seeded pods to the pleiotropic effect of the gene that causes
narrow leaf. Jeong et al. (2011) reported a candidate gene Glyma20g25000.1 that is
associated with the LN encoding gene. Li et al. (2021) finely mapped QTL locus
QNSPFSP07–1 associated with four-seeded pod in soybean.

100-Seed Weight
100-SW is important determinant of seed size of grains so much so that the terms
have been used interchangeably in literature. Small-size grains are sought for a better
quality of soybean sprouts, natto and miso, whereas bold-seeded grains make
excellent raw material for making soy nuts, tofu, edamame (Kato et al. 2014).
Seed size is determined by the onset of cellularization in developing endosperm.
Premature cellularization of the endosperm results in smaller seed size, while its
delayed initiation causes increased seed size in soybean. Rani et al.
(2021) identified Satt684 (Chr05: start 1,800,423–end 180,073) for 100-seed weight
in the proximity of functional gene Glyma05g02470 (Chr05: start 1,817,656–end
1,822,298) for serine-threonine protein kinase which has been reported to regulate
cell cycle growth and may have a role in the cellularization of endosperm (Zhang
et al. 2020). The authors also identified two SSR markers, namely, Sat_263 (LGp
C2, 118.78 cM, LOD-2.39, R2–8.83) and AI856415 (LGp D1b,50.11 cM,
LOD-2.76,R2–10.28) in the proximity of QTL, namely, Staga001 (LGp C2,
119.85 cM) and Satt296 (LGp D1b, 52.61 cM), respectively, reported to be
associated with seed size by Yang et al. (2017) in chromosome substitution lines
derived from N24852  NN1138–2. Further, Satt181 (LGpH, 91.12 cM), which in
our study showed slightly lower LOD value (1.65), was approximately 13 cM distant
from QTL qSW12.1 (104.37 cM) identified with 100-SW in an earlier study (Liu
et al. 2018). Yu et al. (2018) reported four candidate genes, namely,
17 Soybean Breeding 929

Glyma.01G158700, Glyma.01G156800, Glyma.01G125400 and

Glyma.01G147800, related to 100-SW in 147 RILs from cross Charleston 
Dongnong 594 were not found to be significantly associated with this trait in our
results.

17.7 Transgenic Development

Transformation in soybean was first reported in 1988 by Christou et al. (1988) and
Hinchee et al. (1988), and genetically modified soybean was first introduced com-
mercially in 1996. Transgenic soybean plants have been obtained by two predomi-
nant methods for plant transformation, i.e. particle bombardment-based method and
the Agrobacterium-mediated transformation method (Hinchee et al. 1988; McCabe
et al. 1988). Agrobacterium-mediated gene transfer method is preferred over particle
bombardment-based method due to requirement of minimal equipment costs, possi-
bility of transferring relatively large segments of DNA, lower number of transgene
copy integration into plant genomes, rare transgene rearrangement, lower frequency
of genomic DNA interspersion and reduced abnormal transgene expression (Gelvin
2003). Particle bombardment method involves the use of complicated and expen-
sive equipment (McCabe et al. 1988) and results in complex integrations, fragmen-
tation and reconstitution of transgenes that may lead to transgene silencing).
Agrobacterium-mediated transformation method attributes about 85% of the trans-
genic plant production (Yu et al. 2010). This method has been extensively used to
introduce agronomical important traits like herbicide tolerance (Padgette et al.
1995), amino acid modification (Falco et al. 1995), virus resistance (Di et al.
1996), insect resistance (Stewart et al. 1996) and nematode resistance (Yamada
et al. 2012) in soybean cultivar. A detailed list of traits introduced in soybean
through transgenic method is given in Table 17.1.
Despite production of fertile transgenic plants through Agrobacterium-mediated
transformation, reported transformation efficiencies are generally low in soybean
(Somers et al. 2003; Rani et al. 2012; Verma et al. 2014). The transfer of T-DNA and
its integration into the plant genome is influenced by several plant tissue-specific
factors. These factors include plant genotype, explant vigour, Agrobacterium strain,
vector-plasmid and selection system including selection agent and method (Cheng
et al. 2004; Shukla et al. 2020). Additionally, inoculation and co-culture media
composition, osmotic treatments, vir-gene-inducing synthetic phenolic compounds,
tissue damage, suppression and elimination of A. tumefaciens infection after
co-cultivation also affect the transformation efficiency (Klee 2000; Cheng et al.
2004). To develop an efficient genotype-independent Agrobacterium-mediated
transformation system and high efficiency, modification should be done in factors
affecting transformation.
Although a number of factors that affect transformation efficiency have been
studied and manipulated that includes sonication-assisted Agrobacterium-mediated
transformation (Trick and Finer 1997), the use of cystine, dithiothreitol and thiol
compounds (Olhoft et al. 2007), co-cultivation at 22 C and use of Silwet-77 as
930 A. Rani and V. Kumar

Table 17.1 Agronomically important genes transferred into soybean

Target tissue Gene Selectable marker Phenotype References
Half seed AtABF3 Phosphinothricin Drought tolerance Kim et al.
(PPT) (2018)
Half-seed Bar gene PPT Resistance against Li et al.
cotyledonary herbicide (2017a)
explant/
cotyledonary
nodes
Cotyledon γ-TMT PAT 41-fold increase in Lee et al.
α-tocopherol (2011)
Cotyledon CPs NPTII Enhanced accumulation Marra
of isoflavones in seed et al.
(2009)
Cot-node FAD3 PAT Significant reduction in Flores
linolenic acid (18:3) et al.
content, ranging from (2008)
1.0% to 3.1%
Embryonic Cry1Ac NPAT Resistance to cotton Dang and
axes bollworm Wei
(2007)
Cotyledon SbDV-CP CP4 EPSPS and Protection against Miklos
NPTII soybean looper, soybean et al.
podworm and velvet (2007)
bean caterpillar
Somatic CP-SMV HPT Resistance against SMV Furutani
embryo et al.
(2006)
Somatic SMV-HC-Pro HPT Exhibited resistance Tougou
embryo response against SbDV et al.
(2006)
Immature SMV-CP-3’-UTR HPT Bioassay not done Lim et al.
cotyledon (2005)
Somatic Bean-chitinase NPTII Bioassay not done Li et al.
embryo gene (chi) and (2004)
ribosome in
activating protein
gene (rip)
Cotyledon CRC HPT Enhanced accumulation Yu et al.
of isoflavones in seed (2003)
Hypocotyl SMV-CP-3’-UTR NPTII Resistance against SMV Wang
virus et al.
(2001)
Somatic Maize 15 kDa HPT Increased methionine Dinkins
embryo zein protein gene and cysteine content et al.
(2001)
Somatic β-casein HPT Expression of a milk Maughan
embryos protein in soybean et al.
(1999)
(continued)
17 Soybean Breeding 931

Table 17.1 (continued)

Target tissue Gene Selectable marker Phenotype References
Cotyledonary BPMV-CP-P NPTII Resistance phenotype Di et al.
nodes against BPMV (1996)
Somatic Cry1Ac HPT Resistance against corn Stewart
embryo earworm (Helicoverpa et al.
zea), soybean looper (1996)
(Pseudoplusia
includens), tobacco
budworm (Heliothis
virescens) and velvet
bean caterpillar
(Anticarsia gemmatalis)

surfactant (Liu et al. 2007), use of antioxidant during co-cultivation (Wang and Xu
2008), 4-day co-cultivation time period (Ko and Korban 2004) and selection by
direct placement of explant at low concentration of antibiotic (Yan et al. 2000).
Successful transformation using Agrobacterium depends not only on the efficiency
of the plant regeneration systems but also on the subsequent elimination of this
bacterium from transformed cells. The elimination of Agrobacterium is usually
achieved by adding one or more antibiotics to the culture medium and is quite
important because the continued presence of Agrobacterium can present a problem
for identifying transformants or interfere with the growth and development of the
transformed plant cells or cause the death of the cultures (Horsch et al. 1985; Matzk
et al. 1996). Carbenicillin and cefotaxime are the most commonly used antibiotics
for this purpose.
An effective and foolproof selection strategy is very important for successful
transformation. Five different selection markers have been utilized in soybean
transformation. They include cat, npt II, hpt, bar and manA and neomycin
phosphotransferase II (npt II). The most successful and popular selection marker is
the bar gene, derived from Streptomyces hygroscopicus which encodes the enzyme
phosphinothricin acetyltransferase (PAT) conferring resistance to the herbicide
phosphinothricin (PPT) or its analogues Basta (with its active ingredient glufosinate
ammonia) or bialaphos (Harshavardhan et al. 2003).
A new technology for genome editing—the CRISPR (clustered regularly
interspaced short palindromic repeat)/Cas (CRISPR-associated) system—has been
successfully used for genome engineering in many important crops in recent years.
Since 2015, CRISPR/Cas9-mediated genome editing in soybean has shown an initial
success. This technology provides a powerful tool for accurate genetic modification
and gene function identification, but it also relies on transformation efficiency (Chen
et al. 2018). Soybean genetic transformation is limited to few laboratories due to low
transformation and regeneration efficiencies.
932 A. Rani and V. Kumar

17.8 Conclusions

Progress made in soybean breeding through conventional, molecular and transgenic

approaches has been tremendous. Yield-related traits and maturity duration have
been the most important breeding objectives. Breeding for disease resistance has
been gaining importance due to appearance of new diseases and continuous evolu-
tion of pathogens threatening soybean crop. As soybean is a very important source of
edible oil and one of the most economical sources of plant protein, continuous efforts
are being made to improve quantity and quality of both oil and protein fractions.
Genetic improvement in oleic acid in soybean oil has been taken on a priority basis
due to increasing awareness on ill effects of trans fats on human health. Genetic
elimination of Kunitz trypsin inhibitor, a factor responsible for low digestibility of
soy protein, and lipoxygenases responsible for generating off-flavour is gaining
importance.

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Castor Breeding
18
S. Senthilvel, T. Manjunatha, and C. Lavanya

Abstract

Castor, a non-edible, commercial oilseed crop of Euphorbiaceae family, is a

monotypic genus. It is a highly cross-pollinated crop and amenable to all plant
breeding techniques. The present chapter is a comprehensive summary of the
transformation of a wild, tall, shattering, perennial plant type to domesticated,
medium-to-tall, non-shattering, annual plant type grown under rainfed or irrigated
castor-growing regions of India. About 38 high-yielding genotypes including
18 varieties and 20 hybrids are in the seed chain with an average productivity of
1.9 t/ha. The chapter deals with the basic information of the crop, viz. genetics,
floral biology, sex expression and different approaches followed for crop
improvement.

Keywords
Genetic resources · Breeding strategies · Hybrid production · Genomics ·
Improved varieties

18.1 Introduction

Castor (Ricinus communis L.) is grown for its seed oil in more than 30 countries.
India, Mozambique, Brazil and China are the major producers. As per FAOSTAT
(2018), it is cultivated in an area of about 1.3 m ha across the globe with the
production of around 2.8 mt. India ranks first in both area (0.99 m ha) and production
(1.96 mt). It can be grown even in sub-optimal soil conditions with minimal

S. Senthilvel · T. Manjunatha · C. Lavanya (*)

ICAR-Indian Institute of Oilseeds Research, Hyderabad, India
e-mail: c.lavanya@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 945
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_18
946 S. Senthilvel et al.

management. In general, the commercial cultivars contain 48–50% oil, whereas in

germplasm collections, the oil content ranges from 37 to 60% (Wang et al. 2010).
Castor oil is the only known source for ricinoleic acid, an unusual fatty acid. The
higher proportion (>80%) of ricinoleic acid (12-hydroxyl-cis-9-octadecenoic acid)
in the fatty acid composition makes the castor oil unique among the vegetable oils.
The oil and its derivatives are important raw materials for several industries such
as soap, nylon, lubricants, plastic, paper, cosmetic, paint, pharmaceutical, etc. More
than 400 products are manufactured using castor oil and its derivatives. Castor has a
huge potential for production of bioenergy as the oil yield (1250–2500 L/ha) is
higher than any other potential crops for biodiesel. It could supply up to 60% of the
non-edible oil needed to produce biodiesel (Osorio-González et al. 2020). Compar-
ative advantage of castor lies in its ability to adapt to different weather conditions,
possibility of growing even in marginal soils and high ricinoleic acid content
providing characteristics desirable for biodiesel production such as high viscosity,
high miscibility, low iodine content and low freezing point.
Before industrialization, castor was used for varied purposes. The oil was used for
lighting, hairdressing, skin conditioning and as medicine. As medicine, the oil is
mainly used as laxative and to relive the pain caused by sprain. In North Eastern
parts of India and Myanmar, castor leaves are fed to eri silk worm. In some places,
especially Japan, it is used for ornamental purposes. Castor cake is an excellent
source of organic fertilizer.

18.2 Origin, Evolution and Distribution of Species

Castor belongs to Euphorbiaceae family, which contains more than 280 genera.
Under the genera Ricinus, communis is the single species. However, three separate
species, namely, Ricinus communis, Ricinus macrocarpus and Ricinus
microcarpus and a few sub-species such as persicus, chinensis, africanus,
mexicanus, etc. have been reported in literature (Kulkarni and Ramanamurthy
1977; Moshkin 1986; Weiss 2000). However, none of these is botanically qualified
as ‘species’ or ‘sub-species’ because they do not differ in the chromosome number
(all have 2n ¼ 20 chromosomes), and they cross easily with each other (Kulkarni and
Ramanamurthy 1977; Atsmon 1989). They are actually different morpho-types
adapted to specific regions.
Even though ‘Eastern Africa’ is considered as the most probable origin of castor
(Weiss 1971), polyphyletic origins cannot be ruled out. Moshkin (1986) suggested
four centres of origin, namely, Iran-Afghanistan, Palestine-Southwest Asia,
Indo-China and Arabian Peninsula regions. It is found across tropical and
sub-tropical regions of the world. In Ancient Egypt, castor seeds were found in
tombs dating to 4000 BC. Wild castor plants are found throughout the African
continent. India has a rich history of its cultivation and use. An ancient literature
Susruta Atharvaveda (1000 BC) refers castor as an indigenous plant of India. The
earliest castor seeds (125 BC) were found during the excavation in Maharashtra. In
China, castor has been in use as medicine for centuries.
18 Castor Breeding 947

At present, castor is cultivated on a commercial scale in countries such as India,

China, Brazil and Mozambique. In Brazil, about 80% of castor area is concentrated
in the state of Bahia. In India too, more than 80% of area is in the western parts
(states of Gujarat and Rajasthan) under irrigated conditions, while traditional rainfed
castor -growing area is limited to Southern India.

18.3 Plant Genetic Resources

There are at least 30 institutes/organizations worldwide involved in conserving

castor genetic resources. Of these, six major institutions, namely, National Bureau
of Plant Genetic Resources under Indian Council of Agricultural Research (ICAR-
NBPGR); Institute of Crop Germplasm Resources under Chinese Academy of
Agricultural Sciences (ICGR-CAAS); US Department of Agriculture-Agricultural
Research Service (USDA-ARS); Centro Nacional de Pesquisa do Algodao (CNPA),
Brazil; NI Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Russia;
and Institute of Biodiversity Conservation (IBC), Ethiopia, conserve between
510 and 4307 accessions (Anjani 2012). ICAR-NBPGR has the largest collection
(>4307 accessions) followed by China (~2111 accessions) as per the FAO’s Second
Report on the State of the World’s Plant Genetic Resources for Food and Agriculture
published during 2010.
Global efforts in characterization of germplasm collections have shown tremen-
dous variation for morphological traits in castor (Webster 1994; Anjani 2012).
However, the entire genetic diversity is limited to intraspecific diversity mostly
created by hybridizations between local germplasm with exotic lines. Exchange of
breeding materials, breaking of linkages through breeding and independent inheri-
tance of morphological characters played a great role in generating diversity.
Molecular marker analyses have revealed only low to moderate level of DNA
polymorphism (Allan et al. 2008; Qiu et al. 2010; Foster et al. 2010; Senthilvel
et al. 2017). In the pursuit to generate additional diversity, intergeneric hybridization
with Euphorbia lathyris (Moshkin 1986), Jatropha (DOR 2003) and Manihot
esculenta (Gedil et al. 2009) was attempted but remained unsuccessful.
For effective utilization of germplasm, a core set of 165 accessions was identified
from the original germplasm collection of more than 3000 accessions maintained at
ICAR-Indian Institute of Oilseeds Research (IIOR), Hyderabad, India. The
accessions for the core set were selected based on agro-morphological traits. The
core set represented almost the entire variability present in the whole collection
(Sarada and Anjani 2013).
Systematic screening of the germplasm for several biotic stresses led to the
identification resistance sources to Fusarium wilt, Macrophomina root rot, reniform
nematode, leafhopper, capsule borer and serpentine leaf miner. Accessions showing
tolerance to drought (Parvathaneni et al. 2017), early maturity and high ricinoleic
acid content have also been identified (Anjani et al. 2018). A few of the germplasm
accessions carrying useful traits are listed in Table 18.1.
948 S. Senthilvel et al.

Table 18.1 Trait-specific germplasm accessions of castor

S. no. Traits Germplasm accessions/breeding lines
1 Resistance to 48-1, DCS-107, RG-43, RG-72, RG-111, RG-2819 and many
Fusarium wilt more germplasm and improved lines
2 Resistance to root rot RG-111, RG-2722, RG-2818, RG-2819, RG-2822
3 Moderate resistance ICS-324, 48-1, DPC-9, RG-1963
to gray mold
4 Resistance to RG-43, JC-12
reniform nematode
5 Resistance to RG-631, RG-1621, RG-2661, RG-3037, RG-3067
leafhopper
6 Resistance to leaf RG-1930, RG-1771
miner
7 Resistance to capsule RG-898, RG-2774, RG-2800
borer
8 Tolerance to drought RG-27, RG-72, RG-1494, RG-2139
9 Tolerance to salinity 48-1, DPC-9, GC-2
10 Early maturity RG-18, RG-19, JI-258
11 High ricinoleic acid RG-57, RG-66, RG-226, RG-3477
content

18.4 Floral Biology: Emasculation-Pollination Techniques

The inflorescence is a raceme and popularly called as ‘spike’. Separate male

(staminate) and female (pistillate) flowers are located in the same inflorescence
(monoecious). Male flowers appear in the basal and median portions of the spike,
while female flowers are found in the apical part of the spike. Very rarely, one or two
bisexual flowers (hermaphrodite) appear in a spike. Male and female flowers open
asynchronously. Even though the plant is predominantly monoecious, polymor-
phism for sex expression is observed with spike containing only pistillate or pistillate
with interspersed staminate flower (ISF) forms. Sex expression is highly influenced
by environmental conditions (Shifriss 1960). In general, low temperature (<30  C),
early stage of development and high nutrition promote female flowers, and high
temperature (>30  C), old plants and sub-optimal nutrition promote male flowers on
a spike (Lavanya 2002). The role of exogenous and endogenous growth hormones
like gibberellic acid, silver nitrate and ethylene in shifting the female and male
tendency has been well documented (Ramesh et al. 2000; Lakshmamma et al. 2002;
Murthy et al. 2003).
Botanically, both the flowers are described as bracteate, ebracteolate, pedicellate,
actinomorphic and incomplete. Male flowers are apetalous with a simple perianth
consisting of five sepals enclosing a stamen cluster. Each stamen cluster has
1000–1500 anthers borne terminally on branched filaments. Stamens are
polyadelphous, and filaments branched and united to form five branches. Anthers
are dithecous, globose, basifixed, introrse and dehiscing by longitudinal slits. The
18 Castor Breeding 949

ovary is superior, tricarpellary, syncarpous and trilocular with one ovule in each
locule on axile placentation. There are three styles with bifid and feathery stigma.
Due to monoecious nature of the spike, mixed pollinations (both self- and cross-
pollinations) occur in nature. Cross-pollination to the extent of 36 to 76% has been
reported. Upon anthesis, male flowers produce abundant pollen. Due to lightweight,
wind carries the pollen and aids in cross-pollination to a great extent. It has been
observed that pollen can travel to a distance of even 1 km under clear sky and with
normal wind velocity. Bagging the inflorescence with butter paper bags or muslin
cloth bags ensures self-pollination. For attempting crossing between two lines, the
inflorescence of female parent is covered with a paper bag after removing the male
flowers and any opened female flowers in the previous day. For pollination, the male
flowers from the covered inflorescence of male parent are collected in a Petri plate
and kept under the sun for about 30 min for dehiscence of the anther. Then, the
pollen is rubbed on the stigma of female flowers of the designated female parent
using a paint brush and covered with a paper cover. The pollination is done every
alternate day for 10–15 days. The pollen grains are viable for 3–4 days, and the
stigma remains receptive for a period of 5–10 days depending on environmental
conditions.

18.5 Cytogenetics

Castor is a diploid with 20 somatic chromosomes (2n ¼ 2x ¼ 20). However,

Richharia (1937) considered castor as secondary polyploid based on secondary
associations observed during metaphases. The chromosomes are small making
cytogenetic studies difficult. The mean chromosome sizes range from 1.19 to
2.12 μm, and the total length of diploid set is 32.15 μm on average (Vasconcelos
et al. 2010). Jakob (1956) studied the pachytene of meiosis and reported that the
macro chromomere pattern of the chromatic zone is apparently distinct in each of the
ten chromosome pairs. Each chromosome pair was morphologically distinguishable
by the regions, which stained deeply with acetic orcein. He designated the
chromosomes by capital letters on a temporary basis. Later, Jelenkovic and
Harrington (1973) provided a more accurate description of the pachytene comple-
ment. Each bivalent can be recognized by the presence of characteristic heterochro-
matic knobs. Paris et al. (1978) constructed idiogram for the ten pachytene bivalents
showing chromosome length, centromere position as well as lengths and positions of
heterochromatic regions and constrictions. There are five metacentric chromosomes,
four submetacentric chromosomes and one subterminal chromosome in the castor
complement. Chromosomes 2 and 7 contain nucleolar organizer regions (NOR).
Chromosome 3 contains proximal heterochromatic region. Chromosome 4 is the
second longest after chromosome 1. Chromosome 5 is metacentric. In chromosome
6, centromere is flanked by one large chromomere in the long arm. Chromosome 8 is
more or less similar with chromosome 4. Chromosomes 9 and 10 are the shortest.
Recently, molecular tools were used to study the chromosome structure and
organization. Vasconcelos et al. (2010) evaluated mitotic chromosomes using
950 S. Senthilvel et al.

standard staining, fluorochrome staining (CMA/DAPI), fluorescent in situ

hybridization (FISH) and silver impregnation. In contrast to pachytene, more sym-
metrical karyotype was observed in mitotic metaphases with all chromosomes
displaying metacentric morphology except for the submetacentric pair
D. Existence of at least 14 45S rDNA sites was noted. Molecular cytogenetic
analysis revealed knowledge on the repetitive elements in the genome. Alexandrov
and Karlov (2016) studied the chromosomal organization and structure of repeats in
mitotic and pachytene chromosomes using FISH, PCR analysis and bioinformatic
approaches.
Only a very few cytogenetic stocks are available. A naturally occurring haploid
plant was used to generate euploid series consisting of haploid, diploid and tetraploid
individuals (Timko et al. 1980). Artificial induction of polyploidy has been
attempted. Narain and Singh (1968) induced polyploidy by treating the apical
meristem of castor seedlings with colchicine and reported chromosomal
interchanges. Baghyalakshmi et al. (2020) generated tetraploid castor plants by
treating the seeds with colchicine. In the tetraploid plants, the pairing of
chromosomes was abnormal with univalent to octavalent configurations during
meiosis I, but the later parts of meiosis were normal. Variable levels of pollen
fertility were noticed in tetraploid plants depending on the season. The tetraploid
plants were phenotypically comparable with their diploid counterparts but produced
substantially bigger seeds.

18.6 Genetic Studies

18.6.1 Stem Colour

The basic stem colour is green. During the development of plants, the presence and
intensity of anthocyanin pigments turn the stem colour into different shades of red
such as green with reddish-bluish tinge, carmine or rose red, mahogany red, etc. The
intensity of anthocyanin pigmentation varies with sunshine, presence and intensity
of bloom and age of the plant. Earlier genetic studies indicated predominantly
monogenic inheritance for stem colour and dominance or incomplete dominance
of coloured stem over green stem (Solanki and Joshi 2001; Lavanya and Gopinath
2008). A purple morphotype collected in wild showing maternal inheritance has
been reported (Anjani et al. 2007). A spontaneous mutant with yellow stem colour
was identified by Prabakaran and Balakishan (2012).

18.6.2 Waxy Coating

Castor plants differ for the presence of waxy coating, popularly called ‘bloom’ on
different parts of the plants. It serves as a natural protection against extremes of
weather and infestation of insect-pests. Cold injury, thrips and leafhopper incidence
are higher in plants without bloom than in plants with bloom, while it is vice versa
18 Castor Breeding 951

for whiteflies. Plants are classified into four categories (zero bloom, single bloom,
double bloom and triple bloom) based on the presence and distribution of bloom.
‘Zero bloom’ type is devoid of visible waxy coating in all parts of the plant. In
‘single bloom’ type, waxy coating is found in all plant parts (stem, petiole and
inflorescence) except on leaves. In ‘double bloom’ type, waxy coating is found in all
plant parts (stem, petiole, inflorescence, lower surface of the leaf) except on the
upper surface of leaves, whereas ‘triple bloom’ types carry waxy coating in all parts
of plants including the upper surface of leaves. However, there is a wide variation for
the intensity of bloom on different plant parts and among different lines.
The presence of bloom inherits as dominant or partially dominant over the
absence of bloom (Kulkarni and Ramanamurthy 1977; Lavanya and Gopinath
2008). Single bloom was monogenic and dominant over zero bloom while double
bloom had a dominant digenic complementary action of 9 double: 3 single: 4 zero
bloom in a cross between double bloom and zero bloom (Peat 1926). Double bloom
was controlled by two complementary genes B and C, where B alone expresses
single bloom, while C can express double bloom only in the presence of B. The
variation in the intensity of bloom was also controlled by another dominant gene
D. Triple bloom was always dominant to other bloom variations (Narain 1961).
The intensity of bloom within the plants varies with the age of the leaves: mild in
the youngest to traces in matured, senescing leaves but highest in the physiologically
active leaves. In triple or double bloom types, the presence of bloom on the upper or
lower side of the leaf is mostly confined to the latest emerged leaf indicating the role
of penetrance and expressivity of the genes controlling the bloom character or the
role of multiple alleles.

18.6.3 Plant Height

The height of the main stem varies depending on soil type and availability of
moisture. It generally ranges from 45 to 240 cm. However, perennial plants reach
up to 12 m. The inheritance studies on plant height in a cross indicated the
involvement of three non-allelic recessive genes causing dwarfness.

18.6.4 Nature of Spike

Based on the density of capsules, spikes are classified as loose, compact and semi-
compact types. Compactness of spikes influences the pest and disease development.
Compact and semi-compact spikes are highly susceptible to mould and capsule
borer. Compact spikes appear to be completely or incompletely dominant over
loose spike (Solanki and Joshi 2001; Lavanya and Gopinath 2008).
952 S. Senthilvel et al.

18.6.5 Capsule Characteristics

Capsules with purple, mahogany, sulphur white and green colours have been
recorded in germplasm collection. The green colour of capsule was controlled by a
single dominant gene (Patwardhan 1931).

18.6.6 Wilt Resistance

Majority of the published reports indicate that Fusarium wilt resistance in castor
inherits as either single or two genes, and two gene situations are predominant. Both
dominant and recessive expressions were observed. Shaw et al. (2018) noted differ-
ent modes of inheritance when different susceptible parents were crossed with the
same resistant source. Two susceptible parents, namely, JI-35 and JC-12, were
crossed with the common resistant parent (48–1). In both the crosses, the F1 showed
susceptible reaction, but the F2 population showed different modes of inheritance,
namely, monogenic [3 (susceptible), 1 (resistant)] in the cross JI35  48–1 and
digenic with complementary gene interaction [9 (susceptible), 7 (resistant)] in the
cross JC12  48–1.

18.6.7 Sex Expression

Three types of femaleness have been recorded and designated as N, S and NES. The
N type carries a recessive sex-switching gene (Katayama 1948). The homozygous
genotype will produce female plants, whereas the plants are monoecious under
heterozygous condition. The pistillate system is maintained by sib-mating. The
hybrid seed production using this system is tedious because the progeny of seeds
produced from female plants segregates for female and monoecious plants in 1:1
ratio and the monoecious plants are to be removed before anthesis. Nevertheless,
several commercial hybrids have been developed especially in the USA using
N-type pistillate lines.
The S type is governed by the mechanisms of sex reversal and expression of
interspersed staminate flowers (ISF). The ‘sex reversals’ are plant variants, which
start out as female and then revert to monoecism (Shifriss 1956). This reversion may
occur at any time after the first inflorescence. Such pistillate lines are developed and
maintained by selection of females of late-reverted type in every generation. Another
group of non-reverted females carries sensitive interspersed gene at a high fre-
quency. The penetrance and expressivity of interspersed female state are determined
by the environment. VP-1, the widely used pistillate line in Indian breeding
programmes, carries both the systems of sex reversals and environmentally sensitive
gene for the expression of staminate flowers.
An NES-type pistillate line CNES-1 was derived by backcrossing an N-type
pistillate line (N145–4) to a variety ‘Cimarron’ and selecting for ISF (Zimmerman
and Smith 1966). This line is homozygous for N pistillate gene and contains
18 Castor Breeding 953

environmentally sensitive gene for ISF. The NES is advantageous over S type due to
the single recessive gene for femaleness, whereas the S pistillate genes behave like
polygenic complex with both dominance and epistasis.

18.7 Breeding Objectives

The breeding efforts in castor have transformed the tall, highly monoecious,
shattering, wild type into a medium tall, high-yielding, non-shattering commercially
viable crop. Systematic breeding efforts in castor date back to 1800 AD. Extensive
breeding activities were undertaken predominantly by the USA and erstwhile USSR.
In India, crop improvement research was initiated during the 1930s as selections
from populations with an emphasis on seed yield and branching habit. After that,
non-shattering character and oil content were given importance during the 1950s.
Later, development of cultivars with high seed yield and wilt resistance was the
focus.
At present, important breeding objectives include development of short duration
genotypes with plant type suitable for high-density planting and mechanical
harvesting and development of cultivars resistant to biotic stresses (mould, capsule
borer, leafhopper, thrips and whitefly). Among the abiotic stresses, drought tolerance
assumes significance as the crop is cultivated under rainfed situations or with limited
irrigation. In addition, attempts are being made to remove or reduce the ricin content
in castor seeds.

18.8 Breeding Approaches

Castor is a unique crop in breeding perspective. The plant is largely monoecious with
some exceptions. Both self- and cross-pollinations occur under natural conditions.
The considerable level of heterosis is observed without any marked inbreeding
depression. Heterosis has been commercially exploited in castor as early as 1960.
However, there is no CMS system reported so far in castor. Hybrid development
relies on the use of lines producing predominantly female flowers as female and the
normal monoecious lines as male parents.
All the breeding methods suitable for self- and cross-pollinated crops are amena-
ble for use in castor. During 1900, pure line selection was attempted to develop high
oil lines in the USA. Mass selection is used mainly for selection of female plants,
long primary spike and reduced plant height. Due to minimum inbreeding depres-
sion on selfing, inbreeding was used to develop and maintain varieties and parental
lines.
Hybridization followed by selection is the most widely followed method. Fol-
lowing hybridization, the pedigree selection is used to select simultaneously several
heritable and morphological traits. The possibility of recombinants is usually high,
when parents are genetically diverse. A large (>1000 individuals) F2 population is
desired because the generation of diversity is limited to the initial population size.
954 S. Senthilvel et al.

Bulk method of selection is more successful for selecting segregating generations

under abiotic and biotic stress conditions.
Recurrent selection has been successfully used for altering the plant stature for
mechanical harvest (Auld et al. 2009). To combine high seed yield and oil content,
both non-additive and additive gene actions are to be exploited simultaneously. To
achieve such a goal, parental mating and recurrent selection approach may be
followed. Chen et al. (2016) found that recurrent selection was an effective method
to improve oil content in castor. They could raise the mean oil content of a variety,
Impala, from 50.3 to 54.5% by two cycles of selection. The oil content in the base
population ranged from 40.1 to 57.5% with an average of 50.3%.
Mutation breeding was successful in castor in inducing variability for morpho-
logical characters, sex expression and resistance to Fusarium wilt. Even though both
physical and chemical mutagens have been used, physical mutations were found
more successful. Irradiation of HC-6 with thermal neutron treatment led to the
isolation of a short duration mutant, NPH-1, which was later released as Aruna
variety. Gamma ray irradiation of VP-1, a wilt-susceptible stable S-type pistillate
line led to several wilt-resistant pistillate lines like M-574 and M-619 (Lavanya et al.
2003).
To generate novel variability, distant hybridization is a potential approach. Since
castor belongs to a monotypic genus, interspecific hybridization is not feasible.
Therefore, intergeneric hybridizations were attempted by crossing castor with its
close relatives such as cassava (Manihot esculenta Crantz) and jatropha (Jatropha
curcas L.). Laosatit et al. (2017) performed intergeneric hybridization between
jatropha and castor in both directions. The pollen tube grew normally and reached
the style base within an hour after pollination, but the embryo aborted a few days
later indicating post-fertilization barriers. They cultured the excised ovules in vitro
and obtained one intergeneric hybrid plant. Similarly, Premjet et al. (2019) generated
intergeneric hybrid between jatropha and castor through embryo rescue and doubled
the chromosome number of the hybrid using colchicine to improve fertility.
Modern scientific tools are being harnessed for addressing the formidable issues
in castor breeding. As there are no resistant sources available in the germplasm for
lepidopteron pests, incorporating resistance through transgenic approaches were
attempted. Transgenic events carrying Bacillus thuringiensis (Bt) cry1Aa gene
showing resistance to castor semilooper and Spodoptera have been developed and
characterized at ICAR-IIOR. Transformation of decotyledonated embryo axes
through Agrobacterium tumefaciens, particle gun bombardment and in planta
methods resulted in transformation frequencies of 2.4%, 1.1% and 2.1%, respec-
tively. Eight events showing Mendelian segregation were advanced. The laboratory
insect bioassays showed up to 80% of larval mortality and up to 87% of weight loss
among Spodoptera litura and Achaea janata larvae. In field bioassays, the event
AMT-894 was the most promising with 43% of plants showing less than 25% leaf
damage (Muddanuru et al. 2019).
The desirable level of resistance for mould is not found in germplasm. Therefore,
transgenic approach is being followed to impart resistance to mould in castor using
multiple genes imparting resistance to fungal pathogens. Two polygene cassettes
18 Castor Breeding 955

were developed using genes that impart partial resistance to Botrytis cinerea in
Arabidopsis thaliana. In the first construct, three genes ERF1 (ethylene response
factor 1), BIK1 (botrytis-induced kinase 1) and AtEBP (Arabidopsis thaliana
ethylene-responsive element binding protein), involved in signal transduction during
plant-pathogen interaction of necrotrophic fungi, were used. These genes were
cloned under three independent promoters with known inflorescence-elevated
expression pattern, and the resultant cassettes were cloned in tandem within a single
T-DNA of the binary vector so that the transgenic plants realized with this vector will
express all the three gene cassettes independently. In the second polygene construct,
three genes RsAFP2 (Raphanus sativus – antifungal protein 2), chitinase and
AceAMP1 (Allium cepa – antimicrobial peptide 1) were cloned under the same
promoter (35S, a constitutive promoter) and are separated by 2A signal peptide
sequence so that three genes are expressed as a single polycistron and subsequently
as a self-cleaving polyprotein (Prasad et al. 2016).
Efforts to breed for low ricin types have met with limited success. Varieties with
70–75% lesser ricin content have been developed, but they are still very toxic to
mammals. As per genome sequence data, there are several putative genes in the ricin
family, including potential pseudogenes or gene fragments, forming clusters. There-
fore, generating detoxified genotypes using classical mutation techniques is not
feasible. Sousa et al. (2017) explored the RNA interference (RNAi) concept to
silence the ricin gene in castor seeds. RNAi is a post-transcriptional gene silencing
mechanism that regulates the expression of protein-coding genes. Constructs to
express self-complementary RNA transcripts form a dsRNA, which is processed
into small interfering RNAs (siRNAs). These siRNAs trigger a sequence-specific
mRNA degradation, leading to gene silencing. Using this technique, a bio-detoxified
line TB14S-5D has been developed, which is free from ricin (Sousa et al. 2017).

18.9 Precise and High-Throughput Phenotyping Protocols

for Key Traits

18.9.1 Screening for Fusarium Wilt Resistance

Wilt caused by the fungus Fusarium oxysporum f. sp. ricini is the most important
soil-borne disease of castor. It occurs in all castor-growing areas across seasons.
Historically, screening for wilt resistance is done based on disease incidence in wilt
sick plots under field conditions, which had been very effective but with limitations
in terms of the number of lines that can be screened. Shaw et al. (2016) described a
high-throughput screening method for large-scale phenotyping of castor genotypes
for resistance to Fusarium wilt disease. As per this method, the screening is done in
plastic pots (30  15  13 cm) filled with 4 kg of sterilized potting mixture (red soil,
black soil and farmyard manure in the proportion of 5:3:1). The pathogen is mass-
multiplied on sorghum (Sorghum bicolor) grains as substrate. Semi-cooked sorghum
grains (100 g in 250 ml of conical flask) are sterilized by autoclaving at 15 psi for
20 min at 121  C. The flasks are inoculated by actively growing fungal mycelial
956 S. Senthilvel et al.

culture grown on PDA and incubated at 28  2  C for 15 days. The flasks are hand
shaken daily to ensure complete fungal colonization on the sorghum grains. The
15-day-old fungal culture is added to the potting mixture at the rate of 3 g/kg and
thoroughly mixed. The pots are watered and kept for incubation for 24 h before
sowing. Control pots are maintained with only sterile soil. The test lines are sown
along with standard resistant (48–1) and susceptible (JI-35) checks. The plants are
observed for disease reaction up to 75 days after sowing. Genotypes are categorized
on the basis of ‘days to wilt’. For each genotype, the days to wilt is recorded when
80% of the plants died. The genotypes are scored on a 1 (susceptible) to 4 (highly
resistant) scale based on ‘days to wilt’: susceptible (<30 days), moderate (31–50
days), resistant (51–65 days) highly resistant (>65 days).

18.9.2 Screening for Resistance to Gray Mold Disease

Gray mold in castor is caused by the fungus Botryotinia ricini (Godfrey) Whetzel.
Screening for mould disease is tricky because it is highly weather dependent and
affects only the developing inflorescence. Several methods of screening under field
and glasshouse conditions such as detached spike technique, detached capsule
technique, field fogging technique and poly-house screening have been tried (Prasad
et al. 2016). The detached spike technique involves spraying the spore suspension of
pathogen (106 conidia/ml) on 15–20-day-old spikes cut from the plants and kept in
conical flask containing 2% sucrose solution. The flasks with spikes are kept in
glasshouse, where a humidity of 80%, temperature of 25–27  C and continuous
capsule wetness through fogging are maintained. Initial symptoms of mould infec-
tion appear 5 days after inoculation. At the seventh day, the disease severity is scored
based on percent capsule damage. In the case of detached capsule technique, 15–20-
day-old capsules are detached from the spike of castor plants, and surface sterilized
and dipped in spore suspension of pathogen (106 conidia/ml). Inoculated capsules
are kept in growth chamber at 20  C and 90% humidity. Wetness on capsules is
maintained by spraying water at 8 h of interval. Symptoms will appear on capsules at
3–4 DAI. By the sixth day, capsules are fully covered with mycelium. The disease
severity is scored at 6 DAI.

18.9.3 Screening for Root Rot Disease

Root rot disease is caused by the fungus Macrophomina phaseolina. Screening

against root rot is done using sick plot under field conditions and stem tape inocula-
tion technique under greenhouse conditions. Screening of genotypes are done in the
permanent root rot sick plot along with susceptible (GCH-4) and resistant (JI-357)
checks planted after every five test entries. The pathogen isolated from naturally
infected castor plants and grown on sorghum sand medium for 14 days is applied in
furrows at the time of sowing. Root rot incidence at 120, 150 and 180 days after
sowing is recorded. In the case of ‘stem tape inoculation’, plants are maintained in
18 Castor Breeding 957

pots containing sterilized soil under greenhouse conditions for 20 days. The hypo-
cotyl region of the test plants are superficially wounded by peeling the epidermis at
2–3 cm above the soil surface. An agar disc (4 mm in diameter) containing mycelium
with abundant sclerotia replaced on the wound and covered with cellophane tape. In
control, plants are inoculated with a sterile PDA disc. The inoculated plants are
observed for root rot symptoms up to 20 days after inoculation (DAI). The percent-
age of dead plants and length of lesion on stems are recorded.

18.9.4 Screening for Resistance to Leafhopper

The leafhopper (Empoasca flavescens F.) is one of the major pests of castor across
growing seasons. The screening for resistance to leafhopper is done under field
conditions as culturing the insect in laboratory for artificial screening is not feasible.
The susceptible plants of DPC-9 are grown 15 days before sowing of test entries in
order to build up the leafhopper population naturally. The test entries are sown
during the second fortnight of October along with susceptible check (DPC-9) placed
after every two rows of test entries. DPC-9 plants (70- to 75-day-old) from the
infester block are cut at the base, removed and distributed in the screening plot
uniformly near the base of the test plants at the rate of one infester plant per metre.
The test entries were scored for the extent of hopper burn and number of nymph and
adults when the susceptible check is completely dried up. Leafhopper counts
(nymph) will be recorded on three leaves in each plant selecting one leaf from top
(excluding two topmost leaves), middle (medium maturity) and bottom (leaving one
or two bottom-most leaves) on the main shoot. Population will be reported as the
number of leafhoppers/three leaves per plant. The hopper burn is scored on a 0–4
scale based on leaf area burnt per plant (average of five plants): 0, no injury; 1, hopper
burn up to 10%; 2, hopper burn 11 to 25%; 3, hopper burn 26 to 50%; and 4, hopper
burn above 50%.

18.10 Emerging Challenges at the National

and International Level

The use of pistillate mechanism in hybrid development has been successful since the
1970s. However, maintaining genetic purity in hybrid seed lot in commercial
production is becoming a challenge. Variations in weather parameters induce devel-
opment of male flowers in pistillate line leading to a considerable proportion of
selfed seeds of female plant in the hybrid seed lot. A clean genetic or cytoplasmic
genic male sterility (GMS) system is essential to overcome the issues related to the
stability of pistillate lines. There were a few isolated attempts to identify sources of
male sterility through interspecific crosses and induced mutations, but no male
sterility system yet available in castor for use in hybrid seed production.
Cultivation of castor is labour intensive. Labour scarcity is a major issue faced by
the castor farmers. The nature and growth of castor make it unsuitable for
958 S. Senthilvel et al.

mechanization. There is an immediate need to restructure the plant so that the

harvesting can be done through machines.

18.11 Breeding Progress/Varietal Development

18.11.1 Conventional Breeding

Systematic breeding efforts in castor started during the 1920s in the USA and
erstwhile the USSR. The major breakthrough is the identification of dwarf-internode
mutants followed by identification of pistillate-type plants facilitating hybrid breed-
ing (Claassen and Hoffman 1950). Castor was the first oilseed crop in which
variability for duration, plant height and oil content were induced using ionizing
radiations, viz., X-rays, gamma rays and chemical mutagens.
In India, organized breeding work was initiated under the All India Coordinated
Research Project (AICRP) on castor during the 1960s. AICRP breeding programme
was highly successful in increasing the seed yield, reducing duration and plant
height and improving the sex expression. Heterosis has been well exploited in castor.
With the introduction and development of pistillate lines, hybrid development took a
momentum. The first castor hybrid in the world, GCH-3, with high-yielding ability
(88% yield increase over the variety S-20), drought resistance, medium maturity
(140–210 days) and high oil content (46.6%) was released during 1976. Since then,
several hybrids suitable for specific locations have been developed by IIOR and
AICRP centres. The introduction of hybrids resulted in a spectacular rise in produc-
tion and productivity. The productivity at the national level has increased from
270 kg/ha during the 1970s to 1900 kg/ha at present.
Major threat to castor cultivation was the wilt disease. The release of GCH-7, a
high-yielding (3000 kg/ha) hybrid, resistant to wilt-nematode complex, leafhopper
and root rot, made a dramatic impact in irrigated castor-growing regions of Gujarat
and Rajasthan during the last decade. Extensive cultivation of GCH-7 in Gujarat
state led to the decrease of wilt incidence from about 50% to 10%.
Castor oil is being considered as a potential source for biodiesel production.
However, the high viscosity due to methyl ester of ricinoleic acid is a hindrance for
biodiesel production. A line with more than 78% of oleic acid content has been
identified (Rojas-Barros et al. 2004), which can be used for developing cultivars
suitable as biodiesel feedstock.

18.11.2 Genomics-Assisted Breeding

In contrast to the major food crops, the genomic resources are lacking in castor. As a
consequence, progress in molecular breeding is very limited. Even though a draft
genome assembly in the form of 25,828 scaffolds accounting 92.8% of the genome
was published way back in 2010 (Chan et al. 2010), no further efforts were made to
improve the assembly further. A skeletal linkage map with 331 markers, mostly SSR
18 Castor Breeding 959

was constructed (Liu et al. 2016). So far, QTLs linked to plant height (Chen et al.
2014), Fusarium wilt (Tomar et al. 2016), root rot (Tomar et al. 2017) and seed size
and weight (Yu et al. 2019) have been mapped. Very recently, genome data were
generated by ‘whole genome sequencing’ of 14 diverse castor genotypes with an
average of 34X coverage through next-generation sequencing (NGS) technologies.
Further sequence analyses resulted in detection of a total of 2,179,759 putative
SNPs; of which, 6000 high-quality SNPs were used to design a genotyping array
(Infinium BeadChips). Using this genotypic array, a consensus linkage map
consisting of 1978 SNP loci was constructed with an average inter-marker distance
of 0.55 cM using two recombinant inbred line (RIL) populations produced from the
crosses: JC12  48–1 and DCS9  RG1139 (Senthilvel et al. 2019). The SNP array
provides a valuable tool for high-throughput and cost-effective genotyping and
mapping applications in castor. The genotyping array will provide the required
resolution for discovery of marker-trait association through linkage and association
analysis, evaluation of genetic variations, unravelling the genetic architecture of key
quantitative traits and exercising genomic selection in castor.

18.12 Status of Varietal Development

In India, the release of cultivars is governed by two entities, namely, Central Varietal
Release Committee (CVRC) and State Variety Release Committee (SVRC) under
Seed Act 1966. The CVRC and SVRC notify the varieties/hybrids of agricultural
crops recommended by research systems of ICAR. After notification, the commer-
cial seed production of varieties and hybrids is allowed for popularization among the
farmers for cultivation.
About 26 varieties with long duration (240–270 days) and tall plant type like HC
1 to HC 8, EB 16 A, S-20, Junagadh 1, Punjab castor 1, EB 31, Rosy, MC-1, etc.
were developed by hybridization and selection method prior to inception of AICRP
(Kulkarni and Ramanamurthy 1977). Under AICRP, 18 varieties and 20 hybrids
have been developed till 2020. The state-wise varieties and hybrids notified under
seed act from 1976 to 2020 are given in Table 18.2.

18.13 Maintenance Breeding

Due to cross-pollinating nature, complexity of sex and high sensitivity to genotype-

environment interaction, degeneration of genetic stocks happens very often. If seed
multiplication is done without required selection pressure, the parental lines degen-
erate very quickly. Since pollination occurs mostly by wind, genetic purity should be
maintained by maintaining an isolation distance of at least 1000 m from other castor
plants.
The initial source of seed for nucleus seed multiplication of male parental line
should be from 50 to 100 selected and selfed progenies of preceding crop season.
Selfed seeds of 200–300 selected plants are to be planted in progeny rows with at
Table 18.2 Varieties and hybrids of castor notified for cultivation in India
960

Year of Oil
release/ Recommended areas/ content
Name notification Developer situations Seed yield (kg/ha) (%) Salient features
Varieties
GAUC-1 1976 Oilseeds Research Station, Irrigated and rainfed areas 1200 (Rainfed), 1500 46–47 –
Junagadh, under Gujarat in Gujarat (irrigated)
agricultural university,
Gujarat
TMV-5 1985 Oilseeds Research Station, Rainfed areas of Tamil 920 47–49 Resistant to leafhopper
Tindivanam under Tamil Nadu
Nadu agricultural
university, Tamil Nadu
GC- 1993 Castor and Mustard Irrigated areas of Gujarat 2165 47–49 Resistant to fusarium wilt
2 (SKI-273) Research Station under
S. K. Nagar,
Sardarkrushinagar
Dantiwada agricultural
university, Gujarat
Jyoti 1994 ICAR-Indian Institute of Rainfed areas of Andhra 1030 48 Resistant to fusarium wilt,
(REC-9/ oilseeds research, Pradesh, Telangana, early maturity
DCS-9) Hyderabad, Telangana Tamil Nadu and
Karnataka
Kranthi 1996 Regional agricultural Rainfed areas of Andhra 1365 48–50 Drought tolerant
(PCS-4) Research Station, Palem, Pradesh and Telangana
under prof. Jayashankar
Telangana state agricultural
university, Telangana
TMV-6 1997 Oilseeds Research Station, Rainfed areas of Tamil 930 52 Resistant to wilt,
Tindivanam under Tamil Nadu moderately resistant to
Nadu agricultural Alternaria leaf spot and
S. Senthilvel et al.

university, Tamil Nadu rust

 18

AKC-1 1998 Dr. Panjabrao Deshmukh Rainfed areas of Vidarbha 1200 45 Easy threshability
Krishi Vidyapeeth, Akola, region of Maharashtra
Maharashtra
Kiran 2002 Regional agricultural Rainfed and late-sown 1200–1500 48–51 Moderately tolerant to gray
(PCS-136) Research Station, Palem, conditions of Andhra mold and drought; suitable
under prof. Jayashankar Pradesh and Telangana for rice fallows
Castor Breeding

Telangana state agricultural

university, Telangana
Haritha 2002 Regional agricultural Light soils of southern 1400–1600 48–51 Resistant to fusarium wilt
(PCS-124) Research Station, Palem, Telangana, Rayalaseema
under prof. Jayashankar and Prakasam districts of
Telangana state agricultural Andhra Pradesh
university, Telangana
Jwala (48–1) 2007 ICAR-Indian Institute of All castor-growing 1100 (rainfed), 2000 48 Tolerant to gray mold,
oilseeds research, regions of India (irrigated) saline and drought
Hyderabad, Telangana conditions
MCI- 2008 Agricultural Research Irrigated areas of 3327 47.9 Resistant to fusarium wilt
8 (RCV-1) Station, Jodhpur, under Rajasthan and root rot
Mandore agriculture
university, Rajasthan
DCS-107 2011 ICAR-Indian Institute of All castor-growing 1200–1430 (rainfed), 45–47 Resistant to fusarium wilt
oilseeds research, regions of India 2140–2510 (irrigated)
Hyderabad, Telangana
GC-3 2012 Main oilseeds Research Irrigated areas of Gujarat 2310 49.7 Resistant to fusarium wilt
(JI-273) Station, Junagadh under and root rot
Junagadh agricultural
university, Gujarat
Pragathi 2016 Regional agricultural Rainfed areas of 1500–1800 47–49 Resistant to fusarium wilt
Research Station, Palem, Telangana
under prof. Jayashankar
Telangana state agricultural
961

university, Telangana
(continued)
Table 18.2 (continued)
962

Year of Oil
release/ Recommended areas/ content
Name notification Developer situations Seed yield (kg/ha) (%) Salient features
Jawahar 2018 Zonal agricultural Research Irrigated areas of Madhya 2640 46–47 Resistant to fusarium wilt
Castor-4 Station, Chhindwara under Pradesh and root rot
(JC-4) Jawaharlal Nehru Krishi
VishwaVidyalaya,
Jabalpur, Madhya Pradesh
Jawahar 2018 Zonal agricultural Research Sole crop-irrigated and 2745 45–46 Resistant to fusarium wilt
Castor-24 Station, Chhindwara under intercropping-rainfed and root rot
(JC-24) Jawaharlal Nehru Krishi conditions
VishwaVidyalaya,
Jabalpur, Madhya Pradesh
YTP-1 2019 Tapioca and Castor Rainfed and irrigated 1450 (annual), 3110 49 Non-lodging,
Research Station, Yethapur perennial ecosystem (perennial) non-shattering, perennial
under Tamil Nadu
agricultural university,
Tamil Nadu
GAC-11 2019 Regional Research Station, Irrigated and rainfed areas 2360 (rainfed), 3230 48
Anand and Agricultural in middle Gujarat (irrigated)
Research Station, Sansoli,
under Anand Agricultural
university, Gujarat
Hybrids
GAUCH-1 1973 Oilseeds Research Station, Irrigated and rainfed areas 1520 46–47 –
(VHB-44) Junagadh, under Gujarat of Gujarat
agricultural university,
Gujarat
S. Senthilvel et al.
 18

GCH-2 1984 Oilseeds Research Station, Irrigated and rainfed areas 1750 47–49 Resistant to root rot
Junagadh, under Gujarat of Gujarat
agricultural university,
Gujarat
GCH-4 1986 Main Castor and Mustard All castor-growing 1985 48–50 Resistant to leafhoppers
(SHB-18) Research Station, regions of India
Castor Breeding

S.K. Nagar, under Gujarat

agricultural university,
Gujarat
GCH-5 1995 Main Castor and Mustard All castor-growing 2800 50 Resistant to wilt and
(SHB-145) Research Station, regions of India tolerant to root rot, jassids,
S.K. Nagar, under Gujarat whitefly, capsule borer and
agricultural university, water stress
Gujarat
GCH-6 1997 Oilseeds Research Station, All castor-growing 1300 (rainfed), 2300 48 Tolerant to fusarium wilt,
(JHB-665) Junagadh, under Gujarat regions of India (irrigated) resistant to Macrophomina
agricultural university, root rot
Gujarat
Deepti 1998 ICAR-Indian Institute of All castor-growing 1030 (rainfed), 2460 48 Resistant to leafhopper,
(DCH-32) oilseeds research, regions of India (irrigated) suitable for early sown
Hyderabad, Telangana conditions
TMVCH-1 1998 Oilseeds Research Station, Rainfed areas of Tamil 1180 47–49 Resistant to leafhoppers
Tindivanam under Tamil Nadu and moderately resistant to
Nadu agricultural gray mold
university, Tamil Nadu
Deepak 1999 ICAR-Indian Institute of Rainfed areas of 1550 (rainfed), 2130 49 Resistant to fusarium wilt
(DCH-177) oilseeds research, Telangana, Andhra (irrigated) and whitefly, resistant to
Hyderabad, Telangana Pradesh, Tamil Nadu and lodging, non-shattering,
Karnataka and irrigated moderately tolerant to
areas of Maharashtra botrytis gray mold
963

(continued)
Table 18.2 (continued)
964

Year of Oil
release/ Recommended areas/ content
Name notification Developer situations Seed yield (kg/ha) (%) Salient features
RCH-1 2000 Agricultural Research Irrigated areas of 3000–3200 49 Resistant to leafhopper
(RHC-1) Station, Mandore under Rajasthan
Rajasthan agricultural
university, Rajasthan
DCH-519 2006 ICAR-Indian Institute of All castor-growing 1740 (rainfed), 2130 46–51 Resistant to fusarium wilt,
oilseeds research, regions of India (irrigated) leafhopper
Hyderabad, Telangana
GCH-7 2007 Main Castor and Mustard Irrigated and rainfed areas 3000 48–49 Resistant to nematode-wilt
Research Station, S. K. of Gujarat complex
Nagar under
Sardarkrushinagar
Dantiwada agricultural
university, Gujarat
YRCH-1 2010 Tapioca and Castor Rainfed and irrigated 780 49 Moderately resistant to
Research Station under areas of Tamil Nadu capsule borer
Yethapur, Tamil Nadu
agricultural university,
Tamil Nadu
PCH-111 2012 Regional agricultural Rainfed areas of Andhra 1400–1500 (rainfed), 49 Resistant to fusarium wilt
Research Station, Palem Pradesh and Telangana 2200–2500 (irrigated) and moderately tolerant to
under prof. Jayashankar sucking pests, semilooper
Telangana state agricultural and Spodoptera
university, Telangana
PCH-222 2012 Regional agricultural Rainfed and irrigated 1600–1800 47–48 Resistant to fusarium wilt
Research Station, Palem areas of Andhra Pradesh (rainfed), 3500–2800
under prof. Jayashankar and Telangana (irrigated)
Telangana state agricultural
S. Senthilvel et al.

university, Telangana
 18

HCH-6 2016 Zonal agricultural Research Central dry zone of 1830 50 Resistant to fusarium wilt
Station, Hiriyur under Karnataka and whitefly
University of Agricultural
and Horticultural Sciences,
Shivamogga, Karnataka
GNCH-1 2017 Oilseeds Research Station, Irrigated castor-growing 2500 47–48 Resistant to wilt and
Castor Breeding

Navsari under Navsari regions of Gujarat leafhopper

agricultural university,
Gujarat
YRCH-2 2018 Tapioca and Castor Rainfed and irrigated 2089 49 Resistant to wilt, tolerant to
Research Station, Yethapur areas of Tamil Nadu leafhopper
under Tamil Nadu
agricultural university,
Tamil Nadu
GCH- 2018 Main Castor and Mustard All castor-growing 1895 (rainfed), 3000 48–49 Resistant to wilt and root
8 (SHB-896) Research Station, S. K. regions of India (irrigated) rot
Nagar under
Sardarkrushinagar
Dantiwada agricultural
university, Gujarat
GCH-9 2019 Oilseeds Research Station, Irrigated areas in Gujarat 3820 48 Resistant to wilt and root
(JHB-1018) Junagadh under Junagadh rot
agricultural university,
Gujarat
ICH-66 2019 ICAR-Indian Institute of Rainfed areas of 1560 49 Resistant to wilt, root rot
oilseeds research, Telangana, Andhra and leafhopper
Hyderabad, Telangana Pradesh, Karnataka,
Tamil Nadu, Odisha and
Maharashtra
965
966 S. Senthilvel et al.

least 30 plants per progeny row, and 100–200 uniform looking progenies are to be
selected. In each selected progeny, five to ten representative plants which have same
node number and conform to all other morphological characteristics of the genotype
are to be labelled, and three to four spikes other than primary are to be selfed. At
maturity, spike length, number of productive capsules, yield, 100-seed weight and
oil content are measured in the open-pollinated primary spike. The progenies
exceeding the general mean by one standard deviation and showing least intra-
progeny variations are selected. About 50 seeds from each selected progenies are
used for further maintenance, and the remaining portion of seeds are bulked and used
as source for breeder seed production.
The pistillate lines need to be raised in ideal location and season so as to assess the
sex expression. The selfed seeds of individual plants obtained from 6th or later order
spikes of preceding crop season are to be sown in progeny row ensuring a minimum
of 30 plants per progeny. At the stage of primary spike initiation, about 50 plants
may be selected based on the uniformity for various morphological characters and
femaleness, and all other plants are to be removed. Within selected progeny, plants
confronting to the desired node number may be retained, and all other plants may be
removed. The environmentally sensitive interspersed staminate flower should serve
as pollen source. Care should be taken to observe all the plants regularly for
reversion to monoecious status. The plants showing monoecious spike before the
sixth order should be destroyed. The remaining plants are selfed to provide seed for
breeder seed production.

18.14 Coordinated System of Testing

In India, applied research on castor is undertaken by a network of research centres

spread across different agro-climatic regions of the country under All India Coordi-
nated Research Project (AICRP) administered by the Indian Council of Agricultural
Research (ICAR). The project started in 1967 with four centres, viz., Rajendranagar
(Andhra Pradesh), Vijapur (Gujarat), Raichur (Karnataka) and Salem (Tamil Nadu).
At present, AICRP on castor is being operated at nine centres, namely,
Ananthapuramu (Andhra Pradesh), Bawal (Haryana), Bengaluru (Karnataka),
Bhawanipatna (Odisha), Junagadh (Gujarat), Mandore (Rajasthan), Palem
(Telangana), Sardarkrushinagar (Gujarat) and Yehtapur (Tamil Nadu) under the
coordination of ICAR-IIOR. The new cultivars developed by different institutions
are being tested across these centres for 3 years to test their performance against the
existing cultivars as checks.

18.15 Future Thrust Area

The following are the major thrust areas of research on castor in the coming years:
18 Castor Breeding 967

• Bridging the knowledge gaps in the understanding of many issues related to

castor growth and development, which is essential for breeding of high-yielding
varieties adapted to each growing environment.
• The genome assembly is highly fragmented, which needs to be improved, and
chromosome-scale assembly is required for furthering the genomic research.
• Understanding the mechanism of resistance for sucking pests, capsule bore and
mould disease and identifying reliable resistant sources.
• Improving oil quality to increase wider adaptability and uses, viz., reduction of
ricin in castor.
• Development of cultivars suitable for high-density planting and mechanical
harvesting.
• Development of gray mold-resistant castor lines through genetic engineering and
marker-assisted breeding.

18.16 Conclusions

The present chapter summarizes the overall improvement of castor as a perennial,

wild-type plant to an annual, high-yielding plant with inbuilt resistance to wilt and
leafhopper. India still retains the number one position with the highest productivity
(1.97 t/ha) and is the major source of supply of castor oil to the USA, Europe, Japan,
China etc. with a net revenue worth of US$ 400 million in 2020. A high geno-
type  environment interaction in castor necessitates the development of several
locally adaptable and high seed/oil yielding genotypes with a major emphasis on
production conditions. Further enhancement of productivity levels up to 5–6 t/ha
under irrigated conditions needs to be explored with intensified efforts on genetic
enhancement of parental lines through biparental mating and recurrent selection
methods. While the traditional rainfed castor area needs early maturing, drought-
resistant castor hybrids with an emphasis on resistance to mould, capsule borer and
sucking pests. AICRP network needs to be strengthened with additional manpower
and facilities for full-proof evaluation and screening for major pests and diseases.

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Sunflower Breeding
19
H. P. Meena and M. Sujatha

Abstract

Sunflower (Helianthus annuus L.) is one of the important oilseed crops cultivated
worldwide for its oil and confectionary purposes. Among the crops where
heterosis has been successfully exploited, sunflower assumes importance as that
of maize. Identification of the PET-1 cytoplasm along with the complementary
fertility restoration system is a landmark achievement which paved the way for
transformation of an ornamental crop to a commercial oil yielding crop. Breeding
objectives are directed towards development of cultivars with high seed yield,
early maturity, resistance to diseases (downy mildew, powdery mildew, rust,
necrosis disease, Alternariaster leaf spot), insect pests (Helicoverpa, sucking
pests) and tolerance to herbicides, besides improved content and quality of seed
oil and protein. Genetic enhancement for widening the trait base exploited
traditional breeding methods, mutation breeding and interspecific gene transfer.
Interspecific hybridization was adopted as one of the key tools by various
research groups due to the existence of a rich repertoire of genes in the wild
Helianthus species, and several economically important traits such as cytoplas-
mic male sterility, resistance to biotic and abiotic stresses, herbicide tolerance and
seed quality traits were successfully introgressed. The past two decades witnessed
advancements in molecular marker technology and genomics which have been
successfully used in marker-assisted breeding for simple inherited traits, while
traits governed by quantitative trait loci still remain a challenge for the breeders.
Despite the availability of genes in wild Helianthus species, successful transfer to
cultivar germplasm is hampered by crossability between cultivated sunflower
(annual diploid) and Helianthus species varying in habit (diploid perennial) and

H. P. Meena · M. Sujatha (*)

ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, India
e-mail: mulpuri.sujata@icar.gov.in

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 971
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_19
972 H. P. Meena and M. Sujatha

ploidy (tetraploids, hexaploids) warranting the use of genetic engineering

approaches. This chapter presents a comprehensive account of the history, bot-
any, the extent of genetic diversity in cultivated and wild Helianthus species.
Strategies are adopted for development of inbreds and hybrids, seed production
methodology and progress with regard to exploitation of molecular marker and
genomic resources in marker-assisted breeding.

Keywords
Hybrids · Breeding techniques · Oil content · Breeding approaches · Genetic
engineering · Genomics

19.1 Introduction

Sunflower is an important annual edible oilseed crop of Asteraceae family grown

globally over an area of 27.36 m. ha with a production of 56 mt (FAOSTAT 2019)
and world average yield of 2048 kg/ha. Because of its wide adaptability to diverse
agro-climatic situation, it is grown in all the countries crossing climatic and geo-
graphical boundaries. Being photo-insensitive and day neutral, it can be grown
throughout the year, i.e. kharif, rabi and spring/summer, and it is an ideal crop for
contingency cropping plan. Being a short duration crop, it can fit into various inter-
and sequence cropping systems. Leading producing countries are Ukraine, Russia
and Argentina, while countries like Belarus, France, Hungary, Romania,
Kazakhstan, Turkey, Tanzania, China and India produce relatively smaller quantity.
The highest-yielding countries are Hungary (3025 kg/ha), China (2847 kg/ha),
Turkey (2794 kg/ha), Romania (2782 kg/ha), Ukraine (2560 kg/ha), Bulgaria
(2375 kg/ha), France (2149 kg/ha) and Argentina (2039 kg/ha) with an average
yield of >2.0 t/ha as against the lowest-yielding countries like India and Myanmar
with <1.0 t/ha. The crop has become one of the important oilseed crops in India with
an area of 2.4 lakh ha and a production of 2.6 mt of seed (2019–2020).
In India, sunflower is mostly grown in the Southern and Central Peninsula
comprising Karnataka, Andhra Pradesh, Telangana, Maharashtra and Tamil Nadu.
The highest (>50%) area of sunflower is covered by only a single state (Karnataka)
with productivity of 785 kg/ha. It has spread to non-traditional states like Punjab,
Haryana and Uttar Pradesh as an important oilseed crop and is grown in West
Bengal, Bihar and Odisha as well. The productivity (891 kg/ha) of sunflower in
India at present is far lower than the world average (2048 kg/ha). Despite high
productivity in Punjab (1950 kg/ha), Gujarat (1820 kg/ha), Haryana (1743 kg/ha)
and Telangana (1698 kg/ha), area under sunflower has declined drastically due to
unavailability of better hybrids that can give more than 3.0 t/ha seed yield, price
fluctuations, shift in cropping pattern, profitability of other crops compared to
sunflower, withdrawal of private players from sunflower research, bird damage
and vulnerability to several biotic and abiotic stresses during various stages of
crop growth.
19 Sunflower Breeding 973

19.2 Economic Importance

In pre-historic times, the North American Indians for the first time found that the
seeds of wild sunflowers were a rich source of food and domesticated the plant.
Different colour dyes like purple, black and yellow extracted from ray florets of wild
sunflowers were used to dye basketry materials. The Hopi Indians obtained a purple
dye from deep purple achenes (Heiser Jr 1976) to decorate their bodies. In the
southwest, people used it as an antidote to snake bites and to cure rattlesnake bites
by chewing the fresh or dried root followed by sucking the snake bite wound
(Camazine and Bye 1980). The Europeans also used oil as a remedy for heart
diseases, pulmonary infections, cold and whooping coughs (Heiser Jr 1976). It
was cultivated as an ornamental or garden plant, where the blooms were cherished
for their beauty and the seeds were eaten by both humans and wildlife. The oil is
used for human consumption, salad oil, making paints, soaps, as biofuel and candles.
Sunflower oil has potential applications in the cosmetic industry (Oliveira et al.
2019). Sunflower meal is an excellent source of protein for human consumption and
as a supplementary diet which enhances the animal growth and milk production.
Sunflower cake is used in South Africa and Tanzania as the main component of
livestock feeds. Some species of sunflowers are grown for fodder or silage.

19.3 Origin and History

The genus Helianthus is derived from the Greek word helios meaning sun and
anthos meaning flower and belongs to the subdivision Tubiflorae and tribe
Heliantheae. It is a member of the Asteraceae (Compositae) family and has a typical
composite flower. The cultivated sunflower originated in North America from a
diploid (2n ¼ 34) annual wild H. annuus species (Smith 2014). Sunflower is native
to North America, but commercialization of the plant took place in Russia. The
American Indians were the first to domesticate the multi-headed ornamental plant
into a single-headed plant with a variety of seed colours.
The beginning of domestication and the first steps of sunflower breeding date
back to the time when it was cultivated by native Americans over 4000 years ago
(Seiler et al. 2017). It was used in food, to obtain oil, for medical purposes, and as an
ornamental plant. From its wild weedy forms, the crop has spread to Europe during
the sixteenth century and later to former USSR wherein the crop was domesticated.
Sunflower as a cultivated plant was reintroduced to North America from Europe in
the late nineteenth century. After the Second World War, the introduction of Russian
varieties into Europe and America had a decisive impact on the development of
sunflower as a commercial oilseed crop. Sunflower oil on commercial scale was first
produced in Russia between 1830 and 1840.
974 H. P. Meena and M. Sujatha

19.4 Floral Biology

In sunflower, the inflorescence which is a capitulum or head is most prominent

because of its large size and conspicuous yellow colour of the ray florets. The
capitulum is made up of two distinct flower types: outer single row of ray florets
which are male sterile and the inner disc florets which are hermaphrodite and fertile.
The disc florets are arranged in arcs radiating from the centre of the head. Each disc
floret is made up of inferior ovary, two pappi (modified sepals) and a tubular corolla
formed by the fusion of five petals except at the tip. The five anthers are also fused to
form a tube (syngenesious) with filaments attached independently at the base of the
corolla tube. The style is inside the anther tube with stigma divided at the tip. When
the flower is fully developed, the style elongates and the bifid stigma curls outward.

19.5 Pollination Mechanism

The unfolding of outer ray florets indicates the beginning of flowering in sunflower.
Opening of disc florets follows from the periphery proceeding gradually towards the
centre of the head at the rate of one to four whorls per day. The flowering in the
capitulum is completed in 7–10 days depending upon the size of the capitulum and
prevailing weather. Anthesis takes place in the morning between 6:00 and 8:00 AM
on warm sunny days. Anthesis is delayed if weather is cool, cloudy or wet. The
staminal filaments rapidly elongate and exert the anther tube from the corolla. Pollen
is dehisced within the anther tube. The style elongates and forces the two lobed
pubescent stigmas up the anther tube. The stigma is not receptive at this stage
because the two lobes are held together covering the inner receptive surface. The
stigma pushes the dehisced pollen through the upper end of the anther tube, and the
lobes separate exposing inner receptive surface. The sunflower to a large extent is
protandrous as anthesis takes place first, accompanied by a time lag of 10:00–12:
00 h in the maturation of male and female elements. Because of this, cross-
pollination is favoured as a rule, and insects, particularly bees, play an important
role in pollination. The pollen is spiny and well adapted for transmission by insects
mainly by honey bees. Pollination and fertilization occur when the spiny viable
pollen is transferred to the stigmatic surface. The achene is the fruit of the sunflower
that consists of outer pericarp (hull), thin and papery inner seed coat and embryo
(kernel). The achene is attached by a funiculus, but the seed coat is free from the
inner wall of the pericarp. Seed is nonendospermic, and the embryo is the major
portion and is made up of mostly cotyledons. The endosperm is largely made up of a
single layer of aleurone cells coalesced with the seed coat.

19.6 Genetic Resources

Availability of appropriate genetic resources with wide diversity is the key to any
crop improvement programme. Several germplasm collections have been stored in
different gene banks across the world. The highest number of collections are
19 Sunflower Breeding 975

maintained at USDA, USA (total 5217 accessions, of which 2616 are cultivated
H. annuus accessions, 2597 are wild accessions including 1693 annual and
904 perennial and 4 are diverse CMS sources) (Terzić et al. 2020). The France
collection at INRA maintains 3933 accessions, 2703 cultivated H. annuus
accessions, 10 diverse CMS sources and 1214 wild accessions of which
804 accessions are annual and 410 are perennial species. In India, ICAR-Indian
Institute of Oilseeds Research, Rajendranagar, Hyderabad gene bank maintains 3102
sunflower accessions. The collection includes exotic collection, augmented germ-
plasm, inbreds, populations, genetic stocks, gene pools for high oil, high seed yield,
autogamy, backcross-derived lines and wild species including their derivatives.
Other countries that maintain sunflower germplasm accessions are Russia (1210),
Argentina (922), Romania (681), Serbia (593), Germany (503) and Bulgaria (423).
The lowest numbers of accessions are maintained in Spain (196). The collection may
help improve economical traits related to yield and quality and also serve as the
source for biotic and abiotic resistance genes. Further, the elite germplasm may help
initiate sunflower breeding programmes in many countries. The details of germ-
plasm collections in gene banks in different countries are presented in Table 19.1.

Table 19.1 Sunflower germplasm resources maintained in gene banks of different countries
No. of
genetic
S. no. Country resources Type of material
1. USA 5217 Cultivated lines, CMS, wild H. annuus, other annual
Helianthus spp., perennial Helianthus spp. and other
genera
2. France 3933 Cultivated lines, OPV and other populations, CMS, wild
annual H. annuus, other annual Helianthus spp.,
perennial Helianthus spp., other genera
3. India 3102 Cultivated lines, OPV and other populations, CMS, wild
annual H. annuus, other annual Helianthus spp.
4. Russia 1210 Cultivated lines, OPV and other populations, CMS, wild
annual H. annuus, other annual Helianthus spp.,
perennial Helianthus spp.
5. Argentina 922 Cultivated lines, OPV and other populations, CMS, wild
annual H. annuus, other annual Helianthus spp.
6. Romania 681 Cultivated lines, OPV and other populations, CMS, wild
annual H. annuus, other annual Helianthus spp.
7. Serbia 593 Wild H. annuus, other annual Helianthus spp., perennial
Helianthus spp.
8. Germany 503 Cultivated lines, OPV and other populations, CMS, wild
annual H. annuus, other annual Helianthus spp.,
perennial Helianthus spp.
9. Bulgaria 423 CMS, wild annual H. annuus, other annual Helianthus
spp., perennial Helianthus spp., other genera
10. Spain 196 Open-pollinated varieties and other populations
Source: Modified from Terzić et al. (2020)
976 H. P. Meena and M. Sujatha

19.7 Wild Helianthus Species

Cultivated sunflower is diploid with chromosome number 2n ¼ 2x ¼ 34. The genus

Helianthus includes 53 species, of which 39 are perennials and 14 annuals being
maintained at the USDA-ARS, North Central Regional Plant Introduction Station
(NCRPIS) in Ames, IA (Seiler and Jan 2014; Seiler et al. 2017). The 14 annual
species are diploid (2n ¼ 2x ¼ 34), and the 39 perennial species include 26 diploids,
three tetraploids (2n ¼ 4x ¼ 68), seven hexaploids (2n ¼ 6x ¼ 102), one mixoploid
of either diploid or tetraploid and two mixoploids of tetraploid or hexaploid (Liu
et al. 2017). Some species occur in dual ploidy series, such as H. ciliaris L., which
displays both teraploid and hexaploid states, and H. decapetalus L., which exists in
diploid and tetraploid forms (Atlagic 2004).

19.7.1 Utilization of Helianthus Species

The wild Helianthus species exhibit high variability for several agronomic attributes.
Sunflower is one of the few crops where the use of wild Helianthus species in
sunflower breeding programmes has produced significant results. Genes for disease
(Seiler 2010) and insect resistance (Thompson et al. 1981), oil (Jovanka 2004) and
protein content and quality (Miller et al. 1992), cytoplasmic male sterility (Horn
2002), herbicide tolerance (Al-Khatib et al. 1998; Al-Khatib and Miller 2000) or
agronomic and physiological traits (Seiler et al. 2017) have been identified in wild
Helianthus species and transferred into cultivated lines in the USSR, the USA and
many East European countries. Interspecific hybridization paved the way for hybrid
breeding in sunflower wherein several CMS and fertility restorer gene sources were
derived from wild Helianthus species (Horn and Friedt 2006). The single most
important breakthrough has been the discovery of cytoplasmic male sterility
(CMS) via interspecific hybridization and Rf genes involving H. petiolaris, which
allowed practical use of heterosis and development of hybrids worldwide (Leclercq
1969; Kinman 1970). In India, the sunflower variety LSF-8 with tolerance to downy
mildew, rust and Alternariaster was derived from the cross involving H. tuberosus.
The variety CO-5 (COSFV-5) with moderate resistance to Alternariaster leaf spot,
rust and necrosis disease was derived from the gene pool of H. annuus x H. praecox
(Sujatha et al. 2019). Using conventional methods of crossing, several prebred lines
with altered plant architecture, high yield and oil content, maturity duration and
inbuilt tolerance to major biotic stresses have been developed from crosses involving
diploid annuals (Sujatha et al. 2008). Prebred lines derived from
H. annuus  H. argophyllus crosses were found resistant to leafhopper (unpub-
lished). Jacob et al. (2017) identified one sulfonylurea-based accession of H. praecox
(PRA-1823) resistant to herbicides as well as to powdery mildew. Different diploid
annual wild species like H. debilis, H. petiolaris, H. argophyllus, H. praecox and
wild H. annuus are being utilized for broadening the genetic base of cultivated
sunflower in India. Concerted efforts are warranted to overcome the deleterious
effects of distant hybridization and combine desirable traits with high seed and oil
19 Sunflower Breeding 977

yield. Information on the global scenario of the progress made in augmentation and
maintenance of wild Helianthus sources and utilization for introgression of gene
(s) for resistance to biotic and abiotic stresses and oil content and quality is reviewed
in the article of Seiler et al. (2017).

19.8 Evolution of High Oil Sunflower

Transformation of an ornamental sunflower into a high oil yielding crop occurred in

the USSR by 1769 and by 1830, and the manufacture of sunflower oil was done on a
commercial scale. During the early nineteenth century, the Soviet plant breeder,
Vasilii Stepanovich Pustovoit, in 1860, initiated selection for high oil content from
local varieties which contained 30–33% oil content, and concerted efforts at several
agricultural stations resulted in the gradual stepping up of oil content in the cultivars
from 33 to 50%. Consequently, the seed oil content increase was 21%. In 1927,
V.S. Pustovoit bred a new sunflower variety with 35% oil content. High oil sun-
flower varieties such as VNIIMK-3519, VNIIMK-6540, VNIIMK-8931, Peredovik,
Armavirsky-3497 and VNIIMK-309 developed by Pustovoit and his associates
enabled the spread of sunflower as an oilseed crop (Pustovoit 1964). Much of the
change was achieved by breeding for thin hulls surrounding the kernels. Following
Pustovoit’s method (Fig. 19.1), new early, broomrape-resistant, high oil content
(45–48%) and high seed yielding varieties such as Krasnodarets, Armavirets,
Chrnyanka-66 and Enissei were developed. These high oil selections found their
way later on to all the continents, and most of the recently bred varieties owe their
origin directly or indirectly to the materials bred in the USSR.

19.9 Inbreeding, Heterosis and Development of Hybrids

Inbreeding as a method for improving sunflower was used as early as 1922. Cardon
(1922) described the available variation in sunflower varieties and attempted to
isolate different types by self-pollination. Inbreeding was used in the Soviet Union
during the 1920s to develop lines with improved oil percentage, strong single stems
and resistance to diseases and insect pests (Calson et al. 1972; Jagodkin 1937;
Voskoboinik and Soldatov 1974). Unrau and White (1944) recorded a 35% decline
in seed yield after one generation of inbreeding in the cultivar Mennonite. Breeders
soon realized that the value of inbreeding was to develop inbreds with certain
desirable characteristics for subsequent crossing to produce synthetic cultivars or
interline hybrids. Attia et al. (2014) observed 2.25% decrease in oil content due to
inbreeding. Some of the results involving hybridization of inbred lines showed
heterosis for plant height, head diameter, seed size and seed yield. To reduce
inbreeding depression, Kovacik and Skaloud (1975) recommended sib cross in
early inbred generation. Shvetsova (1979) observed no substantial differences
between fertile lines and their male sterile counterparts for oil content in inbreeding.
Schuster (1980) studied inbred lines for 25 generations and revealed mean
978 H. P. Meena and M. Sujatha

Fig. 19.1 Pustovoit method for developing high oil content material

inbreeding depressions for seed yield (61%), plant height (20%), capitulum diameter
(21%), kernel/husk ratio (3%), crude oil content of achene (7%) and 1000 seed
weight (22%). Tuberosa (1983) observed 41.7% decrease in achene yield, 4.2% in
19 Sunflower Breeding 979

oil content and 44% in oil yield in S4 generation due to inbreeding. Gurev and
Osipova (1986) studied a number of varieties and hybrids for the degree of
inbreeding depression and found that the yield decreased by 33.0% in I1, 53.5% in
I2, 46.5% in I3 and 45% in I4 generations.
As early as 1940, Putt in Canada carried out preliminary studies on heterosis
breeding. Unrau and White (1944) reported 60.8% increase in seed yield and great
uniformity in a hybrid compared to unimproved Mennonite. Heterosis studies
carried out in sunflower have been presented for interline, inter-varietal and
top-cross hybrids involving genetic and cytoplasmic male sterility. In a study of
inter-varietal crosses, Kovacik (1959, 1960) observed good response with an
increase in seed yield to the extent of 1 to 20% over the parents. While comparing
progenies from selfed and crossed seeds, Kurnik and Zelles (1962) observed 18.7%
more height, 4.2% higher seed yield, 10.8% higher 1000 seed weight and 3 days of
delayed flowering in the plants from crossed seeds. Putt (1964) reported highly
significant values of heterosis for seed yield and plant height in a diallel study
involving ten inbred lines. In eight sunflower hybrids, Putt (1966) observed heterosis
for plant height and seed yield. Reports from various countries indicate (Gundev
1966; Fick and Zimmer 1974; Putt and Dorrell 1975) heterosis to an extent of 61% in
the crosses of inbred lines for seed yield and much greater uniformity in hybrids.
Kolczowskii (1971) observed an average 10.4% heterosis in the F1s from 20 crosses
among varieties of diverse origin in comparison with the better parent. Stoyanova
et al. (1971) studied heterosis in 140 F1 hybrids obtained from crosses among
192 stabilised inbred lines and reported a heterosis of 25 to 29%. Ge (1971) observed
heterosis of 15.9% for head diameter and 47.0% for a total number of seeds per head
in certain sunflower hybrids. Heterosis of 12 to 21% for seed yield is reported by
Klimov and Ermoshin (1977) in certain top-cross hybrids developed from 29 Soviet
varieties and 3 testers. In India, Seetharam et al. (1977) studied the performance of
hybrids produced by crossing four CMS and two fertility restorer lines and observed
a significant positive heterosis for days to flowering, plant height, head diameter, test
weight, oil content and seed yield. Sudhakar and Seetharam (1980) reported hetero-
sis for seed yield up to 41.31% over the mid-parent and up to 5.24% over the better
parent in 27 top-cross hybrids. Choudhary and Anand (1984) observed 62.8%
heterosis for seed yield, 23.1% for oil content and negative heterosis (7.7%) for
days to flowering over better parent. Singh et al. (1984) in a study on performance of
variety  inbred crosses observed heterosis for yield to an extent of 47.0–206.0%.
The studies of Shivaraju (1984) on ten F1 hybrids indicated an average heterosis to
an extent of 175.0% for seed yield, 129.0% for the number of filled seeds and 6.87%
for oil content. Giriraj et al. (1986) observed 15.2% heterosis for head diameter,
7.7% for days to flowering and 37.7% for the number of filled achenes.
The advantages of maize and other crops stimulated sunflower researchers to
work towards hybrid development in the crop. Introduction of male sterility using
GA3 tried on a large scale in many countries had inherent problems in exploiting
heterosis satisfactorily in sunflower. Several workers (Luciano et al. 1965; Putt
1962) tried to develop hybrids based on the self-incompatibility mechanism. The
occurrence of a higher proportion of selfs in hybrid seed plots came in the way of
980 H. P. Meena and M. Sujatha

large-scale seed production of hybrids based on this system. Before the discovery of
cytoplasmic male sterility and the corresponding fertility restoration system, genetic
male sterility discovered as early as 1934 was tried to produce hybrids (Leclercq
1966; Putt and Heiser 1966). This system was widely explored in France and
Romania despite the major disadvantage of removal of 50% plants in seed produc-
tion plots and higher costs associated with seed production.
The most significant development leading to the large-scale exploitation of
heterosis was the discovery of cytoplasmic male sterility (CMS) and restorer system
first developed by Leclercq (1969) working at the French National Institute for
Agricultural Research (INRA) from the interspecific cross H. petiolaris
Nutt.  H. annuus L. (the variety Armavirsky-9345) back crossed to H. annuus
L. and identification of fertility restorer lines RHA-265 and RHA-266 derived from a
composite cross by Kinman (1970) in the USA. After this discovery there has been a
shift in the breeding emphasis from open-pollinated varieties (OPV) to development
of single- and three-way cross hybrids. The first hybrid using CMS and genetic
restoration system was available as early as 1972, and within a span of 5 years, the
hybrids spread to many countries in Europe and America replacing the open-
pollinated varieties. Today hybrids are predominantly cultivated worldwide,
and > 95% of the area is covered by them.

19.10 Development of Sunflower Hybrids in India

The commercial cultivation of sunflower in India started in 1972 with the introduc-
tion of five Russian varieties [VNIIMK-8931 (EC-68413), Peredovik (EC-68414),
Armavirskii-3497 (EC-68415), Armaverta (EC-69874) and Vashod (Sunrise)]. The
value of hybrids and importance of heterosis breeding were recognized early with
the inception of the All India Coordinated Research Project (AICRP) on Oilseeds in
1972–1973. A special project on ‘Promotion of Research and Developmental Efforts
on Hybrids in Selected Crops-Sunflower’ was launched in 1989 as a thrust
programme to develop hybrids for diverse situations. Experimental hybrids were
developed at Bangalore in 1974–1975 using four CMS lines, namely, CMS-2A,
CMS-124A, CMS-204A and CMS-234A, and two restorer lines, viz. RHA-266 and
RHA-274, introduced from the USA. Based on seed yield, oil content, yield stability
and synchronization of flowering in male and female parents, the first public sector
hybrid BSH-1 (CMS-234A  RHA-274) was released for commercial cultivation
from public sector in 1980 (Seetharam 1980). Since then, the hybrid base has been
further widened in the country through AICRP centres. Till today, a total of
30 hybrids and 19 varieties were released in India from public sector (Sujatha
et al. 2019). The salient features of hybrids released since 1980 are given in
Table 19.2.
 19

Table 19.2 Salient features of sunflower hybrids released from 1980 to 2020 in India (by public sector)
Oil
Year of content
S. no. Hybrids Pedigree release Maturity Yield (kg/ha) (%) Salient features
1 BSH-1 CMS- 1980 85–90 1200–1300 41 Resistance to rust and downy
234A  RHA-274 mildew
2 LSH-1 CMS- 1990 85–90 1000–1100 38 Resistance to downy mildew
Sunflower Breeding

338A  MRHA-II
3 LSH-3 CMS- 1990 90–95 1200–1300 39 Resistance to downy mildew
207A  MRHA-1
4 KBSH-1 CMS- 1992 90–95 1300–1500 43 High yield with high oil content
234A  RHA-6D1
5 PKVSH-27 CMS-2A  AK-1R 1996 85–90 1300–1400 39 Moderate resistance to downy
mildew
6 DSH-1 DSF-15A  RHA- 1997 85–88 1200–1300 38–40 Resistance to downy mildew
857
7 TCSH-1 CMS- 2000 – – – –
234A  RHA-272
8 KBSH-41 CMS- 2001 90–92 1300–1500 39–41 Tolerant to moisture stress
234A  RHA-95- (R) 2500–3000 (I)
C-1
9 KBSH-42 CMS- 2001 90–92 1300–1500 38–41 Tolerant to moisture stress
851A  RHA-95- (R) 2500–3000 (I)
C-1
10 NDSH-1 CMS- 2002 88–90 1400 40 Early hybrid
234A  RHA-859
11 KBSH-44 CMS-17A  RHA- 2002 95–98 1400–1600 36–38 High yield
95-C-1
12 LSFH-35 CMS- 2003 Medium 1400–1500 39–41 Resistance to downy mildew
234A  RHA-1-1
981

(continued)
Table 19.2 (continued)
982

Oil
Year of content
S. no. Hybrids Pedigree release Maturity Yield (kg/ha) (%) Salient features
13 PSFH-118 CMS-10A  P-61- 2004 85–88 1400 40 Resistance to basal stem rot and
R head rot
14 HSFH-848 CMS-91A  RHA- 2005 90–95 1800–2400 41–42 Resistance to Alternaria leaf spot
298 and Rhizoctonia
15 DRSH-1 (PCSH- ARM-243  RHA- 2005 95–98 1300 43 High oil hybrid
243) 6D-1
16 TUNGA (RSFH- CMS-103A  R- 2005 95–100 1300–1500 39–41 –
1) 64-NB
17 PSH-996 CMS-11A  P- 2012 96–100 1957 37–38 Suitable for late sown conditions
93R
18 RSFH-130 CMS-104A  R- 2008 95–100 1800–2000 39–42 Tolerant to necrosis
(Bhadra) 630
19 KBSH-53 CMS- 2008 95–100 750–1250 38 Tolerant to powdery mildew
335A  RHA-95C-
1
20 KSFH-437 (Phule CMS-17A  R-437 2009 90–95 1800–2000 34 –
Raviraj)
21 CO-2 COSF-1A  CSFI- 2010 85–90 1900–2200 38–40 Early
99
22 LSFH-171 CMS-17A  RHA- 2016 90–95 2000–2400 34–35 Resistance to downy mildew
1-1
23 PSH-1962 CMS-67A  P- 2015 99 2050 41.9 High yield and high oil content
93R
24 RSFH-1887 CMS-38A  R- 2016 95–100 1800–2500 38–40 Tolerant to necrosis and Alternaria
127-1 leaf blight
25 NDSH-1012 NDCMS-30A  R- 2016 90–95 2000–2500 40–41 Moderately resistant to downy
(Prabhat) 843 mildew
H. P. Meena and M. Sujatha
 19

26 PDKVSH-952 CMS- 2016 90 1800–2000 36.8 –

302A  AKSF-6R
27 COH-3 (CSFH- COSF-6A  IR-6 2018 90–95 2200–2400 42 –
12205)
28 KBSH-78 CMS- 2018 82–85 1700–2300 39–41 Short duration and medium height
1103A  RHA-92
29 DSFH-3 CMS- 2018 90–95 2000–2500 37–39 High seed yield
Sunflower Breeding

234A  RHA-IV-
77
30 PSH-2080 CMS-67A  P- 2019 97 2441 43.7 High seed and high oil content
160R
Sources: Meena et al. (2013), Sujatha et al. (2019)
983
984 H. P. Meena and M. Sujatha

19.11 Major Breeding Objectives

19.11.1 Seed Yield

The main goal of plant breeding is to increase yield. Seed yield is a complex and
polygenic controlled trait and strongly influenced by environmental conditions, and
hence both additive (Sheriff and Appandurai 1985; Singh et al. 1989; Petakov 1992)
and non-additive (Bajaj et al. 1997; Rether et al. 1998; Kumar et al. 1998; Goksoy
et al. 2000; Cecconi et al. 2000) genetic effects play an important role in the
inheritance of seed yield. Because of the importance of environmental effects, the
heritability for seed yield is relatively low compared with other agronomic traits.
Recurrent selection for general combining ability (gca), reciprocal recurrent selec-
tion, which capitalize on additive genetic variance, and recurrent selection for
specific combining ability (sca), which capitalize on the non-additive portion of
genetic variance, would be more effective breeding methods in improving seed
yield. Seed yield consists of three main components: number of plants per hectare,
seeds per plant and 1000 seed weight. Yield per unit area can be increased in a
number of ways. One of the main approaches is to increase the seed number and seed
size per head while maintaining or increasing plant number per unit area (Merrien
1992). To realize high seed yield in sunflower, parents that have good gca and sca
for most yield components can be used in sunflower breeding (Tyagi 1988). Another
most effective way of increasing the yield of sunflower is to exploit heterosis through
hybrids. Sunflower seed yield may be increased significantly by breeding for seed
size. According to Morozov (1947), the increase in 1000 seed mass by only 1.0 g
brings an increase in seed yield of 40.0 kg/ha. To achieve high seed yield per unit
area, many breeders consider it essential to develop a genotype capable of providing
more than 1500 seeds per capitulum. A head size of 20 to 25 cm and flat shape are
important in attaining this goal.

19.11.2 Oil Content and Quality

Sunflower seeds are mainly used for oil extraction, which is predominantly used for
human nutrition. The oil concentration in sunflower may be reaching a plateau, but
most breeders believe that selecting for higher oil content and oil quality in seed is
still a very important and realistic objective when breeding for high oil and quality
sunflower varieties and hybrids. According to Borodulina and Khachenko (1976),
oil accumulation in sunflower seed begins on the first day after flowering and
continues until physiological maturity. The period of most intensive oil accumula-
tion takes place between the 15th and 22nd day after the beginning of flowering. It is
a quantitatively inherited trait, and genetic variation is affected by additive genes.
The heritability of this trait is relatively high to medium (Mokrani et al. 2002), and
progress has been made in increasing oil content in sunflower. Hence, it can be
improved through breeding methods like simple recurrent selection or through
population improvement. Miller et al. (1987) reported that oleic acid was controlled
19 Sunflower Breeding 985

by a major gene with partially dominant gene action. Hence, it is clear that breeding
for high oleic content is possible in sunflower. Wild Helianthus species may also be
utilized for increasing oil, protein content and quality in cultivated sunflower.
Thompson et al. (1978, 1981) reported that H. niveus (Benth.) and H. salicifolius
are potential sources for oil content. ‘Pervenets’ breeding lines contain a dominant
mutation, which increases oleic acid content to more than 89% in the sunflower oil.
Several QTLs have been identified on various linkage groups for seed oil content and
altered fatty acid composition of sunflower oil. These QTLs had additive to domi-
nant effects and closely related to domesticated related traits in sunflower (Leon et al.
2001; Burke et al. 2005; Ameena et al. 2016).

19.11.3 Diversification of Cytosterility System

Although more than 72 diverse CMS systems have been reported in sunflower, until
now only one system based on PET-1 cytoplasm has been exploited commercially
due to the non-availability of proper restorers and maintainers for other CMS lines.
Such type of dependency on a single source of male sterility could lead to a narrow
genetic base leading to a potential risk and high degree of genetic vulnerability in
hybrid sunflower cultivation which can predispose the crop for some unforeseen
situations of biotic and abiotic stresses in future years. Sunflower yields have
plateaued with the currently available genotypes. Hence, it is essential to diversify
the parental material (CMS and restorer base) to develop hybrids and varieties with
high yield potential. Development of newer CMS sources should be complemented
by identification of suitable restorers for effective hybrid seed production. Among
several strategies available to overcome this problem, diversification of CMS
sources itself is possibly the inexpensive and most effective method.

19.11.4 Biotic Constraints

Biotic stresses cause significant losses in crop plants and management of biotic
stresses (diseases and pests) not only increases the cost of production but also has
implications on environment and ecology (Bainsla and Meena 2016). The important
diseases that cause significant yield losses in sunflower are Alternaria leaf spot
[Alternariaster helianthi (Hansf.) Tub. and Nish.] (Carson 1985), powdery mildew
(Golovinomyces orontii (Castagne) V.P. Heluta), downy mildew [Plasmopara
halstedii (Farl.) Berl. & De Toni] (Gulya et al. 2013), sunflower necrosis disease
(SND) (Bhat and Reddy 2016) and rust (Puccinia helianthi Schwein.) (Shtienberg
and Zohar 1992). Sunflower production in India is constrained by the susceptibility
of the released varieties/hybrids to a wide array of biotic stresses. In India, the major
diseases and insect pests prevalent in sunflower-growing areas are SND,
Alternariaster leaf spot, powdery mildew, downy mildew, Spodoptera litura and
leafhoppers (Basappa and Santhalakshmi Prasad 2005). Sunflower leaf curl virus
(SuLCV) also has become severe in India, and there reports on resistance sources for
986 H. P. Meena and M. Sujatha

Table 19.3 Disease resistance genes identified in wild Helianthus species

Biotic
S. no. stresses Resistant/tolerant wild species References
1. lternariaster H. tuberosus Skoric (1988)
leaf spot H. maximiliani, H. mollis, H. divaricatus, Sujatha et al.
H. simulans, H. occidentalis, H. pauciflorus, (1997)
H. decapetalus, H. resinosus, H. tuberosus
H. occidentalis, H. tuberosus Madhavi et al.
(2005)
H. tuberosus, H. resinosus Sujatha and
Prabakaran (2006)
H. tuberosus, H. maximiliani, H. strumosus Santhalakshmi
Prasad et al. (2017)
2. Rust Wild H. annuus, H. argophyllus, H. petiolaris Quresh et al. (1993)
Wild H. annuus Gong et al. (2012)
Prebred (PS-1089) derived from Sujatha et al.
H. argophyllus  cultivated sunflower (2003)
3. Downy AD-66 derived from wild H. annuus Vranceanu and
mildew Stoenescu (1970)
H. argophyllus Qi et al. (2019)
4. Powdery H. tuberosus, H. praecox, H. bolanderi Acimovic (1998)
mildew H. decapetalus, H. divaricatus, H. laevigatus Dedic et al. (2012)
5. Sucking H. argophyllus Seetharam and
pests Ravi Kumar (2003)
Tobacco Backcross inbreds derived from Sujatha and
caterpillar H. argophyllus, H. petiolaris Lakshminarayana
(2006)
Sunflower H. tuberosus, H. maximiliani Seetharam and
pests Ravi Kumar (2003)
Leafhoppers Prebred lines derived from H. argophyllus Unpublished

SuLCV from wild species are not available (Govindappa et al. 2011). Insect pests of
sunflower are different in tropical and temperate countries. Crop losses due to insect
pests in sunflower vary from place to place. Continuous cultivation of the crop
subjected it to disease pressure with overlapping disease cycles. Host plant resistance
is a major objective in most of the breeding programmes across the crop species
including sunflower and is considered as one of the most viable options for enhanc-
ing the productivity. The level of resistance available in cultivated species/primary
gene pool for some of the diseases and insect pests is rather low, and only a limited
number of resistance sources are available. This limited resistance is inadequate to
manage more virulent pathogenic strains of diseases that arise during intensive crop
production. Therefore, the discovery and incorporation of new genes from wild
species provide a means of complementing crop improvement programmes
(Table 19.3). The chances of finding dominant genes containing resistance to
economically important diseases are higher in wild species which if deployed
19 Sunflower Breeding 987

effectively using new breeding tools including molecular and biotechnology can be
an effective means of combating virulent pathogens.

19.11.5 Abiotic Constraints

Sunflower is generally grown in marginal lands, often in semiarid conditions, where

abiotic stresses always act as a major limiting factor for its production and produc-
tivity in many parts of the world (Škorić 1987). Therefore, development of a heat-
resistant sunflower breeding population or hybrid or breeding for resistance to
drought, high temperature and salinity assumes priority for sustainable yield under
abiotic stress conditions.
Drought is considered as the single most devastating environmental stress, which
decreases crop productivity more than any other environmental stresses (Lambers
et al. 2008). Chimenti et al. (2002) reported 5–56% yield reduction in sunflower if
drought occurs immediately prior to anthesis. An appropriate strategy and criteria of
selection are essential in selection for drought resistance. Restorer gene pool lines
RGP-46-P3 and RGP-60-P1 developed through simple recurrent selection at ICAR-
IIOR, Hyderabad, recorded low drought susceptibility index and good seed yield
under moisture stress and were found promising for drought breeding. The use of
landraces, cultivated hybrids and varieties has produced some positive results, but
not to the extent that would secure stable sunflower production under drought
conditions. The best results in enhancing drought resistance of cultivated sunflower
have been achieved using wild Helianthus species. Some wild sunflower species
have been reported as drought-tolerant species, and the introgression of traits from
these species is expected to increase drought tolerance in cultivated breeding lines
(Saucă et al. 2014). Among the related species, H. argophyllus was identified as
particularly drought tolerant (Belhassen et al. 1996; Jan et al. 2014; Saucă et al.
2014; Hussain et al. 2017).
Seiler (2012) indicated that H. anomalus Blake and H. deserticola Heiser are
highly adapted to desert and sandy areas and could be used as germplasm source for
heat stress studies. Sideli et al. (2013) reported H. cusickii to be a potential source for
genes for drought resistance.
Salinity is also another factor reducing sunflower yield in many countries includ-
ing India. Identification of resistance sources from cultivated sunflower is very
important for improvement of salinity tolerance of sunflower. Based on plant growth
and survival, hybrids CSFH-12205, CO-2, KBSH-44 and DRSH-1 and inbreds, viz.
COSF-1A and CMS-103A, were found tolerant at Gangavathi, and CSFH-12205,
CO-2, KBSH-44, COSF-6A and COSF-7A were found tolerant at Machilipatnam
(Anonymous 2018). Seiler et al. (1981) and Rogers et al. (1982) suggested that
H. paradoxus would be a likely candidate for salt-tolerant genes. Miller and Seiler
(2003) transferred salt-tolerant genes from H. paradoxus into cultivated sunflower
and released two salt-tolerant maintainer lines, HA-429 and HA-430. Hajjar and
Hodgkin (2007) suggests that H. paradoxus has a great potential to breed more salt-
tolerant cultivated sunflowers, with hybrids developed using this trait potentially
988 H. P. Meena and M. Sujatha

providing a 25% yield premium in saline soils. Shtereva et al. (2015) suggested that
the diploid perennial species H. mollis could serve as an excellent candidate of salt-
tolerant genes. Breeders should apply effective screening methods to identify the
donor wild species that possess genes useful in breeding for abiotic stresses and
equally effective breeding methods to transfer these genes into cultivated sunflower
genotypes.

19.12 Breeding Approaches

19.12.1 Conventional Approaches

Sunflower is a highly cross-pollinated (allogamous) crop, and therefore breeding

procedures suitable for cross-pollinated crops are utilized for improvement of
sunflower. In general, introduction, mass selection, pedigree method, backcross
breeding, recurrent selection and Pustovoit method of reserves and mutation breed-
ing were used for sunflower improvement. The choice of the suitable breeding
programme for the development of tolerant cultivars to a defined abiotic stress
depends upon a number of factors: screening techniques, sources and mechanism
(s) of tolerance, modes of gene action and heritability and their relationship to
agronomic traits (Meena et al. 2016).

19.12.1.1 Introduction
Plant introduction consists of taking a genotype or a group of genotypes of plants
into new environments where they were not grown earlier. In India, the first
sunflower variety ‘EC-68415’ was developed in 1976 by AICRP (Sunflower)
Centre, University of Agricultural Sciences, Bengaluru, and released for Karnataka
state through an introduction. Another short-duration (80–82 days) popular variety
‘Morden’ was developed through introduction from Canada in 1978. It was released
for all India cultivation. Morden was very popular among sunflower growers due to
its short stature, short duration and high seed yield.

19.12.1.2 Mass Selection

Mass selection is a method of selection of desirable plants from a population based
on their phenotypic characteristics. This method has been used for cultivar improve-
ment in sunflower for many years and was effective in developing cultivars with
early maturity, higher oil percentage and resistance to diseases. The efficiency of
mass selection depends on gene effects of the selected traits, their heritability,
sample size and genotype  environment interaction. Mass selection is effective
for characters controlled by additive genes (Gowda and Seetharam 2008). Many
varieties like Fuksinka-3, Fuksinka-10, Omskiy Skorospeliy, etc. were developed in
the Soviet Union through this method (Skoric 1992). Varieties like Guayacan INTA,
Cordobes INTA, Manfredi INTA, etc. were also developed using mass selection in
Argentina (Luciano and Davreux 1967). In India, the variety Surya (PKV-SUF-72-
37) was developed by mass selection from Latur bulk and released for Maharashtra
19 Sunflower Breeding 989

state in 1982. Still, this is one of the important breeding methods for sunflower
improvement for many traits.

19.12.1.3 Pedigree Method

Pedigree selection is the most common procedure used to develop sunflower inbred
lines. The procedure involves self-pollination of phenotypically desirable plants
within existing cultivars, breeding populations or segregating generations of planned
crosses. Fick and Swallers (1974) used this method to develop the first downy
mildew-resistant restorer lines, viz. RHA-271, RHA-273 and RHA-274. Hulke
et al. (2010) also developed new rust and downy mildew-resistant restorer line
RHA-464 (Reg. No. GP-325; PI-655015; experimental ‘05187’), using pedigree
method. In India, a large number of fertility restorer lines have been developed using
the pedigree method (Meena et al. 2013). Jaffar et al. (2019) developed high oleic
lines through pedigree method using PI-1806  B-124 parents. In India, this is the
only breeding method utilized by breeders for development of restorer lines and
inbreds.

19.12.1.4 Backcross Method

Backcross selection refers to a form of breeding that uses a superior inbred that may
nevertheless lack a particular trait. It is mainly used for the transfer of disease-
resistant traits in superior inbred lines. But the fertility restorer lines are also
developed by incorporating dominant restorer gene(s) by backcrossing using inbred
lines of proven performance as the recurrent parent (Vranceanu and Stoenescu
1976). Backcross is also used for the transfer of disease resistance from related
species to cultivated species. This method is also employed to transfer male sterility
trait from a donor. New CMS lines are mostly developed in sunflower through the
backcross method. High oleic acid (>90%) was identified in AOP-l and was used as
a donor of this character in a backcross programme to incorporate the trait into
commercial material. Liu et al. (2013) introgressed fertility restoration gene Rf6 for
CMS-514A from an interspecific amphiploid (Amp) of H. angustifolius/P-21
(2n ¼ 68) into cultivated sunflower by backcross method.

19.12.1.5 Recurrent Selection

Recurrent selection refers to the method of selecting special gene traits from the best
sunflower family. Presently, recurrent selection appears to be the most promising
method of increasing the frequency of desirable genotypes in a source population,
thus enhancing the chance of isolating superior inbred lines. It is a useful method in
sunflower breeding, especially for the establishment of the gene pool for different
purposes, primarily of increased productivity and resistance to diseases, insects,
drought and other stresses. The recurrent selection method has not been exploited in
breeding programmes in India even though considerable progress has been achieved
using this method in other countries like the USA and France (Virupakshappa 1987).
Miller et al. (1977) obtained an increment of 12.2% of oil content after three cycles
of simple recurrent selection. Miller and Hammond (1985) reported an increase in
seed yield by 6.3% after three cycles of selection. Resistance for Sclerotinia
990 H. P. Meena and M. Sujatha

sclerotiorum was obtained by Vear and De Labrouhe (1984) through three cycles of
recurrent selection. Dr. Pustovoit in the USSR was a pioneer to practically utilize
recurrent selection for oil improvement in which selection was based on progeny
performance and subsequent cross-pollination is allowed only among superior
progenies. Pustovoit (1964) was highly successful in improving oil content from
about 30% in the early 1920s to over 50% in the present-day varieties. Shobha Rani
and Ravikumar (2006) also improved partial resistance to Alternariaster leaf blight
through sporophytic and gametophytic recurrent selection. Vear et al. (2007)
reported significantly improved Sclerotinia head rot resistance after 15 cycles of
recurrent selection. Harinarayana et al. (1980) noticed an improvement in seed yield,
seed set and oil content through intra- and inter-population improvement. Powdery
mildew-resistant restorer inbreds RGP-21-P4-S1–3 and RGP-50-P2-S1 were devel-
oped through population improvement after three cycles (Anonymous 2018). A wide
range of variability was observed by Seneviratne et al. (2004) for plant height, days
to maturity, head diameter, number of filled seeds and seed yield in C3 cycle
(Anonymous 2018). Emphasis has to be laid on using recurrent selection for
population improvement to act as a source for development of new parental lines,
and the improvement of existing parental lines should receive more attention to
achieve a real breakthrough in yield.

19.12.1.6 Mutation Breeding

This method was mostly used in cultivated sunflower for creating genetic variability
through irradiation with gamma rays or chemical mutagens. Seed treatment with
gamma irradiation has been extensively used to increase variability for several
characteristics, such as days to flowering, seed weight, seed coat colour and oil
content (Giriraj et al. 1990; Jambhulkar and Joshua 1999; Encheva et al. 2003) in
cultivated sunflower. Genetic variability for resistance to Alternariaster leaf spot
disease was induced by radiation or chemical mutagens (De Oliveira et al. 2004).
Orobanche-resistant lines were developed through mutation breeding by Encheva
et al. (2008, 2012, 2014). Cvejić et al. (2014) found changes in fatty acid and
tocopherol content and composition in sunflower oil. Lofgren and Ramaraje-Lers
(1982) isolated plants with resistance to sunflower rust in M2 and M3. Herbicide-
resistant sunflower mutants were generated by induced mutagenesis (Bervill et al.
1992; Sala et al. 2008). Drumeva (2012) developed 159 new downy mildew,
Phomopsis and Alternaria-resistant fertility restorer lines with desirable breeding
characteristics by using the gamma ray-induced parthenogenesis method. Jan and
Rutger (1988) reported induced male sterility in M1 heads of HA-89 treated with
mitomycin C and streptomycin. Soldatov (1976) produced high-oleic sunflower
variety ‘Pervenets’ by treating the seed of variety VNIIMK-8931 with 0.5% solution
of dimethyl sulphate. In India, the sunflower variety Gujarat Sunflower-1
(GAUSUF-15) was developed through mutation breeding and released in 1993 all
over India. Another variety CO-3 (TNAUSUF-10) was developed from CO-2 using
5KR gamma rays and released for Tamil Nadu state in 1995. The variety TAS-82
(TAS-82-8-1/3) was developed from Surya variety through mutation breeding in
2006 and recommended for Vidarbha region of Maharashtra state. Readers
19 Sunflower Breeding 991

interested in additional information on mutations can refer to the article of Vasko and
Kyrychenko (2019) on induced mutagenesis for the creation of new starting material
in sunflower breeding.

19.12.2 Hybrid Seed Production

19.12.2.1 Development of A, B and R Lines

Hybrids developed using the CMS fertility restorer system require three parental
lines, viz. CMS or ‘A’ line, fertility maintainer or ‘B’ line and a restorer line or ‘R’
line (male line). In hybrid development programme, inbred lines are developed by
selfing or sib mating from adapted varietal populations, gene pools, local varietal
populations, inter-varietal hybrids, composites, synthetics, single-cross and
multiple-cross hybrids and interspecific hybrids, etc., over the generations and
essentially evaluated for combining ability by inter-crossing among the best by
following standard genetic model. Once the best combinations are identified based
on high combining ability and per se performance, the female line is converted into
cytoplasmic male sterile line (A line) with the original inbred as the isogenic
maintainer line (B), and the male inbred line is converted into restorer line
(R line). CMS lines are developed by repeated backcrossing using known CMS
lines as a non-recurrent parent (female parent). About five to six backcrosses are
required to derive a new CMS line genetically similar to the recurrent parent. The
inbred, which was used as a recurrent parent (male parent), serves as a maintainer
(B line). Derived CMS line will be employed as the female in seed production of
hybrids along with the selected male line based on the combining ability and
productivity. Wherever the hybrids show 100% fertility in F1, the ‘R’ lines may be
used directly as the male parent. If the fertility restoration is partial or low in the F1
plants, fertility restorer lines are developed by crossing the selected best combiner as
a recurrent parent to a known restorer line of proven performance. By six to seven
backcrosses, R gene(s) may be transferred to the selected male line.

19.12.2.2 Maintenance of Parental Lines

Two methods of planting, viz. row method and block method, are followed for
maintenance of the ‘A’ line (Fig. 19.2). The A  B crosses are used to maintain the
‘A’ line following separate row and block method of sowing. To take up the breeder/
foundation seed production of female (A) line, the planting ratio of ‘A’ and ‘B’ is 3:
1. To facilitate better pollination, mark the first two rows and last two rows of the
seed plot and subsequently every fourth row with a wooden peg to plant these lines
with ‘B’. The sowing of ‘A’ and ‘B’ lines should be taken up by engaging labourers
separately. A and B lines in breeder/foundation stages are planted in 3:1 proportion
in separate blocks. During anthesis, the pollen is collected from the ‘B’ line and
pollinated on to ‘A’ line in respect of breeder/foundation seed production. This
method ensures the production of high-quality hybrid seeds and meets the genetic
standards.
992 H. P. Meena and M. Sujatha

Fig. 19.2 Maintenance of

‘A’ line through row and Row method
block method
BB AAA B AAA B AAA B AAA BB
BB AAA B AAA B AAA B AAA BB
BB AAA B AAA B AAA B AAA BB
BB AAA B AAA B AAA B AAA BB
BB AAA B AAA B AAA B AAA BB

Block method

Breeder/Foundation seed production

Block-I Block-II
AAAAAAAAAAAA BBBB
AAAAAAAAAAAA BBBB
AAAAAAAAAAAA BBBB
AAAAAAAAAAAA BBBB
AAAAAAAAAAAA BBBB
19 Sunflower Breeding 993

19.12.2.3 Certified Hybrid Seed Production

To realize high productivity levels in the commercial scale, the supply of quality
hybrid seed assumes importance. The production of high-quality seed of parental
lines and the certified seed of hybrid requires systematic planning and management
on the part of the seed producers (Fig. 19.3). As in the production of ‘A’ line, two
methods, viz. row method and block method, are being followed to produce hybrid
seed in sunflower (Fig. 19.4). The proportion of female to male is 3:1, i.e. three rows
of female (seed parent) to one row of male (pollen parent). In recent times, the seed
production agencies have faced serious seed quality problems as the seed lots of
hybrids containing a high amount of ‘R’ line plants are contaminated during
harvesting/drying in addition to different stages of post-harvest operations followed
in the above 3:1 method.
In the suggested block system, A and R lines are planted in separate bocks in 3:1
ratio. At the time of anthesis, the pollen is collected separately from R lines and
pollinated on to ‘A’ line in respect of certified seed production. This method ensures
the production of high-quality hybrid seed and meets the genetic standards.

19.12.3 Limitations of Conventional Breeding

Traditional approaches to breeding crop plants with improved abiotic stress

tolerances have so far met with limited success (Richards 1996). This is due to
several contributing factors including the following: (1) the focus has been on yield
rather than on specific traits; (2) the difficulties in breeding for stress tolerance traits,

Fig. 19.3 Procedure of

certified hybrid seed
production
994 H. P. Meena and M. Sujatha

Breeder/Foundation seed production Row Method

Row method
RR AAA R AAA RAAA R AAA RR
RR AAA R AAA RAAA R AAA RR
RR AAA R AAA RAAA R AAA RR
RR AAA R AAA RAAA R AAA RR
RR AAA R AAA RAAA R AAA RR

3 rows of A line 1 row of R line

Certified seed production Block Method

Block-I Block-II
AAAAAAAAAAAA RRRR
AAAAAAAAAAAA RRRR
AAAAAAAAAAAA RRRR
AAAAAAAAAAAA RRRR
AAAAAAAAAAAA RRRR
R line block A line block

Fig. 19.4 Certified hybrid seed production through row and block method

which include complexities introduced by genotype by the environment, or G  E

interactions and the relatively infrequent use of simple physiological traits as
measures of tolerance; and (3) desired traits can only be introduced from closely
related species.

19.12.4 Molecular Breeding

Despite the large genome size (2871–3189 Mbp) of cultivated sunflower, concerted
efforts led to the genome assembly up to the chromosome level with a total length of
3010 (Mb), protein count of 75,695 and GC content of 38.8% (PRJNA396063).
Molecular markers have played a significant role in accelerating sunflower breeding
programmes through marker-assisted selection (MAS) by virtue of their abundance,
technical ease and detection at any development stage of the plant besides being not
affected by environmental factors. To facilitate MAS, a number of molecular marker
systems, namely, restriction fragment length polymorphism (RFLP), randomly
amplified polymorphic DNA (RAPD), amplified fragment length polymorphism
(AFLP), simple sequence repeat (SSR), sequence characterized amplified region
(SCAR), cleaved amplified polymorphic sequence (CAPS), insertion/deletion
(INDEL), single nucleotide polymorphism (SNP) and target region amplification
polymorphism (TRAP) markers, have been developed and used for various molecu-
lar applications in sunflower (Berry et al. 1995; Gentzbittel et al. 1995, 1998; Jan
19 Sunflower Breeding 995

et al. 1998; Flores Berrios et al. 2000; Burke et al. 2002; Mokrani et al. 2002; Bert
et al. 2003, 2004; Langar et al. 2003; Yu et al. 2003; Rachid Al-Chaarani et al. 2004;
Lai et al. 2005; Hu et al. 2007; Poormohammad Kiani et al. 2007; Yue et al. 2008).
These markers have been extensively used in several applications like assessment of
genetic relationships among genotypes, construction of linkage maps, tagging and
mapping genes/QTLs of agronomic interest, development of genomic and cDNA
libraries, map-based cloning and marker-assisted selection.
In sunflower, the first map was developed using RAPD markers (Rieseberg et al.
1993), followed by RFLP markers (Berry et al. 1995; Gentzbittel et al. 1995; Jan
et al. 1998), AFLP markers (Gedil et al. 2001), SSR markers (Tang et al. 2003; Yu
et al. 2003) and SNP markers (Lai et al. 2005; Bowers et al. 2012; Talukder et al.
2014; Celik et al. 2016; Livaja et al. 2016) covering the 17 linkage groups. These
maps were further enriched with gSSRs, EST-SSRs, INDELs, TRAPs and SNPs
(Hu et al. 2007; Heesacker et al. 2008), and a consensus map with 10,080 loci was
constructed (Bowers et al. 2012). Recently, studies on large-scale SNP detection and
generation of large sets of markers through genotyping by sequencing have been
undertaken by several groups (Baute et al. 2016; Celik et al. 2016; Talukder et al.
2016; Mangin et al. 2017; Ma et al. 2017; Qi et al. 2017; ). For more information of
molecular markers and marker-assisted breeding, readers may refer the articles of
Dimitrijevic and Horn (2018).
Molecular markers for simple inherited traits like fertility restoration, herbicide
tolerance, resistance to downy mildew, Orobanche cumana, rust, high stearic and
oleic acid contents (β and γ tocopherols) have been successfully deployed in marker-
assisted breeding programmes (Sujatha and Sujatha 2013). QTLs have been
identified, but genome-wide association studies are required. However, for
investigating complex traits controlled by polygenes, such as seed yield, oil content,
resistance to Sclerotinia mid-stalk rot, black stem and abiotic stresses like drought,
salinity and chilling. Of the various traits that have been improved through MAS,
resistance to downy mildew was highly successful as the resistance was dominantly
inherited (Dimitrijevic and Horn 2018).
With regard to the genetic resources, initial studies focused on development of
biparental populations based on crosses involving elite breeding and introgressed
lines (Berry et al. 1995; Horn et al. 2003; Livaja et al. 2016), land races (Kim and
Rieseberg 1999), wild Helianthus species (Quillet et al. 1995; Ma et al. 2017) or the
recombinant inbred lines (Tang et al. 2006; Talukder et al. 2016). These populations
were used to map genes conferring resistance to downy mildew, QTLs governing
Sclerotinia stalk rot resistance and seed quality traits, but owing to the disadvantages
of the time and costs involved for deployment of individual populations, low
resolution of mapping, mortality of the populations besides evaluation of only two
alleles per locus alteration strategies were adopted. Understanding the need for
assembling the association panels, researchers have directed their efforts towards
this goal. Accordingly, association panels consisting of 433 cultivated accessions
from the USA and Europe maintained at USDA and INRA, respectively (Mandel
et al. 2011); 170 accessions representing Argentinian collections maintained at
INTA (Filippi et al. 2015), which distinguished the maintainer and restorer gene
996 H. P. Meena and M. Sujatha

pools; and 196 Spanish confectionery accessions maintained at CRF-INIA (Velasco

et al. 2014) were characterized which disclosed large genetic variation for seed oil
content, test weight and seed quality traits.

19.12.5 Trait Improvement Through Genetic Engineering

Despite the successes with traditional breeding methods and interspecific gene
transfer for several traits such as cytoplasmic male sterility, fertility restoration
gene(s), seed quality traits, resistance to biotic and abiotic stresses, biotechnological
interventions are required for introgression of beneficial traits into cultivated sun-
flower. Direct and callus-mediated shoot organogenesis from different tissues such
as cotyledons, hypocotyls, petioles, leaves and immature embryos is reported
(Witrzens et al. 1988; Knittel et al. 1991; Pugliesi et al. 1991; Sujatha et al.
2012a). Regeneration through somatic embryogenesis using immature zygotic
embryos, mature seeds and seedling tissues is also reported (Finer 1987; Mc-Cann
Wilcox et al. 1988; Espinasse and Lay 1989; Sujatha and Prabakaran 2001). The key
factors favouring organogenesis include genotype, explant type, age and physiolog-
ical state of the cultured tissue, exogenous growth regulator combinations and their
balance with endogenous growth regulators, etc. Shoot regeneration and quality of
shoots are reported to be enhanced through the use of ethylene inhibitors like
cobaltous chloride (CoCl2) and silver nitrate (AgNO3) molecules (Chraibi et al.
1992), preconditioning of explants with 5 mg/l BAP (Zhang and Finer 2015) and
short-pulse treatments coupled with micrografting (Zhang and Finer 2016). Preco-
cious flowering, hyperhydricity, poor rooting and abnormal morphogenesis are few
other problems encountered in sunflower shoot cultures (Lupi et al. 1987; Freyssinet
and Freyssinet 1988). Even after four decades of research carried out at several
laboratories, availability of a reliable, efficient, reproducible and genotype-
independent tissue culture-based regeneration system still continues to be a major
limitation for application of genetic engineering tools in sunflower.
Genetic transformation experiments were largely through Agrobacterium-
mediated techniques using explants with pre-existing meristems as target tissues
such as shoot tips, mature embryos, immature embryos and cotyledons from mature
seeds. The initial studies were chiefly aimed at optimization of variables for enhanc-
ing the transformation efficiency and mostly confined to characterization of primary
transformants and the T1 generation plants. Owing to the amenability of sunflower to
Agrobacterium tumefaciens infection, high frequency of transient expression is
observed in most of the transformation experiments. However, conversion efficiency
of transient to stable integration was rather limited besides leading to chimeras
(Schrammeijer et al. 1990; Malone-Schoneberg et al. 1994; Grayburn and Vick
1995; Weber et al. 2003). Further, formation of chimeric shoots, low regeneration
rate from transformed cells/calli, low Agrobacterium virulence, bacterial strain,
extreme sensitivity to antibiotics, genotype dependence and lack of stable transmis-
sion of the introduced gene are major factors limiting the overall efficiency of the
transformation systems reported so far. Attempts made at enhancing transformation
19 Sunflower Breeding 997

efficiency by imposing wounding treatments using glass beads (Grayburn and Vick
1995; Alibert et al. 1999); sonication at 50 MHz (Weber et al. 2003); vacuum
infiltration (Hewezi et al. 2003); digestion with macerating enzymes like cellulose,
pectinase and macerozyme (Alibert et al. 1999; Weber et al. 2003); incubation with
acetosyringone (Laparra et al. 1995); co-transformation with cytokinin synthesis
(ipt) gene (Molinier et al. 2002); and dehydration and rehydration of target tissues
(Hewezi et al. 2002) met with limited success. Among the commonly used reporter
genes for selection of putative transformants (hygromycin, kanamycin and basta),
kanamycin is used widely as the plant selection agent in sunflower due to ease of
identification of green shoots (putatively transformed) from bleached shoots
(untransformed). The problem of premature flowering has been overcome to some
extent by incorporation of cytokinins like 2-isopentenyl adenine (2-iP) and kinetin,
incubating the tissues at a temperature of 20  C with 8/16 h light/dark photoperiod
cycle or grafting of in vitro recovered putative transformants onto healthy root stocks
(Weber et al. 2003; Sujatha et al. 2012b). Step-wise protocols for sunflower trans-
formation are described by Lewi et al. (2006), Radonic et al. (2015) and Manavella
and Chan (2009) for development of transformants and for transient expression
analysis which can be used for gaining valuable insights of several biological
processes through functional validation of genes.
While most of the genetic transformation studies undertaken in sunflower are
aimed at establishment of the transformation system, transgenic development for
agronomically desired traits was mainly for incorporation of resistance to biotic
stresses (Sclerotinia sclerotiorum, Alternariaster helianthi, necrosis disease) and
resistance to abiotic stresses (drought, salinity). S. sclerotiorum is an economically
important disease in the temperate regions causing root rot, mid-stalk rot and head
rot, and oxalic acid has been identified as the key component in Sclerotinia infection.
Genetic engineering for enhanced resistance to S. sclerotiorum is aimed at strategies
to degrade oxalic acid and was through deployment of candidate genes like wheat
germin oxalate oxidase (OXO) (Lu et al. 2000; Scelonge et al. 2000); coumarin
phytoalexins (ayapin and scopoletin) (Urdangarin et al. 1999); and antifungal genes
like glucanase, chitinase, osmotin gene and a ribosome inhibitor protein (Radonic
et al. 2008). For conferring resistance to A. helianthi, transgenic lines harbouring
β-1,3-glucanase (Manoj Kumar et al. 2011) and TVD1 gene (Sirisha et al. 2011) were
developed. Sunflower necrosis disease (SND) incited by Tobacco streak virus of
Ilarvirus group accounts for yield losses ranging from 10 to 80% in the tropics and
sub-tropics (Jain et al. 2003). Deployment of TSV-CP gene in sense and antisense
directions was undertaken for conferring resistance to SND (Pradeep et al. 2012;
Singareddy et al. 2018; Sunderesha 2017).
Abiotic stresses like drought, salinity and heat have their effects not only on seed
yield but also on the oil content. Candidate genes were deployed to increase
tolerance to abiotic stresses such as suppression of proline dehydrogenase
(ProDH1) gene for drought and salinity (Tishchenko et al. 2014). Studies at meta-
bolic engineering towards improving oil stability and nutritional quality are targeted
at development of high-oleic sunflower by knocking out delta-12-desaturase gene
998 H. P. Meena and M. Sujatha

which encodes linoleic acid and lines with increased linoleic acid using PTGS
technology (Lacombe et al. 2009; Chen et al. 2010).
Genome editing through CRISPR/cas9 technology is still in its infancy in case of
sunflower. Innovative Genomics Institute, California, is at establishing tools for
genome editing in sunflower (https://innovativegenomics.org/projects/establishing-
tools-sunflower-genome-editing/).

19.13 Conclusions

One of the major challenges in sunflower would be to enhance productivity to the

level of the world’s average. To achieve this, populations and hybrids superior to the
presently grown cultivars need to be bred which should combine high seed yield
(>3.0 t/ha), high oil content (>42.0%) and resistance to major pests like leafhopper
and diseases like Alternariaster leaf spot, powdery mildew, downy mildew, necro-
sis, rust, stem rot, etc. Another important area of breeding research would be to
enhance tolerance/resistance to abiotic stresses. Intensive and monocropping of
sunflower has been the major cause for outbursts of diseases like rust, leaf spots,
powdery mildew, sunflower necrosis disease, leaf curl virus and downy mildew
which require immediate attention. Root rots are becoming severe in some parts of
the country. Hence, development of hybrids with multiple resistance(s) will have to
be the major thrust areas in the years to come. Public-private partnership is also very
important for area expansion and development of high heterotic hybrids. Utilization
of information being generated through genomic resources and tools assumes
importance in tackling problems such as abiotic stresses and identification of
physiological traits contributing to seed yield through genomic selection and
GWAS. Wild Helianthus species displayed extensive variability for various qualita-
tive and quantitative traits including tolerance/resistance to biotic and abiotic stresses
which can be incorporated in cultivated sunflower through introgressive breeding
and novel breeding techniques (cisgenics, genome editing).

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Chickpea Breeding
20
G. P. Dixit, A. K. Srivastava, V. Jayalakshmi, Shayla Bindra,
and Sarvjeet Singh

Abstract

Chickpea is the major pulse crop of India, and it accounts for about 45% of the
total area and production of pulses grown in the country. Impressive progress has
been made in development of cultivars suited to rainfed ecology. This has helped
India in expanding chickpea area in central and southern India and compensating
the loss in chickpea area that occurred earlier due to expansion of wheat in
irrigated areas of northern India. The genetic variability available in the germ-
plasm, particularly in wild species, should be exploited for broadening the genetic
base of varieties and introgressing useful traits, such as resistance to insect pests
and diseases. The barriers to interspecific hybridization have restricted utilization
of several wild species, and, therefore, dedicated efforts are needed to access
genes from these species. High-throughput precision phenotyping protocols need
to be developed and used for screening of germplasm and breeding materials for
different traits related to stress tolerance and nutritional quality. Rapid
advancements in development of chickpea genomic resources during the past
decade have made it possible to initiate genomics-assisted breeding in chickpea
improvement. Molecular markers associated with several useful traits have been
identified. Some of these markers have been validated and are being used in the
breeding programmes. Efforts should be made on increasing the number of
validated/diagnostic markers, so that genomics-assisted breeding becomes an

G. P. Dixit (*) · A. K. Srivastava

All India Coordinated Research Project on Chickpea, ICAR-Indian Institute of Pulses Research,
Kanpur, India
V. Jayalakshmi
RARS Nandyal (ANGRAU), Nandyala, Andhra Pradesh, India
S. Bindra · S. Singh
PAU, Ludhiana, Punjab, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1009
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_20
1010 G. P. Dixit et al.

integrated approach in chickpea breeding programmes. Marker-assisted selection

can accelerate breeding process and facilitate combining different desired traits.
Integration of these approaches would be important for improving precision and
efficiency of chickpea breeding programmes. In this paper, we have reviewed the
status of current research efforts and advancements in Indian and future research
priorities to tackle newer challenges.

Keywords
Breeding · Chickpea · Genetic improvement · Improved varieties · Research
strategies

20.1 Introduction

Chickpea (Cicer arietinum L.) is cultivated in almost all parts of the world covering
more than 50 countries spread over Asia, Africa, Europe, Australia, North America
and South America continents and is the second most important food legume crop
after common bean (Phaseolus vulgaris L.). In India, chickpea is grown almost in all
parts of the country mainly as a rainfed crop (68% area). There has been an
impressive growth in area, production and productivity of chickpea in India during
the past decade. During 2019–2020, chickpea production has been estimated to be
about 10.90 million tonnes, which is about 47% of the total pulse production
(23.01 mt) in India. Madhya Pradesh, Rajasthan, Maharashtra, Uttar Pradesh,
Andhra Pradesh, Karnataka, Chhattisgarh, Bihar and Jharkhand contribute more
than 95% of the total chickpea production in the country. In India, both desi- and
kabuli-type chickpea varieties are grown. India continued to remain the major
importer of desi chickpea but has emerged as a major exporter of kabuli chickpea
during the past decade. India has made remarkable progress in expanding chickpea
area and production. Among pulses, chickpea has the longest history of research in
India.
It started as early as 1905 when Imperial Agricultural Research Institute, Pusa,
made a modest beginning by taking up breeding work on chickpea. Breeding
programme to select high-yielding types and its purification from the existing
heterogeneous land races were initiated mainly at Kanpur (Uttar Pradesh), Lyallpur
(now in Pakistan), Bombay (Maharashtra) and central India (Madhya Pradesh). With
the establishment of the All India Coordinated Pulses Improvement Project
(AICPIP) in 1967, a systematic research on chickpea in India started in the
disciplines of plant breeding, agronomy, plant pathology, entomology, microbiol-
ogy, and plant physiology. Research activities carried out in these disciplines helped
in the development of high-yielding chickpea varieties and matching production and
protection technologies for different agro-ecological zones. Realizing the impor-
tance of crop and providing focussed attention on every aspect of chickpea, a
separate All India Coordinated Research Project on Chickpea was established
in 1993.
20 Chickpea Breeding 1011

20.2 Origin, Evolution and Distribution of Species and Forms:

Wild Relatives

Chickpeas are extensively cultivated in India, Mediterranean area, the Middle East
and Ethiopia since antiquity. During modern years, they are also significant in
Mexico, Argentina, Chile, Peru, Australia and the USA. Chickpeas were first
domesticated in the Middle East as early as 12,000–10,000 years past along with
other crops of wheat, barley, rye, peas, lentil, flax and vetch (Harlan 1971) in the
Fertile Crescent (Zohary and Hopf 1973; Bar-Yosef 1998). van der Maesen (1972)
believed that the chickpea is originated in the southern Caucasus and northern Persia.
However, reported the centre of origin to be southeastern Turkey. Later on van der
Maesen (1987) recognized the southeastern part of Turkey adjoining Syria as the
possible centre of origin of chickpea based on the presence of the closely related
annual species, C. reticulatum Ladizinsky and C. echinospermum. However, the
present distribution of wild relatives may not reflect distribution at the period of
domestication (Diamond 1997). The crop diversity may have evolved outside of the
centre of origin (Harlan 1971).
Cicer, which was classified under Vicieae Alef., was later reported to belong to
the monogeneric tribe, Cicereae. The genus was revised by van der Maesen (1972),
who largely adhered to the classification of Popov (1929). The species is divided into
two subgenera, Pseudononis Popov and Viciastrum Popov; four sections, Monocicer
Popov, Chamaecicer Popov, Polycicer Popov and Acanthocicer Popov; and
14 series. The major taxonomic divisions were made on the basis of flower size,
life span, growth habit, whether the plants are woody or herbaceous and form of leaf
apex, terminating in a tendril and spine or resulted in definite improvement (van der
Maesen et al. 2006).
Wild species of chickpea were most abundant in Turkey, Iran, Afghanistan and
Central Asia (Duke 1981). Recent discoveries have raised the number of Cicer spp.
to 44, with 34 perennials and 9 annuals (van der Maesen 1987). Using the Harlan and
deWet (1971) gene pool concept, the gene pool is grouped into:

GP1 a: Cicer arietinum.

GP1 b: C. echinospermum, C. reticulatum.
GP 2: C. bijugum, C. judaicum, C. pinnatifidum.
GP 3: Other Cicer species.

The list of known species of genus Cicer is furnished below:

20.2.1 Annual Species

1. C. arietinum* L.
2. C. judaicum* Boiss.
3. C. bijugum* K.H. Rech.
4. C. pinnatifidum* Jaub. and Sp.
1012 G. P. Dixit et al.

5. C. chorassanicum* (Bge.) M. Pop.

6. C. reticulatum* Ladiz.
7. C. cuneatum* Hochst. ex Rich.
8. C. yamashitae* Kitamura.
9. C. echinospermum* P.H. Davis.

20.2.2 Perennial Species

1. C. acanthophyllum Boriss.
2. C. macracanthum M. Pop.
3. C. anatolicum* Alef.
4. C. microphyllum* Benth.
5. C. atlanticum Coss. ex Maire.
6. C. mogoltavicum (M. Pop.) Koroleva.
7. C. balcaricum Galushko.
8. C. montbretii* Jaub. and Sp.
9. C. baldshuanicum (M. Pop.) Lincz.
10. C. multijugum van der Maesen.
11. C. canariense* Santos Guerra and Lewis.
12. C. nuristanicum Kitamura.
13. C. fedtschenkoi Lincz.
14. C. oxyodon Boiss. and Hoh.
15. C. flexuosum Lipsky.
16. C. paucijugum (M. Pop.) Nevski.
17. C. floribundum* Fenzl., C. pungens* Boiss.
18. C. graecum Orph.
19. C. rassuloviae Lincz.
20. C. grande (M. Pop.) Korotk.
21. C. rechingeri Podlech.
22. C. heterophyllum* Contandr et al.
23. C. songaricum* Steph. ex. DC.
24. C. incanum Korotk.
25. C. spiroceras Jaub. and Sp.
26. C. incisum* (Willd.) K. Maly.
27. C. stapfianum K.H. Rech.
28. C. isauricum* P.H. Davis.
29. C. subaphyllum Boiss.
30. C. kermanense Bornm.
31. C. tragacanthoides Jaub. and Sp.
32. C. korshinskyi Lincz.
20 Chickpea Breeding 1013

20.2.3 Unspecified

C. laetum Rassulova and Sharipova.

*Species with confirmed somatic chromosome number of 2n ¼ 16.
Source: The CGIAR System-Wide Information Network for Genetic Resources
(SINGER; http://singer.cgiar.org/Search/SINGER/search.htm and van der Maesen
1987).
The wild relatives of chickpea have a very narrow geographical and ecological
range (Abbo et al. 2003). C. reticulatum and C. echinospermum are limited to a few
provinces of southeastern Turkey (Berger et al. 2003). It is possible that they also
occur in similar habitats in Iran or Iraq, although verification of this is not currently
possible. C. reticulatum and C. echinospermum rarely co-occur, except for a few
likely hybrid populations in the Euphrates valley north of Cermik, but do have
adjacent distributions. C. echinospermum typically occurs on more basaltic
substrates at lower elevations in open pastures and disturbed meadows with lower
tree cover than for C. reticulatum, which occurs more frequently on sand-stone or
granitic substrates in mixed pastures and some disturbed habitats (von Wettberg
et al. 2018). Taxa in the tertiary gene pool have somewhat ecologically and geo-
graphically broader distributions. C. pinnatifidum, in particular, occurs in drier
habitats in southeastern Turkey.
The cultivated chickpea (Cicer arietinum L.) and C. reticulatum are interfertile,
with similar seed proteins, and are morphologically similar, but some domestic
accessions may differ from C. reticulatum by a reciprocal inversion, by a paracentric
inversion or by location of chromosomal satellites, whereas C. echinospernum differ
from the Cicer arietinum L. by a single reciprocal translocation, and hybrids
between these tend to be sterile (Ladizinsky 1998). All other annual and perennial
Cicer spp. are genetically isolated in the tertiary gene pool and equidistant from the
domestic species as per amplified fragment length polymorphism (AFLP) diversity
analyses (Nguyen et al. 2004).

20.3 Plant Genetic Resources

Chickpea germplasm accessions are conserved worldwide in more than 30 gene

banks. Most of these accessions originated in India, Iran, Syria and Turkey. Out of
97,400 accessions available worldwide, ICRISAT holds the largest collection of
chickpea, i.e. 20,764 accessions, which comprises 20,456 of cultivated types and
308 accessions of 10 wild Cicer species collected from 60 countries (Chandora et al.
2020). Of the entire cultivated chickpea accessions, 75.2% are of desi small seed
type, 23.1% are of kabuli large seed type and the rest are of intermediate type
(Upadhyaya 2003). ICARDA gene bank has collected and conserved 15,734
accessions including 540 accessions of wild Cicer species in its global germplasm
repository from 61 countries across six continents (Asia, Africa, the Americas,
Europe and Australia). The Indian National Gene Bank at NBPGR, New Delhi,
conserves 14,704 chickpea accessions which represent a large proportion of the
1014 G. P. Dixit et al.

Table 20.1 Ex situ Cicer collections in gene banks

Institute Wild Cultivated Total
International Crop Research Institute for the Semi-Arid Tropics 308 20,456 20,764
(ICRISAT), India
International Centre for Agricultural Research in the Dry Areas 540 15,194 15,734
(ICARDA), Beirut, Lebanon
National Bureau of Plant Genetic Resources (NBPGR), New 69 14,635 14,704
Delhi, India
Australian Temperate Field Crops Collection (ATFCC), 246 8409 8655
Australia
Western Regional Plant Introduction Station, USDA- ARS, 194 7844 8038
USA
National Plant Gene Bank of Iran, Seed and Plant Improvement – 5700 5700
Institute (NPGBI-SPII), Iran
N.I. Vavilov All-Russian Scientific Research Institute of Plant – 2767 2767
Industry (MR), Russian Federation
Plant Genetic Resources Program (PGRP), Pakistan 89 2057 2146
Plant Genetic Resources Department, Aegean Agricultural 21 2054 2075
Research Institute (AARI), Turkey
Institute of Plant Production n.d. a. V.Ya. Yuryev of NAAS, – 1760 1760
Ukraine
Estación de Iguala, Instituto Nacional de Investigaciones – 1600 1600
Agricolas, Iguala, Mexico
Institute of Biodiversity Conservation (IBC), Ethiopia – 1173 1173
Research Centre for Agrobotany (RCA), Hungary 9 1161 1170
Uzbek Research Institute of Plant Industry (UZRIPI), – 1055 1055
Uzbekistan
Total 1476 85,865 87,341
Source: http://www.fao.org/wiews-archive/germplasm_query.htm?i_I¼EN

cultivated diversity found in India and some genotypes introduced from other
countries.
Other gene banks like Australian Temperate Field Crops Collection (ATFCC),
Victoria, Australia, and Western Regional Plant Introduction Station, USDA-ARS,
USA, conserve 8655 and 8038 accessions, respectively. All these collections also
include duplicates which generally happen in the process of collection, conservation
and exchange. Wild species of Cicer represents only less than 1% of the total
accessions (conserved in about 10 gene banks worldwide). Due to the narrowed
gene pool of cultivated chickpea, recent utilization of wild species through
pre-breeding programmes has significantly increased. Therefore, now priority is
being given to the collection and conservation of wild species. Chickpea germplasm
collection held in various major gene banks (ex situ) across the world is presented in
Table 20.1.
Systematic characterization and evaluation is necessary to facilitate effective
utilization of available genetic resources in crop breeding programmes and for
efficient management of germplasm. Since the 1970s, a large number of chickpea
20 Chickpea Breeding 1015

germplasm accessions have been characterized and evaluated, in batches, for mor-
phological and agronomic traits (Singh and Pratap 2016). About 99% of germplasm
accessions of chickpea at ICRISAT have been characterized and evaluated for agro-
morphological traits (Sharma et al. 2005; Upadhyaya et al. 2006). The first large-
scale evaluation of 5477 accessions was carried out by Narayan and Macefield
(1976), who observed substantial amount of genetic variability for plant type, flower
colour, days to flowering, days to seed maturity, pod size, number of seeds per pod,
weight of 100 seeds and seed colour from different geographical locations. This was
followed by various joint evaluations by collaborative research at several national
and international organizations (Muehlbauer and Sarker 2017). In India, systematic
research in chickpea started with the inception of All India Coordinated Pulse
Improvement Program (AICPIP) during 1967 (http://www.aicrpchickpea.res.in)
followed by the establishment of a separate All India Coordinated Research Project
(AICRP) on chickpea during 1993. However, characterization of Indian chickpea
collections was mainly taken care by NBPGR, which is also the host institute for the
Indian National Gene Bank. Along with characterization, NBPGR is also actively
carrying out evaluation of conserved chickpea germplasm.

20.4 Floral Biology, Emasculation and Pollination Techniques

Chickpea belongs to the family Fabaceae (Leguminosae), subfamily Faboideae

(Papilionaceae), tribe Cicereae and the genus Cicer (http://plants.usda.gov/core/
profile?symbol¼CIAR5).

20.4.1 Floral Biology

The inflorescence is an axillary raceme with generally a single papilionaceous

flower. Sometimes two to three flowers were also reported to occur rarely at the
same node. Peduncle is 6–30 mm long, while the pedicel is 6–13 mm long. Both the
peduncle and pedicel look like a single part because they are straight in line up to
fertilization, and then the pedicel bends down. Size of flower may vary from 8 to
10 mm. Flowers are zygomorphic with papilionaceous corolla. Each flower has five
petals: a large standard petal, two lateral wing petals and two fused keel petals. The
flower contains diadelphous stamens (nine fused and one free) of 6–8 mm and a style
(3–4 mm) with a slightly broadened stigma (Auckland and van der Maesen 1980).
Colour of the petals may be pink or purple in desi chickpeas, while kabuli flowers are
white to cream in colour.

20.4.2 Anthesis

The chickpea flower goes through five stages of development: closed bud, hooded
bud, half-open flower, fully open flower and fading flower. The stigma is receptive to
1016 G. P. Dixit et al.

pollen over a 3-day period from the hooded bud to the fully open flower stage. Pollen
matures and anthers dehisce at the half-open flower stage, resulting in self-
pollination. The keel petal remains closed at this stage, preventing the entry of
foreign pollen. Mature pollen is yellow in colour and slightly sticky. Flowering in
chickpea is indeterminate, starting at the lower nodes and continuing to the upper
nodes until the whole plant matures (Loss et al. 1998). Anthesis continues through-
out the day.
Plants produce a large number of flowers, but only around 20–50% of flowers
will develop into pods (Loss et al. 1998). Pods start appearing about 6 days after
fertilization and may take up to 4 weeks for completing seed development.
Outcrossing rates in chickpea are very low. When outcrossing is observed in close
plantings, rates are in the range of 0–1.9%. Outcrossing rate up to 5.9% has been
seen in open-flower mutation (Srinivasan and Gaur 2012).

20.4.3 Technique of Emasculation and Pollination

Due to cleistogamous nature of the flower and due to its small flowers, crossing is
difficult and tedious. Artificial hybridization with and without emasculation has been
followed in chickpea. The success of the artificial hybridization ranges from 10% to
50% depending upon the weather, particularly temperature and humidity, besides the
genotypes involved. Artificial hybridization techniques have been reviewed by
Argikar (1970), van der Maesen (1972), Smartt (1976) and Auckland and van der
Maesen (1980). For emasculation, the flower bud that is due to open the following
day is selected. The selected flower bud is held at the base between the thumb and
forefinger. The front sepal is stripped off with the help of forceps, and the keel is
pushed downwards. The exposed anthers are then gently removed. After that, a
coloured cotton thread or a tag is tied around the internodes below the emasculated
bud. Kalve and Tadege (2017) have shown that the crossing by keel petal incision or
petal removal is an effective approach which significantly increases the crossing
success rate.
Pollination is generally done in the morning on the following day. Half-opened
flowers are the best source of matured pollen. Such flower buds are collected from
the intended male parent in a Petri dish or a glass tube. At the time of pollination, the
standard and wings of the selected buds are removed, and the upper portion of the
keel is lightly pressed between the thumb and the forefinger to shed enough pollen
on the stigma of the emasculated flower. Pollen grains germinate in nearly 30 min
after pollination. The germinated pollen tube takes 4 h to reach the base of the ovary
(Malti and Shivanna 1983). However, it takes 24 h for fertilization after pollination.
In order to increase the success rate of artificial hybridization, the following points
are taken care of:

1. Selection of large flower buds.

2. Selection of lateral buds rather than the terminal ones since the success is reported
to be better on the lateral buds (Sindhu et al. 1981).
20 Chickpea Breeding 1017

3. Avoiding mechanical injury to the floral parts at the time of emasculation and
pollination.
4. Attempting hybridization after the formation of the first pod (Bahl and Gowda
1975).

Timing of pollination and fertilization is also important in deciding the success

rate. Under the conditions of low temperature, emasculation in the afternoon
followed by pollination in the following morning gives better results. However,
when the temperatures are high, morning emasculation followed by immediate
pollination or pollination in the same afternoon is reported to be successful
(Khosh-Khui and Niknejad 1972; Singh and Auckland 1975; Bejiga and Tessema
1981; Pundir and Reddy 1984).
Tullu and van Rheenen (1989) showed that field environment is more favourable
for crossing chickpea than green house. They have reported that the time of
emasculation and pollination has no significant effect on crossing success. In
contrast, emasculation followed by pollination was found to be more effective in
some parts of the world, while evening emasculation and next-day pollination were
found to have better results in other parts. Selection of parents for crossing has also
been found crucial for successful hybridization. It has been reported that crossing
success may be influenced by the parental identity and the environment in which
plants are growing (Pittman and Levin 1989). The female parent plays a crucial role
in determining the crossing success between both the parents. It was reported that for
better crossing in chickpea, parent with small seed size should be used as female
parent (Anbessa and Warkentin 2005). Moreover, female flower with anthocyanin
pigmentation is better than the one without pigmentation which often scheduled for
natural flower drop.
Crossing devoid of emasculation was found as a second option for chickpea
crossing (Arora and Jeena 2000; Dahiya 1974 ; Retig 1971; Arora and Singh 1990).
For this method to succeed, identification of flower stage is very important so that the
artificial pollination can be done before its pollen grains are shed naturally. When
hybridization without emasculation is attempted, there is always some chance of
self- pollination. Therefore, this technique should only be used when parents are
chosen on the basis of marker genes which can be used to eliminate self-pollinated
progenies in the F1 generation. In chickpea, sufficient information is available on
inheritance of various traits (Dahiya 1974; Retig 1971). Therefore, monogenic traits
with complete or incomplete dominance can be used as ‘markers’ to identify selfs.
The reduced damage to flowers and the reduced time taken when flowers are not
emasculated while making crosses can result in more flowers setting seed for the
same amount of effort even when some selfed plants are discovered (Singh 2001).
1018 G. P. Dixit et al.

20.5 Molecular Cytogenetics and Breeding

All chickpea cultivars and their wild relatives are self-fertilizing diploids
(2n ¼ 2x ¼ 16 chromosomes) (Ahmad and Godward 1980; Mercy et al. 1974;
Singh and Singh 1997) with a genome size of 740 Mbp (Varshney et al. 2013c). A
few chickpea species have 2n ¼ 14 chromosome number. An attempt to cytogeneti-
cally characterize the perennial Cicer species was carried out by many researchers.
In 1972, van der Maesen estimated 2n ¼ 14 or 2n ¼ 16 as the chromosome number
in the perennial Cicer species. The initial description of the karyotype of the
perennial C. anatolicum (Ahmad 1989; Hejazi 2011) established 2n ¼ 16 as the
chromosome number, as is the case for the annuals. Ensuring analysis revealed much
similarity in the karyotype of C. songaricum with that of C. arietinum,
C. reticulatum and C. echinospermum.
Abbo et al. (1994) and Staginnus et al. (1999) reported first sequences localized
through fluorescence in situ hybridization (FISH) technique as the ribosomal RNA
genes. While only one chromosome pair carries a visible satellite, two sites hybridize
with a 45S rDNA sequence, which was interesting in light of the presence of two
satellited chromosome pairs in C. reticulatum (Abbo et al. 1994; Ohri and Pal 1991).
Additionally, two sites with 5S rRNA and 45S rDNA sequences have been
recognized on chromosome B (Vlacilova et al. 2002). About 50% of the chickpea
genome is composed of repetitive DNA (Jain et al. 2013; Varshney et al. 2013c).
These repetitive sequences are very informative and hence serve as cytogenetic
markers, particularly where the chromosomal distribution is non-random (Jiang
and Bikram 2006; Schwarzacher 2003). Five microsatellite motifs {(A)16, (CA)8,
(TA)9, (AAC)5, (GATA)4} were selected (Sharma et al. 1995) using FISH tech-
nique, but did not produce any chromosome-specific karyotypes. All these five
microsatellite motifs are localized within each chromosome but show a varied
distribution and intensity from repeat motif to repeat motif (Gortner et al. 1998).
Zatloukalova et al. (2011) and Staginnus et al. (1999) reported a site in the peri-
centromeric region of chromosome A and a major cluster on the short arm of
chromosome B. Nonetheless, the potential of repetitive DNA sequences was
demonstrated in several studies. For instance, Staginnus et al. (1999) isolated the
two tandemly organized chickpea-specific repeats from a genomic library (CaSat
1, CaSat 2) which were very informative. CaSat 1 defined a large cluster of sites in
the sub-telomeric region of both chromosomes A and B, while CaSat 2 proved to be
present at each of the eight centromeres.
Individual chickpea chromosomes have been successfully sorted by flow
cytometry (Vlacilova et al. 2002) and utilized for mapping specific DNA sequences
and genes to individual chromosomes. Thus, specific genes (coding for various
rRNA loci), major random repetitive DNA sequences, sequence-tagged microsatel-
lite site (STMS) markers, En/Spm-like transposon sequences, simple sequence
repeats and Arabidopsis-type telomeric sequences have been successfully hybridized
to, and localized on, the chickpea chromosomes by fluorescence in situ hybridization
(FISH) (Abbo et al. 1994; Galasso et al. 1996; Gortner et al. 1998; Staginnus et al.
1999; Vlacilova et al. 2002; Valarik et al. 2004). Using polymerase chain reaction
20 Chickpea Breeding 1019

(PCR) and FISH, Vlacilova et al. (2002) have successfully associated two STMS
markers belonging to linkage group 8 of Winter et al. (2000) to the shortest
chromosome of the chickpea genome. Recently, FISH analysis on super-stretched
flow-sorted chickpea chromosomes has revealed spatial resolution of neighbouring
loci that has not been obtained by any other method (Valarik et al. 2004).
Owing to early operating and strong post-fertilization crossability barriers
(Bassiri et al. 1987; Ahmad et al. 1988; Stamigna et al. 2000; Ahmad and Slinkard
2003, 2004), only a few authentic interspecific hybrids are known in the genus Cicer.
Ladizinsky and Adler (1976a, b) studied meiotic chromosome associations in six
interspecific hybrids of Cicer. The interspecific hybrid C. arietinum  C. reticulatum
is easy to make, develops normally, has regular meiosis with eight bivalents and is
fully fertile (Ladizinsky and Adler 1976a, b). In contrast, the hybrid
C. arietinum  C. echinospermum is characterized by six bivalents plus a quadriva-
lent (Ladizinsky and Adler 1976a, b), which along with other cryptic structural
hybridities renders the F1 or F2 plants highly sterile. A reciprocal translocation also
differentiates the genomes of C. reticulatum and C. echinospermum, which results in
complete sterility (Ladizinsky and Adler 1976a, b). Chromosome association data
indicate a close chromosome homology between C. bijugum, C. judaicum and
C. pinnatifidum (Ladizinsky and Adler 1976a, b; Ahmad 2005). Univalent formation
was lowest in C. pinnatifidum  C. bijugum and highest in
C. judaicum  C. pinnatifidum. The only hybrid between C. judaicum and
C. chorassanicum has been reported by Ahmad et al. (1987) and is characterized
by a high number of univalents and very low pollen fertility. Authentic interspecific
hybrids of C. arietinum  C. pinnatifidum (Badami et al. 1997) and putative hybrids,
C. chorassanicum  C. pinnatifidum and C. chorassanicum  C. yamashitae
(Ahmad et al. 2005), have been produced, but no chromosome pairing data are
available due to the albino nature of the hybrids. Genetic studies among interspecific
hybrids between cultivated chickpea and accessions from six recently identified wild
C. echinospermum sites in southeastern Turkey indicated that both hybrid sterility
and hybrid breakdown distinct subgroups of C. echinospermum are conditioned by
one to few genetic loci (Kahraman et al. 2017).
Despite their narrow distribution, the annual wild Cicer species have a great
potential for chickpea improvement through base broadening (von Wettberg et al.
2018) and by providing adaptive traits lost in the cultigen. Because wild and
domestic Cicer have very contrasting evolutionary trajectories, there are good
reasons to expect different adaptive traits among the wild species. There is no robust
reproductive chilling (Berger and Turner 2007; Berger et al. 2012) or vegetative cold
tolerance in domestic chickpea relative to wild Cicer, whereas heat tolerance is
relatively common (Devasirvatham et al. 2012a). Wild versus domestic differences
are also evident in phenology. These responses differ in wild Cicer, where vernali-
zation and photoperiod responses become much more important (Berger et al. 2005;
Sharma and Upadhyaya 2015). These differing behaviours suggest that wild versus
domesticate differences are likely to emerge in responses to both biotic and abiotic
stresses, as the current round of phenotyping attests (Kozlov et al. 2019).
1020 G. P. Dixit et al.

The annual wild Cicer species have long been recognized as a promising source
of resistance or tolerance to a range of important biotic stresses (Fusarium wilt, leaf
miner, bruchids and nematodes) (Singh et al. 1998). However, the narrowness of the
world’s wild Cicer collection at that time made it impossible to evaluate whether this
resistance (Singh et al. 1998) was prescriptive of the species as a whole or merely a
symptom of a limited collection (Berger et al. 2003). For example, C. reticulatum
was rated as highly susceptible to Ascochyta blight and C. echinospermum as
moderately susceptible to susceptible (Singh et al. 1998), but these scores were
based solely on the evaluation of material derived from 18 and 10 independent
accessions, respectively. Making matters worse, 5 of these 18 independent
C. reticulatum accessions were collected from the Savur region, recently identified
as a single megapopulation (von Wettberg et al. 2018). To address this constraint, the
newly collected germplasm is currently being evaluated for a wide range of biotic
resistance in Australia (Ascochyta blight, Phytophthora, Pratylenchus thornei and
Pratylenchus neglectus tolerance; Reen et al. 2019) and Turkey (Fusarium,
P. thornei and P. neglectus tolerance). Although many of the activities are ongoing,
there is a history of wild Cicer exploitation in chickpea improvement (Singh and
Ocampo 1997). C. echinospermum, in particular, has been used as a source for
Ascochyta resistance.
An evaluation of global chickpea genetic resources from contrasting reproductive
phase temperature habitats showed no reproductive chilling tolerance in the cultigen
but promising tolerance among wild Cicer (Berger et al. 2012; Berger and Turner
2007). However, this evaluation was subject to the same constraints as the earlier
ICARDA work and was equally unbalanced. Recent evaluation of the new, much
wider Cicer collection in Turkey and southern Australia has identified a wide range
of C. echinospermum and C. reticulatum accessions that can set pods earlier and at
lower temperatures than the domestic checks. This material is also being evaluated
for short- and long-term water use and water-deficit response using mini-lysimeters
and is showing markedly different behaviours than domestic chickpea. The same
applies to regulation of phenology, where variation in flowering response (Kozlov
et al. 2019) may be useful for adapting chickpea to new systems niches, such as the
development of a vernalization response of winter chickpea for use in cold areas.
Spatially accurate GPS data exist for the recently collected C. echinospermum and
C. reticulatum accessions (von Wettberg et al. 2018), plus from the expanded
collection. This would enable identification of key climatic variables associated
with these sites and prioritization of accessions as potential sources of heat, cold
and drought stresses, in both the vegetative and reproductive growth phases (Li et al.
2018). It also allows natural sites to be prioritized for in situ preservation, such as the
lowest and highest elevation sites, or those on particular substrates, or those with
unique rhizobial associates (Greenlon et al. 2019).
20 Chickpea Breeding 1021

20.6 Genetic Studies on Qualitative and Quantitative Traits

Web-searchable International Crop Information System (ICIS) database is being

developed in various crops to incorporate information on genetic studies pertaining
to qualitative and quantitative traits (Balachandra 2005). Collective responsibility is
being given to International Center for Agricultural Research in the Dry Areas
(ICARDA), Morocco; International Crops Research Institute for the Semi-Arid
Tropics (ICRISAT), Hyderabad, India; United States Department of Agriculture
(USDA); and the Australian Temperate Field Crops Collection (ATFCC),
Australia in conjunction with the International Rice Research Institute (IRRI),
Philippines.

20.7 Qualitative Traits

Qualitative traits are characterized by distinct phenotype groups, and Mendelian

genetics are used to study inheritance patterns of these traits. A comprehensive list of
qualitative traits in chickpea and their gene nomenclature is given by Muehlbauer
and Singh (1987) and Pundir et al. (1985). They were further updated as a descriptor
list by the International Board for Plant Genetic Resources (IBPGR) in 1993.
Examples of qualitative traits include leaf shape and arrangement, plant habit,
stem and foliage characteristics, flower colour, seed and cotyledon characteristics,
podding, nodulation and disease resistance. Rubio et al. (2004) identified useful
qualitative genes in chickpea, viz., erect or bushy, single or double and early or late
qualitative genes across a range of environments. Resistance to iron chlorosis (Toker
et al. 2010), seed coat thickness (Gil and Cubero 1993), vigour (Sabaghpour and
Kumar 2003) and speed of germination (Dahiya et al. 1994) are other examples.
Numerous potentially beneficial phenotypes, which may be qualitatively inherited,
have been identified in species closely related to chickpea (Croser et al. 2003).
However, to date few have been confirmed as being qualitatively inherited as
phenotypes once incorporated into chickpea backgrounds. Examples of genes of
interest include virus, insect, disease and nematode resistances. Dehydrin has been
identified in Cicer pinnatifidum (Bhattarai and Fettig 2005), which may confer
drought resistance. Purple flower colour, pigmentation and single-podded traits in
C. reticulatum were governed by a dominant single gene (Adak et al. 2017). Efforts
are also under way to use GM methods to confer Helicoverpa resistance (Gupta et al.
2020; Khatodia et al. 2017; Sanyal et al. 2005) in chickpea.

20.8 Quantitative Traits

In quantitative traits which are governed by many genes, phenotypic variation

expressed as phenotypic continuum. Biometrical tools are employed in quantifying
the genetic components of quantitative traits. In the two botanical cultivar groups,
microsperma (desi) and macrosperma (kabuli), dominance of lower magnitude was
1022 G. P. Dixit et al.

observed for leaflet length, width and shape index, whereas dominance of higher
values was recorded for seed per pod. Overdominance was recorded for pod number,
seed number and seed yield per plant (Martinez et al. 1979; Moreno and Cubero
1978). The most comprehensive documentation of quantitative traits in chickpea was
given in the ICRISAT chickpea germplasm catalogue (Pundir et al. 1988). After
screening thousands of entries, Pundir et al. (1988) obtained bell-shaped frequency
distribution curves (or nearly so) for the following traits: days to flowering, duration
of flowering, plant height, canopy width, seed weight, days to physiological matu-
rity, number of primary and secondary branches, number of pods per plant, seed
yield and seed protein concentration. Analysed 28 diallel trials carried out over
8 years and estimated the genetic variance for several agronomic traits. Although
days to flowering, plant height and seed size were predominantly affected by
additive gene action, both additive and non-additive effects were important for
seed yield. This observation is partly in line with the earlier work of Jaiswal and
Singh (1989), who reported preponderance of non-additive gene effects on yield and
yield components among C. arietinum  C. reticulatum hybrid progeny.
Consequently, Jaiswal and Singh (1989) anticipated poor yield gain under selec-
tion in such crosses. However, impressive yield improvement following introgres-
sion in such interspecific crosses was reported by Singh and Ocampo (1997)
pointing to the importance of additive effects on yield in chickpea. The genetic
basis of freezing tolerance at the seedling stage was investigated, and additive,
non-additive as well as their respective interaction gene effects were identified
(Malhotra and Singh 1991). Root traits confer advantage in drought-prone
environments, and a polygenic control of root length density and root mass with
broad-sense heritability values of 0.23 and 0.27, respectively, was demonstrated in
recombinant inbred lines (Kashiwagi et al. 2006; Serraj et al. 2004). Additive
inheritance of root length and speed of radical emergence, two important adaptive
traits for rainfed farming, were reported by Waldia et al. (1993). The ability to
maintain dry matter accumulation in the seeds is a major adaptive trait under
terminal-drought conditions (Palta et al. 2004). Leport et al. (1999) studied the
yield physiology of a number of Australian chickpea cultivars in water-limited
conditions with and without irrigation after flowering. They reported multifactorial
inheritance of dry matter distribution after flowering.
Seed coat thickness is an important parameter for processing, with desi seeds
having thicker coats compared with those of kabuli type. A number of genes appear
to control this trait, with thick seed coat partly dominant to thin seed coat. Farmers
(producers) prefer to produce large-seeded chickpeas due to consumer preference,
since a larger seed size commands a higher price in regional and international
markets. The inheritance of seed size was determined as monogenic, digenic and
polygenic (Upadhyaya et al. 2006; Sundaram et al. 2019; Kumar and Singh 1995;
Malhotra et al. 1997; Hovav et al. 2003; Hossain et al. 2010; Sharma et al. 2013).
The inheritance pattern of the extra-large-seeded trait was polygenically controlled
by partial dominant alleles (Kivrak et al. 2020). Several other consumer quality traits
like seed mass, seed volume before and after soaking as well as swelling and
hydration capacity show considerable phenotypic and genotypic variation Yadav
20 Chickpea Breeding 1023

et al. 2003; Sharma et al. 2013). The inheritance of seed colour, shape and size as
well as a range of nutraceutical characteristics such as cotyledon and seed coat
flavonoids has been studied and carotenoids (Abbo et al. 2005) and seed Ca
concentration (Abbo et al. 2000). Narrow-sense heritability values of 0.5–0.9 were
reported with negative correlation with seed weight (Abbo et al. 2005). The protein
content showed continuous distribution suggesting that it is a quantitative trait
controlled by multiple genes (Gaur et al. 2016). A number of QTLs for
pro-vitamin A carotenoids were identified on the chickpea genetic map, with one
linked to a QTL for seed weight as expected from the correlation analysis (Rezaei
et al. 2019).
Molecular mapping of the quantitative trait loci (QTLs) and development of
linked and/or perfect DNA markers have blurred the distinction between qualitative
and quantitative traits. Ascochyta resistance gene with a qualitative effect as part of
the overall quantitative gene management has been provided by Cho et al. (2005).
Complex genetic linkage maps have been developed (Cho et al. 2002; Flandez-
Galvez et al. 2003) that include qualitative information on DNA sequences
representing known chickpea morphological or phenotype genes, biochemical
genes (e.g. isozymes), analogues to genes in other species (e.g. lentils and pea)
and DNA sequences without known function. Tekeoglu et al. (2000) and Santra et al.
(2000) identified several QTLs for Ascochyta blight response in several chickpea
crosses. Flandez-Galvez et al. (2003) and Collard et al. (2003a, b) identified QTLs
for Ascochyta blight resistance in interspecific and intraspecific chickpea crosses,
thereby corroborating previous reports on the oligogenic nature of this trait (Santra
et al. 2000; Tekeoglu et al. 2000). Fusarium wilt resistance in chickpea was also
studied using both Mendelian (Upadhyaya et al. 1983; Kumar 1998) and quantitative
approaches (Winter et al. 2000; Jana et al. 2003; Cobos et al. 2005).

20.9 Breeding Objectives

Chickpea is grown in more than 50 countries of the world, and the productivity of
chickpea is usually low in important chickpea-growing countries, with the average
yield ranging from 1041 kg/ha in India to 1730 kg/ha in the USA. Genetic enhance-
ment through breeding is essential to achieve increased yield coupled with stable
productivity. Chickpea breeding objectives generally differ in different regions
depending on the problems and priorities of farmers and consumer preferences of
the province. The major concern for any chickpea breeding programme is its narrow
genetic base which imposes a lesser degree of genetic variability and potential
genetic gain. To achieve the desired level of genetic improvement, broadening of
the genetic base of chickpea is very much required.
The major objectives of breeding in chickpea are:
1024 G. P. Dixit et al.

20.9.1 Breeding for Higher Yield

Chickpea is indeterminate in its growth habit, photo-sensitive as well as thermo-

sensitive (Bahl et al. 1979), and is characterized by poor partitioning of the
photosynthates resulting in very low harvest index values (Jain 1975). High yield
potential can be achieved by improving biomass and its favourable partitioning.
Another way of enhancing yield potential is by breeding cultivars responsive to
fertilizer and irrigation. This is a long-term objective since there is no variability for
this trait in the existing germplasm, and therefore some novel techniques including
the modern biotechnological tools need to be used for realizing this objective.

20.9.2 Breeding for Quality Characters Including Biofortification

Breeding programmes have given greater emphasis to market-preferred seed traits in

recent years. In desi chickpeas, most markets prefer small- to medium-size seeds
(100-seed weight 16–22 g) and pay only modest premiums for the large grades.
There is preference for yellow to light brown seed coat colour, and small niche
markets exist for green- and black-seeded types. More than 70% of desi chickpea is
used for making dhal, and a portion is further processed into flour (besan). High
milling efficiency (dhal recovery) is therefore an important trait. In kabuli chickpeas,
larger seeds get a high price premium. There is generally a preference for white or
beige seed coat colour and ram’s head seed shape. As the bulk of kabuli chickpea is
cooked as whole grain, cooking time and seed volume expansion (on soaking) are
considered important quality traits. Most kabuli-breeding programmes have shifted
an emphasis from medium (around 25 g/100 seed) to large (>30 g/100 seed) seed
size; there is also an increasing demand for extra-large kabuli (>50 g/100 seed)
chickpea, as this variety commands very high premium. Earlier the demand for
extra-large kabulis in the Indian subcontinent was met through import, mainly from
Mexico and Turkey. The extra-large kabuli germplasm introduced in India from
other countries was found poorly adapted (Yadav et al. 2004). The Indian National
Programme, in partnership with ICRISAT, has ongoing breeding programmes for
development of fusarium wilt-resistant, extra-large-seeded kabuli varieties adapted
to local environments. A few varieties like Phule G 0517, PKV 4-1 and MNK-1 have
been developed with seed size more than 50 g/100 seeds (Dixit et al. 2019).
There has been negligible input into the improvement of nutritional quality of
chickpea. Protein content of existing cultivars is generally in the range of 18–22%,
but much larger variability (12.4–32.5%) exists in the cultivated and wild species,
and this could be exploited to breed higher protein (up to 25%) varieties. The
nutritional value of off-grade chickpeas was found to be acceptable in ruminant
and pig diets (Mustafa et al. 2000). The sulphur containing-amino acids methionine
and cystine are the limiting amino acids. Transgenic technology is being used to
enhance the level of sulphur-containing amino acids because the required variation is
absent from the primary gene pool. Transgenics developed by introducing a
seed-specific chimeric gene encoding sunflower seed albumin (SSA) produced
20 Chickpea Breeding 1025

24–94% higher methionine but 10–15% lower cysteine than comparable

non-transgenic chickpea (Higgins et al. 2004).
There is a need to assess genetic variability for various nutritional and
antinutritional traits in the germplasm of cultivated and wild species. Studies are
also needed on G  E interactions and genetics of these traits. Identification of
contrasting parents for the content of each nutritional and antinutritional trait would
be required for development of genetic populations needed for mapping of genes
controlling these traits. Availability of such basic information on genetic variability
and genetics of nutritional and antinutritional traits would help in development of
breeding strategies (both conventional and biotechnological approaches) for
improvement of these traits in chickpea.

20.9.3 Breeding for Tolerance to Biotic Stresses

The serious damage caused by disease and pest results in yield instability. Ascochyta
blight, wilt and root rot are the major diseases; pod borer and leaf minor are the major
pests; and cyst, root knot and root lesion nematodes are the major soil
microorganisms that cause considerable yield losses. Obviously, breeding for resis-
tance to these stresses will help stabilize chickpea production.

20.9.4 Breeding for Abiotic Stress Resistance (Climate Change)

Considerable yield losses occur due to abiotic stresses like drought, salinity, cold and
frost. Resistance or tolerance to these stresses is more complex. However, resistant
germplasm against these stresses has been identified. Therefore, breeding for resis-
tance or tolerance to abiotic stresses is also an important objective. Chickpea
production faces many challenges due to unpredictable climate change as it increases
the frequency of drought and temperature extremes (Gaur et al. 2013a, b; Kadiyala
et al. 2016). Therefore, breeding chickpeas for such stress conditions is essential for
development of high- and stable-yielding varieties of chickpea (Devasirvatham and
Tan 2018).

20.9.5 Exploitation of Heterosis and Prospects of Hybrid

Development

Although exploitation of heterosis is difficult in chickpea due to many problems

including difficulty in producing large quantity of hybrid seeds coupled with very
high seed rate. Male sterility will be useful to employ in population improvement
schemes. In the absence of stable male sterility, development of stable and useful
male sterile genotypes becomes an important objective in chickpea. This may
however be considered as a long-term objective.
1026 G. P. Dixit et al.

20.10 Breeding Approaches: Conventional

and Non-Conventional Including the Use of Genomic Tools

Significant improvement has been made in chickpea by following various conven-

tional breeding approaches. Selection from indigenous and exotic landraces led to
the development of most of the chickpea varieties during the early phases of
chickpea breeding. This invariably led to the further narrowing down of the genetic
base, thereby diverting the focus to hybridization-based breeding programmes with
an aim to broaden the genetic base. One of the commonly used hybridization-based
methods is pedigree method—not practised in original form as it is cumbersome and
only limited number of crosses could be handled. It was found that 120 desi and
53 kabuli parents were used to develop 138 varieties (105 desi and 33 kabuli). The
pedigree analysis revealed that these varieties were developed through hybridization
using IP 58 (27), C 1234 (26), JG 62 (18), S 26 (18) and Chaffa (15) in desi, while
Rabat (26), Pb 7 (24), Banda Local (14), Etah Bold (14), Guamchil 2 (14), P
458 (14) and GW 5/6 (14) as the frequently used parents for the development of
kabuli varieties, thereby evidently specifying that very few genotypes were utilised
for the development of chickpea varieties released in India. Instead of pedigree
method, bulk method and its modifications are commonly used by following
hybridization. It is well recognized that individual plant selection is not effective
for yield in early segregating generations in chickpea. Thus, the selection is preferred
for simple traits such as seed traits, maturity and resistance to diseases in early
generation (F2, F3) while yield, etc., based selection is done in later generations. A
recombinant-derived family method that uses early-generation selection for yield in
F2-derived F4 or later-generation families to eliminate inferior crosses and inferior
F2-derived families has also been suggested (Slinkard et al. 2000) and is used at the
University of Saskatchewan, Canada, thereby necessitating to involve more and
diverse germplasm lines, primitive landraces and wild Cicer species in the
hybridization programme for the cultivar development (Verma et al. 1990; van
Rheenen et al. 1993; Nadarajan and Chaturvedi 2010; Mishra et al. 2013a, b;
Singh et al. 2014).
Most of the chickpea breeding programmes were earlier confined to intraspecific
hybridization by involving desi  desi, kabuli  kabuli or desi  kabuli crosses.
Crosses between desi and kabuli parents are extensively used for transferring genes
for Fusarium wilt, Ascochyta resistance and drought tolerance to kabuli from desi
and genes for improved seed quality, especially large seed size from kabuli to desi
chickpea. Desi  kabuli hybridization programmes have consistently led to high-
yielding progenies and have served as the source for many new cultivars (Yadav
et al. 2004). Efforts have been focussed to utilize interspecific crosses for enhancing
the genetic variability by introgressing useful genes into the cultigen(s) from wild
Cicer species which have been inadvertently being lost at the time of domestication
such as for stable disease resistance for Ascochyta blight, Fusarium wilt, root rot,
botrytis grey mould, cold tolerance, heat tolerance, drought tolerance,
nodulation, etc.
20 Chickpea Breeding 1027

Only two annual wild species, Cicer reticulatum and C. echinospermum, have so
far been exploited in the breeding programmes, as the crossing of the cultigen with
other species has remained a challenge even with embryo rescue techniques. Inter-
specific derivative lines have been developed from a successful Cicer
arietinum  C. pinnatifidum cross at PAU, Ludhiana, expressing significant
variability for yield traits and disease resistance (Kaur et al. 2013; Salaria 2020).
Continuous efforts are required for exploiting wild Cicer species. There is a need to
exploit species belonging to the tertiary gene pool, as they contain many useful
genes, particularly resistant to biotic and abiotic stresses (Ahmad et al. 2005). A desi
chickpea variety, Pusa 1103, developed by the ICAR-Indian Agricultural Research
Institute (IARI), New Delhi, India, from an interspecific cross of C. arietinum with
C. reticulatum, has been released for commercial cultivation in north India, and
recently the Punjab Agricultural University, Ludhiana, developed a high-yielding
variety PBG 8 from an interspecific cross of C. arietinum with C. judaicum for
commercial cultivation in Punjab state. PBG 8 is moderately resistant to Ascochyta
blight and botrytis grey mould and higher level of tolerance to pod borer.
As conventional breeding takes 6 to 7 years to develop homozygous lines after
hybridization, therefore breeding programmes have been focussed to reduce the
number of years required to reach homozygosity by taking more than one generation
per year for the development of a variety. One of the methods to have more than one
generation in a year is by taking the advantage of off-season nurseries or greenhouse
facilities. Another method for generation advancement is rapid generation advance-
ment (RGA) technology for accelerating the breeding cycle by involving the use of
immature seeds to produce miniature plants in artificial medium under controlled
conditions and allowing them to produce few flowers bearing seeds which are
harvested before normal seed maturity (Samineni et al. 2020).
Whole of this process is based on providing extended photoperiod (15–16 h)
through artificial lighting as long days induce early flowering in chickpea provided
until flower initiation (Sethi et al. 1981). But only single seed descent (SSD) method
could be followed using RGA whereby one or more early generations are advanced
without selection in the greenhouse. As by following SSD, large populations could
be accommodated depending on the greenhouse facility and other resources. Results
obtained by Samineni et al. (2020) have implicated the utility of RGA in breeding
programmes such as rapid progression towards homozygosity, development of
mapping populations, reduction in time, space and resources for the cultivar devel-
opment (speed breeding).
Besides above-mentioned breeding methods, mutation breeding has also been
used in chickpea improvement for enhancing genetic variability. Sufficient efforts
have been put forth in chickpea to study the effect of various mutagen treatments
(physical and chemical mutagens) on yield potential, resistance/tolerance to biotic
and abiotic stresses, effect on chlorophyll, tolerance to herbicides and quality
parameters along with elucidation of its origin. Sarma et al. (1991), Charumathi
et al. (1992) and Khan et al. (2005) reported that a significant amount of variability is
produced particularly with the increase in grain yield across the different mutagenic
treatments of gamma radiations (50 kR) in combination with gibberellic acid (John
1028 G. P. Dixit et al.

1995). However, Rao (1988) found that gamma radiations have an adverse effect on
the grain yield in chickpea. Gamma rays have also been found effective in the
development of disease resistance (CM 98 against Ascochyta blight and wilt (Haq
et al. 1999)). As far as quality is concerned, gamma rays brought a significant
increase in degree of softness of seed, thereby improving the cooking quality
(Graham et al. 2002). Some mutants have been directly released as varieties, whereas
many other mutants have been used as parents in the crossing programmes. At least
12 varieties have been developed through mutation breeding. These include seven
varieties (Pusa 408, Pusa 413, Pusa 417, Pusa 547, RS 11, RSG 2 and WCG 2)
developed by IARI and State Agricultural Universities in India; four varieties
(CM 72, CM 88, CM 98 and CM 2000) developed by the Nuclear Institute of
Agriculture and Biology, Faisalabad, Pakistan; and one variety (Hyprosola) devel-
oped by the Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh.
Recent advances in the in vitro culture, transformation and plant regeneration
protocols for chickpea offer unique opportunities to realize the full potential of
chickpea production. Transgenic technology can be utilized to improve those traits
for which adequate variability is not available in the gene pool. These include
resistance to pod borer and other biotic and abiotic stresses, as well as sulphur-
containing amino acids. However, as of date, no transgenic chickpea variety has
been approved for cultivation anywhere in the world.
With the advent of the molecular markers, marker-assisted selection (MAS) is
being considered for improving the precision and efficiency of conventional plant-
breeding methods by understanding the genetic basis of the traits. MAS is consid-
ered to be useful for improving traits wherein direct selection is difficult or is
convenient (e.g. root traits for drought avoidance, antinutritional factors, quality
traits). MAS finds a significant role in pyramiding genes for resistance from different
sources particularly when the resistance is controlled polygenically (e.g. resistance
to Ascochyta blight), combining genes conferring different resistance mechanisms
(e.g. antixenosis, antibiosis and tolerance for pod borer) and resistance against two or
more stresses (e.g. fusarium wilt and pod borer). Besides this MAS is exploited for
the introgression of genes from wild species into cultivated germplasm with mini-
mum linkage drag and mapping of quantitative trait loci (QTLs) governing econom-
ically important traits. The molecular tools hasten the conventional breeding and are
a rapid precise alternative for the improvement of quantitative traits like yield and
resistance/tolerance to various biotic and abiotic stresses. During the last decade,
significant improvements have been made in the generation of plenty of genomic
resources. It has been even made possible to locate genomic regions of various
quantitative traits for use in MAS by various molecular marker technologies, thereby
encouraging the usage of molecular breeding approaches in chickpea breeding
programmes such as marker-assisted backcrossing (MABC), marker-assisted recur-
rent selection (MARS), advanced backcross quantitative trait loci (AB-QTL) analy-
sis and genomics-assisted breeding (GAB).
Development of molecular markers in chickpea on a large-scale have been made
possible through next-generation sequencing technologies leading to the construc-
tion of dense linkage maps and identification of several molecular markers
20 Chickpea Breeding 1029

associated with agronomically important traits. The application of a holistic

approach combining genomics with breeding and physiology, termed as
genomics-assisted breeding (GAB) (Varshney et al. 2005), provides strategies for
improving component traits of biotic and abiotic stress tolerance that should prove
more effective and efficient than the conventional methods. Various functional
genomic approaches like suppression subtractive hybridization (SSH), microarray
and EST sequencing, serial analysis of gene expression (SAGE) and their
modifications such as super serial analysis of gene expression (SuperSAGE) and
deep SuperSAGE have been utilised for the identification of transcripts for different
abiotic stress-responsive genes in chickpea for quantification of global gene expres-
sion (Matsumura et al. 2005; Buhariwalla et al. 2005; Molina et al. 2008).
Considerable reduction in sequencing costs has been made on utilization of
advances in next-generation sequencing (NGS) technology (Varshney et al. 2009)
and has led to the evolution of genotyping methods from individual marker- to
whole-genome sequence-based genotyping. This brought about the development of
large-scale genomic resources, including genome sequence assemblies,
resequencing of few thousand lines, high-resolution genetic maps and a range of
low- to high-density genotyping platforms. Even the identification of alleles and
haplotypes associated with agronomic traits in chickpea has been made possible on
utilization of such genomic resources (Varshney et al. 2019b). Fine mapping of the
QTL-hotspot region from ~ 7.74 Mb to ~ 300 kb, for drought tolerance-related traits
(Jaganathan et al. 2015; Kale et al. 2015), is done by genotyping-by-sequencing and
skim sequencing-based bin mapping. ‘Axiom®CicerSNP Array’, a high-throughput
single-nucleotide polymorphism (SNP) genotyping platform, has facilitated the
construction of dense genetic maps for the advancement of genetics and breeding
efforts in chickpea (Roorkiwal et al. 2018). Whole-genome resequencing (WGRS)
has led to the dissection of genetic diversity, population structure, domestication
patterns, linkage disequilibrium and the unexploited genetic potential for chickpea
improvement (Varshney et al. 2019a). Modern genomics technologies have the
potential to hasten the process for trait mapping, gene discovery, marker develop-
ment and molecular breeding in addition to the enhancement of the rate of produc-
tivity gains in chickpea. Integration of genome-wide sequence information with
precise phenotypic variation permits to capture accessions with low-frequency
alternatives responsible for essential phenotypes such as yield components, abiotic
stress tolerance or disease resistance. Chickpea breeding programmes are focussed
on improving yield and its component traits under biotic and abiotic stress
conditions. But, the changes in climatic patterns have levied challenges to enhance
yield levels of chickpea, in addition to meet the growing demands w.r.t. health
benefits of consumers. Therefore, breeding efforts need to be focussed for the
development of superior climate-resilient chickpea varieties to meet out the
nutritional issues of developing countries.
1030 G. P. Dixit et al.

20.11 Emerging Challenges at National and International Levels

Climate change has played a key role in the evolution. Under present context, effects
of global warming are experienced in the form of climate change like erratic rainfall
patterns (reduction in the number of rainy days, more drought and flood incidence,
etc.), abrupt rise or drop in temperature and humidity, longer consecutive foggy days
leading to low intensity of sunlight during crop growth, etc. Under such adverse
climatic conditions and selection pressure leading to the newer diseases (Alternaria
blight, stem rot, collar rot, rust, etc.) along with the incidence of prevalent diseases
(Ascochyta blight, botrytis grey mould, wilt, dry root rot, etc.), increased infestation
of the insect pests (gram pod borer, cut worm, etc.) under high humidity or foggy
climatic conditions is becoming a consistent phenomenon of climate change not only
in India but also in other chickpea-growing countries worldwide. Even the availabil-
ity and utilization of macro- and micro-nutrients in soil or nutrients applied to the
crop is hampered due to low intensity of sunlight (due to fog) during chickpea-
growing season. Under harsh environmental conditions, even the nodulation may
also be affected. Chickpea being a sensitive crop is susceptible to a large number of
biotic (diseases, insect pests, nematodes, weeds) and abiotic (drought, heat, cold,
salinity, alkalinity, etc.) stresses. Low productivity levels of chickpea are due to
abrupt rise (terminal heat stress) or drop in temperature (cold or frost stress), terminal
soil moisture stress or excess rainfall during crop growth. The emerging challenges
in chickpea have been discussed as biotic and abiotic constraints, ideal plant type and
hastening breeding cycle.
In chickpea a large number of biotic stresses (fusarium wilt, Ascochyta blight,
botrytis grey mould, pod borer, bruchids) and abiotic stresses (drought, heat, cold)
limit the realization of yield potential at farmers’ fields. To curtail losses due to these
stresses, several strategies including genetic options have been recommended and
adopted (Nadarajan and Chaturvedi 2010; Kaur et al. 2013) to enhance chickpea
productivity and production.

20.11.1 Biotic Stress

20.11.1.1 Fusarium Wilt

It is a major problem reported from 32 countries across 6 continents in the world
causing 10 to 90% losses (Jimenez-Diaz et al. 1989; Singh and Reddy 1991).
Initially symptoms of wilt vary among different chickpea genotypes. Resistance to
wilt is controlled by a few major genes that are part of oligogenic resistance
mechanism, thereby delaying the onset of disease symptoms. Resistance against
Fusarium wilt has been reported in the indigenous chickpea germplasm (Singh et al.
2012). Around eight pathogenic races of Foc (races 0, 1A, 1B/C, 2, 3, 4, 5 and 6)
have been reported worldwide (Jendoubi et al. 2017). For the management of
Fusarium wilt, the most effective and efficient method is the development of
resistant cultivars. Reliable and efficient screening methods have been established
by developing sick-plots for evaluating a large number of genotypes under field
20 Chickpea Breeding 1031

conditions at several AICRP centres. Till date conventional breeding methods are
followed for the development of Fusarium wilt-resistant varieties, but it is time-
consuming and depends on inoculum load and specific environmental factors that
influence disease development. The utilization of molecular markers closely linked
to genes/QTLs controlling Fusarium wilt offers a great potential for the identifica-
tion of resistant genotypes.

20.11.1.2 Ascochyta Blight

It is one of the most important foliar diseases of chickpea leading to yield losses as
high as 100% (Nene and Reddy 1987; Singh 1990) and prevalent in many parts of
the world including India. Ascochyta rabiei (causal organism) isolates have been
classified based on their levels of virulence (Udupa et al. 1998; Chen et al. 2004;
Jayakumar et al. 2005) into either a two- or three-pathotype system (I, II and III). It is
speculated that the disease might have spread from its site of origin to distant
continents through chickpea germplasm exchanges. Two most damaging symptoms
of this disease are stem breakage along with girdling and collapse of twigs. The
frequency of resistant and moderately resistant-type accessions is observed to be
comparatively higher in accessions originated from Southwestern Asian countries
particularly Iran and Syria than the accessions originated from Indian subcontinent
(Gayacharan et al. 2020). Presently, chickpea breeders have shifted to gene
pyramiding in elite genotypes instead of incorporating vertical resistance for the
incorporation of stable resistance. Besides this, deployment of different lines having
resistance to different races of the pathogen prevalent in different regions can be
effective in minimizing yield losses caused by Ascochyta blight.

20.11.1.3 Botrytis Grey Mould

Botrytis grey mould (BGM) is the second most important foliar disease of chickpea.
BGM is predominant in 15 countries including India, Bangladesh, Nepal, Pakistan,
Australia, Argentina, Myanmar, Canada, Columbia, Hungary, Mexico, Spain, Tur-
key, the USA and Vietnam. Maximum crop losses are observed in seasons with wet
spring, particularly when crops develop dense canopies. Earlier it was reported that
there is no reliable source known to have resistance to BGM (Singh and Reddy
1991) in cultivated germplasm. Interspecific derivative lines of
C. arietinum  C. pinnatifidum crosses, developed at PAU, Ludhiana, have
exhibited a moderate to high level of genetic resistance against BGM (Kaur et al.
2013; Salaria 2020) and can be utilized to incorporate such durable resistance into
elite genotypes for the development of high-yielding chickpea cultivars.

20.11.1.4 Pod Borer

One of the major insect pests infesting chickpea crop is pod borer (Helicoverpa
armigera). It predominantly causes damages across Asia, Africa, Australia and some
other chickpea-growing regions. Pod borer is a polyphagous insect and known to
cause damage to more than 182 plant species. The breeding approach followed for
conferring pod borer resistance in chickpea is an integrated one involving both the
antixenosis/antibiosis and avoidance mechanisms (Clement et al. 1992). The
1032 G. P. Dixit et al.

development of cultivars resistant or tolerant to H. armigera could be integrated in

the pest management strategy by identifying, characterizing and utilizing the genetic
mechanisms conferring durable resistance to pod borer (Dua et al. 2002). More than
14,000 chickpea germplasm accessions screened under field conditions at ICRISAT
for resistance against H. armigera (Lateef and Sachan 1990) led to the identification
and release of moderately resistant/tolerant chickpea cultivars (Lateef 1985; Lateef
and Pimbert 1990). Still complete resistance against pod borer is far from reach.
Different chickpea cultivars express differential inhibition activity of gut proteinases
of H. armigera, indicating that H. armigera is adapted to a wide range of host protein
inhibitors (Singh et al. 2008). A high-throughput AxiomCicerSNP array led to the
construction of a dense linkage map comprising of 3873 loci spanning a distance of
949.27 cM. This genomic region, after validation, could be useful to improve
H. armigera resistance component traits in elite chickpea cultivars (Barmukh et al.
2020).

20.11.1.5 Bruchids
Significant losses by storage pests occur in the Mediterranean region and in India.
Bruchid (Callosobruchus chinensis) infestation levels can cause losses ranging from
13% (Dias and Yadav 1988; Mookherjee et al. 1970) to total loss (Weigand and
Tahhan 1990) in storage. Talking about resistance to storage pests like bruchids,
there is no resistant genotype available in the cultivated chickpea germplasm.
Chickpea grains with higher sugar and lower phenol contents were found to be
more susceptible to bruchids (Swamy et al. 2020), whereas wild chickpea accessions
have exhibited variable resistance to bruchids (Singh et al. 1994, 1998). Owing to
crossing barrier, it has not been possible to transfer this trait to the cultivated
background. Thus, it is advised to go for chemical control measures (Duke 1981).
Recent studies in legume crops indicated that seed storage in three-layered polythene
bag resulted in effective control of bruchids and their further spread (Vales et al.
2014; Sudini et al. 2015).

20.11.1.6 Weeds
Besides above-mentioned biotic factors, seasonal weeds associated with chickpea
crop such as Phalaris minor (L-Retz), Avena fatua, Lolium temulentum (L), Trifo-
lium spp., Chenopodium album (L), Melilotus spp., Lathyrus tuberosus (L), Convol-
vulus arvensis (L), Anagallis arvensis (L), Asphodelus tenuifolius (Cavan),
Medicago denticulata (L. wild), Rumex dentatus (L), Fumaria parviflora (Lamk),
Circium arvense (L. Scop), Cyperus rotundus (L) and Cynodon dactylon (L. Pers)
pose a serious threat to chickpea productivity by causing a smothering effect to the
crop. It is specifically observed to be a major problem during winter rains when the
weeds become a major yield-limiting factor. Under present situation when the farm
labour days are becoming expensive, there is a need to have varieties tolerant to
herbicides (Sandhu et al. 2010; Gaur et al. 2012). Significant levels of genetic
variations against post-emergence herbicide (imazethapyr) have been observed to
be present on screening reference set and elite breeding lines in chickpea (Gaur et al.
20 Chickpea Breeding 1033

2013a; Gupta et al. 2018). These have paved the way for the development of post-
emergence herbicide-tolerant chickpea varieties.

20.11.2 Abiotic Stress

20.11.2.1 Drought
Globally one of the effects of climate change is drought responsible for high-yield
losses in chickpea. Usually, terminal drought has adverse effects on the crop
productivity (Khanna-Chopra and Sinha 1987). Cultivation of early maturing
cultivars is suggested for areas frequently affected by drought as it helps in judicious
utilization of the available soil moisture and escape of the crop from drought.
Recently, studies on root traits have gained much importance as genotypes with
longer root systems have better potential for the extraction of moisture from deeper
layers of soil, thereby exhibiting better drought tolerance. Among wild Cicer species
screened, a few accessions of C. pinnatifidum and C. reticulatum were found to be
resistant/tolerant to drought (Toker et al. 2007). The ICC 4958 genotype from
cultivated germplasm is a potential donor extensively utilized for the incorporation
of drought tolerance. Chickpea introgression lines with improved drought tolerance
(ICC 4958, used as donor) gave promising results in India and Kenya (Gaur et al.
2012). The introgression lines with improved root traits screened at several locations
in central and southern India exhibited high G  E interaction.

20.11.2.2 Heat Stress

Chickpea is a cool season crop. In the era of climate change and varying cropping
pattern, the crop is being exposed to high temperature (>35  C) during the repro-
ductive phase, leading to severe yield penalties. Reproductive period is most sensi-
tive to heat stress conditions, if temperature rises above the threshold level, the pod
formation and seed set is affected adversely, thereby, in turn, leading to reduced
grain yield (Summerfield et al. 1984; Wang et al. 2006; Basu et al. 2009; Kumar
et al. 2013). Additionally, adverse effects of high temperature are experienced during
seed germination, respiration, membrane stability, photosynthesis, hormone level,
nutrient absorption, protoplasmic movement, fruit maturation and materials trans-
port leading to withering, burning of lower leaves, desiccation of poorly developed
plants, stunting flower and pod abortion, reduced root nodulation and nitrogen
fixation affecting quality of seeds and seed yield (Saxena et al. 1988; Kurdali
1996; Chen et al. 1982; Wahid and Close 2007). Even though chickpea is compara-
tively more tolerant to heat stress compared to other cool season legume crops
(Summerfield et al. 1984; Erskine et al. 1994; McDonald and Paulsen 1997; Patrick
and Stoddard 2010), still severe heat stress leads to high-yield losses and crop failure
(Devasirvatham et al. 2012b). Large genetic variations for heat tolerance in
chickpea-cultivated germplasm have been observed as revealed from multi-location
screening of reference set against heat stress in India (Krishnamurthy et al. 2010). A
field screening technique standardized by Gaur et al. (2014) for heat tolerance led to
the identification of several sources of heat tolerance. The JG 14, a heat tolerant
1034 G. P. Dixit et al.

variety, released in India is found to be promising for normal as well as late planting
situations in central and southern states.

20.11.2.3 Cold Stress

Chickpea being a winter season crop is more productive than the traditionally grown
spring season crops in the Mediterranean region (Singh and Hawtin 1979). This is
mainly due to the long cropping season and better moisture availability. Chickpea
crop grown during winter season experiences difficulties such as flower drop and
pod abortion, thereby leading to severe yield losses particularly when the mean day
temperature falls below 15  C (Savithri et al. 1980; Srinivasan et al. 1999; Clarke
and Siddique 2004; Nayyar et al. 2005). Studies have revealed lack of cold/chilling
tolerance in the domesticated gene pool, while significant tolerance potential has
been observed in the annual wild relatives of chickpea (Berger and Turner 2007;
Berger et al. 2003, 2012). Preliminary studies in Australia demonstrated that the wild
relatives that readily crossable with chickpea (C. reticulatum, C. echinospermum)
have considerably more cold tolerance at vegetative stage and chilling tolerance at
reproductive stage compared to domestic chickpea. Therefore, significant efforts are
required for the identification of novel sources for cold tolerance followed by the
development of the breeding population(s) meant for the identification of cold-
tolerant genotypes.

20.11.3 Ideal Plant Type

Today when the effects of global warming experienced in the form of climate change
are leading to the changes in the cropping pattern, there is an urgent need to
restructure existing bushy/semi-spreading chickpea plant types for the enhancement
of photosynthetic and input use efficiency, reduction in the cost of cultivation,
minimizing foliar diseases, varieties amenable to intercropping, mechanical
harvesting and to ease the intercultural operations. Two different ideotypes were
identified to be suitable for winter and spring sown crops under Italian conditions. It
was suggested that winter types should be resistant to Ascochyta blight, cold tolerant,
longer vegetative cycle, erect growth habit and bearing of pods on upper parts of the
branches to facilitate mechanical harvesting, whereas, for spring sown crop, short
vegetative cycle, good adaptability to southern and central environments, high yield
and good grain quality were suggested by Saccardo and Calcagno (1990). Several
mutants with desirable traits like cymose inflorescence having more than three
flowers per node (Gaur and Gour 2002), brachytic growth habit (Gaur et al.
2008a, b) and determinate growth habit (Hegde 2011) and mutant with short
internode (E100Y) and erect growth (Chaturvedi et al. 2010) offer ample scope to
alter the ideotype of chickpea varieties for their suitability to mechanized harvesting
(Sandhu et al. 2010; Gaur et al. 2012).
20 Chickpea Breeding 1035

20.11.4 Reduction in Breeding Period

Significant efforts have been put forth at national and international levels for
hastening the chickpea breeding programmes to tackle the repercussions of climate
change. Considering the importance of rapid generation advancement for shortening
the breeding cycle, Punjab Agricultural University, Ludhiana, has off-season nursery
facility at Keylong (H.P), and few years back, ICAR-Indian Institute of Pulses
Research has also established off-season nursery centre at Dharwad (Karnataka).
The Dharwad centre helps other chickpea breeding centres for rapid generation
turnover. More than 200 high-yielding varieties with varying levels of tolerance to
biotic and abiotic stresses have been developed with significant gains in production
and productivity with more than 51% chickpea’s share in total pulse production
(19.27 mt) in India during 2013–2014.
Still, to improve the complex traits wherein phenotyping/selection in the
segregating generations is difficult, deployment of molecular markers linked with
targeted genes/QTLs is suggested to hasten the breeding cycle. Recent advances in
the development of hefty numeral of molecular markers linked with useful genes/
QTLs governing traits of breeders’ interest have encouraged applications of marker-
assisted breeding in chickpea improvement. One of the successful examples is
deployment of MABC (marker-assisted backcrossing) wherein a ‘QTL-hotspot’
containing QTLs for several root and drought tolerance traits was transferred from
the drought-tolerant line ICC4958 to a popular desi chickpea variety JG
11 (Varshney et al. 2013c). They have suggested ways to go for marker-assisted
breeding for the development of future varieties in chickpea on reviewing the status
of genomic resources available for chickpea improvement. Further, Gaur et al.
(2013b) reported identification of improved lines with significantly higher yield.
Recently, besides utilising off-season nurseries along with molecular breeding,
RGA (rapid generation advancement) technology is gaining impetus for accelerating
the breeding cycle. This technique offers the flexibility to take about six generations
in a year compared to conventional breeding with two generations per year using
off-season nurseries. This technology involves the usage of immature seeds for the
production of miniature plants in artificial medium under controlled conditions,
thereby allowing them to produce few flowers, bearing seeds, which are harvested
before normal seed maturity. The whole process is based on providing long days of
conditions with 15–16 h photoperiod through artificial lighting for the induction of
early flowering in chickpea (Sethi et al. 1981). The only drawback perceived is that
out of all the chickpea breeding methods only single seed descent (SSD) method
could be followed for the RGA whereby one or more early generations are advanced
without selection in the greenhouse. As by following SSD, large populations could
be accommodated depending on the greenhouse facility and other resources.
Samineni et al. (2020) suggested the utility of RGA in breeding programmes such
as rapid progression towards homozygosity, development of mapping populations,
reduction in time, space and resources for the cultivar development (speed breeding).
1036 G. P. Dixit et al.

20.12 Precise and High-Throughput Phenotyping Protocols

for Key Traits

The term ‘phenotype’, derived from the Greek words ‘phainein’ and ‘typos’ (mean-
ing show and type, respectively), was explained as ‘all types of organisms distin-
guished by direct inspection or with finer methods of measurement or description’ by
Wilhelm Johannsen in 1911 (Johannsen 1911). Fiorani and Schurr (2013) defined
plant phenotyping as the set of methodologies and protocols used to accurately
measure plant growth, architecture and composition at different scales. Traditionally
phenotyping methods deal with either one or few specific plant characteristics at a
given time without thorough functional analysis of constituent traits linking geno-
type with the phenotype. One of the key difficulties with conventional (direct)
measurements of basic plant traits is that they are laborious and often destructive.
This is mainly evident while working with larger plants and plant species with many
small leaves. Additionally, measurement of many traits in segregating generations
becomes difficult as they are invasive, labour-dependent and time-consuming,
thereby decreasing the breeding efficiency as selection is delayed to later genera-
tion(s). Besides this, often the environmental and soil variables are not taken into
consideration while monitoring, aggravating the phenotypic bottleneck(s). Many
times, depending upon the study conducted, other important factors (other than
those under consideration) are overlooked. Therefore, phenotypic prediction based
on the genetic composition of lines or cultivars must be considered to address all the
above-mentioned issues (White et al. 2012). In plant breeding, field experiments
conducted at multiple locations are indispensable for evaluating the adaptability of
new candidate genotypes in order to examine their pattern of genotype  environ-
ment interaction (Chapman et al. 2014). Plant phenotyping techniques have impres-
sively evolved over the last two decades. In today’s era of genomics, data generated
by plant phenotyping needs to be high-quality quantitative data to adapt to the needs
of modern breeding techniques. Modern plant phenotyping is all about increased
accuracy, precision, throughput at all levels with reduction in costs and automation
to minimize labour demand.
On realizing the need for rapid and precise phenotyping of multiple traits, many
next-generation and high-throughput plant phenotyping platforms (HTPPs) have
been developed (Hartmann et al. 2011) to measure trait values accurately for the
assessment of variation among individuals, thereby enabling better HTPPs
approaches to address the relationship between traits, plant development, growth
and reproduction under various conditions. Now, high-throughput phenotyping
strides for non-invasive technologies and is one of the rapidly advancing fields
(Berger et al. 2010; Furbank et al. 2009). These are based on various imaging
techniques to record plant structure, estimation of biomass, analysis of phenology,
plant health, tissue-water relations, transpiration, photosynthetic activity, etc. Such
phenotyping systems can work well under field setting or controlled environment
where individual plants are automatically weighed and watered. Owing to the high
cost involved in HTPPs, cost-effective automated and semi-automated methods for
data acquisition and analysis are now being developed (Gehan and Kellogg 2017).
20 Chickpea Breeding 1037

These HTPPs provides physiological and morphological data along with simulta-
neous analysis of the massive data generated and can give better understanding of
the whole phenome of the plant under a wide range of environmental and growth
conditions.
Mainly HTPPs are categorized into two types, viz., ground-based HTPPs
(enabling the data to be captured at a plot level) and aerial HTPPs (involving a
very high level of automation and precision to cover larger plots and even the entire
fields). Ground-level HTPPs involve the usage of carts, tractors or gantry-mounted
sensors, while aerial HTTPs generally involves small airplanes, helicopters and
unmanned aerial platforms (UAPs) such as polycopters and drones. The recent
alternatives to airplanes in aerial HTPPs include ‘phenotowers’ (Rascher et al.
2011) and ‘blimps’ (Losos et al. 2013). A few HTPPs deployed for phenotyping
several crop plants are available for Arabidopsis (Granier et al. 2006; De Diego et al.
2017), cotton (Andrade-Sanchez et al. 2013), barley (Hartmann et al. 2011), maize
(Trachsel et al. 2011), wheat (Bai et al. 2016; Zhang et al. 2017), rice (Yang 2012),
sorghum (Hartmann et al. 2011; Golzarian et al. 2011), etc. mostly run by large seed
companies and advanced crop research institutes around the world. Some of the
popular HTPPs are LemnaTec; Digital Phenotyping-KeyGene; International Plant
Phenotyping Network; Julich Plant Phenotyping Centre; LEPSEMontpellier Plant
Phenotyping Platform; PPHD-INRA; Dijon; Phenopsis; Arabidopsis Platform,
INRA; PhenoFab, Wageningen; The Biotron, Canada (KeyGene + LemnaTec);
and Australian Plant Phenomics Facility.

20.12.1 Phenotyping for Abiotic Stresses

High-yield losses have been recorded due to the abiotic stresses, especially owing to
adverse agro-climatic conditions experienced at the time of reproductive phase,
leading to instability in chickpea production worldwide. Breeding for tolerant
chickpea types with wider adaptation to different and diverse growth conditions
and regions is the best strategy. But this requires a fine-tuned amalgamation of
advanced phenotyping and genotyping methods. It is suggested that for abiotic
stresses due consideration should be given for the phenotyping of plant phenology,
early vigour, root traits, stomatal conductance, canopy temperature and stay-green
trait, pollen viability, biomass, harvest index and grain yield. Chickpea breeders
generally focus on selecting lines with adaptation to wider agro-climatic conditions.
However, adaptation is dependent on the season, sowing date and water regime
combinations. These combinations often affect phenological development of ther-
mal time to flowering, duration of flowering, end of flowering and pod set, with
accelerated development under late-sown and dry conditions (Sadras et al. 2016).
In chickpea, flowering and podding (reproductive and grain filling stages, respec-
tively) are generally the most critical stages affected by adverse conditions. Conven-
tionally, flowering is recorded visually based on the percentage of plants per plot
(Mallikarjuna et al. 2017), which is subjective and prone to human errors. For this,
an image-based phenotyping method can be opted to measure such qualitative traits
1038 G. P. Dixit et al.

effectively as a replacement of the visual method. There are successful examples of

HTP technology utilized to phenotype heading and flowering (Sadeghi-Tehran et al.
2017) of various crop species (wheat, maize, barley, rice, Brassica), thereby
suggesting that the assessment of flowering time in chickpea by HTPP is very
feasible and should be explored to avoid errors between scorers and days.
Early vigour is an adaptive trait for drought and chilling stress in chickpea (Croser
et al. 2003). Several conventional methods to assess early vigour involve visual
scores based on a pre-determined scale (Sivasakthi et al. 2017, 2018) or vegetative
biomass harvest (Berger et al. 2004). Although effective, these methods are highly
subjective and/or labour intensive and, thus, not suitable on large-scale field trials. A
robust and rapid assessment of early vigour is offered by HTP technology using
sensors or multispectral imagery in various grain crop species such as wheat (Kipp
et al. 2014), barley (Di Gennaro et al. 2018) and field pea (Nguyen et al. 2018) and
can also be utilised for boosting genetic gains in chickpea.
Talking about chickpea root traits, root length density, root volume, root depth
and root mass play a critical role in drought and heat adaptation (Kashiwagi et al.
2015; Ramamoorthy et al. 2017). Several QTLs controlling root traits have been
reported (Gaur et al. 2008a, b; Varshney et al. 2013a, b, c; Kale et al. 2015; Samineni
et al. 2016). So far, the commonly utilized methods for characterizing root traits in
chickpea such as polyvinyl chloride cylinder (PVC) growth systems (Varshney et al.
2013a, b, c), soil cores (Purushothaman et al. 2017), semi-hydroponic systems (Chen
et al. 2017) and shovelomics (Burridge et al. 2016) with subsequent WinRHIZO
imagery analysis are time-consuming and labour intensive. Advanced image-based
root phenotyping methods such as X-ray computer tomography, magnetic resonance
imaging, positron emission tomography and GROWSCREEN-Rhizo have shown a
promise in chickpea germplasm improvement against drought and heat stresses as
they simultaneously combine phenotyping of shoot and root (Tracy et al. 2020).
Stomatal conductance and canopy temperature (CT) are well recognized adaptive
traits for terminal drought and heat tolerance in chickpea. Canopy temperature can
be measured by handheld (Sivasakthi et al. 2017; Biju et al. 2018) or airborne
(Rutkoski et al. 2016; Bian et al. 2019) thermal and hyperspectral imagery to screen
crop genotypes for drought and heat adaptation. Stay-green trait is termed as the
plant’s ability to retain green leaves and photosynthetic activities for an extended
period. Functional stay-green has shown positive association with deeper roots and
cooler CT (the adaptive traits for heat and drought). Proximal and remote sensing
technology using sensors and cameras can be a method of choice for HTP screening
of stay-green phenotypes for different crop species (Blancon et al. 2019; Sadras et al.
2019) along with chickpea (Cai et al. 2016).
To assess the effect of heat, cold and drought stresses during reproductive growth,
pollen viability is a key adaptive trait. Screening of pollen traits using standard
microscopy is cumbersome, tedious and labour intensive. Nowadays with the help of
advanced image-based phenotyping methods, automated quantitative analysis of
pollen fertility has been made possible. Costa and Yang (2009) developed an
image processing pipeline to effectively count the number of stained viable pollens
from digital microscopy RGB images. A novel method utilizing Pollen Counter
20 Chickpea Breeding 1039

software has been introduced by Tello et al. (2018) to successfully quantify fertile
pollen grains within stained aliquots of pollen suspension under a microscope.
Any kind of stress has a direct effect on grain yield which is a function of biomass
and harvest index. Therefore, they are most important targeted traits for phenotyping
in any breeding programmes as it is an outcome of G  E interactions. High-
throughput estimation for biomass is a typical approach in various crop species
and can be conducted fairly straightforward by proximal and remote sensing tools
(Araus and Cairns 2014). Normalized difference vegetation index (NDVI) is an
inexpensive screening tool to capture physiological characteristics such as yield and
crop growth rate in chickpea (Lake and Sadras 2016). Recently, airborne multispec-
tral imagery has been deployed to evaluate yield potential in chickpea, where the
mean NDVI was found to be consistently correlated to dry seed yield (Quirós et al.
2019).
Phenotyping for salinity by Vadez et al. (2015) utilized a high-throughput, 3D
scanning technique to monitor leaf area development in relation to plant water use in
cowpea and peanut. Several studies in cereals utilize high-throughput phenotyping
technology under controlled environmental conditions to gain a better understanding
of the physiological processes associated with salinity stress (Hairmansis et al. 2014;
Pound et al. 2016; Rajendran et al. 2009). In contrast, similar studies examining
salinity response in legume species have not been reported. Similarly, salinity
response, measured as the effect of salt on growth rate at different developmental
times, possibly could explain genotypic variation for salinity tolerance in chickpea.
Atieno et al. (2017) utilized an image-based phenotyping platform (Fig. 20.1) to
enable quantitative, non-destructive assessment of temporal responses of chickpea to
salinity and related the responses to seed yield under saline conditions and proposed
seed number as a selection trait in breeding salt-tolerant chickpea cultivars.

20.12.2 Phenotyping for Biotic Stresses

20.12.2.1 Ascochyta Blight

Chickpea production is limited by several biotic factors. One such biotic factor is
Ascochyta blight (Ascochyta rabiei) disease in chickpea. To minimize the impact of
Ascochyta blight, timely information on disease outbreak and epidemics is essential
for the implementation of disease control methods. One such example for the
utilization of HTPPs for AB screening is by Zhang et al. (2019). They studied the
feasibility of monitoring Ascochyta blight disease severity in chickpea using remote
sensing techniques. Disease severity was monitored using an unmanned aircraft
system integrated with different types of sensors (three-band multispectral, five-
band multispectral and thermal cameras). It was observed that different flight
altitudes (60 m and 90 m above ground level) that lead to different image resolutions
did not influence the disease detection efficiency, especially with the three-band
camera. Hyperspectral sensing was found to be useful in predicting disease severity
demonstrating that the disease severity of Ascochyta blight in chickpea can be
monitored using remote sensing methods under active field conditions. With timely
1040 G. P. Dixit et al.

Fig. 20.1 Salinity tolerance phenotyping in The Plant Accelerator. Plants were imaged at 28 DAS
for 3 consecutive days prior to 40 mM NaCl application in two increments over 2 days. Plants were
daily imaged until 56 DAS. Right pane shows 6-week-old chickpea plants on conveyor belts
leaving the imaging hall proceeding to an automatic weighing and watering station. (Adapted
from Atieno et al. 2017)

and accurate disease severity information from high-throughput phenotyping

technologies, the effects of Ascochyta blight on chickpea yield and quality can be
minimized with timely application of appropriate management techniques.

20.12.2.2 Phytophthora Root Rot

Chickpea is grown as a rotational crop for its ability to fix atmospheric nitrogen
through symbiotic fixation (Yadav and Chen 2007). Susceptibility of chickpea to
soil-borne pathogens is a major limitation for the expansion of chickpea production
area particularly owing to the depleting soil health. An in planta infection method to
screen chickpea for PRR resistance was developed by (Amalraj et al. 2019) using
hydroponically grown seedlings inoculated with P. medicaginis zoospore suspen-
sion culture. They utilized three chickpea genotypes for the initial pilot scale study,
viz., Rupali (susceptible), Genesis 114 (moderately susceptible) and highly
PRR-resistant breeding line 04067-81-2-1-1 (a backcross derivative from
C. echinospermum). They conducted the experiment in a temperature-controlled
growth room at the University of Adelaide, Waite Campus, South Australia,
Australia, at 20/14  2  C day/night temperatures with a 16 h photoperiod. Covered
plastic pots (4.5 L) were utilized to grow plants in continuously aerated nutrient
solution.
The composition of the full-strength nutrient solution was as per buffered with
1.0 mM MES {2-(N-morpholino)ethanesulfonic acid} and adjusted to 6.5 pH using
20 Chickpea Breeding 1041

Fig. 20.2 Phenotypic variation for PRR in chickpea grown in hydropnics at 9 days after inocula-
tion with P. medicaginis zoospores. (a) Wilting symptoms (04067-81-2-1-1 on the left, Rupali on
the right) of chickpea genotypes grown in hydroponics at 9 days after inoculation with
P. medicaginis zoospores. (b) Root symptoms (04067-81-2-1-1 on the left, Rupali on the right).
(c) Lateral and tap root death in Rupali. (Adapted from Amalraj et al. 2019).

KOH. Seeds were washed with commercial bleach (0.042% (w/v) sodium hypo-
chlorite) added to de-ionized water for 5 min, rinsed twice in tap water and imbibed
at 4  C for 48 h. Imbibed seeds were germinated on mesh in 10% aerated nutrient
solution in the dark for 3 days, and seedlings were then transferred to continuously
aerated 25% nutrient solution and exposed to light. Each pot had one healthy
individual from each genotype, and the pots and position of each genotype were
set up in a completely randomized block design with six replicates in control
(no inoculation) and in treatment (with inoculation) pots. P. medicaginis zoospore
suspension culture was added to the treatment pots at a concentration of
1.5  105 spores/mL. Plants were examined daily after inoculation for PRR
symptoms including canker development, chlorosis and wilting/death (Fig. 20.2).
The experiment was terminated at 16 days after inoculation and repeated three times.
To visualize the progression of PRR disease over the duration of the experiments,
the KME-survival was plotted, based on the initial observation of PRR symptoms
after inoculation until the termination of the experiment. The experiment completion
was based on the death of the PRR-susceptible parental genotype included in each of
the RIL mapping population. To visualize the spatial progression of PRR disease
across the experiment, heat maps were plotted for each RIL population to graphically
display the KME-survival and canker length at the termination of the experiment.
1042 G. P. Dixit et al.

20.13 Breeding Progress/Varietal Development

20.13.1 Conventional Breeding

Chickpea breeding in its nascence started with selection from either indigenous or
exotic landraces. After selection, chickpea breeding grew to hybridization-based
programmes with an aim to have an ideal genotype by combining useful traits from
superior parents that invariably led to the narrowing of the genetic base. The
breeding programmes consequently started aiming towards increasing the genetic
variability by utilising diverse germplasm be it from primary, secondary or tertiary
gene pool or by creation of new variation by mutation breeding. The detailed account
of how chickpea breeding kick started in India is given below.
Systematic chickpea breeding started in 1905 at Imperial Agricultural Research
Institute, Pusa (Bihar), followed by other centres focussing mainly on the collection
of landraces. In the early 1970s, varietal development majorly emphasised on
increasing yield potential over superior landraces. Henceforth most of the varieties
like Dahod Yellow, Chaffa, Annegri-1, Ujjain 21, BR 78 and Gwalior 2 were
developed directly by selection and purification of local germplasm or existing
landraces. In the early 1980s, significant crop losses in northern states like Punjab,
Haryana, North West Rajasthan and Jammu region were caused by the outbreak of
Ascochyta blight. Focussed breeding efforts to develop Ascochyta blight-resistant/
tolerant varieties for such areas subsequently brought about the release of high-
yielding Ascochyta-resistant varieties like PBG 1, PBG 5, GNG 469, Gaurav, PBG
7 and GNG 2171. Therefore in the 1980s, breeding was mainly aimed towards
disease resistance to cater AB problem in northern states and wilt problem in central
and southern regions of the country. This led to the identification and development
of disease-resistant/disease-tolerant donors/varieties with Fusarium wilt and
Ascochyta blight resistance by following systematic breeding programme(s). This
initiative led to the development of varieties with the potential to minimize wilt
incidence such as KWR 108, H 82–2, GPF 2, Vijay, JG 11, Vishal, Gujarat Gram
1, Gujarat Gram 2, GNG 663, JG-16, KPG 59, Digvijay, Rajas, BGM 547, BGD
128, GNG 1581, etc.
In 1981–1982, two separate trials were initiated under All India Coordinated
Pulses Improvement Project (AICPIP) for the evaluation of kabuli and desi
genotypes. Then in 1982–1983, trials for desi chickpea were split into two
categories, viz., normal and late-sown. This initiative led to the identification of
JG 74 for central and northern Indian conditions, and simultaneously a special trial
for screening against Ascochyta blight (AB) was also started. To identify and release
high-yielding and large-seeded desi chickpea varieties, a new trial for ‘bold seeded’
types was constituted in 1983–1984 to fit pulse crop(s) in wheat rice cropping system
and to gain back the chickpea area lost in the northern states due to the incidence of
AB. A key drive was initiated to breed for short duration, multiple resistance,
drought tolerance and high input responsive varieties in the 1990s. This was chiefly
instituted to escape from terminal drought and heat for successfully raising a crop
particularly for the environment(s) with short growing season. The drive for
20 Chickpea Breeding 1043

breeding short-duration (90–110 days) genotypes directed the development of

varieties like JG 16, JG 11, Vijay, Vikas, Vishal, JGK 1, KAK 2, ICCV 2, ICCV
10, etc., thereby expanding unexplored chickpea area in southern and central parts of
the country.
In spite of the reduction in maturity duration, the yield potential remained almost
similar to the long-duration varieties. Correspondingly, early maturing varieties
amenable to late planting like Pusa 372, Udai, RSG 963, BGM 547 and Rajas
were developed for the states like Uttar Pradesh, Bihar, parts of Chhattisgarh,
Jharkhand, Haryana and Punjab after the harvest of rice or cotton, as fields are
vacated quite late. Owing to the depleting soil health, two special trials for the
evaluation of genotypes under high input conditions and for salinity tolerance were
instituted in 1991–1992. Later in 1995–1996, a trial to evaluate breeding lines for
drought was started with an aim to cater effects of global warming. Large-seeded
desi-type varieties, Pusa 256, JG 11, Samrat, Phule G 5, Vishal and BGM 547, were
developed and identified through coordinated testing system for large-seeded desi
(>20 g/100 seeds) and kabuli (>25 g/100 seeds) varieties, implemented in
1983–1984 and 1995–1996. Likewise, large-seeded kabuli-type varieties, BG
1003, BG 1053, Haryana Kabuli Chana 1, Haryana Kabuli Chana 2, KAK 2, JGK
1, Vihar and Virat, were also developed.
Similarly, to address the location-specific problems, DCP 92–3, a wilt-resistant
variety was released for the areas receiving frequent winter rains with high soil
moisture and/or high fertility responsible for more vegetative growth followed by
subsequently lodging of the crop. Later for the poor soils with moderate salinity
levels, CSG 8962 variety for mild salinity conditions was identified for North-
Western Plains Zone; for heat stress, JG 14 in central India and RSG 888 for rainfed
conditions of Rajasthan, Haryana and Punjab were released to address moisture
stress. Recently, new kabuli varieties, viz., HK 05–169, L 555 (GLK 26155), GNG
1969 and L 556 (GLK 28127), were released for northern Indian conditions, whereas
cold-tolerant kabuli varieties such as CSJK 6 and Phule G 0027 were released for
northern hilly regions and JSC 55 and JSC 56 for central India (late-sown
conditions). Presently, due importance is being given for the development of
extra-large-seeded kabuli chickpea (>40/100 seeds) varieties. Besides this, work is
in progress for the development of varieties with more than 50 g 100-seed weight.
Several promising lines are in advanced varietal trails, while a few varieties such as
Phule G 0517, PKV 4-1 and MNK-1 have been developed with more than 50 g/100-
seed weight to capture market for premium prices. The promotion of varieties among
farmers is done through FLD’s by SAUs and State Agriculture Department.
Currently with the hike in the labour wages along with labour shortage, the Indian
farming community is gradually on the way of opting mechanization of field
operations as it improves efficiency along with the reduction in the cost of cultiva-
tion. Besides this, there is an increase in the demand of machine-harvestable
chickpea cultivars also. The chickpea cultivars available that are of semi-spreading
and semi-erect growth habit with short to medium stature are not well suited for
machine harvesting. The minimum standard requirement for the development of
machine-harvestable chickpea cultivars is that the genotypes must have >70 cm
1044 G. P. Dixit et al.

height with erect growth habit. NBeG 47, Phule Vikram, RVG 204 and BG 3062 are
the few machine-harvestable varieties released recently for southern and central
Indian conditions. Since the inception of AICRP (All India Coordinated Research
Project) on chickpea, more than 210 chickpea varieties have been developed suitable
for cultivation under different agro-climatic conditions of the country. The
milestones in chickpea varietal development during the past 100 years as adopted
from Kushwah et al. (2020) are given in Table 20.2.
AICRP on chickpea is currently emphasising on the collection, evaluation,
characterization and utilization of germplasm for the development of the improved
varieties. Partnerships with national and international institutions have been made to
take the advantage of innovative knowledge in the frontiers like biotechnology,
information technology, etc. Overall, there is a need to have dedicated research
efforts for the development of irrigation and high-fertility responsive cultivars to
regain back chickpea area in northern Indian states. With the alarming climate
change-related issues, drought tolerance would be the most important trait for
two-thirds of the rainfed chickpea area. Besides this, precise and efficient breeding
efforts are required for the enhancement of resistance/tolerance to abiotic and biotic
stresses to achieve yield stability. This would encompass novel methods to widen the
genetic base of the breeding populations, genomics-assisted breeding, precision
phenotyping, rapid generation advancement and efficient breeding data management
system.

20.13.2 Genomics-Assisted Breeding

Amalgamation and usage of genomic tools in breeding practices for the development
of superior lines with enhanced biotic or abiotic stress tolerance along with higher
yield levels is termed as genomics-assisted breeding (GAB). Conventional breeding
approaches were able to improve yield but still could not break the yield plateau and
address the issue of narrow genetic base significantly. Efforts have been put forth at
various international platforms to generate genomic resources. GAB tends to estab-
lish and utilize relationship between genotype and phenotype for the crop improve-
ment including range of approaches, viz., genomics, transcriptomics and proteomics,
for the identification of the molecular markers associated with traits of interest. This
acts as a tool for breeders to predict phenotype from the genotype. ICRISAT along
with its partners fast-tracked the development of genomic resources during the past
few years. The genomic resources have been integrated with breeding via GAB and
are making an impact on chickpea improvement (Pandey et al. 2016).
For the development of biotic or abiotic stress-tolerant genotypes with improved
yield levels, GAB holds a promise, as it is one of the unconventional breeding
approaches utilizing several genomic tools. As mentioned earlier GAB encompasses
genomics, proteomics and transcriptomics for the detection of tightly linked molec-
ular markers associated with economically important traits for the prediction of
phenotype from the genotype. With the advent of NGS technologies, high-
throughput genotyping has made possible to develop large-scale genome-wide
20 Chickpea Breeding 1045

Table 20.2 Achievements made during the past 100 years in chickpea improvement
Technique used/first of its kind/
Year Variety adaptation
1926 NP 17, NP 25, NP 28 and NP 58 Direct selection
1940s C12/C34 and type 87 Hybridization
1948 Chaffa Wide adaptability
1960s Annigeri 1 First variety for southern India
1960 C 104 First wilt-resistant
C 235 Widely adaptable in northern India states
1969 GNG 114 First release through All India
Coordinated Pulse Improvement Project
(AICPIP)
1970 Radhey Bold (large)-seeded variety for central
India
1970 RS 11 Spontaneous mutation from RS 10
1976 L 144 First kabuli variety
1979 Hare Chhole First green-seeded variety
1982 GL 769 First Ascochyta blight-resistant variety
1984 Pusa 256 First variety developed by desi  kabuli
introgression
1985 Pusa 408, Pusa 413, Pusa 417 Mutation breeding
1985 Pusa 261 Tall variety from Russian tall donors
1992 KPG 59 (Udai) First variety for late-sown condition by
AICRP
1993 ICCV 2 (Swetha) First short-duration kabuli variety
1994 Vijay First drought-tolerant variety for rainfed
condition
1998 DCP 92-3 First lodging-resistant variety for high
input conditions
1998 CSG 8962 First salinity-tolerant variety
1999 JGG 1 First officially released Gulabi gram
1999 JG 11 First variety developed through polygon
breeding
1999 KAK 2 First large-seeded kabuli variety
2002 RSG 888 First drought-tolerant variety
2003 Vihar First large-seeded kabuli variety for
South India
2005 Pusa 1088 First variety through interspecific
hybridization
2008 IPCK 2002-29 Large-seeded kabuli variety for Central
India
2009 MNK 1, Phule G 0517, IPCK02, PKV 4–1 Extra-large-seeded (>50 g/100-seed wt.)
kabuli varieties
2011 JG 14 Heat-tolerant variety
2017 Andhra Pradesh (NBeG 47), Karnataka Machine harvestable
(GBM 2) and Maharashtra (Phule Vikram)
2019 Phule G 08108, JG 20016-24, BG 3062 Machine harvestable for Central India
(continued)
1046 G. P. Dixit et al.

Table 20.2 (continued)

Technique used/first of its kind/
Year Variety adaptation
2019 BGM 10216 (drought tolerance) and Marker-assisted backcrossing (MABC)
MABC WR SA 1 (Fusarium wilt
resistance)
2020 PBG8 First variety from
C. arietinum  C. judaicum-interspecific
hybridization
2020 Manav (Fusarium wilt resistance) Marker-assisted backcrossing (MABC)
(Adapted from Kushwah et al. 2020)

markers. To pyramid traits of interest governed by several major genes/QTLs

together in a specific genetic background, marker-assisted backcrossing (MABC)
is the most preferred approach. Though the most preferred method of choice, MABC
approach becomes less efficient in cases where characters are polygenically con-
trolled. Consequently marker-assisted recurrent selection (MARS) has been consid-
ered as an alternate option for improving polygenic traits. Simultaneously, genomic
selection (GS) or genome-wide selection approach adopted from human and veteri-
nary sciences is emerging as a powerful approach for the selection of desirable
progenies obtained from the desirable crosses (Jannink et al. 2010). To simulta-
neously identify as well as transfer desirable alleles from wild species or wild
relatives into elite ones, advanced backcross QTL (AB-QTL) approach has been
exploited to accumulate several superior alleles for tolerance to biotic and abiotic
stresses from wild species. Successful utilization of AB-QTL approach has been
used by Singh (2005) for the introgression of productivity and disease resistance
traits from C. reticulatum into cultivated chickpea.
Genetic resistance in chickpea to Ascochyta blight is recessive, exhibiting com-
plex inheritance patterns, and MABC approach has made it possible to unravel QTLs
for resistance to AB. The successful example of MABC is from Tar’an et al. (2013)
where in introgression QTLs for double podding and for resistance to AB have been
simultaneously transferred in elite chickpea cultivars via continuous backcrossing of
moderately resistant donors to susceptible but adapted cultivars. A stepwise MABC
approach by Varshney et al. (2014a, b) is given for the development of Fusarium
wilt (FW) and AB-resistant lines wherein two QTLs for AB and foc 1 locus for FW
are incorporated into C 214 (elite cultivar). On undergoing three rounds of
backcrosses and three rounds of selfing, 22 FW-resistant lines and 14 AB-resistant
lines were generated (Varshney et al. 2014b), thereby resulting into the development
of three FW-resistant lines and seven AB-resistant lines. This method has also been
employed to introgress resistance against two races ( foc2 and foc4) discretely along
with the gene pyramiding for FW resistance to two races ( foc1 and foc3) and two
different QTLs conferring AB resistance in chickpea (Varshney et al. 2014b). Genes
from five germplasm lines displaying FW resistance against foc 2 race have been
introgressed by SSR markers into the genetic background of an elite cultivar Pusa
256 (Pratap et al. 2017).
20 Chickpea Breeding 1047

Similar efforts by various national institutes like ICAR-Indian Agricultural

Research Institute (New Delhi), Punjab Agricultural University (Ludhiana) and
ICAR-Indian Institute of Pulses Research (Kanpur) are underway for the transfer
of FW and AB resistance into promising high-yielding chickpea cultivars. In
addition, introgression of genomic regions has also been performed for drought-
and yield-related traits. The genomic region responsible for drought tolerance,
located on LG 4 and labelled as QTL-hotspot, is introgressed into an elite cultivar
of chickpea, JG 11, using MABC approach (Varshney et al. 2014a). The
introgressed lines have shown yield advantage of 24% under irrigated conditions
and 12% under rainfed conditions. Furthermore, drought tolerance-related traits
controlled by the LG 4 QTL-hotspot harbouring several drought tolerance QTLs
have been transferred into elite chickpea cultivars via MABC approach (Thudi et al.
2014).
Coming to MARS, its competence depends on the total genetic gain attained
following selection accuracy, selection efficiency and marker-trait associations
along with the distribution of desirable alleles across the parents. In chickpea, for
the accumulation of the required set of alleles against drought stress, MARS has
been exploited on utilizing crosses, viz., ICCV 04112  ICCV 93954 and
ICCV05107  ICCV 94954 (Thudi et al. 2014). Two crosses, JG 11  ICCV
04112 and JG 130  ICCV 05107, were attempted in chickpea with an aim to
combine the desirable yield QTLs through MARS approach (Thudi et al. 2014). For
this, overall 188 F3 plants each from two crosses (mentioned above) were genotyped
by SSR markers, while for phenotyping F3:5 progenies were assessed at multi-
locations. Association of genotypic with phenotypic data led to the identification
of a few major and several minor QTLs related to yield and yield component traits.
Based on the QTL information for several yield and yield-related parameters in F5
progenies, four lines and three lines from JG 11  ICCV 04112 and JG 130  ICCV
05107 crosses, respectively, were selected for recombination cycle for several
combinations of favourable alleles. The shortlisted lines were further subjected to
two recombination cycles, and F1 plants from both the crosses with favourable
homozygous alleles for yield and yield-related traits were recognized and grown.
Further, the selected F1 plants were advanced to F4 generation for further evaluation,
thereby increasing the frequency and accumulation of favourable alleles for econom-
ically important traits following the number of MARS-based recombination cycles.
To utilise genomic selection (GS) approach, efforts are underway for chickpea
yield improvement in the near future. This has been made possible by the availability
of precise phenotyping techniques and large linkage disequilibrium (LD) blocks in
chickpea breeding populations along with the availability high-throughput
genotyping systems like DArT and SNP markers. ICRISAT has made pioneer efforts
for the exploitation of GS approach in chickpea breeding by utilizing a set of
320 elite chickpea lines genotyped by DArT markers. Phenotyping was carried out
at Patancheru and New Delhi for yield and yield-related traits. Six different statistical
GS models were employed, utilizing phenotypic and genotypic data giving results
with higher prediction accuracies (up to 0.91) for yield and yield-related traits
(Roorkiwal et al. 2016). Higher prediction accuracies could be expected on inclusion
1048 G. P. Dixit et al.

of G  E effects by GS approach by considering multiple variables simultaneously

in chickpea breeding programmes (Roorkiwal et al. 2018). Additionally, an alternate
way to increase the prediction accuracies is by incorporating information regarding
the large-scale genome-wide significant markers obtained from the results of GWAS
to diverse GS models (Li et al. 2018). GS models hold a promise in pre-breeding
programmes as it will help in screening for the identification of introgressions
(Crossa et al. 2017). Varshney et al. (2018) have outlined sequence-based breeding
based on GS approach wherein sequencing at higher depth is suggested for all
possible parental lines of a specific breeding programme. These founder genotypes
can be sequenced for the development of GWAS approach or HapMap that could be
further utilized for the selection of desirable superior parental combinations with
higher frequency of favourable alleles.
If a greater number of lines are to be selected, then a large number of crosses have
to be attempted followed by early-generation selection. GS can now be done on
selected lines srepresenting the lines from such crosses by means of the training
model developed from the germplasm set. Although not feasible for large-scale
breeding programmes, the best genotyping platform for GS approach could be a
fixed SNP array. Consequently, segregating F6/F7 populations could be sequenced at
lower coverage using skim sequencing or 384-plex-based genotyping platform.
Practical haplotype graph (PHG) could be developed via high-throughput genotypic
data generated for parental lines and other available germplasm lines as PHG is
helpful in the identification of SNP markers. By means of sequence-based
approaches, such SNP markers can be evaluated using rhAmp-SNP genotyping
technology or DArT-seq SNP genotyping technology. Thereby exploiting GS
approach-based breeding programme(s) utilizing segregating populations and elite
lines for the selection of genotypes with higher genomic estimated breeding values
(GEBVs) will be quite useful.

20.13.3 Development of Transgenics

Genetic improvement, either by traditional or molecular methods, has been ham-

pered by the limited genomic resources coupled with narrow genetic diversity in the
elite gene pool. However, most intractable stresses like insect pest (gram pod borer,
aphids, bruchids), weeds, drought, salinity and low methionine content in the seeds
are challenging because breeding efforts for these traits are limited, due to cross-
incompatibility and lack of resistant sources in the available germplasm (Acharjee
and Sarmah 2013). Genetic engineering can provide a potential alternative to address
the issue by employing genes available across kingdoms. Recent advances in the
transformation and plant regeneration protocols for chickpea now mean that trans-
genic technology can be used to improve those traits for which adequate variability is
not available in the primary gene pool. These include resistance to pod borer and
other biotic and abiotic stresses, as well as sulphur-containing amino acids. In
chickpea, the combination of recombinant DNA technology and plant tissue culture
has paved the way for the creation of novel options for biotic stress management,
20 Chickpea Breeding 1049

especially insect pests. Special attention has been focussed on insecticidal Bt

expressing transgenic plants that provide tolerance to herbicides (Shelton et al.
2002). The development of transgenic chickpea lines showing resistance to
H. armigera is considered as one of the best approaches to counter yield loss
(Asharani 2009). The genes utilized for development of resistance against pod
borer, bruchid, aphid, drought and salt tolerance, namely, Bt, alpha amylase inhibi-
tor, ASAL, P5CSF129A and P5CS, respectively, are discussed by several
researchers (Das et al. 2017; Kumar et al. 2018; Aggarwal et al. 2018; Bhowmik
et al. 2019). Till date, confined field trials of transgenic chickpea for insect-resistant
trait are reported; however, the efforts require constant support to bring forth viable
transgenics, addressing all regulatory issues. Efforts should be directed towards
development of a large number of transgenic lines, evaluate them in open-field
conditions and identify elite event(s) with high trait efficacy. Efforts should also
be initiated for targeted integration of transgene in genome using genome editing
techniques (CRISPR/Cas9systems).

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Pigeonpea Breeding
21
S. J. Satheesh Naik, Abhishek Bohra, Indra Prakash Singh,
and Abha Tiwari

Abstract

In recent years, pigeonpea has witnessed a number of advances in genetic

research and breeding. The availability of the modern genomic resources such
as whole genome sequence provides the basis and validation of plant responses
for future crop improvement. Genome maps and quantitative trait loci (QTLs)
have provided the opportunity to relive the bottlenecks that previously hampered
the breeding progress. Next-generation sequencing (NGS)-based trait mapping
methods allow rapid identification of candidate gene(s) associated with the traits
of interest. Growing sequencing data on multiple genomes and pangenome
analysis unleashes opportunity for the discovery of large-scale structural
variations (SVs) and the mining of superior haplotypes to accelerate breeding
of climate-smart varieties. Refinements in our understanding of male sterility
phenomenon in combination with molecular basis of heterosis hold promises to
enhance gains from hybrid breeding. In this chapter, we discuss the advances in
genomics and breeding of pigeonpea crop. Concerted efforts backed by the
multidisciplinary research would lead to the development of superior varieties
and identification of potential genetic resources for future use by the research
community.

Keywords

Pigeonpea · Gene · Cytoplasmic male sterility · Genetic gain · Breeding

S. J. Satheesh Naik · A. Bohra (*) · I. P. Singh · A. Tiwari

ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1063
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_21
1064 S. J. Satheesh Naik et al.

21.1 Introduction

Pigeonpea [Cajanus cajan (L.) Millspaugh] also known as tur, arhar, and redgram is
a protein-rich food legume. It is an integral part of food diet especially in Asia due to
its affordability and protein-enriched seeds. It is used not only in human diets but
also as fodder and feed for animals and fuel wood for the tribes and rural living, and
it prevents soil erosion too. Pigeonpea is utilized in intercropping systems to avoid
the need of nitrogen fertilizers and boost the nitrogen usage efficiency of the crop
field system, as is the case with all members of the Leguminosae family.
From the last two decades of the twentieth century, the crop witnessed the major
genomic initiatives and related research in pigeonpea. After these advances, under-
standing of these structural and functional aspects of the genomic regions in crop has
helped breeders to deal with many constraints in faster and efficient manner. After
the first decade of this century, development of various molecular markers helped
breeder to identify the relatable traits, and marker-assisted breeding technologies
could be employed since then. Identification of germplasm and resequencing of the
many genotypes have led to the development of many elite varieties, which are used
in backcrossing programs and development of mapping population. Not only
cultivars but also wild breeding lines are identified with resistant genomic loci for
many resistance traits against biotic and abiotic constraints. After the genome
sequencing initiatives, the finding of candidate genes has been made easy by using
functional and system biology approaches that further accelerated the genetic gains.
Not only cultivars and landraces but also wild relatives are exploited under
pangenomic studies to identify more resistant traits and find the more diverse traits
available.
Till date, over 150 varieties are released in India (Naik et al. 2020). Despite many
efforts, the expected yield gain from pigeonpea is not yet exploited (Varshney et al.
2012). Therefore, it is concluded that the efficiency of breeding system is required to
be improved, and moreover a variety of systems suitable for different agroecologies
within India need to be developed (Singh et al. 2017). Also, cytoplasmic male
sterility (CMS) technology is used to produce CMS-based hybrid for exploiting
grain yields in pigeonpea (Bohra et al. 2020a). Many recent advanced protocols are
now being used to increase the genetic gain through genomic selection (GS), speed
breeding (SB) or rapid genetic advancement protocols (RGA), and haplotype-based
breeding (HBB) (Bohra et al. 2020b). All these methodologies are recently under
observation and have been reported to deliver more yield gain in the farmer’s field,
and breeders are also focusing more towards the strengthening of the seed delivery
system and agronomic practices. This chapter highlights about the pigeonpea origin,
morphological characters of flowers, wild relatives, germplasm availability, varietal
development, and molecular and genomic tools with efficient traditional and con-
ventional breeding practices including high-throughput phenotyping platforms.
21 Pigeonpea Breeding 1065

21.2 Origin, Domestication, and Its Wild Relatives

Pigeonpea belongs to the genus Cajanus, which is comprised of 32 species

(Mallikarjuna et al. 2012). Among all the species, the genetic diversity studied by
Kassa et al. (2012) has suggested that the Cajanus cajanifolius is the most probable
progenitor of cultivated pigeonpea found in eastern India, including eastern state
Odisha (Van der Maesen 1986). These two studies complemented each other and
confirm that India is the country where pigeonpea has originated. Based on the Van
der Masen’s wild distribution map, it suggested that, apart from these southern
origins, some eastern coast states such as Andhra Pradesh and Madhya Pradesh
have some landraces and wild relatives exhibiting high level of genetic diversity,
suggesting the domestication (Saxena et al. 2014). The processes of domestication
strongly show severe bottleneck effect by representing 75% less allelic diversity than
the wild species in the clade (Saxena et al. 2014). Pigeonpea archae-botanical
findings are most abundant in India, with a few others coming from Southeast
Asia. The Neolithic sites in Kalaburagi, Karnataka (Sanganakallu), and its border
areas (Tuljapur Garhi in Maharashtra and Gopalpur in Orissa) show the abundance
of pigeonpea and from there it is encountered with Europeans and dispersed in
Southern African states prior to 1650 BC (Fuller et al. 2019). Within these
domesticated processes, the species C. kerstingii, with haploid chromosome
(n ¼ 16), is found to be originated in Africa (Bohra et al. 2010).
The concept of the gene flow highlighting various gene pools was established by
Harlan and de Wet in 1971. On the basis of the crossability barriers, primary gene
pool (GP1), which produces fertile F1 offspring, is comprised of all cultivars and
landraces of C. cajan. Many early taxonomic studies suggested that the Atylosia and
Cajanus are two different species, but Van der Masen later merged them under
Cajanus (1986). The secondary gene pool (GP2) has wild relatives with many
beneficial traits and may produce partially fertile hybrid in interspecific cross. GP2
has many species such as C. scarabaeoides, C. reticulum, C. trinervirus, C. lineatus,
C. latisepalus, C. cajanifolus, C. lanceolatus, C. sericeus, C. albicans,
C. acutifolius, etc. The tertiary gene pool (GP3) has species which are either not
crossable with cultivated species or crossable with the aid of embryo rescue or tissue
culture techniques. Some of the species from GP3 are C. goensis, C. crassus,
C. rugosus, C. cinereus, C. volubilis, C. platycarpus, C. mollis, and
C. confertiflorus. Some other related generas are Rhynchosia, Dunbaria, Flemingia,
Paracalyx, Eriosema, Adenodolichos, Bolusafra, Carissoa, Chrysoscias, and
Baukea, which are from the far reaches of the gene pool (GP4) but anyhow are
connected during domestication process (Bohra et al. 2010).
The importance of the wild relatives cannot be ignored as the genetic base of the
released varieties is mainly contributed by 48% of the top 10 ancestors of pigeonpea
(Kumar et al. 2003). Many high yield traits and resistant genes against various
constraints from biotic and abiotic category have been introgressed into the cultivars
from these potential wild relatives in several other crops (Bohra et al. 2021a), which
are further discussed under trait dissection. The undeniable fact is that domestication,
allopatric and, sympatric speciation, polyploidization and inbreeding have all had
1066 S. J. Satheesh Naik et al.

severe genetic bottleneck impacts on diversity during the course of evolution. In

order to harness the beneficial genetic traits, breeders realized the importance of wild
crops and targeted their germplasm conservation in gene banks (Varshney et al.
2021a).

21.3 Genetic Resources Available

In pigeonpea, the development of genetic resources started by conservation of the

germplasm accessions, development of the reference genetic maps, transcripts
assemblies, experimental population, genotyping platform, and markers associated
with trait of interest.

21.3.1 Collection of Germplasm

Exploration is the process of gathering the diverse genetic germplasm accessions and
preventing them for use in breeding programs in the form of core, mini core, and
composite collections. According to the concept given by Brown in 1989, core
collection is 10% of the entire collection and represents the maximum genetic
diversity ~70% of the total alleles. Similarly, mini core collection reduces it to
10% of the total core collections. Due to its reduced size, mini core collection has
provided an easy access to scientists, which further helped them to evaluate it across
multiple locations for target traits, finally helping them to identify promising germ-
plasm for future use. The core and mini core collections of pigeonpea are composed
of 1290 and 146 accessions, respectively, developed by ICRISAT. Similarly, to
explore diversity, a global composite collection was put forward which is comprised
of 1000 accessions, from the mini core collection (146), mini core comparator (146),
additional representative accessions from 79 clusters of core collection (236), control
cultivars (4), 63 accessions of 7 wild species, diverse sources for biotic (77) and
abiotic (16) stresses, promising germplasm accessions (59), released cultivars (16),
and accessions with distinct morpho-agronomic traits (237) (Upadhyaya et al. 2008).
In total, 94% were cultivated and 6% were wild relatives in composite collections
and contain accessions that were collected in ICRISAT from 54 countries. Among
all the collected accessions, 58.8% accessions were collected from Asia and 12.9%
from Africa (Upadhyaya et al. 2011). In total, 38,735 accessions of pigeonpea have
been collected at various institutes such as ICRISAT, NBPGR, etc. (Saxena et al.
2016).

21.3.2 Genome Assemblies

A draft map of genome was presented by Singh et al. (2012) using 454 GS FLX
platform with mean read length of >550 bp with >tenfold coverage which success-
fully assembled ~511 mb of the genome. The genotype used was “Asha” (ICPL
21 Pigeonpea Breeding 1067

87119), and 20 kb long fragments were generated by GS-FLX. In these studies,

237.2 Gb and 10.1 Gb sequencing data were generated on Illumina sequencing and
GS-FLX sequencing platform, respectively, which was later on assembled on the
Newbler GS de novo assembler. Further gene annotation was done using
Arabidopsis thaliana gene models as a reference which identified 1213 disease
resistance/defense response genes and 152 abiotic stress tolerance genes in
pigeonpea. Using homology-based approaches, they identified a total of 1,127,729
REs in the pigeonpea genome covering a total of 326,671,068 bp of sequence. These
approaches identified REs belonging to six major categories, namely, (a) LINEs
including L1, R1, and RTE-BovB; (b) LTR-retrotransposons including LTR,
Caulimovirus, Copia, and Gypsy; (c) DNA transposons including En-spm, Harbin-
ger, hat-AC, hat-Tag1, hat-Tip100, Rc/Hiltron, MuDr, TcMAR-Pogo, and
RC/Hiltron; (d) unclassified interspersed repeats; (e) simple tandem repeats; and
(f) low complexity repeats.
Varshney et al. (2012) developed the genome assembly of "Asha" variety
using next-generation sequencing (NGS) and Sanger-sequenced BAC (bacterial
artificial chromosome) clones. Using platforms Illumina GA and HiSeq 2000
sequencing system, two libraries were formed: 11 small insert libraries
(180–800 bp) and 11 large insert libraries (2–20 kb), with a set of 88,860 BAC
end sequences generated by using Sanger sequencing platform. On getting the long
reads, data was assembled using the assembler SOAP de novo with a contig N50 of
21.95 Kb, and the longest contig length was 185.39 kb. Total assembled genome
represents 72.7% of the total genome, i.e., 605.78 M of the total 833.07 Mb of
pigeonpea genome. Further, gene annotation was done using gene models, which
resulted into the identification of 48,680 genes with 51.67% of the repeat elements in
total genome.
In general, both studies have taken many steps to sequence the raw sequencing
reads that was further aligned to form contigs and then calculated the amount of
shared PE relationships between each pair of contigs, and then those scaffolds were
assembled into the genome. The BAC end sequences used for mapping the sequence
obtained a final super scaffold, and a genetic map of Cajanus cajan ICP 28  C.
scaraboides (ICPW 94) was created (Varshney et al. 2012). Varshney et al. (2010)
utilized a scaffold of 51,606 kb, while Singh et al. (2012) used 4522 bp of the contigs
in their N50 assembly. The completion of the genome has a significant contribution
in various genetic resources, with a total of 309,052 SSRs markers and 28,104 SNPs
in the study done by Varshney et al. (2012), whereas the study by Singh et al. (2012)
has given 1,89,895 SSRs including di-peptide and hexa-peptide repeats. These
genome studies will contribute in advancing the development of many other genetic
resources and help breeders to develop elite varieties.

21.3.3 Transcriptomic Resources

As the second-generation sequencing technologies start developing, trait-specific

genes were targeted in breeding programs. The importance of gene, their regulatory
1068 S. J. Satheesh Naik et al.

mechanisms, and their participation in various biological processes came into light.
Based on Sanger’s sequencing, the first set of high-quality ESTs (9468) was
developed that further served the identification of 19 and 20 genes responsible for
fusarium wilt (FW) and sterility mosaic disease (SMD), respectively. Using Illumina
and FLX/454, many transcript assemblies are being submitted with 21, 434 tran-
script assembly contigs (TACs) (Kudapa et al. 2012), 48, 726 TACs (Dubey et al.
2011), and 43, 324 TACs (Dutta et al. 2011). Another study by Sinha et al.
(2015b, c) evaluated the genes expressed by crop under stress and validated the set
of reference gene expressed under heat, stress, and drought condition.
Another study by Pazhamala et al. (2017) represented the global expression
analysis of the gene in pigeonpea during its all developmental and reproductive
phases. This study may have worked as the bridge to fill the gap between whole
genomic sequence information and crops phenotype. Cajanus cajan gene expression
atlas (CcGEA) is comprised of 28,793 genes developed by sing RNA sequencing
that highlights all the genes expressed during developmental growth phases, seed
formation, pollen pistil interaction, and fertilizing conditions. The network analysis
of these genes identified 28 hub genes and 3 highly connected genes for flower-
related trait in pigeonpea. Exploring genome sequences in combination with
pangenomic studies will refine and upgrade the expression atlas for future high-
throughput breeding programs (Bohra et al. 2020a).

21.3.4 Experimental Populations

Previously, researchers found that using a biparental population resulting from the
crosses between two inbred lines had a high power to detect quantitative trait loci
(QTLs) as all allelic frequencies are typically close to 50%. Apart from that fact that
many studies rely upon mapping QTLs in biparental population, they lack mapping
precision due to limited effective recombination, low genetic diversity and genetic
bottlenecks effect caused by choosing only two founder parents. This may limit the
number of QTL captured as no more than two alleles segregate at any locus.
Recently, the two most popular designs are employed in plants NAM (Nested
association mapping) and MAGIC (multi-parent advanced generation inter-cross)
populations. NAM is a set of biparental populations all linked by a common parent,
whereas MAGIC is descended from 4, 8, or 16 parents consistent with a simple
funnel breeding design. MAGIC population usually inherits alleles from all parents
and arranged in random mosaic. By increasing genetic recombination frequency and
variations, these designed populations can overcome limitation of biparental
mapping populations (Scott et al. 2020). MAGIC population available in pigeonpea
involves eight founder parents with seven funnels for mapping various genes.
21 Pigeonpea Breeding 1069

21.3.5 Whole Genome Resequencing Approaches

From whole genome resequencing (WGRS), Varshney et al. (2017) resequenced

292 accessions including landraces, breeding lines, and wild relatives, and the
obtained data were mapped into the reference genome of “Asha” that helped
breeders find many structural variations (SVs). The SVs help breeder to understand
the diversity in the species and understand how many important agronomic traits are
being ignored leading to inbreeding depression in the population. In the study, the
researchers comprehended that the extent of genetic bottleneck during domestication
was more intense than the moderate level observed from landraces to breeding lines.
Similarly, the first-generation haplotype map of pigeonpea is based on WGRS data
of 20 Cajanus accessions which revealed 5.5 million of variants including 4.6
million of the SNPs and 0.7 million of InDels along the structural variations such
as CNVs and PAVs (Kumar et al. 2016).

21.4 Floral Morphology and Pollination

Pigeonpea crops have found to be successfully grown between 30 N and 30 S
latitude, with a temperature range from 29 C to 36 C. The growth seems to be
slow during initial days, depending upon the different maturity groups, and then it
becomes large bushy by its flowering time. Depending upon the days to flowering,
the different maturity groups are divided at 17 N at ICRISAT which is categorized
into super early (<50 days to flowering), extra early (51–60 days), early
(61–100 days), medium (101–140 days), and late (141–160 days). Wallis et al.
(1981) suggested that the trait of earliness is linked to photoperiod insensitivity
which is found to be true.
Pigeonpea forms two types of plant types, viz., determinate (DT) and indetermi-
nate type (NDT). The determinate inflorescence forms somewhat corymb shape
bunch, whereas the indeterminate forms a terminal panicle. The peduncle in DT is
almost 1–8 cm long and flowers are clustered at the top end. An individual flower is
comprised of a calyx with five sepals, and a corolla with a standard, two wings, and
two keel petals. In total, flower has 10 stamens in diadelphous condition, 9 fused in a
column, and 1 free, and the ovary consists of 2–9 ovules. Flowers are normally
yellow but could be in shades of yellow such as ivory, light yellow, yellow, and
orange yellow. Streaks found in petals could be red or purple and ranges from
no/sparse streaks to dense/uniform coverage of streaks (Sameer et al. 2017).
Pigeonpea is a daylight plant; therefore its inflorescence development and pod
setting are greatly influenced by the availability of light. No pods are set under the
dense crop canopy. Dry, bright days are favorable for fertilization, while cloudy,
damp weather results in excessive flower drop (Howard et al. 1919; Mahta and Dave
1931). Precise information on the quality, level, and the duration of light required for
fertilization and seed setting is lacking.
The flower found in pigeonpea is cleistogamous which is further supported by the
evidences provided by Saxena et al. (1992a, b). The study stated that the keel part
1070 S. J. Satheesh Naik et al.

usually surrounds the part of standard wing petal which causes a considerable delay
in opening of buds. Therefore, even in an open flower the standard unwraps itself but
the wings still remain enclosed within the keel resulting in partial cleistogamy
(Sultana and Saxena 2019). Cleistogamy promotes self-pollination, whereas in
pigeonpea this statement is ruled out as a considerable amount of out-crossing is
found. Hence, pigeonpea is a well-known example of often-cross-pollinated crop
which ranges from 3% to 40% of out-crossing.
From the report submitted by Onim (1981), pollen in pigeonpea is shed when the
flower is intact in bud and germination is not seen until the flower starts to wither,
i.e., 24–48 h after their anther dehiscence. Dutta and Deb (1970) studied the pollen
tube growth in a style pollinated with pollen from the same flower and observed it to
be very slow, taking 54 h to reach the base of the ovary. Those two mechanisms
provide a sufficient time gap for the foreign pollen to be introduced on to the stigma
by insect pollinators before self-fertilization takes place. The study by Saxena et al.
(1990) and Onim (1981) observed the entomophily in pigeonpea to support many
previous studies such as at ICRISAT Center by Williams (1977) which counted
between 5500 and 107,333 pollen grains on single Xylocopa spp. and Megachile
spp. of insect pollinators, of which pigeonpea pollen accounted for 98–100%. On
this basis, it is found to be beneficial for broadening the genetic base of the
segregating pigeonpea population.
To study pollination, it was observed that anthers dehisce a day before flower
opens. Anthesis starts from 06.00 h. and continues till 16.00 h, and the peak was
observed between 09.00 and 10.00 h and varies from 6 to 36 h. Pollination takes
place with the help of pollen of the same flower, and it requires 54 h to reach to the
ovary, and also the pollen tube is grown within the style (Dutta and Deb 1970). As
pigeonpea is a daylight plant, full-day sunlight works in favor of the anthesis
(Sharma and Green 1977). Temperature also plays a major role in controlling the
fertility as higher temperature can cause sterility (Saxena et al. 2014); therefore
environmental conditions ought to play a major role in fertilization.

21.5 Cytological Studies

The nuclear variation in C. cajan was studied through cytological research and other
related wild species (20). The study supported that all the species have 2n ¼ 22 as
stated in the earlier reports too (Dundas 1990). According to Ohri and Singh’s (2002)
research, the C. cajan and C. cajanifolius are remarkably similar; their origin stories
supported the fact. The similarity found in respect to the number and morphology of
satellite chromosome in both species. This study further helped breeders to under-
stand the chromosomal abnormalities and possible cross-abilities among these
related wild species. Under such observation, hybrid of C. cajan with
C. cajanifolius and C. lineatus shows a normal meiosis, and C. cajan crossed with
C. lineatus shows reduction of pairing in interstitial and terminal regions and two
heteromorphic bivalents (Dundas 1990). Therefore, breeders could find the success
21 Pigeonpea Breeding 1071

of breeding programs between interspecific cross of C. cajan and its related wild
species for some beneficial traits.
Another cytological study attempted to understand cytoplasmic male sterility
(CMS). Among all the CMS systems, only A4 derived by crossing C. cajanifolius
has been further used for hybrid production. To understand this sterility and fertility
transition in near isogenic lines, cytological studies were performed which helped
researchers to understand the sterility in pollen which is caused by the restricted
supply of nutrients and energy (Dalvi et al. 2008; Pazhamala et al. 2020; Bohra et al.
2021b, c, d).

21.6 Quantitative and Qualitative Traits in Germplasm

Collection

The germplasm collection of pigeonpea with 11,402 accessions was analyzed to

study the diversity pattern in 14 qualitative and 12 quantitative traits (Upadhyaya
et al. 2005). Semi-spreading growth habit, green stem color, indeterminate flowering
pattern, and yellow flower color were predominant among qualitative traits. Other
qualitative trait is growth habitat having three categories being compact, spreading,
and semi-spreading, with semi-spreading being the most heterozygous characteristic
(84.22%) followed by the compact (13.22%) type. Plant pigmentation, flowering
pattern, color, streaks, streak pattern, seed color, pod shape, and seed eye color were
all categorized under qualitative characteristics with their diversity explored in
56 diverse countries (Upadhyaya et al. 2005). The rest of the characteristics such
as 50% days to flowering, number of primary and secondary branches, days to 75%
maturity, plant height, seed per pod, seed weight, protein content, shelling, and
harvest index were accountable under quantitative traits.

21.7 Breeding Efforts for High-Yielding and Disease-Resistant

Cultivars

Since the pigeonpea breeders realized the importance of systemic breeding programs
for developing varieties/hybrids that are more resistant to biotic and abiotic stresses,
various varieties/hybrids have been released for farmer’s cultivation. Previously,
when constraints were found while increasing the yield in pigeonpea, breeders
adopted various methods to increase the yield such as pure line selection from
germplasm followed by pedigree breeding and mutational breeding. Using the
same approaches, 150 varieties were released since 1960–2018, 89 were developed
by pedigree selection, 57 by pureline selection, and 3 by mutation and population
improvement breeding programs (Naik et al. 2020). Earlier approaches involved the
collection and selection of landraces from the farmer’s field. Later on, these
landraces were advanced by using pedigree method, and some of the varieties
produced by the same approaches are well known as C11, T7, BDN1, Bahar,
NA1, ICP8863 (Maruti), ICP7035, etc. (Bohra et al. 2017a, b). Many other varieties
1072 S. J. Satheesh Naik et al.

were maintained for their resistance genes such as, IPA8F, IPA9F, IPA16F, and
ICP7035 for both fusarium wilt and sterility mosaic disease, KPL 44 for fusarium
wilt, ICPL366 for sterility mosaic disease, ICP7105 for Alternaria blight, PB 9 for
Phytophthora blight, IPAC79 for water logging tolerant, and many more.
Many varieties were developed by mutational breeding approach using chemicals
such as ethyl methane sulfonate (C3H8SO3), fast neutrons, and gamma rays, which
were found successful in creating useful variability. Mutational breeding has given
some remarkable varieties against traits such as yield, seed size, earliness, and some
biotic constraints. These varieties (viz., Co 3, Co 5, TT5, TT 6, and TAT 10) have
been bred through mutagenesis. Among these varieties, Co3 is produced by EMS,
and Co 5 by gamma rays, and TAT 5 and TAT 10 were produced by fast neutrons.
One of the desirable traits in all geographical regions is earliness, plant type
(determinate and indeterminate), and protein content. Breeding of early maturating
lines was identified first when the late maturating group landraces were grown in
Gorakhpur, Uttar Pradesh, and spontaneously identified an early maturating named
as T-1 which leads to development of T-21 by crossing T-1 with T-190 in Kanpur.
Subsequently, a few more extra early maturating cultivars including Co 2 from PB
4278, Hy 2 from PI 4628, Hy 4 from PI 4839, Hy 5 from PI 3701, Co 4 from S
80, AL 15 from 809, Pusa 855 from T 21, Pusa 992 from ICPL 90306, AKP 1 from
ICPL 87101, and CORG (RG) 7 from PB 9825 were also developed through the
selection of spontaneous mutants. Recently, transgressive segregation selection is
also used to produce such high-yielding varieties.

21.8 Pigeonpea Constraints and Breeding Approaches

21.8.1 Biotic Stresses

Major biotic diseases in pigeonpea are fusarium wilt (FW), sterility mosaic disease
(SMD), and phytophthora blight.

21.8.1.1 Fusarium Wilt

It is a major biotic constraint governed by single dominant gene which results in
yield loss from 30% to 100%. First completely resistant variety against wilt is
(Maruti) ICP 8863 and then ICPL 87119 (Asha), which were produced in India.
Wilt can be diagnosed by symptoms such as loss of turgidity, slight interveinal
chlorosis, browning of xylem vessels, and purple band on the stem. The pathogen
which causes fusarium wilt is Fusarium udum. One of the greatest approaches
targeted by breeders to overcome this problem was to identify the potential resistant
germplasm, including its wild relatives. Many other varieties were identified in
ICRISAT with potential germplasm such as ICPL 20109, ICPL 20096, ICPL
20115, ICPL 20116, ICPL 20102, and ICPL 20094 (Sharma et al. 2016). This
approach was limited till conventional breeding approaches. Later, using the modern
NGS-based technologies, genotyping by sequencing (GBS), leads to the discovery
of 3 QTLs, qFW11.1, qFW11.2, and qFW11.3, from three populations, namely,
21 Pigeonpea Breeding 1073

PRIL_B, C, and F2. Similarly, by using another approach Seq-BSA (sequencing-

based bulked segregant analysis), resistant (R) and susceptible (S) bulks from RIL
population derived from crossing ICPL 20096  ICPL 332 were sequenced. SNP
index was calculated between R and S-bulks by using draft genome of a resistant
parent ICPL 20096. The result provided with seven candidate genes for FW and
SMD. Further, on the same study, in silico protein analysis has revealed two
promising candidate genes C. cajan_03203 for FW resistance that could be further
used in genomic-assisted breeding programs (Singh et al. 2016a).

21.8.1.2 Pigeonpea Sterility Mosaic Virus (PPSMV)

A species of the genus Emaravirus also known as “green plague” of pigeonpea is
characterized by sterility of flower and mosaic-like appearances over the leaf.
Sterility mosaic disease (SMD) induces symptoms like stunted and bushy plants,
leaves of reduced size with chlorotic rings or mosaic symptoms, and partial or
complete cessation of flower production (i.e., sterility). The causal agent of the
disease is PPSMV, a virus with a segmented, negative-sense, single-stranded RNA
genome, transmitted in a semi-persistent manner by an eriophyid mite Aceria cajani
Channabasavanna (Acari: Arthropoda). Both the virus and the vector are highly
specific to pigeonpea and a few of its wild relatives, such as C. scarabaeoides and
C. cajanifolius. SMD is controlled by four independent loci, two duplicate dominant
gene (Sv1 and Sv2), and two recessive (sv3 and sv4) genes. Expression of SMD is
noticed only when one dominant allele at loci 1 and 2 and homozygous recessive
genes at loci 3 and 4 are present.
As explained, SMD virus is transmitted by a mite; therefore, application of spray
against the mite has controlled mite population thus limiting the spread of the
disease. Apart from these conventional methods, introgression breeding through
genomic-assisted breeding programs would be an important strategy for the devel-
opment of disease-resistant varieties. Genotyping by sequencing approach was used
for simultaneous identification and genotyping of SNPs, and the candidate genomic
region identified on CcLG11 was the promising QTL for molecular breeding in
developing superior lines with enhanced resistance to SMD (Saxena et al. 2017a).
Six QTLs explaining phenotypic variation were identified on LG7 and LG9 after
extensive phenotyping for SMD resistance (Gnanesh et al. 2011). An approach
discussed above for Fusarium wilt by Singh et al. (2016a) also identified seven
SNP related to both FW and SMD, and protein expression profiling identified
another candidate gene, namely, C. cajan_01839 for SMD resistance.

21.8.1.3 Phytophthora Blight (PB)

Another major constraint in pigeonpea which results in 100% yield loss even under a
favorable environment is PB. The causative agent, Phytophthora cajani, was first
isolated from India from infected pigeonpea plants with stem canker symptom. The
disease is easily identified with characteristics such as lesion on stem (dark brown or
black) and leaf, stem broken at the point of infection initiation, stem cankers and
galls, and eventually mortality. It is a soilborne fungi which is mostly found as
dormant mycelium in soil and infects plant debris. It is controlled by a dominant
1074 S. J. Satheesh Naik et al.

gene known as Pd1. This fungus holds sporadic in nature, but in the places of heavy
rainfall, it becomes epidemic in proportions. Only conventional method of selecting
resistance germplasm screened in sick plots is the best way for identifying resistance
source for PB (Singh and Chauhan 1992).

21.8.1.4 Helicoverpa armigera and Bruchids

They are the most devastating insects’ pest for pigeonpea since ages. Conventional
breeding alone cannot be the solution of this problem, as the resistance source is not
yet found in any germplasm. Gene pyramiding with two different insecticidal gene
and tissue-specific expression of a chimeric cry1AcF (encoding cry1Ac and cry1F
domains) gene in transgenic pigeonpea has been demonstrated towards resistance to
H. armigera. Apart from this, an advanced generation population from the cross
utilizing “Cajanus acutifolius,” a wild relative from the secondary gene pool as the
pollen parent, has shown considerable resistance for pod borer damage
(Mallikarjuna et al. 2012). Therefore, many insect resistance genes are exploited
from the wild relatives mainly from secondary gene pool. Some of the lines
produced by crossing C. acutifolius showed high level of resistance to pod borers,
pod fly, and bruchid under unprotected field conditions. Bruchid resistance is an
important trait for pigeonpea seeds under storage as resistance to the pest has not
been observed in cultivated pigeonpea. Another species from the secondary gene
pool, C. lanceolatus, showed resistance against bruchids. Bruchid growth and
survival was inhibited in the lines derived from C. lanceolatus. Some of the lines
showed delayed bruchid growth and delayed life cycle, thus showing antibiosis
mechanism of resistance to bruchids. Lines were screened for protein content, and
some of the lines showed higher protein content than both their parents. Further,
biochemical analysis showed higher content of proteinase inhibitor activity in some
of the lines.

21.8.2 Abiotic Stresses

Major abiotic stresses in pigeonpea are water logging, drought, and salinity. As
researchers are targeting the enhanced yield of pigeonpea, the prevailing abrupt
climatic changes are putting checks to the progress towards self-sufficiency.

21.8.2.1 Drought
It is the water limiting condition where the plants experience the shortage of
moisture to complete its life cycle. Drought can occur at any stage of crop develop-
ment, and it mostly depends on onset time, intensity, and duration of water scarcity.
Despite pigeonpea having deeper root system to withstand considerable level of
moisture stress, it poses penalty on grain yield. Long-duration pigeonpea needs
adequate water, but even in short-duration varieties, yield is affected due to water
stress. Stress leads late flowering and hinders early pod development. Since drought
is a complex trait, a candidate gene could be responsive under such stress. The study
by Sinha et al. (2016) showed upregulated gene under drought stress condition.
21 Pigeonpea Breeding 1075

Three genotypes ICPL 151, ICPL 8755, and ICPL 227 showing different responses
under drought condition were analyzed by expression profile of universal stress
protein domain and later validated by q-RT PCR which revealed 6, 8, and 18 to be
>wo-fold differentially expressed in CPL 151, ICPL 8755, and ICPL 227, respec-
tively. From the total 10 differentially expressed genes including plant U-box protein
(four genes), universal stress protein A-like protein (four genes), cation/H(+)
antiporter protein (one gene), and an uncharacterized protein (one gene) were
abundantly expressed under stress condition.
Genes C. cajan_29830 and C. cajan_33874 belonging to uspA were found
significantly expressed in all the three genotypes with two-fold expression
variations. These two candidate genes were specific to this crop only; thus they
confer drought tolerance specifically to pigeonpea. Drought is the only trait whose
haplotype has been investigated (set of gene inherited together by non-random
segregation), and haplotype-based breeding is the ultimate option when using a
whole genome resequencing approach. By using WGRS data of 292 genotypes
from pigeonpea, 10 drought responsive candidate genes were identified. Further
on, using marker trait association and haplo-pheno analysis, three genes were
identified regulating five component drought traits. The haplotype
C. cajan_23080-H2 for plant weight (PW), fresh weight (FW) and turgid weight
(TW); the haplotype C. cajan_30211-H6 for PW, FW, TW, and dry weight (DW);
the haplotype C. cajan_26230-H11 for FW and DW; and the haplotype
C. cajan_26230-H5 for relative water content (RWC) were identified as superior
haplotypes under drought stress condition.

21.8.2.2 Water Logging

Pigeonpea often encounters overflooding at seedling stage, especially in low-lying
areas. Upon exposure to submergence for 3–4 days, the crop experiences hypoxia
with considerable injury to roots, eventually causing death of the plant. Further, the
weather conditions during seedling stage, such as intermittent rains and moderate
temperatures of 25  1 C, favor the occurrence of phytophthora stem blight (PSB)
and the ensuing diseases causing significant loss in crop yield. Recently, ICAR-IIPR,
Kanpur, have identified a pigeonpea genotype, namely, “IPAC 79,” showing
remarkable tolerance against both water logging and PSB based on long-term
observations. The genotype IPAC 79 is an advance line derived from the cross
“Bennur local/BRG 1.” It was found to be tolerant up to 96 h of waterlogging, when
the screening conducted after 20 days of seedling stage. Under waterlogged
conditions, the genotype showed 53.8% survival as compared to only 0.6% survival
in sensitive line (ICPL 7035), and 11.2% and 18.6% survival in national check
varieties, viz., Bahar and NDA 1, respectively. It is important to note that IPAC
79 was also resistant to PSB. Scientists at ICRISAT have developed the advanced
generation derived out by crossing with the wild C. acutifolius lines showed growth
in stress condition. Formation of lenticels marked waterlogging situation, and this
region gives rise to roots which enter the soil through the water surface.
1076 S. J. Satheesh Naik et al.

21.8.2.3 Salinity
Salinity hinders the growth due to increased salt concentration and accumulation of
those in soil (Jha et al. 2019). Higher NaCl/Na2SO4 content in the soil affects crop
yield physiologically. Salinity delays days to 50% flowering by 1–2 weeks and
prolongs the peak period of flowering and reduces the number and weight of the
seeds. The wild relatives of pigeonpea, C. scarabaeoides, C. albicans, and
C. platycarpus, showed a wide range of variation in their salinity tolerance. The
transfer of salinity tolerance from C. albicans to C. cajan would be feasible as the
high level of salinity tolerance in this wild species is expressed as a dominant genetic
trait (Choudhary et al. 2011).

21.8.3 Yield

To understand the yield, many agronomic traits such as days to flowering, maturity,
relative water content, electrical conductivity, seed protein content, seed weight,
high biomass, and water uptake traits were targeted for the QTL identification
(Bohra et al. 2020a; Obala et al. 2020). The study uses the interspecific cross
between Cajanus cajan (L.) Millspaugh acc. ICPL 20340 and Cajanus
scarabaeoides (L.) Thouars acc. ICP 15739 resulting in higher phenotypic variance
which suggested the major contribution made by wild parent.
Further, using SSR marker partial linkage map with 83 loci, 15 maker trait
associations of 4 different linkage groups were identified, i.e., LG01, LG02,
LG04, and LG05. Their study reported genetic variation for six seed traits including
seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT),
electrical conductivity (EC), and water uptake (WU), which resulted in the identifi-
cation of 2, 3, 3, 2, 1, and 4 QTLs, respectively (Bohra et al. 2020a). Similar
approach used by Obala et al. (2020) with SNP genotyping identified 192 main
effect QTLs and 573 epistatic QTLs, and phenotypic variance from 0.7% to 91.3%
and 6.3% to 99.4%, respectively, were detected. Major effect (PVE  10%) of
M-QTLs included 14 M-QTLs for seed protein content, 16 M-QTLs for seed weight,
17 M-QTLs for seed yield, 19 M-QTLs for growth habit, and 24 M-QTLs for days to
50% flowering, and these QTLs were mapped and genotyped using GBS approach in
5 different populations between CP11605  ICP14209, ICP8863  ICP11605,
HPL24  ICP11605, ICP8863  ICPL87119, and ICP5529  ICP11605.

21.9 Hybrid Development and Heterosis Vigor

The constantly increasing gap in the demand to supply for pigeonpea had been the
matter of concern to the pigeonpea researchers in India. The cross-pollination
behavior of pigeonpea is a desirable to develop and establish the hybrid system to
exploit the commercial heterosis. Keeping this in view, pigeonpea research was
directed towards a new initiative on hybrid pigeonpea breeding at ICRISAT,
Hyderabad, immediately after the identification of male sterile line in 1974, which
21 Pigeonpea Breeding 1077

in turn led to the development of new GMS hybrid called ICPH 8 in 1991 which
resulted in 31–40% superiority in farmer’s field in the central zone (Saxena et al.
1992a, b). Then after five GMS hybrids (PPH4, CoPH1, CoPH2, AKPH4101, and
AKPH2022), the early maturing groups were released by the state and central
varietal release committee. Nevertheless, the GMS-based hybrids did not yield
much success due to difficulty in the production of commercial F1 seed.
The bottlenecks of GMS system led to the development of stable and economic
CGMS system in pigeonpea. The first CMS line in pigeonpea was made by Reddy
and Faris (1981) using wild relative of pigeonpea, C. scarabaeoides. Previously,
pigeonpea was believed to be a self-pollinated crop, and natural out-crossing was
treated as a constraint. The first CGMS line GT 288A and its maintainer B line were
registered by Pulse Research Station, SDAU, GAU, SK Nagar, Gujarat, in 2000.
Consequently in 2006 the first CMS hybrid GTH 1 was developed by SDAU,
Gujarat, and released by CVRC for cultivation in the central zone. Subsequently,
ICRISAT released its first CMS hybrid ICPH 2671 in 2010 (Saxena et al. 2013).
There are 39 CGMS lines that have been registered with ICAR-NBPGR and five
CMS-based hybrids (ICPH 2671, ICPH 2740, ICPH 3762, IPH 15-03, and IPH
09-5) that have been released for cultivation as of today.
After the failure of the GMS, CMS came into light with the first concept of hybrid
seed production technology that harnesses the non-functionality of pollen resulting
from the impaired harmony between the nuclear and cytoplasmic genomes (Bohra
et al. 2016; Mishra and Bohra 2018). Mitochondrial genes have been reported in
different crops that confer CMS trait. The fertility in CMS system is rescued because
of fertility-restoring elements located in the nucleus. Therefore, this system could
also be known as cytoplasmic-genetic male sterility (CGMS). In pigeonpea and
many other crop plants, Bohra et al. (2016) reviewed the progress of
mapping sterilizing cytoplasmic elements and fertility restoration loci by the use of
NGS-based technologies. Many other crops tend to be discovered by the molecular
mechanism using the omics-based approaches in sterilizing cytoplasm. The three-
line system used in pigeonpea has three components and the genotype carrying
sterilizing (mitochondria derived) and Rf (nucleus encoded) factors that are referred
to as sterile (A), restorer (R) line, and third line “maintainer” B line. The maintainer
(B) line is essentially required to retain the sterility status in pollen; both A and B line
are isogenic which differ only in sterility-inducing cytoplasm. In simple words,
A  B cross regenerates the genetic constituent of A line, but B line is devoid of
any Rf gene. Now, A  R cross is used to restore fertility; thus, this explains
improved heterosis in the hybrid.
It has long been assumed that wild germplasm was used to introduce sterility
system (Bohra et al. 2021b, c). The very first hybrid was also produced by crossing
with C. scarabaeoides. So far, nine such systems, namely, C. sericeus (A1),
C. scarabaeoides (A2), C. volubilis (A3), C. cajanifolius (A4), C. cajan (A5),
C. lineatus (A6), C. platycarpus (A7), C. reticulatus (A8), and C. lanceolatus
(A9), have been reported in pigeonpea with varying degree of success (Singh et al.
2017; Saxena et al. 2017a; Varshney et al. 2017; Sameer et al. 2017). Out of these,
A4 cytoplasm with gene nad7a (Sinha et al. 2015a; Bohra et al. 2021d) has been
1078 S. J. Satheesh Naik et al.

promising because of its stability under various agro-climate zones and availability
of good maintainers and restorers.
Another form of sterility is conferred in pigeonpea which can be reversed to
fertility or vice versa. Various environmental factors such as photoperiod (PGMS)
and temperature (TGMS) alter the gene expression causing sterility and fertility
transition. This is also known as two-line system where the temperature above
critical temperature (25 C) causes sterility. This system is known as temperature
genetic male sterility (TGMS) in which temperature above 25 C is considered a
restrictive condition (RC) and causes sterility and below 25 C is known as permis-
sive condition (PC). The temperature-sensitive selections were made in advanced
generations of the populations derived between C. cajan (ICPA 85010) as female
parent and C. sericeus as the pollen donor.
The concept of hybrid vigor or heterosis, first introduced by Shull in 1914,
explains the tendency for the progeny of parents to exceed the mid-parent (average
of the two); in simple words F1 hybrid is superior to its parents. Heterosis can be
estimated in three ways: mid-parent heterosis (MPH), better parent heterosis, and
standard heterosis. Mid-parent heterosis (MPH) can be explained by the formula
(F1-MP)  100  MP, where MP is the mean of two parent and F1 is the mean of
F1. Therefore, heterosis is measured over mid-parent which is the average value of
two parents. Superiority over parental lines in the reference of the many yield-related
quantitative traits such as seed weight, days to 50% flowering, days to maturity, plant
height, etc. was used to identify hybrid superiority. Molecular mechanism to under-
stand this phenomenon of hybrid vigor was not yet known which is already known in
many other crops such as rice, maize, and wheat. Using whole genome resequencing
approach (WGRS), multiyear and multilocation phenotyping data from 104 parental
lines and 435 of their single-cross hybrid progenies, combined with 292 lines from a
previous study (Varshney et al. 2017), a total of 396 inbred lines, were used for
identifying hybrid vigor. After the assessment of yield-related traits in different
locations, an analysis for MPH came out to be 78.6% positive MPH values in the
hybrids. Further by using genome wide prediction and association mapping, the
authors identified 129 SNPs and 52 CNVs effectively for studying heterotic effect.

21.10 Breeding Approaches of Post NGS Era

The latest development of the genomic resources led the breeding of pigeonpea to a
new platform for the genetic enhancement.

21.10.1 Marker Technologies

After the availability of marker technologies, trait mapping and diversity analysis
became easier for the breeders. The development of SSR markers catalyzed the
molecular analysis in a population. Initially using Sanger’s platform, SSR markers
were developed by using genomic libraries or mining ESTs from the transcriptome.
21 Pigeonpea Breeding 1079

The same approach was used by Bohra et al. (2011) to discover the first and large set
of SSR marker (3072) in pigeonpea by using BAC end sequences. After the high-
throughput, automated, and cost-effective technologies came into light, the
discoveries of marker have become easier. The trait-associated mapping also became
easy with the genome sequencing and whole genome resequencing approaches.
Diversity array technologies (DArT), hybridization-based genotyping technologies,
generated thousands of polymorphic loci that were further used for designing linkage
map and to study diversity of analysis across the genotypes. Next-generation
sequencing technologies have made SNP marker development very easy. Single-
nucleotide polymorphism (SNP) marker is nowadays a marker of choice; therefore,
development of cost-effective KASP technologies has given 1616 SNPs (Saxena
et al. 2011) for genotyping assay in pigeonpea.
Using Illumina platform, SNP discovery using NGS, RNA-Seq, complexity
reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA
sequencing (RAD-Seq), and genotyping by sequencing (GBS) have simplified the
way enough. GBS offered a way to sequence and genotype polymorphism among
two genotypes simultaneously. Recently a GBS approach was used in pigeonpea for
the trait mapping and identification of candidate gene for FW, SMD, and determi-
nacy (Saxena et al. 2017b, c, d). The molecular map was designed using SNP
marker, GBS approach in the F2 population of CMS line its isogenic line (Saxena
et al. 2018). Using microarray technology, a 62 k genic-SNP array (Singh et al.
2020) “CcSNPnks” and 56k SNP- array (Saxena et al. 2018) is widely used high-
density genotyping platform for pigeonpea to demonstrate population structure
analysis, diversity analysis, phylogenetic study, high-density linkage mapping,
QTL mapping, and screening of haplotypes.
In the field of hybrid breeding programs, the molecular marker technologies lead
researchers to find the affected molecular pathways and candidate gene confer
against CMS trait. Based on mitochondrial genome sequencing, the open reading
frame (ORFs) and gene in the ICPB 2039 and ICPA 2039 have been identified.
Further, on the comparative analysis between ICPA 2039 and ICPB 2039 of
34 mitochondrial genes, the deletion in nad7A gene in CMS line has been provided.
Thus, InDel-based marker (nad7a_del) is used for testing the hybrid purity (Sinha
et al. 2015a). Later on, to test the hybrid purity, many hybrid purity testing kits by
using SSR marker system were used (Bohra et al. 2015, 2017a, b), but due to the
expensive way of testing, it was later replaced by SNP assays (Bohra et al. 2020a).
To differentiate restorer line from non-restorer lines in A4 hybrid system, two
markers, namely, “CcLG08_RFQI1” and “CcLG08_ RFQI4,” have been developed.
Therefore, after the development of the marker system, the phenotyping activities
could be avoided in order to be time effective.
1080 S. J. Satheesh Naik et al.

21.10.2 Candidate Gene Mapping and Breeding Using

Transcriptomics Resources

Based on Sanger technologies, the first set of transcriptomics resources include 9468
ESTs that served for the candidate gene for fusarium wilt and SMD with 19 and
20 genes, respectively, and set of 3583 SSRs. Sinha et al. (2015a, c) discovered and
validated stress-responsive genes for the candidate gene to be responsive to salinity,
drought, and heat,. A major asset to pigeonpea is its expression atlas, a global view
on the gene expression that helps in bridging the gap between whole genome
sequence information and plant phenotypes. From its developmental stages to its
reproductive and later followed by senescence, expression atlases “CcGEA” high-
light the impact of each gene. It basically covers the whole life cycle of pigeonpea,
which is developed using RNA-sequencing technologies. The “C. cajan gene
expression atlas” CcGEA catalogue has a total of 28,793 genes expressed during
different variable stages especially during flower development and fertilization. This
catalogue also suggested the posttranscriptional and epigenetic modification in seed
and embryo development of pigeonpea.
Co-expressional analysis also highlighted the identification of 28 genes and three
highly connected genes known as “Hub genes” (Pazhamala et al. 2017). Multiomics
approach was used to reveal fertility transition of candidate genes contributing
towards hybrid breeding program in two-line system (TGMS); however
transcriptomics by RNA-Seq was largely relied on. The male and female anther
were studied at their developmental stages, and by integrating omics approaches,
transcriptome and proteome revealed 17 DEGs in sterile anther. The study revealed
that this transition of fertility to sterility is mainly due to auxin homeostasis, impaired
cell wall, and sugar transporters. Similarly, Bohra et al. (2020a, b) revealed a set of
505 genes that showed altered expression in response to CMS. From this set,
412 genes were upregulated, while 93 were downregulated in the fertile maintainer
line as compared to the CMS line. The study revealed gene showing impaired
pathways related to glucose and lipid metabolism, ATP production, pollen develop-
ment/pollen tube growth, and reactive oxygen species (ROS) scavenging.
For candidate trait mapping and QTL, discovery methods are still conventional,
and these mapping can be done by using SSR and SNP marker. SNP array and
linkage maps based on GBS approach have helped researchers in trait dissection.
Other similar approaches like WGRS/skim sequencing with the availability of the
reference genome facilitated the efforts. The first generation Hap-map in pigeonpea-
based WGRs data from 20 accessions revealed 5.5 million genome-wide variants
including 4.6 million SNPs and 0.7 InDels along with the structural variations
including copy number variable (CNVs) and presence and absence variable
(PAVs) (Kumar et al. 2016). Similarly, with WGRS data obtained by using
292 pigeonpea accessions revealed large structural variations (SVs) of greater than
or equal to 1000 bp in the breeding lines, viz. 282 CNVs; 35 PAVs, wild has
173 CNVs; 77 PAVs and landraces have 228 CNVs and 37 PAVs.
21 Pigeonpea Breeding 1081

21.10.3 High-Density Linkage Map and QTL Mapping

Prior to the large set of SSR markers discovered by Bohra et al. 2011, there were
inadequate diversity analyses which impaired the development of high-density
linkage map. Later, the team discovered the first map with 239 loci for an interspe-
cific cross between C. cajan (ICP 28)  C. scarabaeoides (ICPW 94). After this
pigeonpea got more linkage map, none of them were of high density. Over the
discovery of high-throughput technologies, high-density map in pigeonpea became
an easy shot. The first high-density linkage map was discovered by SNP marker for
interspecific cross using KASP assay platform with 875 loci (Saxena et al. 2012a, b).
After that, more population maps were made covering 1101 loci (Saxena et al.
2017b), 964 loci (Saxena et al. 2017c), and 787 loci (Saxena et al. 2017d). To
date, the most comprehensive genetic map of pigeonpea harbors 6818 SNPs loci that
span 974 cM of the genome (Yadav et al. 2019). Availability of such density genetic
maps is the key to understand the genomic importance of essential agronomic traits,
for the trait mapping. In the future, this kind of trait mapping has several advantages
over traditional marker-based mapping. In addition to taking much less time, these
approaches identify genes or QTLs for a given trait which can be used as diagnostic
marker(s).

21.10.4 NGS-Based Trait Dissection

As the popularity of NGS-based platform raised, WGRS approaches and next-

generation trait mapping particularly Seq-BSA were employed for trait discovery.
An approach used by Singh et al. (2016a) revealed the candidate gene responsible for
the major biotic stress in pigeonpea recombinant inbred population (RIL) population
ICPL20096  ICPL332. Four SNPs showed the associated with FW, while the
remaining four showed correlation with SMD. A similar InDel approach used to
identify the same traits by Singh et al. (2017) revealed 16 InDels from which five
were validated by WGRS data. Table 21.1 has highlighted the major candidate genes
and high-density QTLs region with their respective traits and approach used for their
validation and identification.

21.10.5 Adopting Speed Breeding Technology and RGT

Technologies

Speed breeding is recently in spotlight for cool season legume; nevertheless the extra
early and early maturing pigeonpea holds immense potential. The concept of speed
breeding was first introduced by Watson (2019). The speed breeding (SB)/rapid
generation advancement (RGA) concept describes the breeding techniques which
focused on enhancing the genetic gain by reducing the length of breeding cycle
which is inversely related to genetic gains (Moose and Mumm 2008). In pigeonpea
as described earlier, photoperiod plays an important role in the completion of its life
1082 S. J. Satheesh Naik et al.

Table 21.1 Major candidate genes and high-density QTLs regions identified in pigeonpea using
WGRS data
Number of
QTLs/candidate Method/
Trait gene Population approach References
Fusarium wilt 3 QTLs ICPB2049  ICPL99050 Genotyping Saxena
(FW) (qFW11.1, ICPL20096  ICPL332 by et al.
qFW11.2, and F2 (ICPL85063  ICPL sequencing (2017b)
qFW11.3) 87119) (GBS)
Two gene (C. BDN 711  ICPL 20096 GBS Saxena
cajan_03691 et al.
and C. (2021)
cajan_18888)
C.cajan_03203 ICPL 20096  ICPL 332 Bulk Singh
segregant et al.
assay (2016b)
(BSA-Seq)
3 InDels ICPL 20096  ICPL 332 BSA-Seq
and WGRS
Sterility mosaic CcLG11 ICPB 2049  ICPL GBS Saxena
disease (SMD) 99050 et al.
ICPL 20096  ICPL 332 (2017c)
F2 (ICPL 85063  ICPL
87119)
Four gene (C. BDN 711  ICPL 20096 GBS Saxena
cajan_07858, C. et al.
cajan_20995, C. (2021)
cajan_21801,
and C.
cajan_17341)
C.cajan_01839 ICPL 20096  ICPL 332 BSA-Seq Singh
et al.
(2016b)
3 InDels ICPL 20096  ICPL 332 BSA-Seq
and WGRS
qSMD4 ICP 8863  ICPL 20097 Biparental Gnanesh
TTB 7  ICP 7035 et al.
(2011)
Drought C. cajan_23080- _ WGRS Sinha et al.
tolerance H2 (haplotypes) (2020)
C. cajan_30211-
H6
C. cajan_26230-
H11
C. cajan_26230-
H5
Cleistogamous qCl3.2 ICPL 99010 and ICP Axiom Yadav
flower 5529 Cajanus et al.
SNP Array (2019)
(continued)
21 Pigeonpea Breeding 1083

Table 21.1 (continued)

Number of
QTLs/candidate Method/
Trait gene Population approach References
Determinacy CcTFL1 ICPA 2039  ICPR 2447 SNP Mir et al.
C. cajan(ICPL genotyping (2014)
85010)  C. volubilis and marker
Blanco (ICP 15774) trait
association
(MTA)
Seed protein 192 main effect ICP 11605 (P1)  ICP GBS Obala
content (SPC) QTLs and 14209 (P2); ICP 8863 et al.
and seed weight 573 epistatic (P1)  ICP 11605 (P2); (2020)
(SW), seed QTLs HPL 24 (P1)  ICP
yield (SY), 11605 (P2); ICP 8863
growth habit (P1)  ICPL 87119 (P2);
(GH) and days ICP 5529 (P1)  ICP
to first 11605 (P2)
flowering (DFF)

cycle, and hence, SB protocol may work on it. A 12-h day length has been
established as the optimum photoperiod in pigeonpea (McPherson et al. 1985). In
cool season, rapid generation from 5 and 3 generations in legumes such as field pea,
chickpea, respectively, can be achieved by regulation of growth condition and
photoperiod exposure (Gaur et al. 2007; Mobini and Warkentin 2016). Mobini
et al. (2015) applied plant hormone in Faba bean and lentils to gain seven and
eight generations, respectively; they used cytokinin and auxin to induce early
flowering and harvested immature seed for generation advancements. In pigeonpea,
Saxena et al. (2019) achieved four generations per year in the early maturing
genotypes, namely, ICPL 85024, ICPL 87093, ICPL 00004, and ICPL 00151, as
they were photo-insensitive lines. Therefore, SB protocol with single seed descent is
extremely useful for preserving genetic variability, and combination of SB recipe
with genomic selection or marker-assisted selection will promote the targeted
breeding (Bohra et al. 2020b).

21.10.6 Genomic Selection (GS) Using Marker Technologies

From conventional breeding approaches, research programs drastically shifted

towards marker-assisted breeding. From the use of effective marker technologies,
pigeonpea has been derived out of many linkage maps and revealed trait-responsive
QTLs. Deploying trait-associated markers for the introgression or selection of QTL
(s) in the elite genetic background for the development of elite pigeonpea varieties is
currently imparted by the national and international breeding programs. Genomics
1084 S. J. Satheesh Naik et al.

assisted breeding efforts have been successful in legume crops (Varshney et al. 2019,
2021a). In general, the transfer of QTLs using the MABC technology is limited with
the major effect QTL instead of minor QTLs responsible for complex traits of plant
phenotype (Varshney et al. 2021b). Due to this inability of MABC program,
genomic selection (GS) can be used to locate minor effect loci by calculating the
estimated breeding values of the model prepared. Prior information of the phenotype
is not required; genotyping works for controlling the polygenic inheritance. In
simple words, the concept of GS was first proposed by Meuwissen et al. (2001) in
animals for the estimation of breeding values of unobserved phenotypes based on
genome-wide marker data. GS needs the genome wide associated markers, and
genome estimated breeding value (GEBV) is the basis for the selection of the
genotypes from the respective breeding programs. In pigeonpea, no GS model yet
has been reported, but in other legume crops such as field pea, soybean, etc., the
result revealed to conclude superiority of GS over phenotypic selection especially in
the case of field pea with respect to yield response (Annicchiarico et al. 2019).

21.11 Challenges for Pigeonpea as International Crop

Pigeonpea being the rainfed crop harbors several challenges starting from evolution-
ary to adoptability to agronomic and crop husbandry.

21.11.1 Limitation Due to Photoperiod Response and Temperature

across the World

Apart from India, pigeonpea is widely cultivated in South Africa, Asia, and Latin
America. These regions have not yet able to produce the potential yield. Traditional
cultivars of pigeonpea cannot fit as preceding or succeeding crop in situations of
rainfed and irrigated ecologies due to high sensitivity to photothermal regimes.
Therefore, photothermal insensitive lines are of particular interest to pigeonpea
breeders to develop cultivars for niches and also to ensure synchrony in flowering.
Short-duration insensitive accessions are very useful in sequential, double or multi-
ple cropping systems. The photothermal insensitivity trait is well distributed across
the classes of flowering pattern and growth habit indicating that the photothermal
insensitivity can be easily combined with other traits in efforts to maximize the
pigeonpea yields (Upadhyaya et al. 2007). However, the biggest challenge is the
inheritance of insensitivity in pigeonpea. But, several high-yielding varieties have
been released for cultivation due to their photothermal sensitivity which is restricted
to their own geographical regions. Pigeonpea needs shorter days and longer hour of
darkness to promote flower induction (Vales et al. 2012). Perfect combination
induces flower induction because this trait restricts pigeonpea to adaptation beyond
30 northern and southern latitudes. Medium maturating and late varieties are highly
connected to photoperiod response; in other words, inverse correlation between
earliness and photo-insensitivity in pigeonpea is recorded (Saxena et al. 1981).
21 Pigeonpea Breeding 1085

Therefore, photoperiod and low-temperature sensitivity have surely restricted the

expansion of pigeonpea across higher latitudes. Not only environmental factors but
also biotic and abiotic factors still block the way out for pigeonpea to a diversely
cultivated crop all around the world.
Drought is the major abiotic constraints in many areas; therefore through multi-
location and multiyear evaluations, medium-duration genotypes such as ICEAP
00673, ICEAP 01170, and ICEAP 01179, as well as long-duration genotypes such
as ICEAP 01423 and ICEAP 01202 possessing, drought tolerance coupled with high
yield has been identified.

21.11.2 Natural Cross-Pollination

It is one of the major constraints to maintain genetic purity of varieties and breeding
material (Howard et al. 1919). To maintain pure breeding lines for a particular trait,
this turns out to be a serious issue due to poor seed production (Sultana and Saxena
2019).

21.11.3 Limited Genetic Diversity in Various Geographical Areas

Focusing on to primary gene pool, we have processed an inbreeding depression of

the Cajanus which has limited diversity and limited access to beneficially agronomic
traits. More breeding programs crossing the elite varieties are leading more towards
limited collections that add on to the lagging genetic enhancements with
interventions of wild relatives (Saxena et al. 2014). To access more in primary
pool, breeders started exploring the secondary and tertiary pools. The utilization of
the wild relatives will provide resistance, quality, and breeding efficiency, which is
highlighted by Khoury et al. (2015). Further, their study highlight the extent of
diversity in pigeonpea, which cultivars lack as compared to the wild pigeonpea.

21.12 Approaches Used for Varietal Development

In the view from geographical regions and different maturating groups, distinct
maturity groups pertaining to the zone of cultivation of pigeonpea have been
explored (AICRP on Pigeonpea Coordinator Report 2018–2019). Developing any
of the cultivars, breeders focused on increasing the seed yield. In total, all
150 varieties have been released till 2018 since 1960. Most of the varieties were
developed following pedigree (89), pure-line germplasm selection (57), and muta-
tional breeding (3). The data presented by IVT-AICRP suggested that hybridization
coupled with pedigree method was observed in 455 varieties. Of the five maturity
groups, medium and early represent large groups comprised of 48 released and
182 IVT entries and 33 released and 142 IVT varieties, respectively (Naik et al.
2020). Further their study suggested that the landmark pigeonpea varieties released
1086 S. J. Satheesh Naik et al.

for cultivation were having the genetic base contributed by T190, C11, UPAS
120, ICP 8863 and T 21 genotypes. The variety UPAS 120 is pureline selected
from P4768 in 1976 for its superior trait, early maturating, and tolerance to pod
borer, initially cultivated in NEPZ. This variety is the most used of genetic bases in
all varieties, as it’s been used as parent 25 times which is further followed up by
Asha. Asha (ICP 87119) has been widely used as parent 44 times, even exploited in
the NAM population as founder parent due to its resistance against FW and SMD. It
is released in 1986, derived out by hybridizing C11 as cytoplasmic donor and ICP
6 male parent. UPAS 120 is used as donor for most of early and medium maturing
groups, whereas Asha is used as parent for late maturity group.
ICP 8863 well known as Maruti is also achieved by a pureline selection from
Hyderabad landrace and now suitable for South zones, and it shows resistance
against wilt. Many more remarkable varieties are released such as BMSR
736, TJT-501, IPA203, IPA 206, Bahar, etc. (Naik et al. 2020) to understand the
contribution of varieties to form the genetic base of the cultivated pigeonpea and
how the development of these varieties has supported the invention of more elite
cultivars. A new landrace “ICP 7035” has been identified in the state of Madhya
Pradesh in Jabalpur (Bedaghat) which offers multiple resistance against all the three
strains of SMD and has sweet immature seeds. It is considered as the “jewel” among
all the germplasms due to its multiple benefits in soil conservation and resistance
against pest and multiple diseases. Its performance has been reported well in
SMD-endemic areas of India, Myanmar, and Nepal (Sharma et al. 2021).

21.13 Hybrid Released in India

21.13.1 GMS-Based Pigeonpea Hybrids

ICRISAT developed the first GMS-based pigeonpea hybrid ICPH 8 and released for
cultivation in India (Saxena et al. 1992a, b). In farmers’ fields, this hybrid recorded
31–40% yield advantage over the best control. This was followed by the release of
five more GMS-based hybrids that exhibited high levels of standard heterosis
(Table 21.2). But, none of these could reach farmers’ fields at commercial level.
As the male sterility is controlled by a pair of recessive gene (msms), it can only be
maintained by crossing it to heterozygous (Msms) plants. The progeny of this cross
(msms  Msms) will segregate in to 50% male-fertile (Msms) and 50% male-sterile
(msms) plants. Therefore, identification of the fertile segregants within female
population was the primary requirement of large-scale seed production, and it was
not found commercially viable.

21.13.2 CMS-Based Pigeonpea Hybrids

CMS results from an inherent disharmony between cytoplasmic (mitochondrial) and

nuclear genomes. A range of mitochondrial genes have been reported in different
21 Pigeonpea Breeding 1087

Table 21.2 Pigeonpea hybrids released in India

Name of the Days to Superiority over check
hybrid Zone Released maturity (%)
GMS-based hybrids
1 ICPH 8 Central 1991 125 30–40
2 PPH 4 Punjab 1994 137 14
3 CoH 1 Tamil Nadu 1994 117 19–22
4 CoH 2 Tamil Nadu 1997 125 35
5 AKPH 4104 Central 1997 135 64
6 AKPH 2022 Maharashtra 1998 190 25–35
CMS-based hybrids
1 GTH-1 Gujarat 2006 140 32
2 ICPH 2671 Madhya Pradesh 2014 175–180 31–34
3 ICPH 2740 Telangana 2015 180 34
4 ICPH 3762 Orissa – 180–190 36
5 IPH 15–03 NWPZ 2019 150–155 28–55
6 IPH 09–5 NWPZ(reconfirm – 138–140 33
trial)
Source: Project Coordinators (Pigeonpea) Report, 2019; Saxena et al. (2010)

crops that confer CMS trait. The fertility in CMS system is rescued because of
fertility-restoring elements located in the nucleus. The first CGMS line GT 288A and
its maintainer B line were registered by Pulse Research Station, SDAU, GAU, SK
Nagar, Gujarat, in 2000. Consequently in 2006, the first CMS hybrid GTH 1 was
developed by SDAU, Gujarat, and released by CVRC for cultivation in the central
zone. There are 39 CGMS lines that have been registered with ICAR-NBPGR and
six CMS based hybrids that are released for cultivation as of 2019.

21.14 Coordinated System and Programs for Pigeonpea

In India, the emphasis on pulse research including pigeonpea has been increasing
since 1967. Systematic research on pulses was started with the establishment of the
All India Coordinated Pulses Improvement Project (AICPIP) in 1967 with its
headquarter at Indian Agricultural Research Institute, New Delhi. In 1978, the
project was elevated to the status of Project Directorate (Pulses), while its headquar-
ter was shifted to the then IARI Regional Research Station, Kanpur, Uttar Pradesh.
The Project Directorate (Pulses) was further strengthened with the inclusion of basic
and strategic research in its mandate and elevated as Directorate of Pulses Research
(DPR) in 1984 at Kanpur, Uttar Pradesh. During VIII five-year plan, the AICPIP was
divided into three projects, viz., chickpea, pigeonpea, and MULLaRP (Mungbean
Urdbean, Lentil, Lathyrus, Rajmash and Pea), and the post of project coordinator
was created to provide independent leadership to respective AICRPs. Subsequently,
in the IX five-year plan, the project proposal on pigeonpea was proposed to nine
1088 S. J. Satheesh Naik et al.

main centers (Badnapur, Varanasi, Coimbatore, Dholi, Gulbarga, Khargone,

Warangal, Bengaluru, and S.K. Nagar) and 11 subcenters. Consequently, during X
and XI plan, the subcenters were increased to 17 (Akola, Rahuri, Faizabad,
Pantnagar, CSAUAT Kanpur, Berhampur, Hisar, Vamban, Sehore, Junagarh,
Lam, Raipur, Ludhiana, Ranchi, Kota, Nagaland, and Tripura).
The organizational restructuring was done with renewed emphasis to cater the
research and development, in which pigeonpea production needs to be increased in
the country to meet the ever-growing demand. At present, AICRP on pigeonpea has
26 centers spread over 17 states comprising of 22 universities and 1 agricultural
college covering the entire pigeonpea growing region of the country. In recent years,
greater emphasis has been laid on the development of high-yielding varieties and
hybrids coupled with appropriate production and protection technologies to bridge
the gap between the potential and realized yields of pigeonpea. In this regard, our
prime concern is also on developing early-duration varieties/hybrids suitable for
breaking the rice-wheat cropping system with resistance to major biotic stresses like
phytophthora stem blight (PSB), fusarium wilt, and sterility mosaic disease (SMD).
Strengthening seed delivery systems, greater seed replacement rate, and
strengthening of community-based services including seed production, input supply,
and marketing support are expected to promote enhanced cultivation of pigeonpea,
which in turn supports the cause of millions of livelihoods of dryland farmers.
The consumption and demand of pigeonpea in the rural India is unstoppable.
However, the present popularity of pigeonpea as a healthy vegetable source of
protein among the urban household created huge market elasticity for pigeonpea
dal. Pigeonpea is nutritionally rich and highly digestible with less flatulence com-
pared to chickpea and peas. It has been a recommended food for all age groups as a
source of protein.
Pigeonpea and other pulses will very soon find its appropriate place especially in
the context of future challenges such as global warming, scarce water supply, needs
for new raw materials, and increasing health awareness among urban and rural
public. In this circumstance, we need to reinforce our efforts in pigeonpea research
and development by innovative research strategies and continue to develop cultivars
and technologies suitable for specific end uses.

21.15 Future Prospects

Breeders have focused to increase the yield in pigeonpea since all time, and yield
being a quantitative trait results from the combination G  E interaction and minor
epistatic gene; therefore, to improve with respect to each and every factor, it becomes
a tedious task (Saxena et al. 2020). The emergence of the omics technologies has
enhanced and opened up the opportunities for rapid crop improvement and over-
come the adverse effect of climatic change (Varshney et al. 2021b). The technologies
such as marker-assisted backcrossing (MABC), genomic selection, rapid generation
turnover with speed breeding, and haplotype-based breeding accelerated the current
research program in pigeonpea. The whole genome resequencing and GBS
21 Pigeonpea Breeding 1089

approaches have led to the discovery of SNPs and genome-wide variations (Bohra
et al. 2020a) which has made possible to exploit “tailor-made” crops by using
superior haplotypes. By using pangenome studies, the wild accession and their
beneficial traits in breeding programs have also been incorporated. Future research
is focusing to increase the protein yield by QTL analysis (Obala et al. 2019), and
hybrid breeding has the potential to exploit more protein as the gene is controlled by
additive gene action. Natural out crossing which is considered as a boon for hybrid
production becomes a major challenge in pure line breeding. Thus, for the varietal
development, it requires lot of resources such as isolation distance, insect proof
cages, and labor cost for proper cleaning and care. These factors have shifting
researcher attention towards cleistogamous trait. Moreover, studies need to be
done on the area of photosensitivity and earliness, as their inverse relation has
possibly made speed breeding impossible in medium and late maturity groups
(Fig. 21.1). Therefore, researchers need to explore the candidate genes and factors
responsible for this relation, and after that GS-based speed breeding can make future
in pigeonpea. In hybrid production, three-line system has given so many potential
hybrids for different geographical regions, but two-line system (TGMS and PGMS)
is not so much explored.
1090 S. J. Satheesh Naik et al.

Fig. 21.1 Diagram highlighting the way ahead for pigeonpea breeding
21 Pigeonpea Breeding 1091

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Mungbean Breeding
22
Gyan Prakash Mishra , Harsh Kumar Dikshit, Kuldeep Tripathi,
Muraleedhar S. Aski, Aditya Pratap, Uttarayan Dasgupta,
Ramakrishnan M. Nair, and Sanjeev Gupta

Abstract

Mungbean (Vigna radiata (L.) R. Wilczek var. radiata), which is also known as
the green gram, or moong, is primarily grown in East Asia, Southeast Asia, and
the Indian subcontinent. Mungbean has its own place due to some very unique
features like short crop duration, low input requirement, wide adaptability, and
tolerance to various abiotic stresses including heat and drought. Besides,
mungbean is also very rich in overall nutrient content which makes it the most
preferred crop for various culinary preparation including dal, soups, sprouts, etc.
In addition to the biotic and abiotic stresses, breeding focus should be on other
economic traits like extra-early maturity and photothermal insensitivity in the
genotypes, which will help in suitable fitting of the developed varieties in various
cropping systems and patterns. Due to its unique health and nutritional properties,
along with soil and environment ameliorative ability, mungbean is one of the

G. P. Mishra (*) · H. K. Dikshit · M. S. Aski · U. Dasgupta

Division of Genetics, Indian Agricultural Research Institute, Delhi, India
K. Tripathi
Germplasm Evaluation Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi,
India
A. Pratap
Crop Improvement Division, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh,
India
R. M. Nair
World Vegetable Center, South Asia/Central Asia, Patancheru, Hyderabad, Telangana, India
S. Gupta
Crop Science Division, ICAR, Krishi Bhawan, New Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1097
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_22
1098 G. P. Mishra et al.

preferred crops for food, nutrition, and environmental security and sustainability.
In brief, this chapter deals with various aspects of the mungbean crop like
breeding opportunities, varietal development, biotic and abiotic stress tolerance,
nutritional and biofortification possibilities, along with emerging challenges and
improvement opportunities at global level.

Keywords
Vigna radiata · Green gram · Breeding · Biofortification · Nutrition · Cultivation

22.1 Introduction

The mungbean (Vigna radiata (L.) R. Wilczek var. radiata) or green gram crop is
the third most important grain legume after chickpea and pigeon pea. Mungbean is
indigenous to India or Indo-Burma region and is known by various names like green
gram, golden gram, green bean, green soy, etc. (Markam et al. 2018). Since various
wild and cultivated mungbean species are extensively distributed in the central Asian
region, it is considered as a primary center of genetic diversity. It is an important
constituent of cereal-based farming systems of South and Southeast Asia and is also
grown in several other parts of the world including east and central Asia, east Africa,
and Australia. Globally this is being cultivated on nearly 7.2 million ha area with a
productivity of nearly 750 kg per hectare (Nair and Schreinemachers 2020).
Mungbean is being cultivated across a wide range of latitudes (40
N or S) covering
tropical and subtropical regions of the world and is amicably adapted to a range of
cropping systems (http://avrdc.org/intl-mungbean-network/). The mungbean grows
on a wide range of soils but prefers well-drained loams or sandy loams, with a pH
ranging from 5 to 8. Mungbean is reportedly growing up to an altitude of 1850 m and
is known to be sensitive to both photoperiod and temperature (Lambrides and
Godwin 2006).
Nearly 90% of world’s production comes from Asian countries including India,
Myanmar, China, Thailand, Indonesia, and Bangladesh (Schafleitner et al. 2015;
Alam et al. 2014b). India is the largest producer, consumer, and importer of
mungbean. In India, this is being grown on an area of nearly 4.32 million ha with
a production of 2.17 million tonnes and an average productivity of 502 kg/ha (IIPR
2018). Mungbean is unique for various features including shorter crop duration, low
input requirements, wider adaptability, tolerance to heat and drought, and high
nutritional content which makes it an ideal crop for various cropping systems and
patterns, especially for smallholder farmers (Pratap et al. 2020). The Rhizobium and
Bradyrhizobium bacteria, which are present in the root nodules, fix the atmospheric
nitrogen and thus improve the soil fertility and benefit the succeeding crops.
Mungbean belong to the genus Vigna, encompassing approximately 150 species,
of which only 7 are cultivated species. The genus is subdivided into (1) Asiatic
subgenus Vigna having V. radiata L. Wilczek, V. mungo L. Hepper, V. aconitifolia
(Jacq.) Marechal, V. angularis (Willd.) Ohwi & Ohashi, and V. umbellata (Thunb.)
22 Mungbean Breeding 1099

Ohwi & Ohashi and (2) African subgenus having V. unguiculata (L.) Walp. and
V. subterranea (L.) Verdc (Dikshit et al. 2012). The Vigna species is largely
distributed in tropics and subtropics due to their wide adaptation range in different
agroclimatic conditions. This chapter discusses on various aspects of mungbean
including their cultivation, nutrition, genetic improvement, use of genomic tools,
varieties, better crop management practices, and policy related issues.

22.2 Origin, Evolution and Distribution of Vigna Species

The center of origin of mungbean is believed to be the Indian subcontinent

(de Candolle 1884; Vavilov 1926). Owing to the wide genetic diversity of cultivated
and wild mungbean species found in India, it is also considered as the region of its
first domestication (Baudoin and Marechal 1988). In cultivated and wasteland areas
of India and also in the wetlands of subtropical, northern and eastern Australia
(Lawn and Cottell 1988), V. radiata var. sublobata, the progenitor species of
mungbean, is found growing naturally as a weed. In India, wild relatives were also
documented from Western Ghats and Himachal Pradesh; V. radiata var. sublobata
was from eastern and western peninsular tract, and carbonized grains of wild Vigna
species from Daimabad, while the maximum diversity for Vigna species has been
reported from Deccan Hills and upper Western Ghats (Chandel 1981; Kajale 1977).
Tomooka et al. (2002) reported West Asia as the region of diversity and proposed
that from India mungbean spread to Southeast Asia, China, and Taiwan. V. radiata
var. sublobata is known to have moved from East to North Australia, Asia, New
Guinea, Madagascar, and Central and East Africa (Tateishi and Maxted 2002). South
and West Asian mungbean genotypes are small seeded with green, green mottled,
black and brown seed color, whereas Southeast Asian germplasm possesses shiny
green testa, tall plants, high branching habit, and late maturity. East Asian mungbean
genotypes are of short stature and have early maturity having green to dull green
testa.

22.2.1 Taxonomy and Gene Pool

• Family—Leguminosae.
• Subfamily—Papilionoideae.
• Tribe—Phaseoleae.
• Subtribe—Phaseolinae.
• Genus—Vigna.
• Subgenus—Ceratotropis.
• Section—Ceratotropis.
• Species—Vigna radiata.
• Variety—Vigna radiata var. radiata.
1100 G. P. Mishra et al.

Table 22.1 The primary, secondary, and tertiary gene pools of Vigna species
Primary gene Secondary gene pool Tertiary gene pool
pool (GP-1) (GP-2) (GP-3) References
V. radiata var. V. mungo var. mungo; V. angularis; Chandel et al. (1984),
radiata; V. mungo var. V. dalzelliana; Smartt (1981), Smartt
V. radiata var. silvestris; V. trilobata; V. glabrescens; (1985), Kumar et al.
sublobata; V. subramaniana; V. grandis; (2004) and Tomooka
V. radiata var. V. grandiflora; V. vexillate; et al. (2011)
setulose V. stipulacea; V. aconitifolia;
V. tenuicaulis; V. angularis
V. trinervia;
V. umbellata
Source: Kumar et al. (2011)

Harlan and de Wet (1971) postulated the gene pool concept which can be used to
devise a pre-breeding program for directed crop improvement (Kumar et al. 2011).
The details of primary, secondary, and tertiary gene pools of the genus Vigna is
presented in Table 22.1. The distinct species have been grouped or pooled as per
their cross compatibility along with their cytogenetic, phylogenetic, and molecular
analyses. The existence of useful genes is persistent in the secondary and tertiary
gene pools, but crossability barriers encountered during hybridization between
various Vigna species of primary, secondary, and tertiary gene pools necessitates
the use of novel techniques such as embryo rescue, polyploidization, reciprocal
crossing, hormonal manipulations, use of bridge species, etc. for obtaining the viable
progenies (Pratap et al. 2018; Nair et al. 2020).
However, some deviations have been reported like V. aconitifolia and
V. umbellata in GP-2 and GP-3, respectively. Recent hybridization showed
V. glabrescens forming fertile offspring upon crossing with V. radiata without any
fertility/crossing barrier, though this is grouped in GP-3 (Pratap et al. 2014). Thus,
there is a need to revisit the classification of Vigna gene pool using both molecular
and conventional crossing-based tools for the more precise grouping of Vigna
species.

22.3 Cytogenetics

The somatic chromosome number of mungbean is 2n ¼ 22 and the haploid genome

size is approximately 579 mb (Lavania and Lavania 1983; Arumuganathan and Earle
1991). Due to its relatively small genome size, mungbean is considered as a model
plant among Vigna species. Several studies have been conducted to measure the size
and shape of mungbean chromosomes. Bhatnagar (1974) proposed
4Lsm + 4Msm + 3Mm as karyotype formula for mungbean, where L is long
(2.7–3.5 μm), M is medium (1.9–2.6 μm), sm is submedian centromere, and m is
median centromere. The details of various chromosomes of mungbean are presented
in Table 22.2.
22 Mungbean Breeding 1101

Table 22.2 Details of mungbean chromosomes

Chromosome Chromosome Short arm Long arm Chromosome
number length (μm) length (μm) length (μm) type
1 2.1 0.65 0.95 Metacentric
2 1.77 0.61 0.72 Submetacentric
3 1.62 0.62 1.00 Metacentric
4 1.53 0.69 0.84 Metacentric
5 1.40 0.63 0.77 Metacentric
6 1.35 0.60 0.75 Metacentric
7 1.27 0.57 0.70 Metacentric
8 1.20 0.44 0.76 Submetacentric
9 1.15 0.52 0.63 Metacentric
10 1.08 0.50 0.58 Metacentric
11 0.96 0.44 0.52 Metacentric
(Derived from Vinora 1974; Vinora et al. 1999)

22.4 Plant Genetic Resources

Overall, 6700 mungbean accessions are being maintained at the World Vegetable
Center, Taiwan (erstwhile AVRDC), from which 1481 accessions are selected for
the development of core collection through cluster analysis using eight descriptors.
This core collection was then genotyped using 20 polymorphic simple sequence
repeat (SSR) markers, and based on molecular diversity, 289 accessions were then
selected as mini core set (Schafleitner et al. 2015). In India, mungbean germplasm
collection was initiated by R. D. Bose during 1925, and he could identify 40 distinct
genotypes based on seed and morphological traits.
In the year 1943, Coordinated Pulse Research Scheme was initiated by Indian
Council of Agricultural Research in which promising genotypes were identified for
large-scale cultivation. During the 1960s, efforts have been made at IARI, New
Delhi, and a total of 1250 diverse mungbean accessions have been collected from
various Indian states (Paroda and Thomas 1988). The National Genebank at ICAR-
NBPGR has documented more than 11,000 accessions including 7453 indigenous
and 3588 exotic accessions. Of these, nearly 3927 accessions, comprising of 3392
indigenous and 535 exotic collections which are from 12 countries, are stored in
long-term storage (20
C). During the past four decades, NBPGR has introduced
approximately 4000 diverse mungbean accessions from a number of countries.

22.5 Wide Hybridization in Vigna Species

Interspecific hybrids have been attempted in different Vigna species and F1s were
found either sterile or partially fertile (Singh and Singh 2006). In some cases, pollen
tubes were unable to pierce the stigma, whereas, in others, after fertilization embryo
1102 G. P. Mishra et al.

Table 22.3 Crossability studies in Vigna species

Wide cross References
V. radiata  V. mungo Verma and Singh (1986a), Ravi and
Minocha (1987) and Pande et al. (1990)
V. mungo  V. radiate Gosal and Bajaj (1983a, b)
V. glabrescens  V. Radiata Chen et al. (1990)
V. radiata  V. trilobata Sharma and Satija (1996), Dana (1966) and
Pandiyan et al. (2012)
V. radiata  V. umbellate Pandiyan et al. (2008)
V. radiata  V. radiata var. sublobata Sharma and Satija (1996)
V. radiata with V. mungo, V. radiata var. Pandiyan et al. (2008)
sublobata, V. radiata var. setulosa, V. trilobata,
V. trinervia, V. hainiana, V. dalzelliana
(incompatibility in chromosomal pairing)
(Derived from Dikshit et al. 2020; Gayacharan et al. 2020)

abortion was observed (Ahn and Hartman 1978a, b). In addition, very high flower
drop under artificial pollination makes crossing in Vigna quite tedious. The anthesis
timing (from 05:00 a.m. to 08:00 a.m.), dehiscence of anthers (10–14 h before
anthesis), and stigma receptivity (from anthesis till 6 to 8 h after anthesis) are
observed nearly identical in three crossable Vigna species, viz., V. umbellata,
V. mungo, and V. radiata (Bhanu et al. 2018).
Mungbean produces successful hybrids when used as female and are crossed with
V. mungo (urdbean), V. umbellate (rice bean), and V. angularis (adzuki bean) as
male or pollen parent. Interspecific hybridizations between mungbean and urdbean
have been attempted for the transfer of high methionine content from urdbean (Nair
et al. 2013). Embryo rescue has been reported for the isolation of hybrids derived
from such wide (mungbean  urdbean) crosses (Verma and Singh 1986a). Further,
some reports mentioning successful mungbean  rice bean crosses have been
reported especially for the transfer of mungbean yellow mosaic virus (MYMV)
resistance in mungbean from rice bean (Verma and Singh 1986b). The details of
possible wide hybridization are presented in Table 22.3. Further, the potential Vigna
species and their useful traits for introgression are listed in Table 22.4. Till now, in
India, there are three varieties which are reportedly developed through wide
hybridization, viz., HUM 1, Pant mung 4, and IPM 99–125.

22.6 Genetic Studies for Breeding in Mungbean

Systematic crop improvement requires complete knowledge about the important

traits, genetic resources available, and genetics underlying the target traits under
consideration for improvement. Mungbean expresses wide variations for a number
of morphological and biochemical traits. Genetics of any trait is very important as it
helps in understanding the nature of gene action which in turn can be used to device
the breeding strategy for the transfer of such economic traits in the elite genetic
22 Mungbean Breeding 1103

Table 22.4 Vigna species and their useful traits for introgression
Hybridization
Vigna species Useful trait(s) amenability
V. radiata var. Salinity, alkalinity, and cold tolerance; MYMV Crossable with
sublobata and bruchid resistance mungbean
V. mungo MYMIV and fungal disease resistance; shattering Crossable with
tolerance mungbean
V. umbellata Bruchids and MYMV resistance; high Crossable with
productivity mungbean but F1s are
sterile
V. aconitifolia High temperature and drought tolerance No report
V. angularis Determinate growth habit; early maturity; high Partially crossable
productivity and high harvest index
V. glabrescens Bean fly resistance F1s can be obtained
through embryo rescue
(Derived from Nair et al. 2020)

background. The genetics of various key traits in mungbean is presented in

Table 22.5.

22.7 Floral Biology and Crossing in Mungbean

Flowers of mungbean are borne on an axillary or terminal raceme, and peduncles are
up to 13 cm in length having clusters of 10–20 flowers. Corolla is yellow in color and
papilionaceous, sometimes curved (5–10 cm). In general, small flowers are borne in
capitate clusters on the end of long hairy peduncles. Petals are five in numbers,
which are of three types, viz., 01 standard, 02 wings, and 02 keels. Androecium or
the male reproductive part has 10 stamens in diadelphous condition (09 + 01).
Gynoecium or the female reproductive part is made up of stigma, style, and ovary.
Gynoecium is monocarpellary having superior unilocular ovary. The stigma is hairy
and placentation is marginal in nature. Keel encloses the reproductive organs
(10 stamens and one gynoecium).
The mungbean, urdbean, and rice bean plant flowers in phases with axillary or
terminal racemes containing a cluster of 10–20 cleistogamous flowers. Flower
shedding to the tune of 60% have been reported, while 2–5% outcrossing is found
common in these Vigna species, which varies as per cultivar and season (Rheenen
1964; Bhadra and Shill 1986). The degree of outcrossing was found ranging between
0% and 8.26% in mungbean, and bold seeded varieties showed more outcrossing
over small seeded ones while rainy season showed greater incidence of natural
outcrossing (Dikshit et al. 2017). Boling et al. (1961) proposed the following
hybridization procedure so as to achieve maximum success in both intra- and
interspecific hybridization in Vigna. Mungbean must be taken as female or seed
parent to make successful interspecific crosses with other Vigna species like urdbean
and rice bean. In reciprocal crosses, either pod abscises in early stage or, if
1104 G. P. Mishra et al.

Table 22.5 The genetics of various morphological traits in mungbean

S. no. Trait Genetics References
1. Twining habit Single dominant gene Sen and Ghosh (1959) and
Khattak et al. (1999)
2. Twining habit Single recessive gene Pathak and Singh (1963)
3. Semi-spreading habit Single dominant gene Pathak and Singh (1963)
4. Indeterminate growth Single dominant gene Talukdar and Talukdar
habit (2003)
5. Days to maturity Epistatic gene action Wilson et al. (1985)
6. Purple hypocotyl color Single dominant gene Swindell and Poehlman
(1978)
7. Anthocyanin Single dominant gene; Pathak and Singh (1963),
pigmentation (peduncle, dominant gene with Virk and Verma (1977) and
petiole, stem, hypocotyl, pleiotropic effect Dwivedi and Singh (1986)
and epicotyl)
8. Anthocyanin Single recessive gene Appa Rao and Jana (1973)
pigmentation
9. Anthocyanin Recessive epistasis Mukherjee and Pradhan
pigmentation (2002)
10. Stem fasciation Single recessive gene Dwivedi and Singh (1990)
with pleiotropic effect on
the number of floral
organs
11. More branches per plant Epistatic interaction Malik and Singh (1983)
12. Plant height Additive and nonadditive Yohe and Poehlman (1972),
effects Malik and Singh (1983) and
Wilson et al. (1985)
13. Pentafoliate leaf shape Single dominant gene Chhabra (1990)
14. Lobed trifoliate leaf Dominant over entire leaf Talukdar and Talukdar
shape (2003) and Chhabra (1990)
15. Trilobed leaves Two dominant genes Sareen (1982)
(Tlb1 & Tlb2); Duplicate
gene action
16. Narrow lanceolate leaf Two recessive genes, Dwivedi and Singh (1986)
‘nl1’ and ‘nl2’
17. Simple inflorescence Two dominant genes (Í10 Sen and Ghosh (1959)
and Í20 )
18. Compound inflorescence Double recessive Sen and Ghosh (1959)
homozygous lines
19. Single cluster per node Dominant gene “C” Singh and Singh (1971)
20. Three clusters per node Recessive gene “c” Singh and Singh (1971)
21. Induced sterility Monogenic recessive Saini et al. (1974)
22. Petal color (light- Singe dominant gene Bose (1939)
yellowish olive)
23. Days to 50% flowering Additive gene action Yohe and Poehlman (1972)
and Wilson et al. (1985)
24. Days to 50% flowering Partial dominance Luthra et al. (1979)
(continued)
22 Mungbean Breeding 1105

Table 22.5 (continued)

S. no. Trait Genetics References
25. Pod shattering to Single dominant gene Verma and Krishi (1969)
non-shattering
26. Swollen pod tip over Single dominant gene Sen and Ghosh (1959)
tapering pod tip
27. Pod pubescence Independent duplicate Khadilkar (1963)
genes
28. Pod length Additive gene effects Luthra et al. (1979) and
Wilson et al. (1985)
29. Pod length Partial dominance Malhotra et al. (1980)
30. Seed-coat color Monogenic inheritance Khattak et al. (1999) and
Lambrides et al. (2004)
31. Seed-coat color Two dominant genes Bose (1939)
32. Seed-coat color Dominant allele (B-) for Chen and Liu (2001)
black and (bb) for green
33. Seed-coat color Three gene pairs Sen and Ghosh (1959)
34. Seed-coat color Dominant allele “A” Rheenen (1965)
(green) over “Sp”
(spotted)
35. Seed-coat color Five major genes with Chhabra (1990)
non-allelic interactions
36. Seed hardness Four loci Humphry et al. (2005)
37. Seed weight Additive gene effects Yohe and Poehlman (1972)
and Wilson et al. (1985)
38. Seed weight Dominant gene action Singh and Jain (1971) and
Rao et al. (1984)
39. Photo-insensitiveness Single dominant gen Verma (1971)
40. Earliness and photo Digeneic control Tiwari and Ramanujam
insensitivity (1976)
41. Sensitivity to photoperiod Dominant or partially Swindell and Poehlman
dominant gene (1978)
42. Photoperiod sensitivity Two recessive genes Islam et al. (1998)
43. Seed yield Additive gene action Yohe and Poehlman (1972),
Luthra et al. (1979) and
Malik and Singh (1983)
44. Seed yield Nonadditive genes Singh and Jain (1971)
45. Seed yield Partial dominance Singh and Jain (1971)
46. Seed yield Overdominance Malik and Singh (1983)
47. Pods per plant Additive gene action Yohe and Poehlman (1972)
48. Pods per plant Partial dominance to Luthra et al. (1979)
overdominance
49. Seeds per pod Additive gene action Luthra et al. (1979)
50. Seeds per pod Partial dominance to Singh and Jain (1971) and
overdominance Luthra et al. (1979)
51. Seeds per pod Epistasis Malik and Singh (1983)
52. Pods per cluster Additive effects Malik and Singh (1983) and
Wilson et al. (1985)
(continued)
1106 G. P. Mishra et al.

Table 22.5 (continued)

S. no. Trait Genetics References
53. Pods per cluster Partial to overdominance Singh and Singh (1971)
54. Total phosphorus and Dominant recessive Sompong et al. (2010)
phytate P epistasis

developed, it contains nonviable seeds. Flower buds having light-green color with
optimum size should be selected and emasculated preferably in the evening around
16:00–18:00 h. During emasculation, it is advised to open only the upper half of the
standard, wing, and keel petals with the help of dissecting needle or fine-tip forceps
so as to expose the stigma and anthers. The anthers are then carefully removed with
the help of forceps. This method increases the success rate of pollination/fertilization
as there are fewer disturbances on style and ovary during emasculation and also
pollination.
Pollination should be done in the next morning between 5:00 and 7:00 h.
However, the time of pollination is directly associated with the prevailing weather
conditions. For mungbean which is grown during summer season, the most optimum
time for pollination is between 5:30 and 6:30 h, while during kharif, it should be
performed between 6:00 and 7:00 h in the morning. It was observed that the
pollination success rate decreases if it is performed after sun shines completely or
if there are rains just after the pollination. For pollination, the feathery part of the
stigma of the previous day emasculated bud is gently rubbed with dehisced anthers
for getting maximum success rate (Fig. 22.1). To avoid any severe load, a total of
8–12 flowers per plant per day should be emasculated besides picking the self-
pollinated flowers/pods (Bhanu et al. 2018).

22.8 Breeding in Mungbean

22.8.1 Breeding Objectives

Besides various biotic and abiotic stresses, there are a number of economic traits
which seek immediate attention by the mungbean breeders. Development of extra-
early and photothermal insensitive genotypes can suitably fit in various cropping
systems. In addition, these can also avoid the terminal drought especially in rainfed
areas. Traits like root architecture influences the nutrient and water uptake efficiency;
dense leaf pubescence reduces leaf temperature and water loss by transpiration and
enhances photosynthesis and vegetative vigor (Du et al. 2009); thus, work on these
traits should also be initiated. The mungbean protein is deficient in sulfur-containing
amino acids (methionine and cystine), and there is need to improve these by taking
an important breeding target. Root extension and higher number of lateral roots can
improve the possibilities of scavenging for P; thus, acquisition and mobilization of P
within plants should also be considered as a key goal for mungbean breeder.
22 Mungbean Breeding 1107

Fig. 22.1 Crossing in mungbean. (a) Flower; (b) emasculation of unopened flower bud (preferably
in the evening); (c) flower buds with protruding stigma after pollination (next day morning); (d) pod
setting in the pollinated flower buds (2 days after pollination)

Besides, there are certain traits which are season specific and require attention of
the mungbean breeders: mungbean which are grown during kharif season should be
of semi-determinate nature with 90–120 days maturity, medium plant height
(70–75 cm), large inflorescence, more clusters/plant, 3–4 branches/plant, 8–10
seeds/pod, 100 seed weight of 3–4 g, tolerance to shattering, and moderate seed
dormancy. However, the mungbean genotypes, targeted for spring or summer
season, should be of short maturity duration (55–65 days), determinate growth
habit and high harvest index, fast initial growth and reduced photoperiod sensitivity,
1108 G. P. Mishra et al.

high pod set in first reproductive flush, long pod (>10 seed per pod), number of pods
at top of plants that remain non-shattering, and vegetative growth should terminate
with flowering.

22.8.2 Breeding Methods and Varieties Developed

There are a number of breeding methods (including introduction, hybridization,

early generation selection, and mutation), which are being used for the development
of high yielding varieties. In addition, a number of molecular markers are also used
to enhance precision of trait selection during breeding for new variety (Ranali and
Cubero 1997). The details of different breeding methods being used in the mungbean
improvement and the varieties developed in India are discussed in this section.

22.8.2.1 Introduction
The introduction involves the direct release of introduced germplasm as a variety.
This is considered as the primary approach in the crop improvement program. In
India, during the last few decades, a number of mungbean germplasm and advanced
breeding lines are being introduced from the World Vegetable Center (Erstwhile
AVRDC), Taiwan. These introduced genotypes possessed a number of economic
traits such as earliness, bold seed size, long pods having nearly 18 seeds per pod, etc.
These unique germplasms were used in the Indian mungbean breeding program for
broadening of the mungbean genetic base and also for their direct release as a variety
(after intensive testing). The varieties like Pusa 105, Pusa 9531, Pant Moong 5, Pusa
Vishal, and SML 668 are the examples of direct introduction. The details of the
mungbean varieties developed directly from exotic germplasm sources are presented
in Table 22.6.

22.8.2.2 Pureline breeding

Pureline breeding or pureline selection is a method commonly used for the self-
pollinated crops like mungbean for the development of a variety. In this method,
selection of desired plant types is made by the breeder from a genetically heteroge-
neous population including landrace (Gupta and Kumar 2006; Tickoo et al. 2006).

22.8.2.3 Recombination Breeding

Through hybridization (both intra- and interspecific), breeders aim to combine a
number of traits of interest and desirable recombinants are selected in the segregating
generations. Interspecific hybridization is mainly aimed to develop pre-breeding
material for the transfer of some key traits which is otherwise not available in the
cultivated genotypes. These pre-breeding materials are subsequently used for the
development of improved varieties. Rare alleles can be identified from exotic lines,
landraces, and primitive genotypes. After crossing, the segregating generations can
be advanced following pedigree, bulk, recurrent, backcross, or single-seed methods
of selection.
22 Mungbean Breeding 1109

Table 22.6 Mungbean varieties developed using exotic germplasm in India

Germplasm Origin/Country Variety developed
V3484 AVRDC, Taiwan Pusa101, WGG2
VC1137–213 AVRDC, Taiwan Pusa105
(M 178)
VC 6368 (46–40- AVRDC, Taiwan UPM 98
4)
VC 6370 (30–65) AVRDC, Taiwan UPM 98–1
V2164 AVRDC, Taiwan SML134
VC 6368 AVRDC, Taiwan Pant mung 5
VC6368 (ML 26) AVRDC, Taiwan Pant mung 2
NM94 Pakistan/AVRDC, SML688
Taiwan
NM9473 Pakistan/AVRDC, Pusa 9531
Taiwan
NM92 Pakistan/AVRDC, Pusa Vishal
Taiwan
China moong China Shining Moong 1, Sunaiana, RMG62, Jalgaon
781, DGGV-2
VC6367 (44–55- Thailand IPM 410–3 (Shikha)
2)
Iranian Iran PS 16
germplasm
CES44 Philippines AAU34
MG50–10 Philippines Co5, Co6
(Source: Gayacharan et al. 2020)

Recurrent selection is being used in case we need to break the undesirable linkage
and accumulate the desirable linkage. Early generation testing was suggested by
Burton (1997) for discarding the undesirable progenies. This involves early-
generation selection in F2, F3, and even F4 generations, and based on the expression
of target traits, undesired families are rejected, which in turn reduces the overall
population load. Interspecific hybridization involving V. radiata  V. mungo have
led to the development of four mungbean varieties (Pant M4, HUM1, Meha, PM6)
having better plant types. Some key traits like sympodial bearing, non-shattering,
YMD resistance, etc. are targeted from urdbean to mungbean. The details of
mungbean varieties developed before the inception of AICPIP program
(Table 22.7), varieties identified/released by All India Coordinated Pulses Improve-
ment Project (Table 22.8), and varieties released by the states of India (Table 22.9)
are listed below. Two high yielding varieties are presented in Fig. 22.2.

22.8.2.4 Mutation Breeding

Mutations may occur naturally or these may be induced, especially for the traits
which are lacking in the primary gene pool. Induced mutation effectiveness is
dependent on the ability of the mutagen to cause the desired mutation(s) per unit
dose of the mutagen, while efficiency of the mutagen is dependent on the undesirable
1110 G. P. Mishra et al.

Table 22.7 State-wise list of varieties developed before the inception of All India Coordinated
Pulses Improvement Project (AICPIP) in India
State Varieties
Maharashtra Sindhkheda 2–3, Chinamung 1/49, Jalgaon 17, Kopergaon, and Jalgaon
781
Madhya Pradesh Krishna II, Gwalior 3, Ujjain 16, Kopergaon, Khargaon 1, Jawahar
45, Kachrod 5, and Bhilsa Green
Uttar Pradesh T 1, T 2, T 44, and T 51
Tamil Nadu Co 1, 367/2, 367/4, ADT 1, Co 2, and KM1
Rajasthan R 288–8, D 66–26 ad RS 4
Bihar Kanke, NP 23, BR 2, BR 1, BR 5, BR 6, BR 7
West Bengal B1, B 105, T 10, Kharif Sona, Kulu type 1, No. 49
Punjab and Himachal Mung 54, Mung 305, Shining Mung 1
Pradesh
Gujarat D 45–6, Gujarat 1 and Gujarat 2
Haryana No. 305
Orissa T 150, Utkal 2, Selections 196, 687, 855, 932, 946, T 1630, and T 2105
(Source: AICRP-MULLaRP)

changes it causes like sterility, injury, and lethality (Goud 1967). Among various
chemical mutagens, ethyl methanesulfonate (EMS) showed higher mutagenic effi-
ciency over others (Khan and Wani 2006). Gamma rays and ethidium bromide were
used for the creation of variation for various agronomic traits (Gunasekaran et al.
1998).
Mutations for high protein and yield (Chakraborty et al. 1998), leaf and pod
mutants and semi-dwarf plants (Srinives et al. 2000; Tah 2006), and resistance to
powdery mildew, Cercospora leaf spot (CLS), and cowpea weevil (Wongpiyasatid
et al. 1999) were reportedly induced in mungbean using gamma rays. In mungbean,
a number of mutations were created for yield and other agronomic traits (Wani et al.
2017; Das and Baisakh 2018). This method of breeding has been used very effec-
tively to develop new mungbean varieties (Ahloowalia et al. 2004; Gopalakrishna
and Reddy 2009). The details of varieties developed using this approach is reported
in Table 22.10. Most of the varieties developed have early maturing and high
yielding and are tolerant/resistant to YMD (Ahloowalia et al. 2004). In addition,
varieties like Pusa Vishal and SML 668 have been developed through selection in a
mutant line NM 94. Mutant varieties NIAB Mung 92 and NIAB Mung 98 are very
popular in Pakistan.

22.8.3 Breeding for Grain Quality

In the entire South Asian regions, mungbean is very frequently consumed as cooked/
boiled dry grains with added spices known as dal, which is a kind of stew (Pratap
et al. 2021). Till date, a few methodical efforts have been undertaken to improve the
nutritional quality of mungbean. Mungbean grains contain very high protein
 22

Table 22.8 List of mungbean varieties identified/released by All India Coordinated Pulses Improvement Project since 1985
Year Average
Name of Developing of yield Days to
S. no. variety center Pedigree release q/ha maturity Area of adaptation
1. ML 267 PAU, ML1  LM987 1987 10–11 75 NWPZ
Ludhiana
2. PDM 11 IIPR, Kanpur Selection from LM595 1987 8.33 75 CZ
3. PDM 54 IIPR, Kanpur Selection from Kundawa 1987 9.11 65 NEPZ
Mungbean Breeding

Bahraich
4. Pusa 105 IARI, New Selection from M178 1987 10.0 75 CZ
Delhi
5. Vamban 1 Vamban S-8  PIMS3 1989 8.0 65 Tamil Nadu
6 RMG 62 Durgapura R 288–8  China mung 1991 7.0 65–70 Rajasthan
7. ADT 3 TNAU, (M70–16  Rajendra)  G65 1991 10.7 65–70 Tamil Nadu
Adutharai
8. Co 5 TNAU, KM2  MG50-10 1991 9.0 70–75 Tamil Nadu
Coimbatore
9. MUM 2 M.U., Meerut Mutant of K851 1992 12.0 60–70 NWPZ
10. BM 4 ARS, Mutant of T44 1992 10–12 65–70 CZ
Badnapur
11. AKM 8803 PKV, Akola PIM53  MH1 1992 10.5 65–70 Maharashtra
12. Narendra NDUA & T, G65  UPM79-3-4 1992 10.0 60–70 Uttar Pradesh
Mung 1 Faizbad
13. Phule M 2 MPKVV, J781  ML 1992 6.9 65 Maharashtra
Rahuri
14. AAU 34 AAU, Assam CES 44/ML5 1992 10.0 60–65 Assam
15. TARM 2 BARC/Akola RUM5  TPH1 1994 9.5 65 Maharashtra
16. Pusa 9072 IARI Pusa106  10–215 1995 9.0 65–75 SZ (Rabi)
17. Warangal APAU, W 75–70  Pusa101 1995 14.0 65–70 Andhra Pradesh
1111

2 (WGG 2) Warangal
(continued)
Table 22.8 (continued)
1112

Year Average
Name of Developing of yield Days to
S. no. variety center Pedigree release q/ha maturity Area of adaptation
18. LGG 407 APAU, Lam Mutant of Pant M2 1995 14.0 70–75 Andhra Pradesh
19. LGG 450 APAU, Lam Mutant of Pant M2 1995 13.0 70–75 Andhra Pradesh
20. Gujarat S.K. Nagar – 1995 – – Gujarat
Mung 3
21. Jawahar JNKVV, ML5  PIMS3 1995 12.4 70–75 Madhya Pradesh
Mung 721 Indore
22. ML 613 PAU, ML2993  ML229 1996 13.0 84 Punjab
Ludhiana
23. PDM IIPR/ – 1996 8.1 65–70 Andhra Pradesh
84–178 Kathalgeri
24. TARM 1 BARC/Akola RUM5  TPM1 1996 12.4 79 Maharashtra
25. TARM 18 BARC/Akola PDM54  TARM2 1996 12.0 68 Maharashtra
26. SML 134 PAU, V2164  ML258 1996 11.0 68 Punjab
Ludhiana
27. Pant Moong Pantnagar T44  UPU2 1997 7.1 68 NEPZ
4 (UPM
92–1)
28 HUM1 BHU, BHUM1  Pant U30 1999 9.4 65 CZ & SZ
(Malviya Varanasi 8.1 60
Jyoti)
29 RMG 268 RAU, R 288–8  J 781 1997 8.9 60 Rajasthan
Durgapura
30. CO6 TNAU, WGG 37  CO 5 1999 10.0 65 Tamil Nadu
Coimbatore
31. Pusa 9531 IARI, New Selection from NM 9473 2000 9.0 60 CZ
Delhi
G. P. Mishra et al.
 22

32. Pusa Vishal IARI, New Selection from NM 92 2000 11.0 62 NWPZ
Delhi
33. Ganga 8 ARS, K 851  Pusa 105 2001 9.2 72 NWPZ
Sriganganagar
34. OUM11–5 OUAT, Mutant of Dhauli 2002 7.3 62 SZ
Berhampur
35. HUM2 BHU, Selection from TVCM-3 2000 10.5 67 Uttar Pradesh & Uttaranchal
Mungbean Breeding

(Malaviya Varanasi
Jagriti)
36. HUM6 BHU, Selection from BHUM 54 2001 10.0 68 Uttar Pradesh
(Malaviya Varanasi
Janpriya)
37. HUM12 BHU, HUM 5  DPM 90-1 2003 11.2 60–62 NEPZ
(Malaviya Varanasi
Janchetna)
38. Meha (IPM IIPR, Kanpur PM3  APM36 2004 9.8 66 NEPZ
99–125)
39. TM B 37 BARC, KopergaonTARM2 2005 11.0 65 NEPZ
Mumbai
40. COGG912 TNAU, MGG 336  COGG 902 2005 8.0 62 SZ
(COGG 7) Coimbatore
41. HUM16 BHU, Pusa bold-1  HUM8 2006 10.9 55–58 NEPZ
(Malaviya Varanasi
Jankalyani
42. MH 2–15 Hisar PDM116  Gujrat1 2007 10.55 67 NWPZ
(Sattaya)
43. Pant Mung-6 GBPUA & T, Pant M2  AMP36 2007 10.52 96 NHZ
Pantnagar
(continued)
1113
Table 22.8 (continued)
1114

Year Average
Name of Developing of yield Days to
S. no. variety center Pedigree release q/ha maturity Area of adaptation
44. KM 2241 CSAU, Samrat  PDM 54 2008 10–11 65–70 NHZ
Kanpur
45. IPM02–3 IIPR, Kanpur IPM99–125  Pusa bold2 2009 11.0 62–68 NWPZ
46. PKVAKM 4 PKV, Akola BM4  PS16 2009 10.0 62–66 CZ & SZ
47. Pusa0672 IARI, New 11/395  ML 267 2009 10.0 64 NHZ
Delhi
48. IPM02–14 IIPR, Kanpur IPM99–125  Pusa bold2 2010 11.0 60–65 SZ
49. DGGV-2 UAS Chinamung  TM-98-50 2014 11–14 70–75 Karnataka
Dharwad
50 MH421 CCSHAU, Muskan  BDYR2 2014 10–12 60–61 NWPZ
Hisar
51. Pusa1371 IARI, New 2016 9–10 81–91 NHZ
Delhi
52 IPM410–3 IIPR, Kanpur IPM03–1  NM1 2016 11–12 65–70 NWPZ/CZ
(Shikha)
53 IPM 205–7 IIPR, Kanpur 2016 10–11 52–56 Punjab, Haryana, Rajasthan, Uttar Pradesh,
(Virat) Bihar, Jharkhand, Madhya Pradesh,
Gujarat, Tamil Nadu, Telangana, Andhra
Pradesh and Karnataka
54 SML115 PAU, SML134  SML715 2016 11–12 65–70 NEHZ
Ludhiana
55. GM6 SDAU, GM 9926  Pusa Vishal 2018 11–12 70–75 NEHZ
S.K. Nagar
G. P. Mishra et al.
 22

56 IPM512–1 IIPR, Kanpur IPM 99–125  Co 5 2020 12–13 60–65 NEPZ

(Soorya)
57 MH1142 HAU, Hisar MH 421 (Muskan  BDYR2) 2020 11–12 60–65 NEPZ & NWPZ
Source: Project Coordinators Report (2020) AICRP-MULLaRP. CZ central zone, NEPZ northeastern plain zone, NHZ northern hill zone, NWPZ northwestern
plain zone, SZ southern zone, AAU Assam Agricultural University, APAU Andhra Pradesh Agricultural University, ARS Agriculture Research Station, BARC
Bhabha Atomic Research Center, BHU Benaras Hindu University, CCSHAU Chaudhary Charan Singh Haryana Agricultural University, GBPUA & T G.B.Pant
University of Agriculture and Technology, HAU Haryana Agricultural University, IARI Indian Agricultural Research Institute, IIPR Indian Institute of Pulses
Mungbean Breeding

Research, JNKVV Jawaharlal Nehru Krishi Vishwavidyalaya, MU Meerut University, MPKVV MP Krishi Vishwa Vidyalaya, NDUA & T Acharya Narendra
Deva University Of Agriculture And Technology, OUAT Odisha University of Agriculture and Technology, PAU Punjab Agricultural University, PKV
Dr. Panjabrao Deshmukh Krishi Vidyapeeth, RAU Rajasthan Agricultural University, SDAU Sardarkrushinagar Dantiwada Agricultural University, TNAU
Tamil Nadu Agricultural University, UAS University of Agricultural Sciences
1115
Table 22.9 Details of mungbean varieties released by the Indian states
1116

S. Year of Average Days to

no. Name of variety Developing center Pedigree release yield q/ha maturity Area of adaptation
1. Asha CCS HAU, Hisar K851  L24–2 1993 10–14 78 Haryana
2. MGG 295 ARS, Madhira Pims-4  cO-3-5-2 1993 12–14 65–70 Andhra Pradesh
3. LGG 410 RARS, Lam Mutant from ML26–10- 1994 14–16 65–70 Andhra Pradesh
3
4. LGG 460 (Lam 460) RARS, Lam LamM2  ML267 1997 15–16 65–70 Andhra Pradesh
5. PBM 1 PAU Induced mutation of 1998 12.50 75 Punjab
ML131
6. K1 ARS, Kovilpatti Co4  ML65 1998 – 70–75 Tamil Nadu
7. Pratap RARS, Shillongani/ ML56  PIMS1 1999 12–14 60–70 Assam
AAU, Assam
8. Pragya IGKV, Raipur Selection from 1999 9–10 90–100 Chhattisgarh
germplasm
9. Suketi CSK HPKV, HAREC, Selection from 2000 10 85 Himachal Pradesh
Dhaulakuan DPM8909
10. Samrat (PDM 139) IIPR, Kanpur ML20/19  ML5 2001 10–11 60–65 Uttar Pradesh
11. AKM - 8802 Dr. PDKV, Akola MH-1  PIMS-4 2000 10–11 61–63 Maharashtra
12. RMG 344 RARI, Durgapura Mung selection-1  J-45 2001 8–9 62–74 Rajasthan
13. G M- 4 S.K. Nagar, Gujarat G M-3  Pusa9333 2001 8.59 61 to 68 Gujarat
14. VBN (Gg) 2 NPRC, Vamban VGG4  MH309 2001 9.00 65–70 Tamil Nadu
15. VRM (Gg)1 ARS, Virinjipuram Selection from K851 2001 – 60–70 Tamil Nadu
16. PDM 139 IIPR, Kanpur ML20–20/19  ML5 2001 10.12 58–62 Uttar Pradesh and
Uttrakhand
17. Pant Mung 5 GBPUA & T, Selection from VC6368 2002 12–15 60–65 Uttar Pradesh and
Pantnagar Uttrakhand
18. MGG 348 ARS, Madhira MGG-329  narp-1 2002 12–14 65–70 –
19. RMG 492 RARI, Durgapura Mutant of RMG 62 2003 9–10 65–70 Rajasthan
G. P. Mishra et al.
 22

20. Pusa Ratna (Pusa IARI, New Delhi VC6368  ML267 2004 11–12 72 NWPZ, National Capital
9972) Region (NCR)
21. Muskan CCS HAU, Hisar PDM116  Gujarat–1 2004 12–15 75 Haryana
22. Shalimar Moong-1 SKUAST-K Selection from Jalgoan 2005 8.0 105–115 Kashmir
Mungbean
23. PKV Green gram Dr. PDKV, Akola BM-86  MH-1 2007 10–12 64–72 Maharashtra
(AKM-9911)
Mungbean Breeding

24. TM-96-2 BARC & ANGRAU, KopergaonTARM-2 2007 9 65 Andhra Pradesh

LAM
25. TJM-3 BARC & JNKVV, KopergaonTARM-2 2007 9.5 65 Madhya Pradesh
Jabalpur
26. PAU 911 PAU ML613  K92–140 2007 12.25 75 Punjab
27. MGG 347 ARS, Madhira K-851  PDM-54 2009 13–15 65–70 –
28. MGG-207 ARS, Madhira LBG-165  LBG-637 2009 12–14 75–80 –
29. VBN (Gg) 3 NPRC, Vamban K1  Vellore local 2009 9.75 65–70 Tamil Nadu
30. Basanti CCS HAU, Hisar Asha  PDM90–1 2010 12–15 64 Haryana
31. Pairymung IGKV, Raipur TARM1  J781 2010 12–14 65–70 Chhattisgarh
32. KM 2195 CSAUA & T, Kanpur K92–140  PDM54 2010 10–11 60–65 Uttar Pradesh
33. TM-2000- BARC & IGKV Raipur JL-781  TARM-2 2010 10.9 88 Chhattisgarh
2 Pairymung
34. SML 832 PAU, Ludhiana SML302  Pusa Bold-1 2010 11.60 61 Punjab
35. DGGV-2 UAS Dharwad ChinamungTM-98-50 2012 11–14 70–75 Karnataka
36. Shalimar Moong-2 Srinagar Centre, PS-7  Larkipora Local 2013 10.0 99 Kashmir
SKUAST-K
37. CO (Gg) 8 TNAU, Coimbatore COGG923  VC6040 2013 – 60 Tamil Nadu
38. MH 318 CCS HAU, Hisar AshaBDYR1 2016 10–14 60–61 Haryana
39. SGC 16 RARS, Shillongani/ PDM91–243  WGG62 2014 13–14 60–65 Assam
AAU, Assam
1117

(continued)
Table 22.9 (continued)
1118

S. Year of Average Days to

no. Name of variety Developing center Pedigree release yield q/ha maturity Area of adaptation
40. BGS 9 (Somnath) UAS, Raichur Selection from local land 2014 12–13 65–68 Karnataka
race
41. Utkarsh Maharashtra State seed Sel7-1-10 from Amainer 2016 12–13 60–65 Maharashtra
(KM 11–584) Corporation
42. Pant Mung GBPUA & T, PM3  NDM99–3 2016 10–11 78–83 Uttarakhand
8 (PM 09–6) Pantnagar
43. Yadadri (WGG 42) PJTSAU, Hyderabad – 2016 10–12 55–60 Telangana
44. Sri Rama (MGG 351) PJTSAU, Hyderabad – 2016 12–14 60–65 Telangana
45. MSJ RARI, Durgapura Mutant of K851 2016 7–8 60–65 Rajasthan
118 (Keshvanand
mung 2)
46. RMG RARI, Durgapura ML613  ML1189 2016 8–9 65–70 Rajasthan
975 (Keshvanand
mung 1)
47. ML 2056 PAU, Ludhiana ML1165  ML1191 2016 11–12 70–75 Punjab
48. GBM-1 NAU, Gujarat 2016 11–12 102–105 Gujarat
49. KM2328 CSAUA & T, Kanpur KM2241  HUM16 2018 10–12 60–62 Uttar Pradesh
50. Pusa1431 IARI, New Delhi Pusa9531  IPM02–19 2018 12–14 56–66 NCR Region, Delhi State
51. SGC16 (Rupohi) AAU, Jorhat, Assam PDM91–243  WGG62 2018 12–13 65–70 Assam
52. GAM 5 AAU, Anand Selection from VM6 2018 18–19 60–65 Gujarat
53. Gujarat Mung-7 Navsari Meha  GM4 2018 10–11 75–80 Gujarat
Source: AICRP-MULLaRP. GAU Gujarat Agricultural University, ANGRAU Acharya N. G. Ranga Agricultural University, IGKV Indira Gandhi Krishi
Vishwavidyalaya, CSK HPKV Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, HAREC Hill Agricultural Research and Extension Centre,
NAU Navsari Agricultural University, NPRC National Pulses Research Centre, PJTSAU Professor Jayashankar Telangana State Agricultural University, RARI
Rajasthan Agricultural Research Institute, RARS Regional Agricultural Research Station, SKUAST-K Sher-e-Kashmir University of Agricultural Sciences and
Technology of Jammu
G. P. Mishra et al.
22 Mungbean Breeding 1119

Fig. 22.2 The seed and plants of high yielding variety Pusa 1371 and Pusa 1431.

(20.97–31.32%) (Anwar et al. 2007; Itoh et al. 2006), carbohydrates (62–67%), fat
(1.4–1.85%), and fiber (3.5–6%) (Selvi et al. 2006). The details of nutrition present
in the mungbean seed are presented in Table 22.11. Mungbean is also an excellent
source of folate, potassium (K), and soluble fiber (Singh and Pratap 2016). Ebert
et al. (2017) reported that the genetic enhancement of mungbean is possible in terms
of protein quality, starch content and quality, mineral contents (iron and zinc), etc.
Huge difference has been reported for the crude protein content in mungbean (Das
et al. 2015). The seed storage proteins, viz., globulin (60%) and albumin (25%), are
also present in good quantity. In addition, this also contains a good amount of
essential amino acids like phenylalanine (1.443%), leucine (1.847%), isoleucine
1120 G. P. Mishra et al.

Table 22.10 Mungbean varieties developed through mutation breeding

Country Varieties
India BM4, Co4, Dhauli (TT9E), LGG407, LGG450, MUM2, ML26–10-3, Pant
mung2, TAP7, TARM1, TARM18, TARM2, TJM3, TM2000–2, TM96–2,
TMB37
Bangladesh Binamoog-1, Binamoog-2, Binamoog-3, Binamoog-4, Binamoog-5, Binamoog-6,
Binamoog-7, Binamoog-8, Binamoog-9
Pakistan AEM-96, NIAB Mung 121–25, NIAB Mung 13–1, NIAB Mung 19–19, NIAB
Mung 2006, NIAB Mung 20–21, NIAB Mung 51, NIAB Mung 54, NIAB Mung
92, NIAB Mung 98, NIAB Mung 28
Indonesia Camar
Thailand Chai Nat 72, Chai Nut 84–1

(1.008%), valine (1.237%), tryptophan (0.26%), arginine (1.672%), methionine

(0.286%), lysine (1.664%), threonine (0.782%), and histidine (0.695%) (Mubarak
2005). As mungbean is rich in lysine, thus it is an excellent complement to rice as
balanced human nutrition (Vairam et al. 2016). A negative correlation has been
noted between mungbean protein content and methionine content (Yi-Shen et al.
2018). The true digestibility of mungbean was reported to be 73% (Tsou and Hsu
1978; Mubarak 2005).
Mungbean carbohydrates are comprised of starch components (available, resis-
tant), fibers (lignin, cellulose), monosaccharides (maltose, glucose, xylose), and
oligosaccharides (raffinose, stachyose, verbascose). Total starch content ranges
between 40.6% and 48.9% (Shi et al. 2016), and thus this is preferred for noodle
preparation (Nair et al. 2020). Interestingly, mungbean starch has low glycemic
index as this contains higher amylose content; thus these can be used in developing
products to prevent the risk of diabetes (Hoover et al. 2010). Since this is also rich in
iron (40–70 ppm), it is good for the lactating and pregnant women (Vairam et al.
2016). Seed size has been reported to have nonsignificant correlation with micronu-
trient content (Nair et al. 2015a, b). Varieties with better grain nutrient content would
definitely have increased nutritive value as sprouts (Ebert et al. 2017). Nair et al.
(2015a, b) have identified the genotypes having improved Fe uptake ability, and
these were utilized in breeding for improving the iron content of commercial
varieties.
Phytic acid (PA) has been reported to provide resistance to the grains against the
bruchid beetle (Srinivasan et al. 2007), but it has negative impact on iron and zinc
bioavailability. The low PA content (2.6–3.8 g/kg) and the presence of phenolic
compounds such as ferulic acid (1540–3400 mg/g) in mungbean may lead to
increased bioavailability of micronutrients (Nair et al. 2015b). Salunkhe et al.
(1982) reported that polyphenols are present in higher amounts in colored and darker
legume varieties than in the light-colored varieties. Muhammed et al. (2010)
reported that the seed coat polyphenols can help the seed against pathogens and
improve seed viability. Sprouting enhances the nutritional properties of mungbean
significantly and makes sprouts a premium breakfast food across the world. The
sprouts are quite high in vitamin C and folate (Nair et al. 2013), while its foliage is
22 Mungbean Breeding 1121

Table 22.11 Nutritional composition of mungbean seed

Nutrition Range References
Protein 14.6–33.0 g/100 g Harper et al. (1996), Mubarak
(2005), Anwar et al. (2007),
Dahiya et al. (2015) and Itoh et al.
(2006)
Fat 1.45–1.85 g/100 g; 2.1–2.7% Mubarak (2005) and Zia-Ul-Haq
et al. (2008)
Fatty acids Palmitic (2.8–4 g), stearic (1.4–1.7 g), Anwar et al. (2007)
oleic (2.1–2.9 g), linoleic (3.4–4.6 g),
linolenic (1.9–2.4 g) and arachidic
(0.23–0.25 g) per kg basis
Crude fiber 3.5–6.15 g/100 g Mubarak (2005) and Dahiya et al.
(2015)
Iron 1.15–12.63 mg/100 g USDA 2010, Harper et al. (1996)
and Dahiya et al. (2015)
Iron 3.5–8.7 mg/100 g (Indian lines/ Nair et al. (2015a, b)
varieties)
Zn 2.1–6.2 mg/100 g; 21–62 mg/kg DW Taunk et al. (2011) and Nair et al.
(2015a, b)
Carbohydrates 50–63.4% USDA (2010), Mubarak (2005),
Dahiya et al. (2015) and Kaur
et al. (2020)
Starch Total starch: 40.6–48.9% in seed; Shi et al. (2016)
resistant starch: 16.1–22.3% (of total
carbohydrates)
Phosphorus 340–367 mg/100 g Kaur et al. (2020) and USDA 2010
Phosphorus 2760–5170 mg/kg DW Nair et al. (2015a, b)
Calcium 77.3 to 247.67 mg/100 g Agugo and Onimawo (2009) and
Kaur et al. (2020)
Calcium 1190–1580 mg/kg DW Nair et al. (2015a, b)
Other minerals Mg (970–1700 mg), Cu (7.5–11.9 mg), Nair et al. (2015a, b)
Mn (9.8–19.6 mg), Se (0.21–0.91 mg),
K (8670–14,100 mg)/kg DW
Amylose 32% Lang et al. (1999)
Ash 3.32–3.76 g/100 g Mubarak (2005)
Energy 338–347 kcal/100 g Dahiya et al. (2015)
Vitamins
Carotenoid 0.5–0.8 mg/100 mg (cotyledons) and Harina and Ramirez (1978)
0.07–0.44 mg/100 mg (seed coats)
Vitamin A 100 lg retinol activity equivalent USDA (2010)
(RAE) in sprouts; 70 lg RAE /kg grain
Vitamin C 0–10 mg/100 g; 1.38 g/kg (sprouts), Prabhavat (1990) and Nisha et al.
0.05 g/kg (grain) (DW basis) (2005)
Riboflavin 0.29 mg/100 g Nisha et al. (2005)
content
(continued)
1122 G. P. Mishra et al.

Table 22.11 (continued)

Nutrition Range References
Folate content 0.0069 g (grain) and 0.0064 g USDA (2010) and Rychlik et al.
(sprouts)/kg DW basis; 0.0028 g/kg (2007)
grain
Tocopherol 12.5 mg/100 g Zia-Ul-Haq et al. (2008)
Phytic acid 1.8–5.8 g/kg grain DW; 2.6–3.8 g/kg Sompong et al. (2010) and Nair
et al. (2015a, b)
Others
Trypsin 56–98 [trypsin inhibitor units Philip and Prema (1998)
inhibitor activity (TIU)/ mg]
Tannin content 3.1–4 g/kg grain Philip and Prema (1998)
Saponins 5.7 g/kg DW Fenwick and Oakenfull (1983)
Total phenolic 0.167–0.192 g ferulic acid equivalent Kim et al. (2012)
and flavonoid (FAE)/kg DW (sprouts);
extracts 0.098–0.101 g FAE/kg DW (dry seed)
2-Acetyl-1- In aromatic mungbeans Attar et al. (2017)
pyrroline
biosynthetic
pathway
Phenolic Phenolic acids (1.81–5.97 mg rutin Lee et al. (2011), Shi et al. (2016)
components equivalent/g), flavonoids and Singh et al. (2017a)
(1.49–1.78 mg catechin equivalent/g),
tannins (1.00–5.75 mg/g)

consumed as fodder and hay. Sprouting also reduces the indigestible

oligosaccharides, tannins, and phytic acid, making it a preferred food (Savage and
Deo 1989).
Due to the presence of easily digestible protein in the seeds, this is one of the
highly recommended foods for the sick (Yi-Shen et al. 2018). Cereals when con-
sumed in combination with mungbean are known to improve the protein quality and
balances sulfur-containing amino acids (of cereals) with that of lysine in mungbean
(Boye et al. 2010). A number of health-related properties known in the mungbean
are presented in Table 22.12. Due to these properties, mungbean is also used as a
component of infant’s weaning food (Bazaz et al. 2016). Mungbean induces less
flatulence and also has very less “anti-nutritive factors” which can be managed by
various types of pre-consumption processing (Dahiya et al. 2014). Pressure cooking
is known to degrade phytic acid, while dehusking and germination reduces the total
tannin content (Wang et al. 2015). In addition, mungbean is being consumed across
the world in different forms with some regional preferences (Table 22.13).
Mungbean is also consumed as microgreens or nutrigreens in different parts of the
world by the health-conscious people (Priti et al. 2021). Thus, while breeding for
high nutrient, care should be taken to breed for the region-specific and preference-
based traits for the wider acceptance of the developed variety.
22 Mungbean Breeding 1123

Table 22.12 Health associated properties in mungbean

Compound Health properties References
Vitexin and Hypolipidemic (lowers inflammatory Inhae et al. (2015) and Yao
isovitexin cytokines) and anti-melanogenic et al. (2011)
(tyrosinase inhibitor)
Ligans and Hypoglycemic (Inhibits alpha- Liyanage et al. (2018) and
flavonoids glucosidase and Alpha amylase activity; Jang et al. (2014)
decreased fat accumulation)
Mungoin (protease Anticancerous Ketha and Gudipati (2018),
inhibitor) and Yao et al. (2016) and Lee
phenolics et al. (2013)
Vicilin protein Antihypertensive (ACE-I inhibitory Xie et al. (2019), Gupta et al.
hydrolysate activity) (2018), Wang et al. (2006)
and Xu and Chang (2012)
Arabinogalactan Immunomodulation (induced release of Luo et al. (2016), Yao et al.
and saponins NO, TNF-α, IL-6, and IL-1β) (2011) and Ali et al. (2014)
Antityrosinase Anti-melanogenesis (inhibited Chai et al. (2018) and Kim
tyrosinase, monophenolase, and et al. (2012)
diphenolase activities)

Table 22.13 Preferred grain qualities by the consumers of different regions

Region Preferred grain qualities by consumer
South Asian regions Medium to bold grains for dal; dehusked and overnight
soaked grains for making porridge, candies, etc.
Indian subcontinent Shiny green and small to medium sized grains
Bangladesh, Sri Lanka, Shiny yellow and small grains (<3.0 g/100 seed)
northeastern states of India
Indonesia, Taiwan, Kenya, and Dull green seeds
Tanzania
India and parts of Southeast Asia Medium-sized grains, thin seed coat, uniform texture for
fried, salted and dehusked dry seeds
Kenya and several African As thick bean stew
countries
China Cooked with rice and sugar to make a sweet desert soup
Throughout the world Sprouts, soup mix, noodle garnish, etc.
(Derived from: Nair and Schreinemachers 2020)

22.8.3.1 Markers Associated with Mineral Biofortification

The process of enrichment in the content of some key micronutrients like Fe and Zn
is called mineral biofortification. For developing a variety with high concentration of
micronutrient like iron and zinc, it is important to identify the germplasm having
high content of micronutrients (Singh et al. 2013a). Aneja et al. (2012) reported
variation for Fe (29.95–00.97 mg/kg) and Zn (20.13–35.70 mg/kg) content in
mungbean genotypes, while Taunk et al. (2012) reported iron and zinc content
varying from 46.31 to 106.15 and 23.31 to 40.46 mg/kg, respectively. Singh et al.
(2013a) reported wide variations for iron (1.6–9.3 mg/100 g) and zinc (1.5–3.9 mg/
1124 G. P. Mishra et al.

Table 22.14 Molecular mapping for grain micronutrient concentration

QTLs/MTAs LG/markers/population References
17 QTLs (2 for Fe and 15 for Zn content) LG4 (qZn-4-3 and qFe-4-1), LG6, Singh
LG7, and LG11 (qZn-11-2 and et al.
qFe-11-1) (2017b)
43 marker-trait associations (MTAs) for Ca, 6486 SNPs (explained 22% PVE) Wu et al.
Fe, K, Mn, P, S, Zn by GBS (2020)
Vradi01g00820, Vradi01g00830, and Chromosome 1 (K content) Wu et al.
Vradi01g00840 (2020)
Vradi05g16350 Chromosome 5 (P content) Wu et al.
(2020)
Vradi07g26320 and Vradi07g26340 Chromosome 7 (P content) Wu et al.
(2020)
Vradi07g14180 Chromosome 7 (K content) Wu et al.
(2020)
Vradi08g22740 and Vradi08g17100 Chromosome 8 (K content) Wu et al.
(2020)
Vradi06g09900, Vradi06g10020, Chromosome 6 (Fe content)) Wu et al.
Vradi06g10060, Vradi06g10120, (2020)
Vradi06g10210
QTLs for phytic acid P (PAP), total P (TP), – Sompong
and inorganic P (IP et al.
(2012)
QTLs for seed Fe and Zn content RIL from ML776  Sattya Singh
et al.
(2017b)
Fe: 01 QTL (qFe-11-1) for Fe on LG11; Zn: RIL from ML446 (high iron Singh
04 QTLs (qZn-11-4, qZn-11-5 on LG11 & content)  Sattya (low iron (2013)
qZn-4-1, qZn-4-2 on LG4) content)

100 g) content in RIL populations. Wu et al. (2020) conducted genome-wide

association study (GWAS) for seven minerals which were analyzed using induc-
tively coupled plasma (ICP) spectroscopy in 95 cultivated mungbean genotypes
chosen from the United States Department of Agriculture (USDA) core collection
representing accessions from 13 countries. The details of markers found linked with
quantitative trait loci (QTLs) governing micronutrient content in mungbean is
presented in Table 22.14.

22.8.3.2 Nutrient Bioavailability

Anti-nutritional factors present in the mungbean seeds like phytic acid can bind with
iron, zinc, calcium, and magnesium and forms insoluble complexes, thereby limiting
the mineral absorption in the small intestine (Weinberger et al. 2002). However,
through various processing methods like fermentation, germination, dehulling,
soaking, and cooking, these anti-nutritional factors can be reduced significantly
(Hemalatha et al. 2007). In the sprouted mungbean, the phytic acid content has
reportedly declined by 76%, which resulted in an increase in the bioavailability of
zinc and iron by 3.0 and 2.4 times, respectively (Nair et al. 2012; El-Adawy 2002).
22 Mungbean Breeding 1125

Similarly, trypsin inhibitors are low-molecular-weight proteins which adversely

affect the protein digestion by inhibiting the proteolytic enzymes. Heat treatment,
soaking, and sprouting of the seeds are known to lower the trypsin inhibitor activity
in mungbean seeds (Chandrashekar et al. 1989).

22.9 Emerging Challenges

The productivity of different mungbean varieties depends upon their genetic consti-
tution and environment in which they are cultivated. Favorable environment at
different growth stages helps the mungbean plant in achieving maximum genetic
potential. Favorable environment in terms of biotic and abiotic stresses is essentially
required for achieving the full yield potential of mungbean crop. MYMV, powdery
mildew, Cercospora leaf spot, bruchids, and sucking insect pests are all important
biotic stresses. Drought, heat, and flooding are the main abiotic stresses affecting
the crop.
Mungbean crop is being affected by a number of biotic stresses. Resistance to
mungbean yellow mosaic virus (MYMV) was reported under the control of a
number of genes including a single recessive gene, two recessive genes, trigenic,
etc. (Mishra et al. 2020). Further, a number of weather parameters regulating vector
activities are equally important factors for the whitefly-transmitted begomovirus
disease management in mungbean. Powdery mildew is a foliar disease caused by
Erysiphe polygoni which causes yield loss to the tune of 20–40%. For Cercospora
leaf spot (CLS) resistance, a number of gene actions have been reported (AVRDC
1980; Lee 1980). Bruchid (Callosobruchus chinensis and C. maculates) may cause
severe post-harvest losses, and they can cause complete destruction of stored seed in
2–3 months (Fernandez et al. 1988). Genetics of various biotic stresses in mungbean
is presented in Table 22.15.
Mungbean is mostly grown as rainfed crop, and drought-tolerant varieties capable
of withstanding soil moisture stress and produce better yield are required to be
developed. Varieties that are found to germinate under reduced water potential do
not usually fail to germinate and establish into seedlings (Kaur et al. 2017). Root
length at seedling stage provides a fair estimate about the root growth in field (Ali
et al. 2011; Vincent 2014). In general, deeper and more profuse root systems could
be able to tap extra water from the soil profile and alleviate drought effects.
Mungbean being rainfed crop sometimes also encounters excessive rains, which
causes damage to the crop due to flooding (Miah et al. 1991). Stagnation of water
impairs the root growth and this more frequently occurs in Eastern India and
Southern Bangladesh. Variation for soil flooding tolerance among mungbean
genotypes has been reported by various workers (Amin et al. 2016). The World
Vegetable Center mungbean mini core collection consisting of 296 genotypes were
screened for 14 root-related traits, and a number of genotypes displaying different
root traits were identified as donors for breeding cultivars with enhanced adaptation
to water-deficit stress and other stress conditions (Aski et al. 2021).
1126 G. P. Mishra et al.

Table 22.15 Genetics of various key biotic and abiotic stresses in mungbean
Genetics of traits References
YMD resistance
Monogenic recessive Malik et al. (1986), Reddy and Singh (1995),
Saleem et al. (1998), Khattak et al. (1999),
Khan et al. (2007), Reddy (2009a), Dhole and
Reddy (2013) and Sudha et al. (2013)
Complementary recessive genes Shukla and Pandya (1985) and Alam et al.
(2014a)
Dominant and complementary recessive genes Sandhu et al. (1985)
Trigenic recessive Mishra and Asthana (1996)
Modifying genes Khattak et al. (2000)
Digenic recessive Dhole and Reddy (2012) and Singh et al.
(2013b)
Trigenic (02 dominant +01 recessive) Markam et al. (2018)
Digenic dominant Mahalingam et al. (2018)
Powdery mildew resistance
Monogenic dominant gene Chaitieng et al. (2002)
Two dominant genes “Pm1” and “Pm2” Reddy et al. (1994)
Single dominant gene Khajudparn et al. (2007)
Single dominant gene (Pm3) Reddy (2009b)
Quantitative and additive gene action Kasettranan et al. (2009)
QTL (PMR1; PVE 65%) Chaitieng et al. (2002)
QTL (PVE 86%) Humphry et al. (2003)
Additive and dominance gene actions Gawande and Patil (2003)
Cercospora leaf spot (CLS) resistance
Single dominant gene Chankaew et al. (2011) and Singh et al.
(2017c)
Single recessive gene Mishra et al. (1988)
01 major QTL on LG03 Chankaew et al. (2011)
Bruchid resistance
Single gene Miyagi et al. (2004) and Sun et al. (2009)
Br1 locus on LG11 Wang et al. (2016)
Seed hardness
Single dominant gene ‘Br’ (V. radiata var. Kitamura et al. (1988), Young et al. (1992) and
sublobata accession-TC1966) or few dominant Humphry et al. (2005)
genes
Mapped the gene on LG8 Kaga and Ishimoto (1998)
Calcareous soil (iron deficiency chlorosis)
Two genes with inhibitory action Nopparat et al. (1997)
Single dominant gene (IR) with a few Srinives et al. (2010)
modifying genes
Preharvest sprouting
Additive and nonadditive gene action; high Durga and Kumar (1997)
G  E interaction
22 Mungbean Breeding 1127

Rise in the temperature by 2050 by 3.2
C in winter and 2.2
C during summer as
a result of climate change may cause flower drop and poor pod filling. Thus, to
sustain the crop production we need to develop climate resilient varieties. Shift in
area, especially total area reduction in northern India while an increase in area in
Central and South India. In many areas, yields have started declining because of
decline in organic matter content in soil and emergence of multi-nutrient
deficiencies. Also, a widespread zinc and sulfur deficiency was reported, and nearly
50% pulse growing districts have Zn deficiency. Further, of 137 pulse-growing
districts, 87 districts have reported 20–60% sulfur deficiency. Thus, a holistic
approach is required for the realization of higher yield from this wonder crop.

22.10 Molecular Breeding and Genetic Engineering

In mungbean, a number of molecular markers have been developed and used for the
mapping of various biotic and abiotic traits, with limited success. Various
researchers have used SSR markers for deciphering genetic diversity in mungbean
(Chen et al. 2015; Liu et al. 2017); however, low SSR polymorphism has been
reported in mungbean (Tangphatsornruang et al. 2009). Transferable SSRs from
cowpea and adzuki bean have also been used in mungbean for tagging of various
QTLs (Kitsanachandee et al. 2013; Gupta et al. 2013). Van et al. (2013) have
identified more than 300,000 SNPs in mungbean, and among them only 43 SNPs
could be validated as competitive allele-specific polymorphism (KASP) markers
(Van et al. 2013; Islam and Blair 2018). To date, a limited studies on GBS-based
GWAS have been undertaken in mungbean for genetic mapping and diversity
assessment (Noble et al. 2018; Reddy et al. 2020a, b, c). Previous genetic diversity
studies of cultivated and wild mungbean germplasm, using both morphological and
molecular markers, have highlighted low levels of genetic diversity in cultivated
mungbean compared to wild Vigna (Pratap et al. 2015). Limited numbers of linkage
maps have been developed in mungbean. A high-density map developed using
whole genome sequences can enable further advancement in trait dissection
(Noble et al. 2018; Sokolkova et al. 2020). The recent release of a reference genome
for mungbean provides new opportunities for mungbean genomic research (Kim
et al. 2015; Dasgupta et al. 2021). Therefore, quantitative trait locus (QTL) analyses
through mapping populations or GWAS using molecular markers and high through-
put sequencing techniques provide valuable ways of identifying the genes underly-
ing various traits (Reddy et al. 2020a, 2021a; Aski et al. 2021; Mishra et al. 2020).
To decipher the genetic basis of PUE traits, 144 diverse mungbean genotypes
were evaluated through GWAS using 55,634 SNPs. In total, 71 protein coding genes
were identified, of which three potential candidate genes VRADI11G08340,
VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence
region were identified (Reddy et al. 2020a, 2021b). RNA-seq analysis was
conducted between a resistant and a susceptible mungbean genotype under infected
and control conditions, and resistance to MYMIV showed a very complicated gene
network, which begins with the production of general PAMPs (pathogen-associated
1128 G. P. Mishra et al.

molecular patterns), then activation of various signaling cascades like kinases,

jasmonic acid, and brassinosteroid, and finally the expression of specific genes
such as PR-proteins, virus resistance, and R-gene proteins, leading to resistance
response (Dasgupta et al. 2021).
Genetic transformation systems have been well developed in mungbean, and
several transgenics targeting both biotic (Bhajan et al. 2019) and abiotic stresses
(Kumar et al. 2017; Mekala et al. 2016) have been developed which are mostly at
proof-of-concept level. Genome editing in mungbean is still in its initial phases, but
researchers are aiming to use CRISPR/cas9 for developing virus-resistant transgene-
free mungbean plants (Khatodia et al. 2018). With the availability of a deep
sequenced reference genome of Asian mungbean, freely available SNPs data, tagged
germplasm for specific traits, and easy regulatory policies, the SNP-trait associations
will mark the future in mungbean breeding.

22.11 Mungbean Production Technology

The mungbean in India is being grown as kharif, spring, and summer crop. The
details of mungbean production technology are described below:

22.11.1 Climate

Although mungbean can be grown in a wide range of climatic conditions, a warm

humid climate with temperature ranging from 25
C to 35
C, with 400–550 mm
rainfall, well distributed during the growing period of 60–90 days, is suitable for the
cultivation.

22.11.2 Soil

Mungbean can be easily grown in a wide range of soils including red laterite soils,
black cotton soils, and sandy soils. A well-drained loamy to sandy loam soil is best
for its cultivation. The crop does not grow well on saline and alkaline soil or
waterlogged soils.

22.11.3 Field Preparation

Mungbean requires proper drainage and ample aeration in the field so that the
activities of nitrogen-fixing bacteria are not hampered at any stage of plant growth.
In case of water-logging, ridges and furrows may be prepared and levelling and
sowing can be performed on the ridges. Otherwise also, ridge sowing gives better
yield over normal sowing.
22 Mungbean Breeding 1129

22.11.4 Manures and Fertilizers

Well-decomposed farmyard manure (FYM) should be mixed at the rate of 10–-

12 tonnes per hectare one month before sowing. This not only provides the nutrient
but also the desired physical quality to the soil. In addition, 5 kg/ha of Trichoderma
viride can be mixed with FYM, and the mixture is kept under partial shade for
4–5 days before its application to the soil. In general, 100 kg DAP per hectare is the
recommended dose for mungbean. If soils deficient in Zn, then 25 kg ZnSO4 per ha
should be applied before sowing. Top dressing of N at 15 kg/ha should be done at
flowering stage.

22.11.5 Seed Rate

For sowing, quality seeds which are healthy, undamaged, and free of insect pests
should be selected. The seed rate depends on the seed size and sowing season. In
case of bold-seeded varieties, seed rate of 20 kg/ha is considered optimum in spring
and autumn, and 16 kg/ha during summer season. It is advised to have approxi-
mately 25 plants/m2 of plant stand in the field for reaping the good yield.

22.11.6 Seed Treatment

Dried seed may be treated with captan or thiram at 3.0 g/kg of seeds against any
seedborne fungal diseases. Seed inoculation with appropriate Rhizobium strain is
highly recommended, especially in those fields where mungbean cultivation is taken
up for the first time.

22.11.7 Isolation Distance

Although mungbean is a self-pollinated crop, some cross-pollination always

happens under field conditions. Thus, an isolation distance of 3.0 m should be
used so as to get the seeds of desired purity.

22.11.8 Method of Sowing

Line sowing is considered advantageous as it not only requires less seed but also
produces more even crop, which is easier to manage and also gives more yield. The
spacing between the ridges/rows should be kept as 25–30 cm, while plant-to-plant
spacing is kept as 10.0 cm. Seed sowing through broadcasting makes various
intercultural operations including weeding very difficult, making harvesting more
labor intensive and thereby having significantly reduced crop productivity and poor
economic return.
1130 G. P. Mishra et al.

22.11.9 Irrigation

Frequency and number of irrigations required by mungbean crop depends upon

season, weather, and soil and field conditions. Usually, first irrigation is required just
after seedling emergence. Later, two to three irrigations may be applied at 10- to
15-day intervals depending on the dryness of the season. The last irrigation should
be stopped at about 50 days after sowing. Generally, no irrigation is needed during
rainy season except under drought-like situation.

22.11.10 Rouging

It is an important task especially in the seed crop to regularly inspect the seed crop
and remove any off-type plants present in the field.

22.11.11 Weed Control

In mungbean, it is recommended to select the field with low weed pressure for
sowing, as weed control options are very limited in this crop. Both manual weeding
and use of herbicides are used for the weed control. The pre-sowing weedicides like
Basalin45EC (fluchloralin) (5.0 mL/L) and Treflan48EC (trifluralin) (4.0 mL/L) or
preemergence weedicide like Stomp 30EC (pendimethalin) (5.0 mL/L) or preemer-
gence weedicide Stomp 30EC at 3.0 mL/L along with one hoeing, four weeks after
sowing, can be used for the effective control of the weeds. Approximately 500 L of
water is sufficient for one hectare, and herbicides should be sprayed immediately
after sowing for preemergence application. In addition, it is recommended to per-
form inter tillage by hand or cultivator once or twice to promote healthy crop growth.

22.11.12 Diseases

The important diseases affecting mungbean crop and their control measures are
briefly discussed below.

22.11.12.1 Seed and Seedling Rot

A number of fungi such as Fusarium sp., Macrophomina phaseoli, and Rhizoctonia
solani cause seed and seedling rot which ultimately results in poor seed germination.
These are serious disease and sometimes re-sowing of the crop has to be done if it is
not controlled well on time. For the control of this disease, (1) treat the seeds with
thiram or captan at 3.0 g/kg of seed, (2) sow fresh and clean seeds which are obtained
from a healthy crop, and (3) adopt suitable crop rotation.
22 Mungbean Breeding 1131

Fig. 22.3 Mungbean genotypes expressing resistant and susceptible reaction to yellow mosaic
disease (YMD)

22.11.12.2 Mungbean Yellow Mosaic Virus

This virus causes yellow mosaic disease (YMD). The symptom starts as small
yellow specks along the veinlets which then spreads over the lamina. In the case
of severe infestation, the pods become thin and curl upward (Fig. 22.3). The disease
is transmitted by an insect vector named whitefly (Bemisia tabaci). For the control of
this disease, (1) spray the crop with neem oil at 20 mL/L or with Metasystox 25EC
(oxydemeton-methyl) at 3.0 mL/L of water so as to control the whiteflies which are
the actual vectors of this disease, (2) grow YMD-resistant varieties, and (3) use
yellow sticky traps against whiteflies.

22.11.12.3 Cercospora Leaf Spot (Cercospora canescens)

This disease can be identified by the appearance of spots on the leaves which are
circular to irregularly shaped, with grayish-white centers and reddish-brown to dark-
brown margins. For the control of this disease, (1) spray the crop with Dithane Z-78
or Dithane M-45 at 3.2 g/L of water, (2) remove all the plant debris from the crop
field, (3) remove all the infected plants and burn, and (4) avoid sowing of the seeds
which are harvested last year from the infested field

22.11.12.4 Powdery Mildew (Erysiphe sp./Podosphora sp.)

This disease commonly occurs under cool weather conditions (20–26
C) and is
favored by cloudy weather. A white-gray powdery mass becomes visible first in
circular patches on the dorsal leaf surface, but later this spreads to all over the leaves,
stems, and pods (Fig. 22.4). For the control of this disease, (1) spray the crop with
neem seed kernel extract (NSKE) at 50 g/L or neem oil at 20 mL/L twice at 10 days
1132 G. P. Mishra et al.

Fig. 22.4 Powdery mildew

on the mungbean leaf surface

interval from the initial disease appearance, (2) spray 10% eucalyptus leaf extract at
the time of disease initiation and 10 days later, and (3) spray the crop with
carbendazim at 1.0 g/L or wettable sulfur with 2.5 g/L of water.

22.11.13 Pests

The important pests infecting mungbean crop and their control measures are as
follows:

22.11.13.1 Tobacco Caterpillar (Spodoptera litura)

The initial stage larvae are black in color, whereas grown-up larvae are dark green
with black triangular spots on body. Its moth lays eggs in masses covered with
brown hairs on the lower side of the leaves. After hatching, first and second instar
larvae feed gregariously and skeletonize the foliage. Besides leaves, they also
damage floral buds, flowers, and pods. For the control of this pest, (1) collect the
egg masses and young larvae with leaves and destroy, and (2) spray the crop with
commercial neem formulations (including neem oil or neem seed kernel extract),
Bacillus thuringiensis formulations, Spodoptera litura nuclear polyhedrosis virus
22 Mungbean Breeding 1133

(NPV), Novaluron 10EC at 1.5 mL/L or Acephate 75SP at 8.0 g/L or Chlorpyriphos
20EC at 15 mL/L of water.

22.11.13.2 White Fly (Bemisia tabaci)

The adults are tiny and very delicate and have white or smoke-colored wings with
which they flitter away from plants on little disturbance (Fig. 22.5). Insects stick to
the lower surface of leaves and leaves of infested plants show yellowish discolor-
ation. For the control of this pest, (1) spray the crop with neem oil at 20 mL/L or with
Metasystox (oxydemeton-methyl) 25EC at 3.0 mL/L of water, and (2) use yellow
sticky traps in the field.

22.11.13.3 Bean Pod Borer (Maruca testulalis) and Asian Corn Borer
(Ostrinia furnacalis)
In recent years, these have become very serious pest, causing substantial damage to
the mungbean crop. They feed on buds, flowers, pods, and grains. The larvae may be
pale green, yellow, brown, or black in color, 3–5 cm in length. Larva presence can be
judged from dark-green feces under the plant canopy. For the control of this pest,
consider the following: (1) Spray the crop with Acephate at 8.0 g/L or Spinosad at
0.6 mL/L or Indoxacarb at 2.0 mL/L of water. (2) Commercial neem-based
formulations or neem oil or neem seed kernel extract or B. thuringiensis
formulations can also be used as organic control.

22.11.13.4 Bean Fly (Ophiomyia phaseoli, O. centrosematis,

Melanagromyza sojae)
This is the most important insect pest of mungbean which causes significant damage
during the seedling stage. The adult flies are too tiny (2.0 mm) and cannot be
recognized easily. The bean fly maggots feed inside the plant stem and their damage
cannot be seen from the outside. For the control of this pest, consider the following:
(1) Spray Metasystox (oxydemeton-methyl) 25EC at 3.0 mL/L of water. (2) Moth

Fig. 22.5 Whiteflies

(in circle) on the dorsal
surface of mungbean leaf
1134 G. P. Mishra et al.

bean, chickpea, lentil, and cluster bean crop could be used as “dead-end trap
crops”—the bean fly adults lay eggs on these crops, but the eggs fail to hatch.

22.11.13.5 Thrips (Megalurothrips distalis and M. usitatus)

Thrips are very small insects found in the flowers and causes flower drop, deforma-
tion of pods, and ultimately reduction in yield. For the control of this pest, (1) spray
Spinosad at 0.6 mL/L of water at flower initiation stage, and (2) do not control the
thrips infestation with broad-spectrum chemical pesticides, as this may cause the
resurgence of thrips.

22.11.13.6 Cowpea Aphid (Aphis craccivora)

Sometimes this pest is also reported to attack mungbean crop. For the control of this
pest, consider the following: (1) Spray Imidacloprid at 150–170 mL per 500 L of
water per hectare. The spray must be done once we notice unusually high aphid
populations (>20 insect per plant). (2) Neem oil may be used either alone or in
combination with the entomopathogenic fungi biopesticides. The ladybird beetles
and green lacewings are efficient predators of aphids. Protect the population of these
predators by avoiding the use of broad-spectrum pesticides.

22.11.13.7 Bruchids (Callosobruchus chinensis and C. maculatus)

This is also known as pulse beetles or cowpea weevils, and they attack mungbean
both in field and storage conditions, but the greater losses occur during storage. The
nutritional quality of mungbean grains gets deteriorated rendering them unmarket-
able. For the control of this pest, consider the following: (1) Maintain proper
cleaning of the storage area and proper drying of the seeds (9–10% moisture). For
large-scale seed storage, fumigate with phosphine or other suitable fumigants.
(2) Treat the grains with clays, sand, kaolin, and ash, as these were proven effective
during storage. In addition, vegetable oils (e.g., olive oil or mustard oil at 15 mL/kg
of seed) can also be used for the grain treatment. (3) Use traps such as pitfall trap or
probe trap to monitor and mass-trap bruchids during storage. (4) Store the seeds in
airtight containers and triple-bag the mungbean grains during storage.

22.11.14 Harvesting

Mungbean can be harvested when the pods get mature and dried, but before they
start shattering. Manual harvesting is usually practiced, but mechanical harvesting
can save labor cost and time. Desiccation of the plants is needed before mechanical
harvesting, for which crop having mature pods and green leaves can be sprayed with
Diquat (2–3 L/ha) or Glyphosate so as to desiccate the plants. In the case of manual
harvesting, threshing must be done as soon as the pods get dried. Pods can be beaten
with a stick until pods are opened by keeping them in a jute bag. All the foreign
materials are removed by winnowing and are sun-dried for 3–5 days. Drying of seed
to 9–10% moisture level is very important for good storage, which can be measured
using seed moisture meter. Use of solar dryers is considered as a better option for
22 Mungbean Breeding 1135

quick drying. It is advised to collect only good seeds which are free from diseases,
seed coat cracking, split, or immature. If using a threshing machine, adjust the speed
of the machine in order to avoid seed damage. Dried seeds can be safely stored for at
least three years. Place the seeds in jars, manila envelopes, cloth or mesh bags, and
plastic or foil envelopes. The best containers are airtight, such as a sealed glass jar,
metal can, or foil envelope. Seeds should be protected from sunlight and stored in a
cool (below 15
C is ideal) and dried conditions. Seeds may be placed in a refrigera-
tor for long-term storage. For short-term storage, seeds can be kept in a cool, shady
and dry place. The recommended storage practices should be followed
(as mentioned above in the pests section) for the control of storage pests especially
bruchids (Tiwari et al. 2017).

22.12 Indian Minimum Seed Standards for Mungbean

The General Seed Certification Standards are basic and, together with the following
specific standards, constitute the standards for certification of mungbean seeds.

22.12.1 Land Requirements

Land to be used for seed production of mungbean shall be free of volunteer plants.

22.12.2 Field Inspection

A minimum of two inspections shall be made, the first during flowering and the
second after flowering and fruit setting stage.

22.12.3 Field Standards (General Requirements)

• Isolation: Mungbean seed fields shall be isolated from the contaminants shown in
column 1 of Table 22.16 by the distances specified in column 2 and 3 for
foundation and certified seed, respectively.

22.13 Social, Political, and Regulatory Issues

Legumes are the most important protein source for the vast majority of vegetarian
population in Asia, which offers a great promise in achieving the nutritional security
(Vision 2050). It has been envisioned to bring an additional area of three to four
million ha under pulses in India including mungbean (nearly one million ha) by
promoting mungbean in rice and wheat fallows, intercropping with sugarcane and
vegetables and intensifying different cropping systems. Clearly, if a sustainable
1136 G. P. Mishra et al.

Table 22.16 The details of contaminants, seed standards, and their respective isolation distances
as required for the quality seed production in mungbean
Minimum distance (m)
Contaminants Foundation Certified
• Fields of other varieties 10 5
• Fields of the same variety not conforming to varietal purity 10 5
requirements for certification
Standards for each class
Seed standard factors Foundation Certified
• Pure seed (minimum) 98.0% 98.0%
• Inert matter (maximum) 2.0% 2.0%
• Other crop seeds (maximum) 5/kg 10/kg
• Weed seeds (maximum) 5/kg 10/kg
• Other distinguishable varieties (maximum) 10/kg 20/kg
• Germination including hard seeds (minimum 75% 75%
• Moisture (maximum) 9.0% 9.0%
(Source: https://agricoop.nic.in/)

development of mungbean production has to be achieved, a three-pronged strategy

needs to be adopted which mainly includes:

1. Vertical expansion of the crop by improving the yield potential of mungbean

cultivars.
2. Horizontal expansion by extending its cultivation in new areas.
3. Intensifying a well-established cropping system with integration of shorter dura-
tion cultivars.

Timely availability of quality seeds of improved varieties is a serious issue in

most of the mungbean-growing countries. Varietal mismatch and late arrival of
quality seeds are the two most common problems in all mungbean growing areas
which require an immediate attention. To address this issue, the Department of
Agriculture and Cooperation (DAC), Government of India, has established
150 seed hubs in the country to ensure availability of 1000 quintals of quality
seeds of pulses through each seed hub every year. Mungbean finds an important
place in many seed hubs, and these have been producing seeds of mungbean
varieties which have been developed in only last 10 years. Likewise, 12 “enhancing
breeder seed production centers” have been established to ensure breeders seed
production of mungbean and other pulses.
Fewer varieties for each pulse producing agro-climatic zones will ensure avail-
ability of pulses. Larger areas under single or fewer varieties will help in adopting
suitable crop management and mechanization. Identification of varieties with
uniform size and shape minimizes adjustments in machine parameters, thus
minimizing the loss in form of breakage. Storage losses account to 15–30% loss in
all stored grains and mungbean is no exception. The current storage protocols
adopted for storage of mungbean are similar to those in major cereal. There is strong
22 Mungbean Breeding 1137

need to develop specific storage protocol for mungbean. Jute bags prone to internal
and external infestations are still being used for pulse storage, whereas for export and
import PP woven bags are used. Adoption of polypropylene (PP) woven or high-
density polyethylene (HDPE) bags at storage level will minimize chances of external
infestation. Initial infestation can be curbed by fumigation of fresh arrival.
Buffer stock should be created for longer period, at least for 5 years and only 1/5
part needs to be replenished with fresh crop. This will minimize transportation cost
and losses. Further the buffer stock should be converted into dal prior to release;
otherwise millers will dictate the market. Nonetheless, for all of these targets, the
cultivation of mungbean has to be made less cost intensive and profitable to farmers.
Unfortunately, short duration crops like mungbean come associated with drudgery
especially when most of the crop is still harvested by hand picking.

22.14 Future Thrust Area

Mungbean, as a crop, is so versatile that it can be grown under varying agro-

ecological conditions and in different seasons (spring, summer, kharif, and winter).
Extensive progress has been made for the development of high yielding short
duration varieties which has resulted in significant increase in the production and
productivity across the world. However, in the scenario of climate change, a constant
pressure is there for the development of climate smart and resilient varieties. In
addition, research is also required for the management of preharvest sprouting,
bruchid resistance, and stacking of genes controlling resistance or tolerance to
various biotic and abiotic stresses. Although much progress has been made for the
development of short duration varieties in India, efforts are still needed to tap the
huge potential which lies in summer mungbean cultivation especially in Indo-
Gangetic plains and rice fallows. Out of 10.5 M ha rice fallows of eastern (Uttar
Pradesh, Bihar, West Bengal, Assam), central (Chhattisgarh), and southern states
(Andhra Pradesh, Karnataka, Tamil Nadu), 2.5 million ha can be utilized by
expanding extra-short duration mungbean and urdbean cultivation. The summer
mungbean is being grown as a bonus crop in a number of Indian states. Thus, very
focused efforts are needed to develop suitable technology for rice fallow to expand
the base of mungbean production in eastern states like Odisha, Chhattisgarh,
Jharkhand, Bihar West Bengal, and Assam.
High yielding and input-responsive genes are yet to be identified and transgressed
in common varieties. There is urgent need to broaden the genetic base by
strengthening prebreeding and mapping of genes/QTLs and marker-assisted selec-
tion for resistance to insect pests and diseases, yield and grain quality, gene
pyramiding for stable resistance, and development of transgenics in Vigna for
problems hitherto unsolved through conventional means. Owing to its health and
nutritional benefits as well as soil and environment ameliorative properties,
mungbean promises to be a preferred candidate crop for food, nutrition, and envi-
ronmental security and sustainability. Realizing its importance as a nutrition-rich
crop, detail studies of the bioactive compounds were advocated. Postharvest
1138 G. P. Mishra et al.

processing and value addition enhance its commercial value tremendously. Several
in vitro and in vivo studies have indicated various health benefits of mungbean;
nonetheless, the mechanisms involved in disease prevention and the metabolic
processes leading them to become a functional food are essential to unravel.
Ample variability exists in different mungbean cultivars and germplasm
accessions for almost all nutrition-related traits suggesting that improvement for
most of these is possible through simple breeding methods. The sprouting segment
represents the high-value segment of the market although the grains need to meet
exacting quality attributes. Pesticide residue, nonuniform grain size, and hypocotyls
pigmentation are some of the issues which need strict monitoring and quality
standard compliance. For milling of pulses, such varieties must be identified which
gives higher dal recovery in milling, indicating lower gum content in between husk
and cotyledons. While efforts must be made to consume pulses as whole to prevent
milling losses, pulses in form of dal are better protected from bruchid infestation as it
does not provide hiding space to insect larvae and can be stored for longer duration.
About 30% whole grain are lost in form of milling by-product which is rich in
proteins and antioxidants. Presently it goes for low-value cattle feed. Powder
component of the milling by-product can be separated and can be utilized as source
for pulse proteins, whereas husk rich fraction can be used as nutraceuticals.
Postharvest storage has a great role to play in maintaining the nutritional and
physical qualities of all pulses. Bruchids (Callosobruchus species) cause huge losses
to the stored grains in terms of both physical and nutritional quality. These are
reported to enhance trypsin inhibitor activity, saponins, and phytic acid in the stored
grains (Modgil and Mehta 1994). Therefore, there is an urgent need to identify
bruchid-resistant donors and molecular markers associated with resistance and
which initiate host-plant resistance breeding immediately. There is a need of inter-
national collaborative efforts towards exploitation of biological variation for various
nutritional parameters and deploying strong and reliable analytical methods to
determine nutritional compounds in mungbean.

Acknowledgments This research was funded by Indian Council of Agricultural Research (ICAR),
Indian Agricultural Research Institute (IARI), New Delhi, and SERB, New Delhi (CRG/2019/
002024). The technical support received from Mr. Dilip Kumar is duly acknowledged.

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Urdbean Breeding
23
Debjyoti Sen Gupta, Jitendra Kumar, Ashok Kumar Parihar,
Anup Chandra, G. K. Sujayanand, and Sanjeev Gupta

Abstract

Urdbean (Vigna mungo L. Hepper) is a warm season food legume grown on a

wide scale in South Asia. India is the largest producer and consumer for this pulse
crop. Besides India, urdbean is grown profusely in ASEAN countries like
Myanmar and Thailand as well as in Nepal, Pakistan, Bangladesh, and
Afghanistan. It is consumed in the form of whole grain or splitted form or flour
is used in different food preparation. Urdbean breeding was initiated formally
since the inception of All India Coordinated Research Project on Pulses in India.
Since then, a number of varieties were released for general cultivation which are
high yielding and resistant to yellow mosaic, powdery mildew diseases, and
crinkle virus. Seed production and distribution of recent varieties in traditional
and newer niches resulted in the enormous production increase in this pulse crop.
Urdbean has contributed to the ongoing pulse production boom in India. This
chapter discusses different methods associated with urdbean breeding and their

D. S. Gupta (*) · A. K. Parihar

Division of Crop Improvement, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, Uttar
Pradesh, India
AICRP on MULLaRP, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh,
India
J. Kumar
Division of Crop Improvement, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, Uttar
Pradesh, India
A. Chandra · G. K. Sujayanand
Division of Crop Protection, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, Uttar
Pradesh, India
S. Gupta
Crop Science Division, ICAR, Krishi Bhawan, New Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1151
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_23
1152 D. S. Gupta et al.

potential impact in terms of increased production and productivity in this high

protein crop. Starting from botanical descriptors, breeding objectives,
hybridization techniques, selection methods to genetic resources, and use of
molecular markers were discussed in detail.

Keywords

Urdbean · Vigna mungo · Phenotyping · Grain legumes · Genetic mapping ·

Genome

23.1 Introduction

Urdbean or uradbean or urid or urd or blackgram or kalai (Vigna mungo var. mungo
L. Hepper) is a highly popular pulse crop in South and East Asia., particularly in
India. It is a crop of tropical or subtropical growing environment. Indian subconti-
nent is considered as the centre of origin of this crop species based on the rich genetic
diversity of this crop species (Arora 1985). The closest progenitor species of urdbean
is V. mungo var. silvestris, which is still found in natural habitats (Singh and Ahuja
1977; Chandel 1984). This wild species is reported to be domesticated in one of the
biodiversity hotspots, i.e. Western Ghats and northern hilly tracts of Maharashtra
(Chandel 1984; Arora 1985). The wild type of urdbean was having smaller seed size
and was having trailing kind of growth habit (Gupta et al. 2020a, b, c). The present-
day cultivated urdbean varieties were developed through accumulation of recessive
mutant genes, resulting in different plant characters which were not dominant in
natural populations (Sen and Murty 1960; Smartt 1985). During this long man-made
and nature-privileged selection process, many adaptive traits like the dehiscent pods
and seed hardiness were negatively selected. Modern urdbean varieties are high
yielding, resistant to multiple disease and insect pests, and shorter maturity duration
compared to what was grown 50 years back (Rao and Jana 1974).
India is the largest producer and consumer as well as importer of urdbean.
Myanmar contributes to 80% of total urdbean import in India. India produces
about 2.45 million tonnes of urdbean annually from about 4.11 million hectares of
area with an average productivity of 696 kg per hectare (second advance estimates,
DES, DAC & FW, GOI 2020–21; Project Coordinator’s Report 2020–2021).
Urdbean production contributes to 14% of India’s total pulses production (24.42
million tonnes in 2020–21). In Uttar Pradesh, it is also grown during Spring season
and sown during the last part of February or the first part of March. Urdbean is grown
as kharif or rainy season crop in Southern and Northern India. In Southern India, it is
also grown as Pre-Rabi or Rabi crop. In Eastern and Southern growing regions of
India, urdbean is predominantly grown as a rice fallow crop. Date of sowing of
urdbean varies based on the local meteorological conditions, for example, in Uttar
Pradesh and Madhya Pradesh state, it is sown in the month of early July to the first
week of August. In many states in Southern India, it is sown in the last part of
October or the first part of November, whereas, in many Southern states like Orissa,
23 Urdbean Breeding 1153

it is sown in October or February. It requires moderate temperature (25–35
C) with

moderate to high humidity (70–90%) during vegetative growth. Bright sunshine
hours during reproductive stage and well-distributed rainfall are key for the success-
ful cultivation of urdbean. Weeklong continuous rainfall during pod filling or
maturity phase damages the crop yield and quality of the seeds drastically (Gupta
et al. 2020a, b, c). Urdbean has the better ability to withstand waterlogging condi-
tion. The hardy nature of this crop species towards draught or waterlogging condi-
tion makes it a unique crop for physiological studies. Limited irrigation during
spring/summer season while cultivating urdbean in heavy black or brown soil
gives satisfactory yield. Although the national average productivity is lower for
this crop species compared to cool season pulses in terms of per day productivity and
diverse growth ecologies, this makes it a popular pulse crop to compete with others.

23.2 Origin, Evolution, and Distribution of Species and Forms:

Wild Relatives

Cultivated urdbean or urdbean (Vigna mungo var. mungo (L.) Hepper) is originated
from wild progenitor, Vigna mungo var. silvestris Lukoki, Maréchal, and Otoul
(Chandel et al. 1984). It was reported further based on excavations that urdbean
originated in India (Zukovskij 1962), and, however, domestication of urdbean
occurred about few thousand years ago (Fuller and Harvey 2006). Urdbean has a
secondary centre of diversity in southeast Asia. It is cultivated throughout the
southeast Asia including Northern Malaysia, Philippines, Thailand, and Myanmar
(Gupta et al. 2020a, b, c). It is also grown in the neighbouring countries of India,
i.e. Afghanistan, Bangladesh, Bhutan, Pakistan, and Nepal. DNA-based analysis
revealed that cultivated urdbean was more closely related to wild urdbean from
South Asia than that from Southeast Asia (Kaewwongwal et al. 2015).
The genus Vigna is a taxon in Fabaceae family with 104 species found in tropical
and subtropical regions of Africa, Asia, America, and Australia (Schrire et al. 2005).
Among these species, three are mostly popular as pulses; V. radiata (urdbean),
Vigna mungo (mungbean), V. unguiculata (cowpea), and urdbean (Vigna mungo
L. Hepper) varieties can be categorized into three groups, i.e. var. mungo, early
maturing, and large seeded; var. viridis Bose, late maturing and greenish dull or
shinning type seed; and var. silvestris Lukoki, Marechal, and Otoul, wild type.
However, all possible types of recombinants are present today in cultivated types
due to extensive breeding efforts done.

Botanical classification of urdbean:

Kingdom—Plantae.
Division—Angiosperms.
Subdivision—Eudicots.
Class—Rosids.
Order—Fabales.
Family—Fabaceae.
1154 D. S. Gupta et al.

Mainly yellow-flowered 21 species of Vigna, with a diverse range throughout

Asia, are known as Asiatic Vigna species. Among these, seven Asian Vigna species,
i.e. mungbean (V. radiata), urdbean (V. mungo), adzuki bean (V. angularis),
mothbean (V. aconitifolia), jungli bean (V. trilobata), rice bean (V. umbellata), and
creole bean (V. reflexo-pilosa), are used as food crops. Taxonomically, cultigens and
conspecific wild forms are recognized in all species except V. aconitifolia (Bisht
et al. 2005). Based on morphological characterization and biochemical evidences,
Asiatic Vigna species were grouped in separate subgenus Ceratotropis of the genus
Vigna savi which were formerly under the genus Phaseolus. Present grouping of
Vigna species is based on morphological, biochemical, and molecular characteriza-
tion. These groupings of crop species are many a times modified based on the
emergence of any new evidence or theories. However, these changes are not
common and vary from species to species.

23.3 Plant Genetic Resources

National gene bank (long-term storage facility) (NBPGR, New Delhi) has 2246
accessions of urdbean. These were mostly germplasm collections made through
explorations throughout India, breeding lines, primitive cultivars, and landraces
over the years. Considerable morphological variability exists for different agronomic
traits like flowering time, plant height, seed size, seed colour, disease resistance, and
maturity duration. The wild species which are crossable to urdbean are also
maintained in this gene bank. The primary crossing species are Vigna sylvestris,
Vigna umbellata, Vigna sublobata, and Vigna radiata or mungbean. A medium-term
gene bank facility is also present in ICAR-Indian Institute of Pulses Research in
Kanpur City in India where different wild Vigna accessions are maintained for
conservation and sharing with research institutions. Currently, more 200 wild
Vigna accessions are maintained in that facility. Besides this, different state agricul-
tural universities, which are plant genetic resource storage and maintenance
facilities, like GBPUAT, Pantnagar, TNAU, Coimbatore, PAU, and Ludhiana
have their own gene bank holding hundreds of accessions of urdbean.

23.4 Floral Biology: Emasculation and Pollination Technique

Urdbean has a typical cleistogamous flower which is bright yellow in colour. The
cleistogamous flower denotes that here anthesis occurs before opening of the flower.
Thereby, urdbean is a self-pollinated pulse crop. Urdbean flowers are emasculated,
and 10 anthers (9 + 1) are removed and pollinated by the pollen dust from other
desirable plants by handheld devices.
23 Urdbean Breeding 1155

23.5 Breeding Objectives

23.5.1 High Yield

Systematic urdbean breeding effort was initiated with the inception All India Coor-
dinated Pulse Improvement project in 1967. The main objective was development of
high-yielding varieties in urdbean. The national urdbean productivity has improved
from 300 kg/ha in 1960s to 842 kg/ha in 2020–2021. The yield potential of recent
urdbean varieties is between 10 and 15 quintals per hectare. However, most of these
high-yielding varieties are longer in duration (80–95 days).

23.5.2 High Yield Combined with Earliness

Many urdbean breeding programmes now targeting reduction in maturity duration

by 10–15 days without much loss in productivity. Recently, Gupta et al. (2020a, b, c)
evaluated 21 urdbean genotypes (14 advanced breeding lines, 7 released varieties)
(IPU19–27, IPU19–11, IPU19–5, IPU19–6, IPU19–7, IPU19–8, IPU19–20,
IPU19–24, IPU19–31, IPU19–44, IPU19–46, IPU19–51, IPU19–53, IPU19–55,
IPU02–43, IPU11–02, IPU94–1, KUG479, WBU 108, Shekhar 3, WBU 109) for
earliness and yield along with many other qualitative and qualitative traits including
days to first flower, days to 50% flowering, days to first branch, days to first pod,
plant height 30 days after sowing, plant height 45 days after sowing, number of pods
per plant, number of seeds per pod, number of clusters per plant, and days to
physiological maturity. Significant variation was observed for test entries as com-
pared to released checks for yield and maturity duration. One advanced breeding line
IPU19–27 matured early (60–65 days) and yield was at par with high-yielding
checks. This line is the product of the cross “SPS 5 x IPU02-33”. This kind of
breeding lines of urdbean has a long way to go for varietal replacement in urdbean
seed chain to provide growers with more time management options, thereby increas-
ing the cropping intensity. In our personal experience, 60 days maturity urdbean with
high yield potential will become popular among urdbean growers.

23.5.3 Quality Characters Including Biofortification

Food legumes are rich in protein, dietary fibres, folates, micronutrients, and many
other nutrients or phytochemicals (Thavarajah et al. 2014; Sen Gupta et al. 2016;
Maphosa and Victoria 2017; Siva et al. 2019; Jha and Warkentin 2020; Gupta et al.
2020a, b, c). Micronutrient or vitamin deficiency which is also known as hidden
hunger is a global problem against achieving millennium developmental goals set by
the United Nations worldwide, and it is estimated that, globally, more than two
billion people are under malnutrition (FAO 2012; FAO, IFAD, UNICEF, WFP and
WHO 2021). To ameliorate micronutrient deficiency, three basic procedures are
operative: (1) direct micronutrient(s) supplementation in the form of tablet or
capsule, (2) food fortification during processing, and (3) biofortification of crops
1156 D. S. Gupta et al.

in which nutritionally rich crop varieties are developed (Singh et al. 2016; Gupta
et al. 2015, 2020a, b, c). However, breeding for biofortified crop cultivars is a
low-cost method for managing malnutrition or hidden hunger (Bouis and Saltzman
2017). After the release, biofortified crop cultivars can be grown with full potential
in different regions with similar agroclimatic conditions. Further, recurrent cost of
developing biofortified varieties are minimized worldwide as once the micronutrient
trait becomes integral part of plant breeding programs (Bouis and Saltzman 2017).
The breeding objective of biofortified crop cultivars has already been set in few
crops like rice, wheat, maize, pearl millet, and cassava; however many are still
pending. Urdbean is a popular candidate for biofortification of crop varieties as it is
consumed by millions throughout the country. In order to find out high sources for
iron and zinc concentration, larger accessions should be tested under precise grow-
ing conditions. The status of released cultivars also needs to be known. In recent
years, only one study has been conducted to know iron and zinc concentration
among 26 urdbean genotypes that showed iron concentration ranging from 71 to
100 mg/kg and zinc concentrations ranging from 19 to 61 mg/kg (Singh et al. 2017).
Gupta et al. (2020a, b, c) evaluated a larger set of urdbean genotypes which were
grown over multilocations or environments to identify stable sources of high iron
and zinc concentration in this crop species. Here, 83 urdbean genotypes of diverse
origin were tested for iron and zinc concentrations over two locations. Analysis of
variance showed that genotype effects were significant for both traits over both
locations. Iron concentration ranged from 19 to 235 mg/kg (mean 117 mg/kg) and
16 to 255 mg/kg (mean 91 mg/kg) among tested genotypes at the first and second
locations, respectively. For zinc concentration, it ranged from 5 to 134 mg/kg (mean
44 mg/kg) at the first location, while at the second location, it was between 12 and
59 mg/kg (mean 29 mg/kg). “Genotype (G)”, “Location (L)”, and “Genotype” (G) 
“Location” (L) interaction effects were also significant for both micronutrient
concentrations (Gupta et al. 2020a, b, c). This study has identified useful donors
with high and stable sources of iron and zinc concentration.

23.6 Biotic Stress Resistance

23.6.1 Disease Resistance

23.6.1.1 Yellow Mosaic Disease Resistance

The begomovirus (family Geminiviridae) causing yellow mosaic disease (YMD) is
the most important limiting factor in the production of urdbean in India (Anjum et al.
2010). YMD of black gram and in other grain legumes, mungbean, cowpea, and
soybean causes yield losses of 100% under epidemic conditions (Nene 1973). The
annual yield loss due to YMD was estimated to be $ 300 million in three leguminous
crops, viz. urdbean, mungbean, and soybean (Varma and Malathi 2003). In the
Indian subcontinent, YMD is caused by at least four different begomovirus species,
mungbean yellow mosaic virus (MYMV), mungbean yellow mosaic India virus
(MYMIV), horsegram yellow mosaic virus, and Dolichos yellow mosaic virus (Ilyas
23 Urdbean Breeding 1157

et al. 2009). MYMIV and MYMV are the two most important begomoviruses in
grain legumes in India. MYMV is the most prevalent in southern and western
regions (Karthikeyan et al. 1996), whereas MYMIV is predominant in northern,
central, and eastern regions of India (Usharani et al. 2004). The management of
YMD is generally addressed through the control of whitefly (Bemisia tabaci) and use
of resistant cultivar.
Though many resistant varieties of black gram and mungbean have been devel-
oped through conventional breeding (Gupta et al. 2005), the resistance does not hold
for a long time due to the narrow genetic base of the cultivars as well as rapid
emergence of new begomovirus species or strains (Varma et al. 2011). Most of the
resistance screening/breeding and molecular work was conducted in mungbean in
India (Mishra et al. 2020). However, with reference to urdbean, a limited study was
conducted in India (Nene and Kolte 1972; Basandrai 1999; Bag et al. 2014).
Presently, the genome sequence of urdbean has been generated in India. However,
the sequence-based identification of resistant gene and validation of its function are
yet to be demonstrated. The comparison of complete nucleotide sequence of DNA A
component of yellow mosaic viruses with other begomoviruses led to clear differen-
tiation of four species, MYMV, MYMIV, DoYMV, and HgYMV, on the basis of
91% species demarcation. The identity between the two species MYMV and
MYMIV is 81%. The relationship is more or less similar with respective isolates
of MYMV and MYMIV from Thailand, Pakistan, Bangladesh, Nepal, and
Indonesia. In the DNA B component, the cognate DNA B of Thailand isolate
MYMV-[TH-Mg1] and one urdbean isolate of Vamban MYMV-[KA 27] identity
with DNA B of MYMIV-Bg3, MYMIV-Cp, MYMIV-Mg, and MYMI-Sb is
only 67%.
The most unusual feature of MYMV is association of one DNA A with multiple
DNA B. One urdbean isolate of MYMV from south India, MYMV-[IN:Vig] is
associated with two distinct types of DNA B component. One type of DNA B
MYMV-[KA 27] which shows 97% sequence identity with DNA B of Thailand
isolate, and other set of DNA Bs, KA22, KA28, and KA34, which show only
71–72% identity with Thai isolate, but exhibited nearly 90–92% identity with
DNA B of MYMIV (Karthikeyan et al. 1996; Balaji et al. 2004). Two types of
DNA B components are also associated with a soybean isolate of MYMV [IN: Mad:
Sb], one being closely related (96%) to DNA B of HgYMV.
Critical comparison of nucleotide sequence of the DNA B components of
MYMV along with one DNA B variant cloned from Gujarat MYMIV-IN Anand
25 (John et al. 2008) revealed how the components have evolved. The four DNA B
components, three associated with MYMV, one with MYMIV between themselves,
share 96% identity in the coding region ORF BVI and ORF BCI. However, they
differ in the non-coding region. While DNA B of MYMV- KA22, KA28, and KA34
exhibited similarity with CR of MYMV-[IN Vig], Gujarat isolate showed maximum
identity with CR of MYMIV (John et al. 2008). These DNA B molecules referred to
as DNA B variants may represent molecules generated by exchange of components
between MYMV and MYMIV. Swapping of CR could have occurred from MYMV
to MYMIV (“origin donation or regulon grafting”) when both the viruses were
1158 D. S. Gupta et al.

present together in mixed infection. This is well borne out by the divergence
observed between A and B components in the CR region in MYMV and MYMIV.
Analyses of LYMV infected samples by RCA let to unexpected identification of
both beta- and alphasatellites. Over the past few years, betasatellite has been found
associated with MYMIV- (Rouhibakhsh and Malathi 2005) and MYMV-infected
plants (Sathya et al. 2013). The symptoms in the presence of betasatellites are severe
like crumpling and severe leaf curl. In all these cases, the betasatellite was identified
as papaya leaf curl betasatellite. Sathya et al. (2013) found that samples of MYMV-
infected urdbean revealed the presence of alphasatellites, which were identified to
belong to the Vernonia yellow vein alphasatellite species. The importance of associ-
ation of these satellites in LYMV pathogenicity is not understood, whether such
tri/tetrapartite is stable and contributes to viral population evolution and diversity
needs to be looked into. Several studies have been conducted to understand the
genetics of resistance to YMV in urdbean. It has been reported to be inherited as
monogenic dominant (Kaushal and Singh 1989a, b; Gupta et al. 2005, 2013a),
monogenic recessive (Pal et al. 1991; Khattak 2000), oligogenic (Singh 1981), and
complimentary recessive (Shukla and Pandya 1985) traits in different studies. These
studies clearly indicate that resistance to this important disease depends upon
combination of genotypes and the virus strains. It can be concluded that in most of
the cases the host resistance is regulated by single gene in urdbean to yellow mosaic
disease.

23.6.1.2 Powdery Mildew Disease Resistance

Powdery mildew is a major problem in coastal humid regions. In the case of
mungbean, quantitative inheritance of resistance loci was reported (Chatieng et al.
2006). The inheritance of resistance is reported to be controlled by a single recessive
gene in urdbean (Kaushal and Singh 1989a, b). Many workers reported resistance
sources in urdbean like Pant U 30 (Jain and Yadava 1994), P 115, Line 6203, and
LBG 642 (Parmeshwara and Setty 1993). Popular varieties or breeding lines such as
LBG 17, LBG 402, Co 5, WBU 108, and WBU 26 combining resistance with high
yield have also been developed. Among them, LBG 17 derived from two susceptible
parents (Krishnaiah et al. 1978) has revolutionized urdbean cultivation in rice
fallows of coastal Andhra Pradesh. Most of the recent varieties of urdbean grown
in coastal regions are carrying this PMD resistance locus.

23.6.1.3 Cercospora Leaf Spot Resistance

Cercospora leaf spot is the most prevalent disease in kharif season causing leaf
spotting and defoliation. Yield reduction from this disease was reported to be 25%
when leaf defoliation reached 75%. The principal pathogen is Cercospora
canescens, although C. cruenza was also identified to cause this disease. Resistant
sources such as IC 11008, HPBU 51, HPBU 98, UPU 95–1, Pant U 26, and UG
407 have been identified, and prominent cultivars such as Jawahar Urd 2, Jawahar
23 Urdbean Breeding 1159

urd 3, Pant U 19, Mash 48, Mash 21, RBU 38, and KB 512 combining resistance
with high yield have also been developed.

23.6.1.4 Leaf Crinkle Virus Resistance

Leaf crinkle virus causes crinkling and rugosity of leaves and malformation of floral
organs. Pollen fertility and pod formations are severely reduced on infected plants.
Nene (1972) reported 62–100% yield reductions depending upon the stage of growth
at which the plant becomes infected. Prasad et al. (1998) reported NDU 94–6 as a
resistant source in India while Iqbal et al. (1991) found S 210, MM 5–60, S 250, and
Mash Sialkot as resistant sources in Pakistan. Among the released cultivars, Pragati
(US 131) and ADT 3 have shown field resistance.

23.6.2 Insect Resistance

The urdbean crop is infested by a range of insect pests. Twelve species of insect pests
were observed to attack urdbean variety Pant Urd 31 at different stages of crop
growth in an overlapping manner (Yadav et al. 2020). The spotted pod borer,
Maruca vitrata (Geyer); gram pod borer, Helicoverpa armigera (Hubner); bihar
hairy caterpillar, Spilosoma obliqua (Walker); and leafhopper Empoasca kerri
(Pruthi) were recorded as major pests. Yadav et al. (2021) screened 15 urdbean
genotypes against pod borers, i.e. M. vitrata and H. armigera. Two genotypes, viz.
KU-99-05 and Azad Urd-1, were found with minimum pod infestation of 7.67% and
9.67%, respectively, and categorized as resistant against M. vitrata. The four
genotypes KU-99-05, Azad Urd-1, Shekhar-2, and PU-6 were classified as resistant
against H. armigera with minimum pod infestation of 5.83%, 6.17%, 8.50%, and
9.83%, respectively. Saleesha et al. (2019) observed that highly susceptible variety
Co 5 had less number of trichomes (2.13/mm2) and trichome length (3.95 mm),
while the resistant variety VBN 6 had dense trichomes (4.13/mm2) and trichome
length (5.01 mm) which is considered to be the main factor to confer resistance in
plants. A total of 17 blackgram genotypes were screened for resistance to major
insect pests, including aphid (Aphis craccivora Koch.), whitefly (Bemisia tabaci
Genn.), hairy caterpillar (Spilosoma obliqua Walker), and pod borer (H. armigera
Hubner) during summer season of 2018 and 2019 (Neupane et al. 2021). It was
reported that three genotypes BLG0069–1, BLG0036–1, and BLG0079–1 were
having lower number of above-mentioned insect populations, exhibited more resis-
tance in both years, and produced higher grain yield (~1.5 t/ha) than other genotypes.
Naik and Mallapur (2019) screened 15 urdbean genotypes for their resistance against
spotted pod borer, M. vitrata. Five genotypes with percent pod damage, LBG-685
(8.25%), WBU-108 (9.25%), COBG-653 (9.35%), VBN-05 (9.30%), and PU-31
(10.10%) were found as tolerant, and LBG-631 (32.35%), VBG10–024 (31.60%),
RUG-10 (32.85%), KUG-586 (32.80%), and PUSA-9531(31.25%) genotypes
showed susceptibility. The maximum pod damage was found in RUG-10
(32.85%), and significantly least pod damage was noticed in LBG-685 (8.25%). In
urdbean, highly resistant lines such as UG 218, PDU 1, PDU 5, AKU 7, Co 305, UP
1160 D. S. Gupta et al.

95–1, and LBG 707 have been identified against stem flies, Ophiomyia spp. (Gupta
and Kumar 2006). At PAU, about 1400 urdbean genotypes have been screened
against whitefly, B. tabaci, jassids, and MYMV and the genotypes LUs 15, 178,
190, 194, 196, 330, 397, 426, 434, UGs 119, 187, 218, 254, 302, 407, UL 29, UL
257, UL 310, UL 338, UL 557, UL 389, UL 407, UL 538, UL 597, UG 600, UG
633, UG 402, and UG 636 were identified as resistant (Chhabra and Kooner 1981,
1993, 1994, 1995a, b; Chhabra et al. 1984; Kooner et al. 1994). Taggar et al. (2013)
categorized urdbean genotypes KU 99–20 and NDU 5–7 as moderately resistant to
whitefly, whereas Chhabra et al. (1993) reported that urdbean entry LU 15, LU
178, LU 190, and LU 194 had resistance against black aphid, A. craccivora Koch.
Chhabra et al. (1986) tested 30 urdbean genotypes and identified LU 335, LU
274, LU 332, and LU 470 as moderately resistant to A. craccivora and M 1–1 as
highly resistant to the aphid. Highly resistant lines such as PDU 5, KB 63, UG
567, and UH 804 have been identified against thrips (Gupta and Kumar 2006). Lines
such as UG 737, PLU 557, and TAU 1 have been identified highly resistant against
pod borers (Gupta and Kumar 2006). VM 2011 and VM 2164 showed high
resistance against bruchids (Nair et al. 2013). List of insect pests of urdbean and
their tolerant genotypes are given in detail in Tables 23.1 and 23.2, respectively.

23.7 Abiotic Stress Tolerance Under Climate Change Scenario

23.7.1 Heat Stress

Urdbean is sensitive to abrupt climate changes like any other crop species. Although
it is adapted to diverse agro-ecologies or growing conditions, the climatic
fluctuations particularly during flowering or pod filing duration impacts the most.
Discussing about the urdbean-growing ecologies, this crop species is grown mainly
in rainy season (July–October), and in southern part, it is grown as winter season
crop (November to February). However, its cultivation is limited during summer
season cultivation. The scarcity of atmospheric humidity is also another reason for
limited cultivation during summer season. Thus, development of heat-tolerant
urdbean varieties can expand urdbean cultivation area in the country. Genetic
variability for heat tolerance has been reported in many food legumes (Sita et al.
2017). However, there is no report of genetic variability study for heat tolerance in
urdbean except done by Gupta et al. (2021) where they evaluated a panel of urdbean
genotypes under field as well as laboratory testing for heat tolerance. Urdbean
growth phenology includes warmer season (25–35
C) along with high humidity
for its normal growth and development. High temperature (>40
C) during
flowering results in deformation/abortion of flower parts or flower drop leading to
negative impact on yield (Gupta et al. 2021). Similarly, in mungbean, higher
temperature of >38/25
C (day and night, respectively) markedly affected the
yield under summer-season cultivation (Nayyar et al. 2017).
Current climate change scenario leads to abrupt changes in mean temperature
during crop growth duration. The physiological processes are highly impacted by
23 Urdbean Breeding 1161

Table 23.1 List of major insect pest of urdbean

Economic threshold
S. No. Common name Scientific name Family level (ETL)
1 Gram pod borer Helicoverpa armigera Noctuidae 10% affected plants
Hubner
2 Spotted pod Maruca vitrata Crambidae 3/plant
borer Fabricius
3 Tobacco Spodoptera litura Noctuidae 8 egg masses/100 m2
caterpillar Fabricius
4 Red hairy Amsacta moorei Noctuidae –
caterpillar Butler
5 Bihar hairy Spilosoma obliqua Erebidae –
caterpillar Walker
6 Blue butterfly Lampides boeticus L. Lycaenidae –
7 Stem fly Ophiomyia phaseoli Agromyzidae 5–10% incidence
8 Galerucid Madurasia obscurella Galerucidae –
beetle
9 Cowpea aphid Aphis craccivora Aphididae 20/2.5 cm length
koch
10 Thrips Megalurothrips Thripidae –
distalis
11 Pod bug Clavigralla gibbosa Coreidae –
12 Whitefly Bemisia tabaci Aleurodidae –
13 Leaf hopper Empoasca kerri Jassidae –
14 Blister beetle Mylabris pustulata Meloidae –
15 Pulse beetle Callosobruchus spp. Bruchidae –
16 Green stink bug Nezara viridula Pentatomidae –
17 Red-banded Piezodorus hybneri Pentatomidae –
stink bug
18 Hawk moth Herse convolvuli Sphingidae –

Table 23.2 List of insect-tolerant urdbean genotypes

Pest Tolerant genotypes
Pod Kalai, 338-3, Krishna, and Co 3, 4, and 5
borer
CBG 08-011 and PLU 54; UH 82–5, IC 8219 and SPS143
Stem fly Killikullam, 338/3, P 58, Co 4 and Co 5
Jassid Sinkheda 1, Krishna, H 70-3 and UPB 1
Thrips PDU 5, KB 63, PDU 88-23, PDU 2, 5, UG 567, DU4, T9, UH80-4,UH90-9, and
UH80-7

heat stress resulting in dramatic yield losses. The processes impacted are pollen or
ovule activity, flower growth, and even growth and development of embryo or seed
in many pulses (Sita et al. 2017). Taxonomically, urdbean is a close relative of
mungbean and cowpea which are extensively cultivated under identical
environments (Ehlers and Hall 1998; Basu et al. 2019). This further indicates the
1162 D. S. Gupta et al.

possibility of identification of heat-tolerant urdbean genotype in germplasm

collections. Trait discovery is an important tool for urdbean improvement, particu-
larly newer morpho-physiological traits (Scafaro et al. 2010). Therefore, characteri-
zation of large number of germplasm under critical field and controlled condition is
required (Gaur et al. 2019). In many field crops, various physiological and biochem-
ical traits such as photosynthetic activity, membrane stability, pollen viability, and
phenolic compounds have been used to identify heat-tolerant genotypes (Asseng
et al. 2015; Murata et al. 2012; Allakhverdiev and Murata 2004; Sita et al. 2017;
Challinor et al. 2007). Trait genetics underlying key morpho-physiological traits
imparting heat tolerance helps researchers to make genetic improvement of field
crops more precisely. In the recent years, molecular markers were used to find out
genetics of morpho-physiological traits imparting heat tolerance in several crops
(Argyris et al. 2008; Roy et al. 2011; Paliwal et al. 2012). However, in urdbean, use
of molecular markers for genetic mapping and gene expression studies for heat
tolerance are not yet in public domain.
In a separate study, a panel of 97 urdbean diverse genotypes was characterized for
yield potential under stress and non-stress conditions to identify heat-tolerant
urdbean genotypes (Gupta et al. 2021). Eight heat-tolerant and 35 highly heat-
sensitive genotypes were identified based on heat susceptibility index (HSI). Heat
susceptibility index was calculated for individual genotype based on the yield
differences under heat-stressed and normal field conditions. Heat-stressed condition
was created by adjusting the sowing date in a way that flowering or pod-filling stage
coincides with critical maximum day temperature. Further, characterization of a
group of heat-tolerant and sensitive urdbean genotypes based on physiological and
biochemical traits showed genotypic variability for leaf nitrogen balance index
(NBI), chlorophyll (SPAD), epidermal flavanols, and anthocyanin contents. It was
found that heat-tolerant genotypes were having higher membrane stability index
compared to sensitive urdbean genotypes. Significant differences among genotypes
for ETR at varying levels of PAR irradiances were observed. PAR  genotypes
interactions were also significant among tested urdbean genotypes. It indicated high
photosynthetic ability of heat-tolerant genotypes under heat-stressed condition.
Further, in the case of highly heat sensitive genotype, PKGU-1 showed distortion
of photosystem II (PS II) as observed from the decrease in different fluorescence
parameters. Fluorescence kinetics showed the delayed and fast quenching of Fm in
highly heat-sensitive and heat-tolerant genotypes, respectively. Biochemically, heat-
tolerant genotype (UPU 85–86) had higher antioxidant activities than sensitive one
(PKGU 1). Molecular characterization placed heat-tolerant (UPU 85–86) and heat-
sensitive genotype (PKGU 1) distantly from each other. These heat-tolerant
genotypes can be used in breeding programmes.

23.7.2 Photosensitivity

Urdbean is a highly photothermosensitive crop. Therefore, its yield potential varies

across locations due to variable day length in addition to varying thermal regimes.
23 Urdbean Breeding 1163

Thus, minimizing the genotype  environment interactions can help to achieve

stable yield of urdbean. The high temperature stress above the threshold across the
locations during the summer season could be the compounding effects of both heat
and photosensitivity. One of the strategies for selecting photothermo-insensitive
lines is to evaluate different genotypes at multilocations having varying day length
and thermal regimes. As a result, genotypes having stable yield across the locations
could be identified as putative photothermo-insensitive lines. This strategy should be
made to screen thermotolerant lines from the panel of photothermo-insensitive lines
so that widely adapted stable heat-tolerant lines could be identified having less
influence of photo-thermoperiods. In the present investigation, this approach has
been followed to identify contrasting genotypes having high level of tolerance or
sensitivity to high temperature.

23.8 Exploitation of Heterosis and Hybrid Development

Nonavailability of male sterile lines and cleistogamous nature of the urdbean plants
impairs hybrid development or utilization of heterosis in this crop species. While
hybridizing distant parents, many a times male sterile (MS) plants are recovered
(personal communication, not published) (Fig. 23.1.). However, these MS genotypes
are not stable and difficult to be maintained in the absence of any identified restorer.
More research is required in this area for utilization of heterosis in urdbean.

23.9 Breeding Approaches: Conventional and Nonconventional

Including Use of Genomic Tools

23.9.1 Precise and High-Throughput Phenotyping Protocols for Key

Traits

Key traits in urdbean breeding are MYMIV/MYMV resistance, powdery mildew

resistance, tolerance to different abiotic stresses including heat stress and salinity and
tolerance to specific niche water logging. Precise phenotyping facilities are required
for disease screening or evaluation of different key morpho-physiological traits
which are key to imparting tolerance towards few abiotic stresses. From breeders’
point of view, these phenotyping facilities are required to be high throughput in
nature allowing hundreds of samples to be tested in a single run. In the following
section, we will be discussing about various methods or phenotyping platforms
available for increasing the selection efficiency in urdbean breeding:

23.9.1.1 Agroinoculation Method for MYMV/MYMIV Screening

The begomovirus (family Geminiviridae) causing yellow mosaic disease (YMD) is
the most important limiting factor in the production of urdbean in India (Anjum et al.
2010). YMD of urdbean and in other grain legumes, mungbean, cowpea, and
soybean cause yield losses of 100% under epidemic conditions (Nene 1973). The
1164 D. S. Gupta et al.

Fig. 23.1 Male sterile urdbean plant with full blooming but without pod formation

annual yield loss due to YMD was estimated to be $ 300 million in three leguminous
crops, viz. urdbean, mungbean, and soybean (Varma and Malathi 2003). In the
Indian subcontinent, YMD is caused by at least four different begomovirus species,
mungbean yellow mosaic virus (MYMV), mungbean yellow mosaic India virus
(MYMIV), horsegram yellow mosaic virus, and Dolichos yellow mosaic virus (Ilyas
23 Urdbean Breeding 1165

et al. 2009). MYMIV and MYMV are the two most important begomovirus in grain
legumes in India. MYMV is most prevalent in southern and western regions
(Karthikeyan et al. 1996), whereas MYMIV is predominant in northern, central,
and eastern regions of India (Usharani et al. 2004).
The management of YMD is generally addressed through the control of whitefly
(Bemisia tabaci) and use of resistant cultivar. Though many resistant varieties of
urdbean and mungbean have been developed through conventional breeding (Gupta
et al. 2005), the resistance does not hold for a long time due to the narrow genetic
base of the cultivars as well as rapid emergence of new begomovirus species or
strains (Varma et al. 2011). Most of the resistance screening/breeding and molecular
work was conducted in mungbean in India. However, with reference to urdbean,
limited studies were conducted in India (Nene and Kolte 1972; Basandrai 1999; Bag
et al. 2014). YMV isolates from mungbean, moth bean, pigeonpea, cowpea, soy-
bean, dolichos, and horse gram have been cloned and sequenced (Malathi 2007).
Agroinfectious clones were developed against different isolates of MYMIV to prove
Koch’s postulates in urdbean (Mandal et al. 1997), mungbean (Sivalingam et al.
2022), cowpea (Malathi et al. 2005), pigeonpea (Chakraborty 1996), and soybean
(UshaRani et al. 2005). The use of agroinfectious clones on a routine basis in
breeding programmes needs to be adopted for MYMIV-/MYMV-resistant urdbean
cultivar development with a durable resistance.

23.9.1.2 Screening for Heat Tolerance

Recently, Gupta et al. (2021) elaborated the high-throughput and precise
phenotyping procedure of a large set of urdbean genotypes and about their biochem-
ical as well as molecular validation to identify heat-tolerant urdbean genotypes. Heat
susceptibility index (HSI) for each individual urdbean genotype was calculated
using the equation by Fischer and Maurer (1978): HSI ¼ (1Yh/Y)/(1Xh/X),
where Yh and Y are the phenotypic means (Yield) for each genotype under heat-
stressed and non-heat-stressed conditions, respectively, and Xh and X are the
phenotypic means (Yield) for all lines under heat-stressed and non-heat-stressed
conditions, respectively. This study identified 8 highly heat-tolerant and 35 highly
heat-sensitive genotypes based on heat susceptibility index. Further, characterization
of a group of six highly heat-sensitive and seven highly heat-tolerant urdbean
genotypes based on physiological and biochemical traits showed genotypic
variability for leaf nitrogen balance index (NBI), chlorophyll (SPAD), epidermal
flavanols, and anthocyanin contents under 42/25
C max/min temperature. Our
results showed higher membrane stability index among heat-tolerant genotypes
compared to sensitive genotypes. Significant differences among genotypes for
ETR at different levels of PAR irradiances and PAR  genotypes interactions
indicated high photosynthetic ability of a few genotypes under heat stress.
Further, the most highly sensitive genotype PKGU-1 showed a decrease in
different fluorescence parameters indicating distortion of PS II. Consequently,
reduction in the quantum yield of PS II was observed in a sensitive one as compared
to a tolerant genotype. Fluorescence kinetics showed the delayed and fast quenching
of Fm in highly heat-sensitive (PKGU 1) and heat-tolerant (UPU 85–86) genotypes,
1166 D. S. Gupta et al.

respectively. Moreover, tolerant genotype (UPU 85–86) had high antioxidant

activities explaining their role for scavenging superoxide radicals (ROS) protecting
delicate membranes from oxidative damage. Molecular characterization further
pinpointed genetic differences between heat-tolerant (UPU 85–86) and heat-
sensitive genotypes (PKGU 1). These findings will contribute to the breeding
towards the development of heat-tolerant cultivars in urdbean.

23.9.1.3 Screening for Salinity Tolerance

Recently, Shanthi et al. (2021) evaluated a set of urdbean genotypes under salinity
stress condition to identify genotypes which are tolerant to salinity stress. Salinity is
one of the most important abiotic stresses that affects the yield in most of the crops
which are grown under degraded soil condition. The area under coastal cultivation of
this crop is shortened due to increasing problem of soil salinity. In this report,
fourteen urdbean genotypes, viz. VBN1, VBN2, VBN3, VBN(Bg) 4, VBN(Bg) 5,
VBN(Bg) 6, VBN 7, and VBN 8 and VBG 12–034, VBG 12–062, VBG 12–110,
VBG 12–111, VBG 13–003, and VBG 14–016, were screened under three EC level
(4.0 EC, 11.0 EC, and 16.0 EC) and compared with 0.0 EC (control). The mean
germination percentage of all the 13 genotypes studied illustrated reduced level of
germination percentage with increasing salinity level.
At the highest salinity level (16.0 EC), the germination percentage was signifi-
cantly affected compared to 4.0 EC and 11.0 EC. The grand mean of plumule length
was more at 4.0 EC and was reduced to half (16.0 EC) as compared to control. The
root grew longer at 11.0 EC (4.91 cm) as compared to 4.0 EC (4.83 cm) and 0.0 EC
(3.02 cm), although it showed drastic reduction at 16.0 EC (1.92 cm). The grand
mean value of dry matter weight increased concomitantly with salinity. The radical
length had positive and significant correlation with dry matter weight at 11.0 EC
(0.657), whereas positive and non-significant correlation with 4.0 and 16.0 EC
suggested that radicle length is the most useful parameter to select salinity-tolerant
urdbean genotypes. Genotypes VBG-14-016, Vamban 4, Vamban 8, and VBG-12-
062 were found promising under salinity stress condition. It is pertinent to mention
that a large set of urdbean accessions of diverse is needed to be phenotyped under
soil salinity condition, so that a potential donor can be identified for this trait. The
soil salinity condition should be monitored on a regular interval during the entire
crop growth period.

23.10 Breeding Progress

23.10.1 Conventional Breeding

Predominant procedures in urdbean varietal development are mass selection, pedi-

gree selection, back-crossing, and mutation breeding. Varieties released during
1940s were direct selections from local landraces. For example, Type 9 variety
was first released by selection from local landrace. Urdbean varieties released in
India from 1949 to 2000 more than 50% were developed from selections (Gupta
23 Urdbean Breeding 1167

Fig. 23.2 (a) Main stem bearing urdbean. (b) Normal bearing urdbean

et al. 2020a, b, c). Later, after 2000, most of the urdbean varieties released were
hybridization based followed by pedigree selection. Development of multiparent or
MAGIC population is part of modern urdbean breeding in leading institutes. In
India, mutation breeding is coordinated by Bhaba Atomic Research Center (BARC),
Mumbai. Intra- as well as interspecific hybridization was initiated to combine traits
in a single variety. Interspecific hybridization has become regular in most urdbean
breeding programmes with the use of improved hybridization techniques using
hormones or other chemicals during pollination which have increased the number
of successful crosses. However, most of these interspecific crosses are with
V. radiata or V. mungo var. silvestris (Gupta et al. 2020a, b, c). Other species are
yet to be fully explored in distant hybridization of urdbean. During the last 10 years,
more than nine urdbean varieties have been developed by interspecific hybridization
in India. Presently, development of main stem bearing or sympodial (soybean type)
type of urdbean is now a priority in urdbean breeding programmes. Recently, in
ICAR-IIPR, we developed a main stem bearing urdbean variety, IPU 13–1
(Fig. 23.2.). The main purpose of manipulating plant types is to accommodate
more number of plants in a same area, thereby increasing yield potential of a variety.
Manipulation of plant type also facilitates mechanical harvesting. In crops like
urdbean, mechanical harvesting is still an unexplored area and a greater number of
varieties are required which will be amenable to mechanical harvesting.
1168 D. S. Gupta et al.

23.10.2 Genomics-Assisted Breeding

23.10.2.1 Mapping or Tagging of Important Traits

Focus of use of molecular markers in urdbean breeding has been on MYMV or
MYMIV resistance breeding. Limited research efforts in relation to the breeding for
YMV disease resistance are in public domain. International efforts are mostly
concentrated on another important food legume of South Asia, Mungbean (Vigna
radiata). So far quantitative trait loci (QTLs) linked to MYMIV resistance loci were
reported by few workers in mungbean (Kitsanachandee et al. 2013; Alam et al.
2014). Kitsanachandee et al. (2013) employed a F8 recombinant inbred line (RIL)
mapping population generated in Thailand from a cross between NM10–12-1
(MYMIV resistance) and KPS2 (MYMIV susceptible). One hundred and twenty-
two RILs and their parents were evaluated for MYMIV resistance in infested fields
in India and Pakistan. Composite interval mapping identified five QTLs for MYMIV
resistance: three QTLs for India (qYMIV1, qYMIV2, and qYMIV3) and two QTLs
for Pakistan (qYMIV4 and qYMIV5). qYMIV1, qYMIV2, qYMIV3, qYMIV4, and
qYMIV5 explained 9.33%, 10.61%, 12.55%, 21.93%, and 6.24% of variation in
disease responses, respectively. Alam et al. (2014) used a F2 and BC1F1 population
derived from a cross between susceptible (BARImung 1; BMl) and resistant
(BARImung 6; BM6) mungbeans to identify quantitative trait loci (QTLs) associated
with resistance to MYMIV.
Composite interval mapping consistently identified two major QTLs, qMYMM
on linkage group 2 and qMYMVT on linkage group 7, conferring the resistance in
both F2 and BC1F1 populations. qMYMIV2 and qMYMIV7 accounted for
31.42–37.60 and 29.07–47.36, respectively, of the disease score variation,
depending on populations and locations. At both loci, the resistant alleles were
contributed by the parent BM6. qMYMIV2 appeared to be common to a major
QTL for MYMIV resistance in mungbean reported previously (Kitsanachandee et al.
2013), while qMYMIVT is a new QTL for the resistance. So, perusal of literature
clearly indicates that no effort at the international level was made so far on mapping
and tagging QTLs against MYMIV in urdbean. However, a field experiment was
conducted at the Indian Institute of Pulses Research in Kanpur, Uttar Pradesh, India,
during the rainy seasons of 2000 and 2001 to evaluate the inheritance of resistance to
mungbean yellow mosaic virus (MYMV) in the F1, F2, and F3 populations of inter-
varietal crosses of black gram involving eight highly resistant cultivars (DPU 88–31,
NP 21, PLU 710, PDU 6, IPU 98–8, UPU 85–86, UG 27, and DUS 19) and six
susceptible cultivars (PDU 1, IPU 99–182, IPU 99–168, PGRU 95013, UH 80–38,
and UH 82–2) (Gupta et al. 2005). The highly susceptible cultivar for MYMV, PDU
1, was used as the indicator-infector and was also sown all around in the field to
increase the MYMV incidence. The plants were classified as symptomless (R), and
susceptible with typical symptoms of mosaic (S) and necrosis (N). Plants showing
necrosis or no symptoms were classified as resistant. Each F3 family was classified
as resistant (homozygous), susceptible (homozygous), or segregating (heterozy-
gous). Disease severity on F2 plants segregated 3:1 (resistant:susceptible; R:S) as
23 Urdbean Breeding 1169

expected for a single dominant resistant gene in all R/S crosses. The results of F3
analysis confirmed the presence of a dominant gene for resistance to MYMV.
ICAR-Indian Institute of Pulses Research (IIPR) has developed recombinant
inbred line (RIL) populations by crossing resistant parent, DPU88–31, with the
susceptible parent AKU9904 to identify and validate markers related to yellow
mosaic disease resistance loci (Gupta et al. 2013b). Transferability of simple
sequence repeat (SSR) markers was studied to increase the availability of molecular
markers for germplasm evaluation, genetic analysis, and new cultivar development
in urdbean. Three hundred sixty-one (361) simple sequence repeat markers devel-
oped for other food legumes were used to amplify genomic DNAs extracted from
24 diverse genotypes of urdbean. Out of these, 245 SSR markers (68%) amplified
though only 39 (16%) were highly polymorphic among 24 diverse genotypes of
urdbean (Gupta et al. 2013b). These identified SSR markers were used for genetic
analysis of the RIL population. MYMIV resistance gene has been further mapped at
a distance of 12.9 cM in LG10 of urdbean using SSR markers (Gupta et al. 2013b).
This genomic region may be enriched with more closely linked molecular markers to
make marker-assisted breeding for MYMIV in urdbean possible. Though various
genomic resources have been developed for mungbean, urdbean, adzuki bean, and
cowpea for enhancing the breeding efficiency, the limited marker polymorphism
within the species makes it difficult to utilize marker-assisted selections in improve-
ment of Vigna species. Comparative genome mapping holds a great opportunity as
mungbean, adzuki bean, common bean, cowpea, and lablab bean exhibited high
level of genomic collinearity (Han et al. 2005; Somta and Srinives 2007). Recently
we have developed a set of polymorphic SSR markers in urdbean mapping popula-
tion (DPU88–31  LBG685) (personal communication from D. Sen Gupta, IIPR,
Kanpur, not yet published) which showed high polymorphism percentage between
the parental lines of the RIL population. This RIL population has 350 lines which are
either resistant or susceptible to MYMIV infection. Polymorphic markers identified
may be used to fine map the region of interest in urdbean.

23.10.2.2 Genome Sequencing

Recently, Jegadeesan et al. (2021) developed the genome assembly and draft
genome sequence of urdbean variety, Pant Urd 31. They used Illumina and Oxford
Nanopore sequencing technology to develop this draft sequence. The assembled de
novo whole genome of urdbean is ~475 Mb (82% of the genome) and has maximum
scaffold length of 6.3 Mb with scaffold N50 of 1.42 Mb. Bioinformatic analysis
identified 42,115 genes with mean coding sequence length of 1131 bp. Nearly half of
the assembled sequence was repeat elements. From this data, primer pairs for 34,816
SSRs were designed. Out of the 33,959 proteins, 1659 proteins showed the presence
of R-gene-related domains (Fig. 23.3). KIN class was found in majority of the
proteins (905) followed by RLK (239) and RLP (188). Previous to this work,
Pootakham et al. (2021) employed the 10X Genomics linked-read technology to
obtain a de novo whole genome assembly of urdbean cultivated variety Chai Nat
80 (CN80). The draft assembly contained 12,228 contigs and had an N50 length of
1170 D. S. Gupta et al.

Fig. 23.3 Gene ontology chart of Vigna mungo depicting R-gene-related domains (adopted from
Jegadeesan et al. 2021, Draft genome sequence of the pulse crop urdbean [Vigna mungo (L.)
Hepper] reveals potential R-genes. Scientific reports, 11, 11,247)

5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques
produced chromosome-level assembly of 499 Mb comprising 11 pseudomolecules.

23.11 Status of Varietal Development and Maintenance

Breeding

Sincere efforts of varietal development in urdbean had been started in the first quarter
of twentieth century at Pusa, Bihar, with the endeavour of improving locally adapted
but genetically variable populations mainly through the pure line and mass selection
method for yield contributing traits. Numbers of genotypes/cultivars were collected
from all important urdbean-growing areas of India and Burma (Myanmar) in 1925
(Bose 1932). Subsequently, large number of cultivars (15 small, green seeded, and
10 large black seeded) comes out, some of which are still popular in certain areas of
the country (Table 23.3). Only two cultivars had a semi-erect plant type and the rest
were spreading type. The breeding work on urdbean accelerated with the inception
of AICRP on pulses in 1967. But before that during 1943–1950, a large number of
urdbean varieties such as Mash 48, Pusa 1, T-122, T 27, T 77, HPU 6, and Amoo
46–5 were also developed in different states. Later on, during 1950–1970, limited
numbers of varieties were developed like Gwalior-2, T-65, CO-1, ADT 1, T-9, and D
6–7. Before 1970, the varieties were developed by research scientists working in the
state department of agriculture and/or in agriculture colleges in different parts of
India, for example, popular variety T 9 was developed at Kanpur. It was an early
maturing (80–90 days) and higher yielding variety. This variety was ruling variety
for several years in areas and season where yellow mosaic disease was not a big
23 Urdbean Breeding 1171

Table 23.3 Decade-wise list of urdbean varieties developed in India after 1920
S. no. Years Names of varieties
1 Before Amoo 46-5, HPU 6, Mash 48, Pusa-1, T-122, T-27, T-77
1950
2 1950–1970 Gwalior-2, D 6-7, T-65, Co-1, T-9,ADT-1
3 1970–1990 Mash 2, Mash 1-1, Keishna, Kulu Mash No-4, , Khargone-3, KM-1,
Co-2, C0-3, G-75, Naveen, Co-4, ADT 2, Kalindi, KM-2, N0.55, Pant
U-19, Pant U-30, Sindhkeda 1-1, TMV, 1, ADT 3, Co-5, Zandewa,
Pragati, Sarla, LBG 402, Mash 218, TAU-1, Jawahar Urd-2, Jawahar
Urd-3, Pant U-35, LBG 17
4 1990–2010 PDU-1, LBG 402, LBG 20, Vamban 1, ADT 4, ADT-5, TPU 4, TAU
2, APK 1, LBG 22, K-1, Narendra Urd 1, WBU 108, PDU 1, UG
218, LBG 648, Pant U 19, LBG 623, LBG 685, VBN 3, AKU-15, LBG
645, PBG 1, PBG 107, KU 309, VBN(Bg)4, GU-1, Mash 1008, P-93,
LBG 709, VBN(Bg) 5, HM-1, DU-1, Mash 114, LBG 752, CO 6, LBG
611, Mash 338, Birsa Urd 1, Mash 414, AKU 4, KBG 512, Vamban
2, WBG 26, TU 94-2, KU 301, KU 92-1, IPU 94-1, RBU 38, KU
300, NDU 99-2, KU 96-3, Pant U-31, Pant U 40, WBU 109, IPU02-43,
NUL 7
5 2010–2020 LU 391, KUG 479, IPU 07-3, VBG 04-008, TU 40, VBN-8, VBN-9,
VBN-10, LBG 787, KPU 405, PU-10, Kota Urd 4, VBN 6, UH-1,
DBGV 5, Pratap Urd-1, SBC 40,MDU-1, Vallabh Urd 1, Indira Urd
Pratham, TBG 104, AKU 10–1, ADT 6, KKM-1, TRC Urd 99-2, Pant
U-7, Pant U-8, Pant U-9, IPU 13-1, IPU 10-26, IPU 11-02, GBG
1, VBN-11, OBG 33, Kota Urd-3, C0-7

issue. Consequently, it became very popular and used as national check in AICRP
trials for several years.
Out of aforementioned cultivars, T 9, ADT 1, and Co 1 were most important lines
as they were not only preferred by farmers’ community but also used extensively in
breeding programme to develop many varieties of urdbean. With the inception of
AICRP on pulses during 1970–1990, many varieties developed were KM-1,
khargone, ADT-2, Pant U-19, Pant U-30, Mash 218, Sarala, and LBG 17. Of
which, Pant U-19, Pant U 35, and TAU 1 are still popular in certain areas and
existed in seed chain. Amid 1970–1980 in collaboration with AICRP, hybridization
work was taken up by different research stations to evolve varieties having
characteristics such as high yield potential, short duration, non-shattering, resistance
to pest and diseases, wider adaptability, and high protein content (Kumar and Singh
2009). It was necessary to diversify the agronomic bases with incorporating YMV
resistance. KM 1 was the first variety developed through hybridization in the year
1977. Other varieties, Pant U19 and Pant U 30, were developed from a cross of UPU
1, a selection from T 9 and UPU2. These varieties are short duration and YMV
resistance and released in 1981. The hybridization followed by selection has played
an important role in the development of resistant varieties in 1980s. This had led to
the development and release of several MYMV-resistant/MYMV-tolerant varieties
like Pant U 19, Pant U 30, Pant U 35, PDU 1, etc. in urdbean. Type 9 in combination
1172 D. S. Gupta et al.

with L 64, Sel. 1, Line 400, NP 19, and 7378/2 leads to development of urdbean
varieties KM 2, Narendra Urd 1, WBG 26, IPU 94–1, and KU 300, respectively.
Simultaneously, it was observed that the productivity of urdbean under rice fallow is
very poor, and a need was felt to enhance the productivity through incorporation of
powdery mildew resistance in the varieties. The first powdery mildew resistance
urdbean variety LBG 17 was developed in 1983 for rice fallow situation. This has
revolutionized the urdbean cultivation in the coastal regions of A.P. Later, few more
urdbean varieties like LBG 20, LBG 625, LBG 685, LBG 402, and LBG 611 led to
its area expansion in rice fallows of coastal peninsular.
Similarly, LBG 17, Pant U 35, and KU 301 are also derived from cross
Netinminumum  Chikkuduminumu, UPU 3  Pant U 19, and 7570/7  Sel.1.
Varieties KM 1 and ADT 4 are the product of three-way crosses (G 31  Khargone
3)  G 31 and (T 9  ADT 2)  Pant U 19.
Furthermore, national crossing programme was initiated in 1980 in order to create
new variability (Singh and Satyanarayana). The number of crosses has been assigned
to different centres. The impact of this programme could be judged from the fact that
about 67% varieties were developed by hybridization during the 90s. By the mid of
the 1990s, substantial reduction in crop duration coupled with photothermo-
insensitivity and synchronous maturity, resistance to major disease, and large seed
size were achieved. During the first decade of twenty-first century, many varieties
have been developed with high yielding potential and biotic stress resistance (YMV,
CLS, and PM). AKU-15 is the product of hybridization for Vidarbha region of
Maharashtra, and it has tolerance to powdery mildew and dry root rot. Systematic
breeding efforts for incorporating MYMV resistance resulted in development of two
resistant cultivars, Pant U 31 and IPU 02–43, which were bred in northern Indian
conditions but had shown resistance against MYMV across the locations and found
promising in southern peninsula. Pant U 31 was released in 2005 and became
popular among farmers in 2009. Other varieties like KU 300, NDU 99–2, Pant
U-40, and WBU 108 developed through hybridization for different agro-climatic
conditions with MYMV resistance. After hybridization and selection, mutation with
gamma rays was also most frequently used in urdbean for varietal development.
Many varieties like Co 4, Manikya, TAU 1, TPU 4, TAU 2, and TU 94–2 have been
developed through mutation breeding approach. The mutant variety TAU 1 was the
most popular variety particularly in Maharashtra.
However, pedigree analysis of urdbean revealed that a small number of parents
with high degree of relatedness were repeatedly used in crossing programme which
narrows down the genetic base. Sixty seven percent of varieties in urdbean have
Type 9 as one of the ancestors in their pedigree. Therefore, keeping in mind this
issue, wide hybridization has been started in urdbean to develop varieties with wider
adoptability and improved plant types. Initially the progress in urdbean has been
very slow, but recently some urdbean lines isolated from mungbean x urdbean and
urdbean  Vigna mungo var. silvestris crosses have been found very promising with
respect to wider adoptability and degree of sensitivity to abiotic stresses.
Till date, a total of nine urdbean cultivars have been developed using interspecific
approach (Table 23.4), and several promising lines are being evaluated in
23 Urdbean Breeding 1173

Table 23.4 Varieties developed through interspecific hybridization

Crop Species used Cultivar developed
Urdbean Vigna silvestris VBN 7, Vamban 5, Vamban 6, Mash 1008
Vigna radiata Mash 114, VBG04-008, TU 40, VBN 8, Mash 1137 (09)
Vigna umbellata

multilocation trial under AICRP. Recently the incidence of MYMV has become
serious in rice fallows of south India, and efforts are being diverted towards
incorporation of MYMV resistance genes along with powdery mildew. During the
last two decades, major emphasis has been to breed short-duration, photo- and
thermo-insensitive varieties of urdbean coupled with resistance to biotic stresses,
viz. yellow mosaic virus and powdery mildew, which contributed significantly to the
national production. Consequently, more than 100 varieties of urdbean have been
developed till date in India.

23.12 Coordinated System of Testing

The coordinated research programme on urdbean along with other pulses started
with the establishment of All India Coordinated Pulse Improvement Project
(AICPIP) in the year 1966 at Indian Agricultural Research Institute, New Delhi.
Later in 1978, the headquarter of AICPIP was shifted to the then regional station of
IARI at Kanpur. The Project Directorate (Pulses) was further strengthened with the
inclusion of basic and strategic research in its mandate and elevated as Directorate of
Pulses Research in 1984. It was also delinked from IARI and started functioning
independently under ICAR. To provide focused attention on each crop, MULLaRP
crops MULLaRP (Mungbean Urdbean, Lentil, Lathyrus, Rajmash and Pea) were
separated from the rest of the pulses under independent coordinated project AICRP
on MULLaRP during VII Plan in 1993 with 6 mandatory and 8 verifying centres.
The post of Project Coordinator (MULLaRP) was created to provide independent
leadership to AICRP on MULLaRP. These centres were also allowed for varietal
testing of one or two other pulse crops besides carrying out the intensive research on
mandated crops of MULLaRP which includes generation of breeding material,
development of location specific production, and protection technologies. During
IX Plan, all 8 verification centres were converted to sub-centres through redeploy-
ment of manpower from other projects and ten new sub-centres, i.e. Kanpur and
Varanasi (Uttar Pradesh), Dholi (Bihar), Sehore (Madhya Pradesh), Dharwad
(Karnataka), Imphal (Manipur), Agartala (Tripura), Ludhiana (Punjab), Hisar
(Haryana), and Coimbatore (Tamil Nadu), were added. Additionally, 10–15 volun-
tary centres were also included in the network to test the location-specific genotypes
and production and protection technologies by providing the additional contingency
grant. This was the great expansion of this AICRP. During X Plan, a new sub-centre
at Kota (Rajasthan) was added to cater the need of southern Rajasthan. During XI
Plan, more emphasis was laid on location-specific focused research activities. The
1174 D. S. Gupta et al.

two sub-centres, one each in Sagar (Madhya Pradesh) and Keonjhar (Odisha), were
created. To give impetus on rice fallow pulses, two sub-centres, one each in
Ghantasala (Andhra Pradesh) and Aduthurai (Tamil Nadu) in southern peninsula,
were added to the project. At present, the project operated through 6 main centres
and 22 sub-centres.

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24
Harsh Kumar Dikshit, Gyan Prakash Mishra, Muraleedhar S. Aski,
Akanksha Singh, Kuldeep Tripathi, Ruchi Bansal, Aditya Pratap,
Sanjeev Gupta, and Shiv Kumar

Abstract

Lentil (Lens culinaris Medikus) is important rainfed winter season grain legume
for diversification of cereal-based cropping system worldwide. The crop
originated in Near East and spread to different region establishing in wide
range of agro-ecology. Lentil is cultivated in more than 50 countries. Lentil
grains are rich sources of protein, prebiotic carbohydrates, micronutrients, and
vitamins. Lentil is important staple food in regions with low income. The
productivity of lentil is low due to poor seedling vigour, high flower drop, low
pod set, poor dry matter accumulation, and susceptibility to biotic and abiotic
stresses. Biotic and abiotic stresses induced by climate change pose challenge to
lentil cultivation. Discovery of new genes and quantitative trait loci offer oppor-
tunity to breeders for improving lentil varieties for higher grain yield, nutritive
value, and tolerance to biotic and abiotic stresses. In this chapter, we discuss the
present challenges and opportunities for lentil improvement.

H. K. Dikshit (*) · G. P. Mishra · M. S. Aski

Division of Genetics, Indian Agricultural Research Institute, Delhi, India
A. Singh
Amity Institute of Organic Agriculture, Amity University, Noida, Uttar Pradesh, India
K. Tripathi · R. Bansal
Germplasm Evaluation Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi,
India
A. Pratap
ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
S. Gupta
Crop Science Division, ICAR, Krishi Bhawan, New Delhi, India
S. Kumar
Biodiversity and Integrated Gene Management Program, ICARDA, Rabat, Morocco

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1181
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_24
1182 H. K. Dikshit et al.

Keywords

Lens culinaris · Origin · Hybridization · Breeding · Biotic and abiotic stresses ·

Nutritional quality

24.1 Importance of Crop

Lentil (Lens culinaris subsp. culinaris) is self-pollinated diploid crop grown in cool
season. Lentil is Old World legume domesticated with wheat and barley. From
Fertile Crescent, lentil cultivation proliferated westwards to the Mediterranean
region, the Nile Area, and Central Europe and in east towards Asia. Later the lentil
was introduced to North America and Australia (Cubero 1984; Matny 2015).
Cultivated lentils are known as masur (Hindi), adas (Arabic), heramane (Japanese),
and mercimek (Turkish). Cultivated lentils are classified in two groups:
macrosperma types and microsperma types (Cubero 1981). Macrosperma types
have large and flat seeds and are predominantly grown in North Africa, Southern
Europe, and North and Latin America. Microsperma types are grown in Afghanistan,
Egypt, Ethiopia, and South Asia. Lentil is grown in 52 countries with global area of
6.1 Mha and production of 6.33 Mton (FAO 2018). Canada, India, Australia,
Turkey, and Nepal were the leading producers of lentil. Canada and Australia
produce lentil for export to South Asia. Nutritive lentil grains are grown for
human consumption and lentil straw is valuable animal feed. Lentil is rich in protein,
carbohydrate, fibre, vitamins, and micronutrient and provides nutritional security
(Kissinger 2016). Lentil straw is nutrient rich with higher ruminal degradation in
comparison to cereal straw and has been successfully utilized for ration of large
ruminants and sheep (Mudgal et al. 2018). In South Asia, lentil is grown in different
cropping systems (rice/lentil, fallow/lentil, and pearl millet/maize/cotton/lentil).
Major lentil-producing regions in South Asia are Northwestern Plains, Northeast-
ern Plains, Central Highlands, and Terai region. Northwestern plains include West-
ern Uttar Pradesh, Haryana, Punjab, and Punjab province of Pakistan. Small-seeded
lentil varieties with bushy growth habit, profuse branching, and maturity duration of
130–140 days are grown. This region occupies 10% of total area under lentil.
Vascular wilt (Fusarium oxysporum f.sp. ciceri), ascochyta blight (Ascochyta
lentis), and rust (Uromyces fabae) are the major diseases (Mishra et al. 2007).
Northeastern Plains include Bangladesh, Myanmar, Eastern Uttar Pradesh, West
Bengal, and Bihar. This region accounts for 35–40% of area. Small-seeded lentils are
grown on rice fields under rainfed conditions, on low-lying areas (Tal area), or on
uplands after jute. Wilt, stemphylium blight, and rust are the major diseases. Central
highlands occupy 35–40% area of South Asia including Madhya Pradesh, Uttar
Pradesh, and Maharashtra. Here lentil is monocropped in kharif rice fallows. Bold
seeded, early maturing varieties with long tap roots, and upright growth habit are
preferred. Wilt and rust are the major diseases. Terai region includes Himalayan foot
hills of Nepal, Pakistan, and India occupying about 15% of total area in South Asia.
This region has high humidity, rainfall, and severe winter. Frost, rust, and wilt are
abiotic and biotic constraints.
24 Lentil Breeding 1183

24.2 Origin and Distribution

The genus Lens Miller is part of the family Fabaceae (Leguminosae), subfamily
Faboideae, tribe Fabeae, or alternatively in subfamily Papilionaceae, tribe Vicieae.
Lens culinaris subsp. culinaris (Bioss.) Ponert is divided into two groups: the small-
seeded, red cotyledon var. microsperma and the large-seeded, red, yellow, green var.
macrosperma. Lens culinaris ssp. culinaris is native to near East and Central Asia.
Lens orientalis is the probable progenitor (Ladizinsky 1979) of lentil. It was found in
the field of farmers cultivating lentil in the Middle East, and plant characteristic and
pollen morphology resembles lentil. Initially Cubero (1981) classified genus Lens in
five species Lens culinaris, Lens orientalis, Lens ervoidis, Lens nigricans, and Lens
montbretti. Later this genus was divided in seven species/subspecies (Ferguson
2000):

(a) L. culinaris.
ssp. culinaris,
ssp. orientalis (Boiss) Ponert,
ssp. tomentosus (Ladizinsky) Fergusan, Maxted, van Slageren and Robertson,
ssp. odemensis (Ladizinsky) Fergusan, Maxted, van Slageren and Robertson.
(b) L. ervoides (Brign.) Grande.
(c) L. nigricans (M.Bieb.) Godron.
(d) L. lamottei Czefr.

The Lens wild relatives originated from areas with variable climatic conditions
and soils. The distribution of CWR in genus Lens is reported by Singh et al. (2014a).
Lens culinaris ssp. orientalis exists in the entire Fertile Crescent including Jordan,
Syria, Israel, Lebanon, and Cyprus and in Armenia, Azerbaijan, Czech Republic,
Iran, Russia, Turkmenistan, Tajikistan, and Uzbekistan in open or shaded habitats on
stony calcareous to basalt soils at 500–1700 m. L. culinaris ssp. tomentosus is
reported from Syria and Turkey. L. culinaris spp. odemensis is distributed in Israel,
Syria, and Palestine in grassy habitat and in calcareous soils of pine groves and on
basaltic gravel, at 700–1400 m. in Turkey. L. ervoides is found in Jordan, Syria,and
Palestine and westwards to Montenegro, Italy, and Croatia and northwards to Russia,
Ukraine Armenia, and Azerbaijan under trees and shrubs in shady and partially
shady habitat. L. lamottei is reported from Spain and France. L. nigricans extends in
open or shady stony habitats in granitic or limestone soil or in terraces, settlements,
and plantations up to 1200 m in Bahrain, Crimea, Croatia, France, Italy Montenegro,
Spain, and Ukraine.
Lentil was domesticated by selection of plants from their wild species. The initial
selection was made primarily for seeds in pod and seed size. Archaeological
evidence indicates the presence of lentil in Syria-Turkey-Iraq region around
8500–600 BC. The crop was probably domesticated in this region. From here the
crop spread to Greece, Nile, Central Europe, and South Asia (Nene 2006). Later
lentil spread to Afghanistan, China, Ethiopia, India, and Pakistan. Invaders of the
Hamites introduced lentil as part of Near Eastern crop assemblage to Ethiopia. From
1184 H. K. Dikshit et al.

Bronze Age, lentil was grown with wheat and barley throughout the Mediterranean
region (Erskine et al. 1989). Lentil cultivation as part of farming system began in
5th–4th millennium BC.

24.3 Plant Genetic Resources

24.3.1 Lens Gene Pool

Cubero et al. (2009) noticed hybridization barriers in the genus Lens. They classified
L. culinaris and L. orientalis in primary gene pool and L. odemensis in secondary
gene pool due to some restrictions in hybridization. L. nigricans and L. ervoides
were grouped in tertiary gene pool. Later, Tullu et al. (2013) reported that
L. nigricans and L. ervoides can be part of secondary gene pool using embryo
rescue. Wong et al. (2015) classified seven taxa in four gene pool (primary,
L. culinaris; secondary, L .orientalis; tertiary, L. tomentosus and L. lamottei; and
quaternary, L. ervoides and L. nigricans).
Several reports are published (Ladizinsky et al. 1984; Abbo and Ladizinsky 1991,
1994; Fratini et al. 2004; Fratini and Ruiz 2006; Muehlbauer et al. 2006) on
crossability of L. orientalis and L. odemensis with L. culinaris. Hybrid embryo
abortion, hybrid sterility, and albino seedling are major constraints in the interspe-
cific hybridization of Lens species. Abbo and Ladizinsky (1991, 1994) and Gupta
and Sharma (2005) reported hybrid embryo abortion in crosses involving
L. culinaris and L. nigricans and L. ervoides. Application of gibberellic acid
(GA3) has led to success of L. culinaris crosses with L ervoides, L. odemensis,
and L. nigricans. Protocol to recover embryo of crosses between L. culinaris and
L. odemensis, L ervoides, and L. nigricans has been reported by Fratini and Ruiz
(2006). The details on leading gene banks and PGR conserved are mentioned in
Table 24.1.
Taxonomic classification of the genus Lens Miller has gone through several
modifications, initially with five species, Lens culinaris, Lens orientalis, Lens
ervoides, Lens nigricans, and Lens montbretii (Cubero 1981), to the present seven
species/subspecies, L. culinaris ssp. culinaris, L. culinaris ssp. orientalis,
L. culinaris ssp. tomentosus, L. culinaris ssp. odemensis, L. ervoides, Lens lamottei,
and L. nigricans (Ferguson 2000). Despite the taxonomic reclassifications, all
studies indicated L. culinaris ssp. orientalis as the most closely related wild progen-
itor of L. culinaris ssp. culinaris (Cubero et al. 2009).
During domestication, successive selection rounds have reduced genetic variation
and the allelic diversity of crops in comparison to their wild progenitor. The reduced
diversity during domestication is the major bottleneck in improving crop productiv-
ity. Effective adaptation strategies are required to meet biotic and abiotic stresses due
to climate change and variability of weather within growing season. Crop wild
relatives (CWRs) have tremendous potential to enhance and sustain optimum pro-
ductivity. Search, characterization, and conservation of CWR is important in lentil
24 Lentil Breeding 1185

Table 24.1 Leading gene banks and PGR conserved

Wild Land Total
Gene bank Country relatives races accessions Reference
ICARDA Global 4% 80% 13958 Coyne
et al.
(2020)
Australian Temperate Field Australia 4% 54% 5254 Singh
Crops Collection et al.
Seed and Plant Improvement Iran 3000 (2017a, b)
Institute
USDA USA 1% 2875
N.I. Vavilov All-Russian Russian 80% 2556
Scientific Research Institute of Federation
Plant Industry
National Bureau of Plant India 1% 42% 2285
Genetic Resources
Inst de Inv. Agropecuarias, Chile 1345
Centro Regional de
Investigación Carillanca
PGRC Canada 56% 1139
Plant Genetic Resources Dept. Turkey 1% 99% 1095
Aegean Agricultural
Research Inst.
General Commission for Syria 1072
Scientific Agricultural Research
General Commission for
Scientific Agricultural Research
Research Centre for Hungary 3% 1061
Agrobotany
NGB Egypt 5% 875
Institute of Crop Germplasm China 60% 855
Resources
Plant Genetic Resources Pakistan 8% 91% 805
Institute, National Agricultural
Research Center
Bangladesh Agricultural Bangladesh 798
Research Institute
Centro de Recursos Spain 10% 87% 703
Fitogeneticos, INIA
Biodiversity Conservation and Ethiopia 70% 678
Research Institute

breeding programme. CWRs are the most potential sources for additional genetic
variation in crop plants.

24.3.1.1 Wild Relatives as Source of Novel Variation

Variation of yield traits (secondary branches, crop duration, biological yield, number
of pods, seed size, and grain yield) in different Lens species have been reported
1186 H. K. Dikshit et al.

(Kumar et al. 2011; Singh et al. 2013a). L. culinaris ssp. orientalis accession ILWL
118 is very valuable source for earliness. Earliness is important for rainfed lentil in
Central India and rice fallows in Eastern India. The utility of L. ervoidis has been
reported as source of seed traits, growth habit, and biomass production (Tullu et al.
2011, 2013). Gorim and Vandenberg (2017a) investigated root trait variation for
improving biomass and grain yield of L. orientalis, L. tomentosus, L. odemensis,
L. lamottei, and L. ervoides. Ferguson et al. (1998) and Gupta and Sharma (2006)
reported that L. lamottei and L. culinaris ssp. orientalis are the potential sources of
genes for seed size and number of seeds and pods. Singh et al. (2014a) evaluated a
large number of Lens species accessions over the years and reported variation for
yield contributing traits and multiple disease resistance in L. ervoidis and
L. nigricans. The study of Singh et al. (2020) exhibited significant variation for
agromorphological traits in Lens wild species.

24.3.1.2 Wild Relatives as Source of Tolerance to Abiotic Stresses

Lentil and its wild relatives evolved in low rainfall areas on marginal soil. The most
important abiotic stress is drought. Accessions in primary gene pool exhibit poor
water extraction and lower growth rate than accessions in secondary and tertiary
gene pool. The potential of L. nigricans, L. odemensis, and L ervoides for drought
tolerance has been reported (Hamdi and Erskine 1996; Gupta and Sharma 2006).
The L. culinaris. spp. orientalis from low rainfall environments in Syria, Azerbaijan,
Jordan, Tajikistan, and Turkmenistan provides sources of drought tolerance. Gorim
and Vandenberg (2017a) studied lentil CWRs for root traits under water stress and
controlled environment. Omar et al. (2019) examined interspecific derivatives and
reported that drought tolerance was associated with pubescent leaves, relative leaf
water content, increased root-shoot ratio, cell membrane stability, and transpiration,
reduced wilting, and canopy temperature. Sanderson et al. (2019) evaluated RILs of
crosses of L. culinaris with L. odemensis, L. orientalis, and L ervoides. Stress
tolerance was associated with reduced transpiration, delayed flowering, deep roots,
and reduced plant height.
Genotypes of L. orientalis and L. odemensis with deep roots exhibited drought
tolerance. Delayed flowering permitted root exploration in deeper soil; however pod
number and seed yield were reduced. L. tomentosus exhibited reduced transpiration
rate. Hamdi and Erskine (1996) reported cold tolerance in L. culinaris ssp. orientalis.
L. lamottei accession, evolved from frost-prone area, exhibited trichomes on leaves,
stems, and pods (Gorim and Vandenberg 2017a). Baute et al. (2015) reported that
the reproductive period in May–June of Lens orientalis genotypes from Tajikistan,
Turkmenistan, and northern Syria makes it potential source for heat tolerance.

24.3.1.3 Wild Relatives as Source of Tolerance to Biotic Stresses

Donors for important biotic stresses (fusarium wilt, ascochyta blight, stemphylium
blight, rust, anthracnose, powdery mildew, bruchids, Sitona weevil, and Orobanche)
have been reported from different Lens ssp. (Meena et al. 2017). Bayaa et al. (1994)
screened 248 accessions of wild germplasm from ICARDA for ascochyta blight
resistance. Resistance was reported in 12 accessions of L. culinaris ssp. orientalis, 3
24 Lentil Breeding 1187

accessions of L. culinaris ssp. odemensis, 36 accessions of L. nigricans, and

03 accessions of Vicia montbretti. Gupta and Sharma (2006) characterized
70 accessions of wild species and reported resistance for both biotic and abiotic
stresses in L. nigricans. Tullu et al. (2006) evaluated 564 accessions of six Lens
species for resistance to anthracnose (Colletotrichum truncatum). Among the studied
species, L. ervoides revealed high resistance to race Cti and Cto followed by
L. lamottei. It was reported that the L. ervoides accessions exhibiting resistance
originated at Turkey and Syria. Cultivated lentil exhibits susceptibility to Ascochyta
lentis.
Fernández-Aparicio et al. (2009) studied screened wild Lens accessions and
reported high level of resistance to broom rape in accessions of Lens odemensis,
Lens ervoides, and Lens orientalis. Tullu et al. (2010) studied 375 accessions of six
wild Lens ssp. for resistance against A. lentis. Several accessions of L. ervoides and
L. nigricans belonging to secondary gene pool exhibited resistance. Laserna-Ruiz
et al. (2012) evaluated 571 accessions of wild Lens against seed bruchids. Relatively
less infestation was recorded in 32 accessions of L. culinaris ssp. culinaris,
L. culinaris ssp. orientalis, L. nigricans, and L. lamottei. Podder et al. (2013)
characterized 70 accessions of six Lens species for resistance to Stemphylium
botryosum. High frequency of resistance was reported in L. lamottei followed by
L. ervoides. Resistance to multiple diseases in L. nigricans and L. ervoides
accessions had been reported by Singh et al. (2014a). Dadu et al. (2017) screened
30 genotypes of five species (L. orientalis, L. odemensis, L. ervoides, L. nigricans,
and L. lamottei) against Ascochyta lentils. About one-third of the studied genotypes
exhibited resistance to ascochyta and L. orientalis accession ILWL 180 exhibited
stable resistance against highly aggressive isolates. Barilli et al. (2020) reported high
level of resistance in L. ervoides accession PI 572330, PI 572334, and PI 572338
against Colletotrichum lentis.

24.3.2 Germplasm Evaluation for Agromorphological Traits

Several reports are available on characterization of germplasm. Few recent reports

on evaluation of germplasm indicating the range of variability in studied germplasm
are presented in Table 24.2.

24.4 Floral Biology: Emasculation (Pollination Techniques)

24.4.1 Flower Structure

The inflorescence is an axillary raceme with 1–4 flowers borne on slender peduncle
(Fig. 24.1a, b). However, 5–7 flowers per peduncle are also reported (Mishra et al.
2020). A genotype bearing up to 15 flowers per peduncle (fasciated stem mutant
line) was also reported recently (Tripathi et al. 2021). The flower consists of five
unequal sepals, five petals (standard petal broadly obviate, two wing petals oblong to
obovate, and keel formed by fusion of two petals), androecium, and gynoecium.
1188 H. K. Dikshit et al.

Table 24.2 The range of variation for agromorphological traits in lentil

Mekonnen and
Anjam et al. Kumar and Hoekstra Pouresmael
Traits (2005) Solanki (2014) et al. (2014) et al. (2018)
Plant height (cm) 28–45 14.60–45.20 20.6–44.7 16.67–33
Days to 50% – 59.00–107 42–78 62–77
flowering
Days to pod – 71.00–115 – 61–73
initiation
Days to maturity – 101.00–145 77–138 81–103
Secondary – 5.80–49.00 – –
branches
Pods/plant 23–160 7.20–302 1.6–73.3 1.42–14.78
Seeds/pod – 1.00–2.00 0.5–2.0 1–4.33
100 seed weight – 0.49–5.17 1.38–4.9 0.21–6.59
Seed yield/plant – 0.19–3.84 – 0–6.33
Pod dehiscence 2–9 – – –
(1–9 scale)
Seed yield (kg/ha) 333–1544 – 0–347.2 –
Biomass (kg/ha) 1667–7292 – – –
Straw yield (kg/ha) 1333–6133 – – –
Viral disease 1–9 – – –
(1–9 scale)
Pods/peduncle 2–4 – – –

Fig. 24.1 (a) Details of a lentil flower; (b) a peduncle bearing seven flowers in cultivated lentil

Gynoecium includes laterally compressed sub-sessile ovary, glabrous style (1–5 mm

long, flat, and abruptly unturned), and stigma (glandular papillate and spatulate). The
stamen is diadelphous (9 + 1), axillary stamen is free, and stamens are winged
24 Lentil Breeding 1189

towards base. Spherical anthers are basifixed with 0.2 mm diameter and light yellow
in colour.

24.4.2 Hybridization Technique

Lentil is a self-pollinated crop with less than 0.8% natural outcrossing. Emasculation
of lentil flower prevents self-pollination. The highest percentage of crossed seed is
produced when pollination is done immediately after emasculation. The average
temperature range of 15–25 degree centigrade is suitable for hybridization. Relative
humidity of 50% and 12–15 h of light ensure good seed set. Hybridization is carried
out in forenoon. The buds with three-fourth length of calyx lobes are selected and are
held between the thumb and the forefinger with the suture of the keel. Pointed
forceps are used to remove one or two calyx lobes adjacent to the suture side of
the keel. The forceps is inserted in keel to split it without damaging it. The stamens
are carefully removed with help of forceps and pollination is done manually imme-
diately after emasculation. Pollen is collected from young flowers immediately after
anther dehiscence. Interspecific hybridization is vital for broadening the genetic base
of cultivated lentil. Hybridization of lentil with species of secondary gene pool
results in degraded and shrivelled embryos and non-viable seeds. To overcome the
problem, embryo rescue technique was employed but the success was low. Embryo
rescue is time consuming and requires controlled growing environment and highly
skilled technical personal. The initial work on interspecific hybridization in lentil has
been reported by Cohen et al. (1984) and Fratini and Ruiz (2006).

24.5 Cytogenetics

Lentil is a self-pollinated crop with 2n ¼ 2x ¼ 14. Sindhu et al. (1983) reported one
metacentric, three acrocentric, and three sub-metacentric chromosome pairs in
karyotype of lentil from somatic tissues of L. nigricans, L. orientalis, and
L. culinaris. Ladizinsky et al. (1984) reported a similarity in karyotype of
L. culinaris and L. orientalis. Three interchange differences were recorded by
Gupta and Bahl (1983) between L. culinaris and L. nigricans. Different workers
have reported different total chromosome length varying with species and seed size.
Gupta and Singh (1981) reported total chromosome length of 39.31 μm for PL
639, (Dixit and Dubey 1986), 31.77 μm for Type 36, and 30.4 μm for L. orientalis
and 21.47 μm for L. ervoides (Sindhu et al. 1983). Dixit and Dubey (1986) reported a
range of 28.2–72.3 μm in different small-seeded lentil cultivars. Mishra et al. (2007)
reported a range of 3.0–9.2 μm.
1190 H. K. Dikshit et al.

24.6 Genetic Studies for Morphological Traits

24.6.1 Growth Habit

Ladizinsky (1979) reported the incomplete dominance of erect growth habit and
proposed gene symbol Gh. Emami and Sharma (1999) reported recessive gene ert
for erect growth habit. Later Kumar (2002) and Mishra (2004) reported that erect
growth habit was completely dominant over the prostrate growth habit and proposed
gene symbol Ert.

24.6.2 Foliage Colour

Kumar (2002) and Mishra (2004) reported that dark-green foliage was dominant
over the light-green foliage, and the gene symbol Dgl was proposed. Red pigmenta-
tion on plant parts has been studied (Ladizinsky 1979, epicotyl (gene Gs for green
stem); Emami and Sharma (1996a), brown leaf (gene Bl); Vandenberg and Slinkard
(1989), pods (gene Grp green pod); and Emami (1996), pods (anthocyanin
developments gene Rdp)).

24.6.3 Leaflet Size, Shape, and Number

Mishra (2004) reported that the higher number of leaflets is dominant trait and
proposed gene symbol Hl. They also reported incomplete dominance of broad
leaflets (gene symbol Blf) over narrow leaflets. Leaflet size varies between
microsperma and macrosperma genotypes.

24.6.4 Plant Pubescence

Pubescent pod (gene symbol Glp) is dominant over the glabrous pod (Vandenberg
and Slinkard 1989). Kumar (2002) reported that plant pubescence is controlled by
single dominant gene (Pub).

24.6.5 Tendril

The genetics of inheritance of tendril in lentil was studied by Vandenberg and

Slinkard (1989). They reported that this trait is governed by single dominant gene
(Tnl).
24 Lentil Breeding 1191

24.6.6 Plant Height

Hadded et al. (2004) reported quantitative inheritance for plant height. Tahir and
Muehlbauer (1994) reported that tallness in lentil is dominant (Ph) over dwarfness.

24.6.7 Stem Fasciation

Stem fasciation is a recessive trait (Sharma and Sharma 1978).

24.6.8 Flowering Time

Sarker et al. (1999) reported that earliness is a recessive trait and proposed gene
symbol sn. Transgressive segregation in F2 is due to interaction of sn with minor
genes for earliness.

24.6.9 Flower Colour

The flower colour depends on colour of standard, wing, and keel. Lal and Srivastava
(1975) reported two genes for flower colour in lentil and suggested gene symbols
VVPP, VVpp, and vvPP for violet white and pink flower. Bluish flower colour in
lentil is governed by single dominant gene (Ladizinsky 1979). Red flower with gene
symbol P was dominant over the white flower (Kumar 2002; Mishra 2004).

24.6.10 Number of Flowers/Peduncle

The number of flowers/peduncle is an important trait influencing grain yield in lentil.

The trait is influenced by environment and declines with plant age. Gill and Malhotra
(1980) reported that flower number is monogenic trait and two flowered phenotypes
is dominant over three-flowered phenotype. However, the studies by Emami (1996)
and Kumar (2002) revealed that higher number of flowers/peduncles was dominant.

24.6.11 Pod Size

Pod size is related to seed size and is a variable trait in lentil. Kumar et al. (2005)
reported the monogenic inheritance of pod size with incomplete dominance.
1192 H. K. Dikshit et al.

24.6.12 Pod Dehiscence

Ladizinsky (1985) reported that pod dehiscence in L. culinaris ssp. orientalis is

governed by two complimentary genes.

24.6.13 Seed Size

Cultivated lentils based on seed size/weight are divided in microsperma and

macrosperma. Indian lentils are characterized as microsperma types with 100 seed
weight between 12 and 35 g. Ladizinsky (1979) studied microsperma  macrosperma
cross (L. orientalis  L. culinaris) and reported intermediate seed size in F1 and
continuous distribution in F2. Abbo and Ladizinsky (1991) reported quantitative
inheritance for this trait.

24.6.14 Seed Coat Colour

Different seed coat colours (black, grey, green, and brown) have been reported in
lentil. The inheritance of black seed coat colour in lentil was studied by Vandenberg
and Slinkard (1987). He reported one dominant gene with codominant expression.
However, Vandenberg and Slinkard (1990) reported two recessive genes for black
seed coat. Studies by Vaillancourt and Slinkard (1992), Emami (1996), Emami and
Sharma (2000), and Sharma et al. revealed monogenic inheritance. Emami and
Sharma (2000) proposed gene symbol Blt for this trait. The dominance of brown
testa over yellowish-grey testa was reported by Ladizinsky (1979). Slinkard et al.
(1990) reported digenic dominance of brown testa over green. Both grey and tan
testa were reported as dominant over green.

24.6.15 Tannins in Seed Coat

The inheritance of tannins in seed coat was studied by Vaillancourt et al. (1986).
They reported that the presence of tannins in seed coat was dominant trait. Bezeda
(1980) reported that the presence of tannins (proanthocyanidins) in seed coat causes
the discolouration of seed coat.

24.6.16 Seed Coat Spotting

The presence of spotting on seed coat is dominant over spotless seed coat
(Ladizinsky 1979; Vandenberg and Slinkard 1990; Emami 1996). Vandenberg and
Slinkard (1990) identified multiple alleles for spotting (Scp locus). They identified
two types of spotting: spotting (Scps) and dotted (Scpd). Later Emami (1996)
24 Lentil Breeding 1193

confirmed two types of seed coat (mottling-Mot and speckling-Spt) in lentil both
dominant over spotless.

24.6.17 Seed Hardness

Seed hardness in lentil is associated with poor water absorption. Ladizinsky (1985)
reported that hard seed coat is monogenically controlled in cross between L. ervoidis
and L. culinaris and proposed gene symbol Hsc. Vaillancourt and Slinkard (1992)
reported that seed hardness is a recessive trait in cross involving L. culinaris
orientalis and L. culinaris.

24.6.18 Cotyledon Colour

Microsperma types are called red lentils due to orange cotyledons, and macrosperma
types have yellow and green cotyledon. Cotyledon is sporophytic tissue and colour
can be recorded in freshly harvested seed. Hybridization of red and yellow
cotyledons (Tschermak-Seysenegg 1928; Wilson et al. 1970; Singh 1978; Slinkard
1978; Sinha et al. 1987; Emami 1996; Kumar 2002) revealed that orange is dominant
over yellow (Slinkard 1978 designated the gene as Yc). In addition to yellow
cotyledon colour, there is phenotype with brown or pink tinge called as brown.
Emami and Sharma (1996b) reported independent nature of Y and B. Double
dominant YB results in orange cotyledon and yybb results in greenish cotyledon
due to the absence of pigment. Emami (1996), Emami and Sharma (1999), and
Sharma and Emami (2002), identified another gene Dg controlling the cotyledon
colour.

24.6.19 Protein Content

Lentil is a rich source of dietary protein. The quantitative inheritance of protein

content was reported by Hamdi et al. (1991), Chauhan and Singh (1995), and Tyagi
and Sharma (1995). Seed protein content is negatively correlated with seed size.

24.7 Breeding Objectives

24.7.1 Breeding for Yield-Related Traits

24.7.1.1 Prebreeding for Broadening the Genetic Base

The genetic base of released cultivars in the Indian subcontinents is narrow.
Sustained use of few genotypes in hybridization programme is the main reason for
yield stagnation. Diverse Mediterranean germplasm and wild species is valuable
repository of useful genes not available in cultivated lentil. Under DAC-funded
1194 H. K. Dikshit et al.

ICARDA-ICAR project “Broadening the genetic base: Pre-breeding and genetic

enhancement in breaking yield barriers in kabuli chicpea and lentil”, Mediterranean
germplasm lines were evaluated and important donors were identified for different
traits (Table 24.3).

24.7.1.2 Breeding for Mechanised Harvesting

Manual harvesting of lentil is expensive and often adequate number of labourers is
not available for harvesting at crop maturity. Delay in harvesting results in shattering
of pods. The use of combined harvestor is hampered due to loss of pods because of
low plant height. New plant types with erect and non-lodging growth habit will suit
mechanical harvesting. ICARDA can facilitate the national research programmes by
providing non-lodging plant types with erect growth habit. For mechanical
harvesting, ground clearance of about 15 cm is required. ICARDA-developed lentil
variety Idlib is suited for machine harvesting (El-Ashkar et al. 2003).

24.7.1.3 Breeding for Herbicide Tolerance

Lentil production suffers parasitic and nonparasitic weeds. The non-parasitic weeds
cause yield loss up to 40% due to competition with crop for nutrient and light (Tepe
et al. 2005). The weeds are controlled by manual hand weeding. Manual weeding is
not cost effective and sometimes adequate labourers are not available for manual
weeding. Herbicide resistance is an alternative strategy to reduce the cost of produc-
tion. Herbicide-tolerant lentil varieties have earlier been developed in Canada and
Australia (Slinkard et al. 2007). In addition, these parasitic weeds like Orobanche
are major threat to lentil cultivation under conservation agriculture in the Mediterra-
nean region (Rubiales et al. 2006). Fernández-Aparicio et al. (2008, 2009) have
screened Lens germplasm for orobanche resistance.

24.7.1.4 Breeding for Nutrient Use Efficiency

Lentil is grown in marginal soils deficient in micronutrients. From India, Syria, and
Ethiopia, iron and boron deficiencies are reported. Fe deficiency in high pH soil
causes yield. Yield loss in susceptible genotypes of 25% and 47% has been reported
from India and Syria (Ali et al. 2000; Erskine et al. 1993). B deficiency is reported
from northern Bangladesh, eastern Terai plains of Nepal, and Eastern India.

24.7.1.5 Breeding for Early Maturity and Bold Seed Size

Several studies have been conducted to decipher the genetics of flowering time in
lentil (Tullu et al. 2008). A number of QTLs controlling flowering duration have
been reported in lentil by Tullu et al. (2008). Several short-duration lentil varieties
escaping terminal heat have been developed in Bangladesh (BARI M4, BARI M5,
BARI M6 and BARI M7, BARI M8 and BARI M9) and India (L 4717). L 4717 is
the first extra-early variety of lentil maturing in less than 100 days. Early maturing
lentil varieties with stemphylium blight resistance are required for rice fallow
cultivation in Eastern India.
Conventionally small-seeded types (100 seed weight 2.5 g/100 seed) are grown in
India. Small-seeded types have shown wider adaptability to different agroclimatic
24 Lentil Breeding 1195

Table 24.3 Donors for important traits identified from Mediterranean germplasm from ICARDA
Trait Donors identified Trait Donors identified
Drought ILL 10040, ILL 10044 Pods/cluster ILWL 15
tolerance
Heat ILL 10174, FLIP 2009-55 L, Short ILWL 17
tolerance IG 2507, IG 4258, IG 2503, IG internode
3101, IG 3563, IG 4079, IG
4098, IG 4312, IG 4380, IG
1539, LC 279–1296, LC
270–804, LC 284–1206
Salinity ILWL 297, ILWL 368, ILWL Higher ILWL 117, ILWL 398
resistance 371, ILWL 417, IG 136670 primary
branches
Fusarium ILWL 76, ILWL 79, ILWL High IL 10732, ILL 10733, ILL
wilt 37, ILWL 1, ILWL 138, ILL biomass 10734, ILWL 30
resistance 3492, ILL 4385, ILL 10956,
ILL 6449, ILL 4649, ILL
3796, ILL 2502, ILL 2505,
ILL 5714
Rust ILWL 15, ILWL 17, ILWL Large seed ILL 1005, ILL 4559, ILL
resistance 19, ILWL 30, ILWL 62, ILWL size 4637, ILL 4649, ILL 5488,
81, ILWL 97 ILL 5628, ILL 8072, ILL
8595, ILL 7946, ILL 7678,
ILL 7943, ILL 9890, ILL
10734, ILL 10736, ILL 10741,
IPLS -09-17, IPSL-09-23,
IPLS-09-33, IPLS-09-35, ILL
45113, ILL 45101
Powdery ILWL 55, ILWL 59, ILWL High grain ILWL 74, ILL 8095, ILL
mildew 334, ILWL 359, ILWL 450 Fe and Zn 7981, ILL 10854, ILL 10072,
resistance concentration ILL 88527, IG 135395, IG
135403
Root knot ILWL 18, ILWL 72 Early ILL 6002, ILL 7663, ILWL
nematode maturity 118, ILL 2585, ILL 4605, ILL
resistance 10848, LIRL-21-50-1-1-1-0,
LIRL-22-46-1-1-10, LIRL-22-
46-1-1-1-0, LIRL-22-46, ILL
45101, ILL 45107, IPLS-09-
17, IPLS-09-35
Unpublished data from DAC-funded ICARDA-ICAR project “Broadening the genetic base:
Pre-breeding and genetic enhancement in breaking yield barriers in kabuli chicpea and lentil”

conditions. In India, large-seeded types are confined to Central India, and small-
seeded types are preferred in eastern, northern, and northern hills. Seed size in lentil
is a quantitative trait controlled by several genes (Abbo and Ladizinsky 1991).
Fedoruk et al. (2013) and Verma et al. (2015) have identified QTLs controlling
seed size in lentil.
1196 H. K. Dikshit et al.

24.7.2 Diseases

24.7.2.1 Wilt
Fusarium wilt is most important disease of lentil caused by Fusarium oxysporum
Schlecht.:Fr. f. sp. lentis Vasudeva and Srinivasan. The disease is reported from
most of the lentil-producing regions. The symptoms of this disease are produced at
pre- and post-emergence stage. Browning of micropylar end occurs in infected
seeds. After seed germination, the radicle browning results in death of seedling.
Plant growth is reduced, leaves become yellow and curled, crown droops, and plant
dies. Roots become yellowish/dark brown. The wall of xylem vessel is discoloured/
turns brown due to the presence of fungal hyphae. Macroconidia, microconidia, and
chlamydospores are the asexual spores produced by the pathogen (Meena et al.
2017). Pathogen survives as dormant mycelium and chlamydospores on seed surface
or as systemic infection besides infected plant debris. Soil water holding capacity of
25% and soil temperature of 17–31  C favour the disease development (Khare
1981). Fusarium wilt occurs both at seedling and reproductive stage.
Screening for fusarium wilt in sick plot using infector row technique was
proposed by Bayaa et al. (1995) following a rating scale of 1–9. Limited wilt sick
plots are available for screening against wilt in lentil. Efforts have been made to
screen lentil varieties and germplasm for identification of donors. Kannaiyan and
Nene (1975, 1976) reported that LWS 14 and LWS 21 were immune to all 5 strains
of pathogen, and Pant 209, Pant 220, Pant 234, Pant 538, Pusa 3, Pusa 4, JL 80, and
UPL 175 also exhibited substantial resistance. Screening of 2000 lentil lines in field
and pots at Jabalpur led to identification of 11 resistant lines (LWS numbers 4, 6,
10, 14, 15, 20, 23, 24, 25, 26, and 50) exhibiting less than 5% wilt incidence (Khare
et al. 1979). Saxena and Khare 1988 reported that lentil varieties with shorter roots or
few secondary roots show low disease incidence. Kamboj et al. (1990) and Abbas
(1995) reported that inheritance of the resistance to vascular wilt is controlled by the
monogenic dominant gene, Fw. Eujayl et al. (1998) and Hamwieh et al. (2005)
identified molecular marker linked to wilt resistance gene in lentil.

24.7.2.2 Collar Rot

Collar rot in lentil is caused by Sclerotium rolfsii. Infection caused by pathogen at
collar region of plant results in yellowish-brown colouration and rotting of tissue.
Damping off symptoms are seen in younger seedlings. Fungus survives in soil in the
presence of organic matter. High soil moisture, high temperature, and sunshine after
rain favour the disease development. Seedlings are more susceptible as compared to
adult plants. Khare et al. (1979) screened lentil germplasm for resistance against
S. rolfsii in the field and under inoculated condition and reported LWS numbers 2, 4,
7, 9, 11, 12, 22, 35, 37, 40, 47, 51, 52, 53, 55, 59, 60, 61, 63, 66, and 74 to be
resistant. Resistance in Pusa 3, Pant 234, and JL80 was recorded by Kannainyan and
Nene (1976) and by Mohammad and Kumar (1986) in Pusa 1, LP 18, and Pant 638.
24 Lentil Breeding 1197

24.7.2.3 Root Rot

Root rot in lentil is caused by Rhizoctonia solani Kuhn (Shukla et al. 1972) and
Rhizoctonia bataticola (Taub) Butler (Khare et al. 1979). The typical symptoms
include change of foliage colour from dull green to reddish brown and then to
yellow. Roots show infection in all tissues except xylem. Roots are ashy brown
with minute sclerotia in the case of R. bataticola. R. solani isolated from field
exhibited yellowish brown to hyaline mycelia and sclerotia of about 2 mm, and
R. bataticola exhibited minute black sclerotia. This disease development is favoured
by high temperature.

24.7.2.4 Stem Rot

Stem rot in lentil is caused by Sclerotinia sclerotiorum (Lib.) de Bary. The disease is
favoured by high humidity during plant growth. The affected plant exhibits white
cottony fungal growth, and sometimes light-brown to dark-brown sclerotia are seen.

24.7.2.5 Rust
Rust is an important disease in lentil caused by autoecious fungus Uromyces fabae
(Pers) de Bary. Singh and Solanki (1980) reported six pathotypes of this fungus.
Initially the development of pycnidia and aecia is seen on the lower surface of
leaflets and pods. Later uredial pustules emerge on leaflets, stem, and pod. Pustules
are nearly 1 mm in size with oval to circular shape. Telia are produced on stem and
branches. Lentil rust occurs in the form of aecia and pycnidia. At a low temperature
of 17–22  C, aeciospores germinate forming secondary aecia or uredia. A Tempera-
ture range of 20–22  C, high humidity, and cloudy weather favour disease develop-
ment. From urediniospores, telia develop. Teliospores survive in soil in the form of
broken leaves and stem and are the source of basic inoculum. Teliospores germinate
at 17–22  C. Nene et al. (1975) reported rust resistance in improved varieties
(L 9–12, T 36, and Bombay 18), germplasm lines (LP 846, UPL 172, UPL
175, and BC 10) and both wilt and rust resistance in JL 599, JL 632, JL 674, and
JL 1005. Agrawal et al. (1976) identified JL 599, 632, 674, and 1005 as resistant
sources. Pandey (1981) identified Pant L 236 as resistant and Pant L 406 as
susceptible. Khare and Agrawal (1978) reported T 36, BR 25, Pusa 10, and UPL
175 and 22 other germplasm lines free from rust. Sinha and Yadav (1989) and Singh
and Singh (1990) reported single dominant gene for rust resistance in lentil.

24.7.2.6 Powdery Mildew

Powdery mildew caused by Erysiphe polygoni DC was first reported from Rajasthan
by Sankla et al. (1967). Plants can be attacked by powdery mildew at any stage but
symptoms are often seen at flowering stage. Initially small white powdery patches
appear on lower leaves and later they become amphigenous. Mishra (1973) reported
resistance to powdery mildew in five lentil lines 10,511, 10,526, 10,528, 10,536, and
10,537.
1198 H. K. Dikshit et al.

24.7.2.7 Ascochyta Blight

Ascochyta blight in lentil is caused by Ascochyta lentis (Kulshrestha and
Vallabhacharyulu 1985). Ascochyta sp. has been detected in lentil seeds imported
from the USA and Syria (Lambet et al. 1985).

24.7.2.8 Stemphylium Blight

Stemphylium blight in lentil is caused by Stemphylium botryosum Waltr. Initially
this disease emerged in West Bengal, and now it is spreading in Indo-Gangetic plains
and even up to Himachal Pradesh. In South Asia, a temperature of 18–22  C and
relative humidity of over 85% favour disease development (Erskine and Sarker
1997). Das et al. (2017) screened lentil germplasm at two locations and reported
immunity in P 3235, LL 1122, and ILL 10832.

24.7.2.9 Nematodes
Root knot (Meloidogyne sp.) nematode is an economically important pest of lentil.
Symptoms include yellowish plant with stunted growth and irregular swelling of
roots. The root knot nematodes of lentil were classified as Meloidogyne incognita
(Mishra and Gaur 1980) and Meloidogyne javanica (Prakash 1981).

24.7.3 Insects Pests

24.7.3.1 Black Aphids

Aphis craccivora Koch is a threatening pest worldwide. Aphids deplete assimilates
and increases respiration rate of plant (van Emden 1973). Lentils are prone to aphid
damage at seedling, flowering, and podding stage. Severe insect infestation causes
stunting and deformation of leaves and shoot and black mould grows on plant on
honey dew deposits of insect. Dry weather favours multiplication and spread of
aphids.

24.7.3.2 Pea Pod Borer

Etiella zinckenella (Treit.) is an important pest damaging 5–15% of pods (DPR
1988). Young larvae feed on flowers and young pods. Older pods with brown spot
can be identified as infested pod. Seeds are consumed by borer and fross and silk can
be seen in damaged pods.

24.7.3.3 Bruchids
Three bruchid species – Callosobruchus chinensis, C. analis, and Bruchidius
minutus F. Lentil seed inpods are attacked by the insects in the field. Eggs are
glued to seeds/pods or lie loose. The preharvest oviposition on pod is an important
source of infestation in storage. Bruchid-infested lentil seeds are not suitable for
consumption and lose germinability.
24 Lentil Breeding 1199

24.7.4 Abiotic Stress

24.7.4.1 Heat Tolerance

Lentil is a sensitive crop to the rising temperature (Choudhury et al. 2012; Bhandari
et al. 2016; Sehgal et al. 2017), and its growth and development is hindered due to
high temperature. At various stages, temperature requirement varies, and it ranges
from 18 to 30  C, and cooler temperature is required at vegetative stage, while
warmer temperatures are needed at the time of maturity (Choudhury et al. 2012).
Under the changing climatic scenario, the length of heat period has been increased in
comparison to chilling period. Some of the responses of plants exposed to heat stress
are sterility of pollen grain and flower drop crops, which are exposed to increasing
temperature stress specifically at reproductive stage (Hasanuzzaman et al. 2013).
The maximum temperature and above 32/20  C (the ratio represents max/min
temperature) at flowering and pod filling stage in lentil can sharply deteriorate the
quality of the grain and also reduce the grain yield (Delahunty et al. 2015).
According to the reports, heat waves (35  C) consecutively for 6 days have a
repercussion on lentil yield, which results in 70% reduction across southeastern
Australia (Delahunty et al. 2015). Heat stress during germination decreases the
germination rate in lentil (Covell et al. 1986). The consequence of heat stress is
reduction in percentage of germination, abnormal growth of seedlings, degeneration
of nodules, loss in cell membrane stability, reduction in plant biomass, early
flowering, increase in lipid peroxidation, and reduction in photosynthetic efficiency
(Ellis and Barrett 1994; Muehlbauer et al. 2006; Chakraborty and Pradhan 2010;
Sehgal et al. 2017).
Studies in lentil report that genotypes tolerant to heat stress exhibit superiority in
functionality of pollen and enhanced level of antioxidants (Sita et al. 2017a, b) and
reduced reproductive period, reduced seed set, pod abortion, and forced maturity
(Gaur et al. 2014; Bhandari et al. 2016). The genetic variability for heat tolerance has
been reported in few studies; however limited studies have been performed for
screening of lentil genotypes for heat tolerance (Gupta et al. 2019).

Screening System for Heat Stress

Screening of lentil genotypes for heat stress can be done by growing them in late
sown conditions so that the temperature at reproductive stage is above 35  C
(Delahunty et al. 2015; Kumar et al. 2016a, b; Sita et al. 2017a, b; Singh et al.
2019b). However screening under field condition is extremely difficult, and hence
precise phenotyping techniques (phenomics) can be employed for evaluating
heat-tolerant traits in the field (Basu et al. 2015). Lentil genotypes have been
evaluated for traits such as rate of photosynthesis, pollen viability, and membrane
stability with high precision laboratory techniques (Kumar et al. 2018a, b). Heat-
tolerant genotype has been also identified by evaluating the genotypes in laboratory
and hydroponics conditions under high-temperature conditions (Roy et al. 2011).
However, the best practice for identifying heat-tolerant genotypes is to combine
the screening under field and controlled conditions as merely screening under
controlled condition would not reproduce similar results in field condition. Some
1200 H. K. Dikshit et al.

other researchers followed different method wherein plants were grown in pots in
field conditions and later on at flower initiation stage transferred into controlled
conditions to expose it to suitable temperature during anthesis (Chen et al. 2019; Sita
et al. 2017a, b).

Donors
The donors for the heat tolerance have been discovered in a wide range of studies IG
3263, IG 3745, IG 2507, IG4258, and FLIP 2009 (Kumar et al. 2016a, b; Sita et al.
2017a, b). Rajendran et al. (2020) screened the FIGS set of lentil germplasm for
tolerance to terminal heat and combined heat stress tolerance at two locations,
namely, Marchouch and Tessaout, in Morocco. Accession ILL 7835 was identified
as a good source of stable tolerance to heat stress and combined heat-drought stress
at both locations (Rajendran et al. 2020). However, there is a need to use these
donors in a breeding program, which is otherwise still limited so far. Simple
monogenic inheritance has been reported for pod setting and seedling survival in
heat stress environment in lentil. However more research is required to confirm the
inheritance of heat tolerance in lentil.

24.7.4.2 Cold Tolerance

Lentils exhibit sensitivity to frost as all the legumes (Murray et al. 1988). Exposure
to frost stress in the early stages of plant growth leads to instant recovery from
underground axillary bud, but if plant gets exposed to frost at maturity stage, then it
results in ceasing of initiation of axillary buds and further restricts the plant to go
further to reproductive stage and consequently to the death of the plant. In lentil,
frost stress hinders the flower initiation and pod development, injures the vegetative
tissue, damages seed coat and leaf (Gupta et al. 2019), and hence impedes the overall
development of seed. Maximum injury due to frost occurs at flowering stage due to
exposure of flowers to frost. Plant exposed to frost continuously becomes susceptible
to disease such as anthracnose botrytis grey mould and pest infestation (Gupta et al.
2019). Frost tolerance in lentil has been characterized in lentil (Erskine et al. 1981;
Summerfield et al. 1985; Murray et al. 1988; Spaeth and Muehlbauer 1991;
Kusmenoglu and Aydin 1995; Ali and Johnson 1999). In some of the recent studies,
frost injury and winter hardiness have been studied in lentil (Kahraman et al. 2004;
Barrios et al. 2007, 2010, 2016).

Donor
The characterization of lentil genotypes for cold tolerance identified genotypes
WA8649041 (Barrios et al. 2017) and WA8649090, ILL-1878, and ILL-669
(Kahraman et al. 2004). Hamdi and Erskine (1996) evaluated lentil accessions for
winter hardiness and reported that L. culinaris ssp. orientalis LC9978057,
LC9977006, Kafcas, Cifei, ILL1878, ILL4400, ILL7155, LC9977116,
LC9978013, ILL759, ILL8146, ILL8611, ILL9832, and Ubek as frost/cold tolerant.
Some of the tolerant genotypes LL1878, ILL662, ILL857, ILL975, ILL1878 (Sarker
et al. 2002), and ILL5865, Balochistan local (Ali and Johnson 1999), have been
reported by the researchers.
24 Lentil Breeding 1201

Genetics
The inheritance of radiation frost tolerance has been suggested to be monogenic in
lentil (Eujayl et al. 1999). In another study, inheritance for winter hardiness has been
reported to be controlled by quantitative traits (Kahraman et al. 2004).

24.7.4.3 Drought Tolerance

Lentil can be grown in dry regions and among all the legumes it exhibits moderate
tolerance (Abraham 2015). It requires minimal water for its growth and develop-
ment, but the productivity gets impeded by variable annual rainfall which magnifies
the incidence of prolonged drought periods (Dai 2011). Drought stress also affects
the metabolism, osmoregulation, and concentration of photosynthetic pigments, in
lentil (Gökçay 2012; Muscolo et al. 2014; Mishra et al. 2016; Biju et al. 2017). The
impact of drought stress varies at different stages of crop development (Shrestha
et al. 2006; Allahmoradi et al. 2013). Drought stress occurring at flowering or
podding stage affects vegetative and reproductive growth leading to reduced leaf
area (48–55%), flower production (22–55%), number of pods and seeds (27–66%),
and total dry matter (32–50%) with significantly higher abortion of pods and flower
drop and aborted pods (Shrestha et al. 2006).
Drought avoidance and tolerance are the two mechanisms involved in lentil for
combating drought stress. Traits related to root are the important components of
drought avoidance mechanism (Idrissi et al. 2016; Biju et al. 2017), and selection for
root-related traits provides drought tolerance to the crop and further improves the
production and productivity of the crop (Gahoonia et al. 2005; Chen et al. 2015).
Drought tolerance in wild lentil species has been evaluated by analysing root-related
traits to understand the underlying mechanism of drought (Gorim and Vandenberg
2017a). In lentil, early-maturing varieties (Precoz, Bakaria, BARI M4, BARIM5,
BARI M6, and Idlib 3) show adaptation to drought stress and reflect drought
avoidance (Erskine et al. 1994; Shrestha et al. 2005).
Above ground level, some of the traits such as early or delayed flowering and
pubescence play a key role in shielding plants exposed to water-deficient conditions.
Singh et al. (2014b) exhibited the association of agro-morphological traits with
drought tolerance. To breed for traits for drought tolerance, two strategies can be
applied: short-term strategy for assessing the genetic variability for drought tolerance
in lentil germplasm and long-term strategy to introgress desirable traits from wild
species to the cultivated one.

Screening System for Drought Stress

Osmotic adjustment (increase in solute concentration in cell) for maintaining turgor
at low water potential (Kumar and Elston 1992) has been reported as an adaptation to
drought. Osmotic adjustment has been reported to enhance in yield of field crop by
maintaining the turgor pressure (Munns 2002; Morgan and Condon 1986; Passioura
1986). Estimation of drought tolerance can be also carried out by evaluating traits
like relative water content (Sinclair and Ludlow 1985; Schonfeld et al. 1988),
stomatal conductance (Terzi et al. 2010), seedling vigour, and water use efficiency
(WUE) (Nagarajan and Rane 2000; Dhanda et al. 2004). Screening methods based
1202 H. K. Dikshit et al.

on biochemical, morphological, and physiological traits have been reported by Hura

et al. (2009) under soil condition. In lentil, rapid screening method was reported by
Singh et al. (2013b). Screening for dehydration avoidance can be done by character-
ization of root and shoot attributes at seedling development and plant growth stages
(Kumar et al. 2012).
Morphological and physiological parameters related to root (depth, length, and
density), shoot (rapid ground cover, early growth vigour), and leaf characteristics are
related to drought tolerance and assist in maintaining the transpiration demand of
plant (Passioura 1981). Root attribute traits, for instance, highly branched roots,
strengthen the capacity of absorption of nutrient and water from the soil (Gahoonia
et al. 2005, 2006). However, limited studies were performed to characterize legume
root system, and in lentil, few researchers reported their work on root and shoot
attributes (Sarker et al. 2005; Gahoonia et al. 2005).

Donors
Lentil genotypes IPL 98/193, DPL 53, and JL 1 have been identified with excellent
root parameters which give these genotypes the ability to sustain in drought envi-
ronment (Kumar et al. 2012). Some genotypes with greater drought escape mecha-
nism (ILL7618, ILL9921, ILL7981, ILL9830, ILL9922, ILL9844, ILL9850,
ILL9920, ILL6024, ILL7504, ILL8095, ILL8138, ILL8621, and ILL9923) have
been reported at ICARDA (Malhotra et al. 2004). Wild species have adapted to a
broad range of environments and developed rich genetic diversities for drought
tolerances. Hamdi and Erskine (1996) exhibited that wild Lens species have greater
tolerance to drought. The primary strategies identified for drought stress are escape,
avoidance, and tolerance, and screening of cultivated (Lens culinaris Eston) and wild
lentils (Lens odemensis IG 72623, both L. erv. Genotypes (IG 72815 and
L-01-827A), Lens lamottei IG 110813, L. ori. PI 572376, L. ori. PI 572376,
L. ori. IG 72643, and L. erv. L-01-827A) identified accessions tolerant to drought
stress (Gorim and Vandenberg 2017b; Fang and Xiong 2015). In a recent study,
Rajendran et al. (2020) identified accession ILL 7835 as a good source of stable
tolerance to combined heat-drought stress at different environments in Morocco.

Genetics
Simple inheritance of drought tolerance (Morgan 1991; Monneveux and Belhassen
1996; Tomar and Kumar 2004) has been reported by several researchers, and few
studies also demonstrated complex inheritance (Ekanayake et al. 1985) for the trait.

24.7.4.4 Flooding and Submergence Tolerance

Submergence and flooding drastically affect the yield of legume crops (Solaiman
et al. 2007; Kang et al. 2017). Lentil cannot withstand flooding or waterlogging; the
production is hindered specifically in poor drainage and fine-textured soil or in
conditions of persistent extreme rainfall (Wiraguna et al. 2017). The amount of
injury occurred is dependent on its severity and growth stages and duration of the
stress, and it further causes absolute loss of crop in the severely affected conditions
(Toker et al. 2011). Waterlogging will affect all the development stages in lentil and
24 Lentil Breeding 1203

subsequently reduce the yield (Materne and Siddique 2009). At germination stage, it
delays the seed germination, and hence leads to suppression in the root growth and
development (Jayasundara et al. 1997), and transient waterlogging is a major
impediment for production of lentil, specifically in early vegetative growth stages
(Materne and Siddique 2009). At flowering stage, waterlogging causes abortion of
pods and flowers and restricts the pod filling, which is referred to as the most
sensitive stage in waterlogging. The plant exhibits variable symptoms such as leaf
senescence and stunted growth, and the plant withers, ultimately causing death of the
plant.

Screening for Flooding and Submergence Tolerance

Waterlogging-tolerant genotypes were identified by its high root porosity, low
biomass, higher stomatal conductivity, early flowering, and maturity (Ashraf and
Chishti 1993; Malik et al. 2015; Erskine et al. 2016). The adverse effect of
waterlogging in lentil can be managed by applying few management practices
such as drainage, paddock selection, seeding rate, and time of sowing (Toker and
Mutlu 2011). Selections for adventitious root growth and more aerenchyma have
been suggested as possible solutions for increased tolerance to flooding (Materne
and Siddique 2009; Jayasundara et al. 1997). Screening of lentil germplasm against
waterlogging tolerance has been studied by Wiraguna et al. (2017), and results
exhibited that genotypes from Bangladesh are more adapted to waterlogged soil at
germination. In rice and Arabidopsis, flooding stress and its subsequent derivatives
like waterlogging, hypoxia, submergence, and anoxia were studied exhaustively, but
in lentil, it is still required to do more research in order to understand the underlying
molecular mechanism related to flooding or submergence tolerance.

Donor
Genotypes identified for the waterlogging tolerance in several studies are ILL6439,
ILL6778, and ILL6793 (Ashraf and Chishti 1993), Nugget (Malik et al. 2015), and
BINAmasur1 (Islam et al. 2009) and can be utilized in future breeding program for
development of tolerant genotypes.

24.7.4.5 Salinity Tolerance

Lentil roots are extremely sensitive to the salinity stress, which results in arresting
the root growth and restricting the rhizobium infection (Rai and Singh 1999; Van
Hoorn et al. 2001). The effect of salinity on different stages of plant growth and
development varies according to the growth stages (Munns and Tester 2008).
Germination stage is less sensitive than the early stages of vegetative growth, and
the most critical stage sensitive to salinity is reproductive stage (Vadez et al. 2007;
Sakina et al. 2016). The response towards stress also varies with the level of salinity,
available nutrients, relative humidity, soil-water status, and temperature (Lachaâl
et al. 2002). Salinity stress involves changes in plant’s metabolic, biochemical, and
the physiological mechanisms such as photosynthesis (AL-Quraan et al. 2014),
γ-Aminobutyric acid (GABA) accumulation (Al-Quraan and Al-Omari 2017), oxi-
dative and membrane damage, ion homeostasis, osmolyte accumulation, and proline
1204 H. K. Dikshit et al.

metabolism (Hossain et al. 2017) depend upon the intensity of the stress and
eventually inhibit crop growth. In lentil, salinity stress results in reduction in
flowering and pod setting and anthocyanin pigmentation in stems and leaves (Van
Hoorn et al. 2001); reduces total biomass, plant height, and biochemical and
enzymatic activity; and further reduces grain yield by 90 to 100% (3 dS/m) and
20% (2 dS/m) at variable electrical conductivity (Tewari and Singh 1991; Van
Hoorn et al. 2001; Ghassemi-Golezani and Mahmoodi-Yengabad 2012). Strategies
need to be evolved to overcome the yield loss due to salinity with the emphasis on
management of soil and water in the salinity-affected regions, but amelioration
processes are very expensive, and more cost-effective methods need to be identified.
Therefore, developing an effective breeding program for the development of salinity
stress varieties is the most effective and sustainable strategy, for stabilizing and
improving yield in salinity-affected areas.

Screening System for Salinity Tolerance

In general, field and hydroponic screening methods are in practice for salinity stress.
But due to lack of homogeneity in the environment and soil conditions, it is difficult
to perform screening in field conditions, and it can be resolved by screening in
hydroponic system. Traits such as reduction in seedling growth; germination; visual
salt injury; biomass accumulation; seedling survival; proline and antioxidant
activities; Na+, Cl, and K+ contents, and hydrogen peroxide (H2O2) production
have been studied by various researchers for the evaluation of salinity tolerance in
lentil and other crops (Singh et al. 2019b). Recently, an image-based screening
method has been developed by Dissanayake et al. (2020) to screen lentil genotypes
for salinity tolerance.

Donor
The genotypes reported for salinity tolerance are PDL-1 and PSL9 (Singh et al.
2019b) SAPNA, RLG-258 and RLG-234 (Kumawat et al. 2017), PDL1, PSL9,
ILWL95, Jordan 1 (Al-Quraan and Al-Omari (2017), Flash (CIPAL0411), Bounty
(CIPAL0415), Nipper (CIPAL0203) (GRDC, 2013), Masoor2002, NL20–3-3,
LN0188, M93, NL9775 (Aslam et al. 2017), Siliana, Local oueslatia, Nefza (Ouji
et al. 2015), Nipper, PBA Flash, ILL2024 (Siddique et al. 2013), Çagıl, AltınToprak
(Kokten et al. 2010), Ustica, Pantelleria (Sidari et al. 2007), DL443, Pant L406,
ILL3534 LG 128, ILL6796 (Materne and Reddy 2007). Crop wild relatives ILWL
368, ILWL 297, ILWL 371, IG 136670, and ILWL 417 of L. culinaris ssp. orientalis
(DAC-ICAR-ICARDA, Annual Progress Report, 2014) were identified as the salt-
tolerant genotypes in various studies for introducing the novel allelic diversity in
breeding programmes.

Genetics
In lentil also, monogenic inheritance was reported by Singh et al. (2019b). Inheri-
tance of traits associated with salinity tolerance has been studied in chickpea,
soybean, and pigeonpea. These traits showed monogenic inheritance pattern and
mapped major QTLs associated with the salt tolerance (Abel 1969; Shao 1994; Lee
24 Lentil Breeding 1205

et al. 2007; Hamwieh and Xu 2008; Hamwieh et al. 2011; Liu et al. 2016; Guan et al.
2014).

24.8 Nutritional Quality of Lentil

24.8.1 Protein and Amino Acid Content in Lentil

Lentil grains are excellent sources of high-quality protein. The average protein
concentration in lentil grain is around 26% crude protein. Lentil protein is comprised
of 70% globulins, 16% albumins, 11% glutelins, and 3% prolamins (Boye et al.
2010). There is extensive variation in the protein content in lentil seeds as suggested
by many studies. One of the primary studies for the protein content in lentil varieties
was performed by Barulina (1930) which exhibited a variation from 27.5% to 31.7%
in lentil varieties (Barulina 1930). The lentil global germplasm was evaluated for
protein content by Hawtin et al. (1978), and it showed broader variation in the
protein content which varies from 23.4% to 36.4% among the 1688 accessions of
lentil.
The variation is also reported by Hamdi et al. (1991) and Kumar et al. (2016a, b).
Cultivated lentils are rich in amino acids like arginine, aspartic and glutamic acids,
and leucine, and they are low in some of the essential amino acids such as trypto-
phan, threonine, phenylalanine, histidine, methionine, isoleucine, valine, and leucine
except lysine, while they have inadequate level of sulphur-containing amino acids
like methionine and cysteine (WHO 2007). As compared to the animal-based
protein, lentil proteins are low in methionine (0.9%) (Van Vliet et al. 2015).
Anabolic properties of diet based on plants can be balanced by combining
cereals and legumes, as cereals are higher in methionine and lower in lysine and
legumes are lower in methionine and higher in lysine (Van Vliet et al. 2015). Some
of the important non–amino acid proteins in lentil seeds are trigonelline (Rozan et al.
2001), erythro-γ-hydroxyarginine 2(S), 4(R)-4-hydroxyarginine γ-hydroxyarginine,
γ-hydroxyornithine, and homoarginine (Sulser and Sager 1976). Grusak (2009)
reviewed the nutritional quality of lentil and reported the protein content range of
15.9 to 31.4%.

24.8.2 Folates/Vitamin B9

The insufficient folate intake affects millions of people globally (De Benoist 2008).
Inadequate intake of folic acid drastically affects pregnancy and raises the risks of
preterm delivery, foetal growth retardation, low birth weight of newborn, and
developmental neural tube defects (NTDs). Low intake of folate along with the
increase in the level of homocysteine levels is closely linked with the occurrence of
cardiovascular diseases, neurodegenerative disorders, and a range of cancers, while
proper intake of folates and folic acid in diets reduces total homocysteine levels in
plasma (Blancquaert et al. 2010). Staple crops such as rice, potato, maize, and
1206 H. K. Dikshit et al.

plantain are low in folate (USDA-ARS, 2012), while legume crops such as lentil
(Lens culinaris L.) and common beans (Phaseolus vulgaris L.) are rich in folates
(Singh 2018). Lentil is a rich source of folate, and according to a study, lentil has a
folate concentration of 255 μg/100 g (on average) which makes it a whole food
source of folates (Sen Gupta et al. 2013).
Moreover, it has been also revealed that lentil has higher folate concentration in
comparison to green field pea, yellow field pea, and chickpea. Rychlik et al. (2007)
also reported variability in the folate concentration of green lentils (110–154 μg/
100 g). The recommended dose of folate for adult is 400 mg, while for pregnant
women, it is much higher around 600 mg (Institute of Medicine, Food and Nutrition
Board, 1998). Serving of 100 g lentil provides 54–73% of folate RDA (Thavarajah
et al. 2008). Characterization of wild species and cultivated lentil quantifies eight
folate monoglutamates, and higher folate concentration in wild lentil species
(195–497 μg/100 g) has been reported than cultivated genotypes (174–361 μg/
100 g) (Zhang et al. 2019). Several studies on lentil and other pulses reported
5-formyltetrahydrofolate (5-FTHF), 5-methyltetrahydrofolate (5-MTHF), and
tetrahydrofolate (THF) as the most prominent folate (Jha et al. 2015; 2020;
Fernandez-Orozco et al. 2013). Along with this, several studies have also revealed
the predominance of 5-MTHF in lentils (Hefni et al. 2010; Rychlik et al. 2007).

24.8.3 Prebiotic Carbohydrates

Prebiotic carbohydrates are the form of complex carbohydrates with poor digestibil-
ity in upper portion of the gastrointestinal tract. They play a major role in stimulation
of health-promoting bacteria. Lentil is rich in prebiotic carbohydrates (Bhatty 1988;
Johnson et al. 2013) and has showed significant variation for prebiotic carbohydrates
(Chung et al. 2009; Tahir et al. 2011; Johnson et al. 2013). Lentils are low in mono-
and disaccharides and oligosaccharides, and starch is the main polysaccharide in
lentil. Resistant starch value of 3.7 g/100 g dry matter of lentil was reported by De
Almeida Costa et al. (2006).
Lentil starch is digested slowly releasing glucose. Lentil has low glycemic index
among food crops (Jenkins et al. 2012). The average concentration of prebiotic
carbohydrates in lentil has been reported around 7,500 mg of resistance starch (RS),
4071 mg of raffinose family oligosaccharides (RFOs), 62 mg of
fructooligosaccharides (FOSs), and 1423 mg of sugar alcohols (SAs) per 100 g
(Johnson et al. 2013). Siva et al. (2019) analysed the simple sugar content in lentil
and revealed that the maximum concentration is of sucrose, followed by glucose,
fructose, mannose, and rhamnose. The concentration of stachyose was the maximum
followed by verbascose and raffinose in RFOs, while in SAs the highest concentra-
tion is of sorbitol followed by mannitol and xylitol. Considering lentil FOSs, kestose
levels were higher than nystose levels. Other prebiotic carbohydrates present were
arabinose, xylose, and cellulose. The concentration of lentil prebiotic carbohydrate
also varies by the growth environment (Johnson et al. 2015).
24 Lentil Breeding 1207

24.8.4 Phenols

Dietary phenolics include polyphenols, phenolic acids, and flavonoids. Of the total
dietary intake, phenolic acids account for about one-third, and the remaining
two-thirds is accounted by flavonoids (Scalbert and Williamson 2000). The antioxi-
dant activities of phenolic compounds and their potential use in processed food as
natural antioxidants have attracted the attention of researchers (Gupta et al. 2021b).
Twenty lentil cultivars have been evaluated and revealed that the major phenolic
compounds in lentil are flavonoids, which includes catechin/epicatechin glucosides,
kaempferol glycosides, and procyanidins (Zhang et al. 2015). The phenolic compo-
sition varies with differentiation in seed coat colours of lentils (Mirali et al. 2017;
Gupta et al. 2018). The total polyphenol content in Canadian lentils ranges from 1.22
to 7.45 mg/g and has exhibited positive correlation with antioxidant activity (Padhi
et al. 2017). The total phenolic content of lentil hulls was reported to be 3 to 8 times
higher in comparison to the whole lentil seeds (Oomah et al. 2011), and hulls have
more diverse phenolic composition than the cotyledon. In lentil seed coat, 43 pheno-
lic compounds have been reported including three anthocyanidins, four
proanthocyanidins, six flavones, one stilbene, one phenolic acid, two flavanones,
seven flavanols, and 15 flavonols (Mirali et al. 2014, 2017). Lentil microgreens are
also found as the rich sources of antioxidants including minerals (Priti et al. 2021).

24.8.5 Micronutrients

A number of studies have been conducted for the estimation of micronutrients in a

wide set of cultivated lentil gemplasms (Gupta et al. 2021a, b; Kumar et al. 2019).
However, significantly low efforts have been done to discover the wild relatives with
high concentration of micronutrients and vitamins. The study conducted by Sen
Gupta et al. (2016) reported wide variability of micronutrient concentrations in
L. lamottei (Fe ¼ 64–80, Zn ¼ 26–40, Ca ¼ 311–434, Cu ¼ 2–6, Mg ¼ 754–839-
mg kg1), L. nigricans (60–70, 33–39, 508–590, 3–4, 445–738 mg kg1), and
L. ervoides (65, 37, 339, 6, 638 mg kg1). One of the recent studies reported
150 ppm Fe in a wild accession of L. orientalis, ILWL 118, and this accession is
being broadly employed in pre-breeding programs (Sarker et al. 2016). Ninety-six
wild accessions were analysed to determine its biofortification potential (Kumar
et al. 2018a, b). Significant variation was observed in species for various mineral
concentrations. L. culinaris ssp. odemensis, L. culinaris ssp. orientalis, and L.
ervoides showed extensive variability for Fe, Zn, Mo, Cu, and Mn, L. ervoides
and L. culinaris ssp. orientalis for Mg content, L. nigricans and L. culinaris ssp.
orientalis for Ca content. This may be occurred due to diverse genetic makeup of
these species or may be due to the sound expression of respective genes of particular
species under given environmental conditions.
However, L. culinaris ssp. culinaris had the minimum variability for some of the
minerals as it is a cultivated species. Significant variability for Zn concentration was
reported in lentils (36.7–50.6 mg kg1) (Ray et al. 2014), and the effect of genotype
1208 H. K. Dikshit et al.

Fig. 24.2 L 4717: An extra-

early and biofortified variety
of lentil from India

and environment interaction has been also observed (Khazaei et al. 2017;
Vandemark et al. 2018). Selenium concentration in lentil has been also evaluated
in lentil grown in dark-brown and brown soil of Western Canada, and high concen-
tration of Se (425–672 μg kg1) has been observed (Thavarajah et al. 2008). In
another study, lentils grown in six major lentil-producing countries, Syria
(22 μg kg1), Northwestern USA (26 μg kg1), Morocco (28 μg kg1), Turkey
(47 μg kg1), Southern Australia (148 μg kg1), and Nepal (180 μg kg1) and had a
significantly less concentration of selenium (Thavarajah et al. 2011). Recent study
by Bansal et al. (2021) indicates that biofortified variety tolerates heavy metal
(Cadmium) stress in soil. Recently two biofortified lentil varieties L 4717 and IPL
220 were released from Indian programme. L 4717 is extra-early lentil variety
maturing in 100 days (Fig. 24.2).

24.9 Emerging Challenges at National and International Level

24.9.1 Climate Change

The average global temperature rose by 0.74  C during the last century but is
expected to increase by 2.6–4.8  C by the end of the twenty-first century (Leisner
2020). Climate changes may affect the global food and nutritional security. The
impact of climate change on productivity, biotic and abiotic stresses, and nutritional
quality requires the attention of researchers.

24.9.2 Nutritional Quality Improvement

Lentils are low in saturated fat and sodium and are rich in folate, fibre, potassium,
and polyphenols. Lentil is low in glycemic index due to slow-digesting resistant
starch. Lentils are valuable sources of prebiotics. There is increasing interest in
24 Lentil Breeding 1209

legume protein for environmental sustainability and nutritional security. Lentil

lowers BP, cholesterol, and blood sugar (Ganesan and Xu 2017; Hanson et al. 2014).

24.9.3 Mechanical Harvesting

Mechanical harvesting is important for reducing the cost of production of lentil.

Scarcity of labourers at maturity sometimes causes shattering losses. For mechanical
harvesting, tall, erect, non-lodging plants with pod set of 10 cm above ground are
required. Such plant types ensure both good straw and seed yield. Erskine et al.
(1991) compared hand harvesting with cutting by mower and cutting with angled
blades. Both mechanical harvest methods resulted in harvest loss as compared to
hand harvesting. Grain yield loss was about 8.6% and straw loss was 16.6%. Labour
harvest cost compensated loss due to mechanical harvest. Sidahmed and Jaber
(2004) developed a experimental harvester for harvesting lentil. Mechanical
harvestor harvests lentil 5.9 cm above ground at 22% moisture with 20% straw
loss and 2% seed loss as reported by Sidahmed and Jaber (2004). Jawad et al. (2019)
evaluated 36 genotypes for mechanical harvesting. Two genotypes from ICARDA
nurseries 09S 83,184–10 and 2009S 96,518–1 were found superior. These can be
used to improve the existing cultivars. In the Mediterranean region and Canada,
lentil varieties are harvested using combined methods. Efforts are being made to
develop suitable varieties for South Asia. In the recent year, ICARDA has developed
a breeding material suitable for mechanical harvest and is providing this material to
national programmes.

24.9.4 Herbicide Tolerance

Lentil was recently introduced in Australia and Canada. Lack of registered and safe
post-emergence weedicide is major bottleneck in controlling the weeds. Attempts
were made to utilize metribuzin (aminotriazinone) as option for weed control.
Metribuzin is a broad-spectrum weedicide used for grasses and broad leafed
weeds. Mutant lines exhibiting herbicide tolerance to metribuzin were reported in
Australia and Canada. Very low mutation rate of 9.4  10–8 was recorded. Devel-
opment of lentil cultivars with metribuzin tolerance would ensure crop safety and
reduce crop phytotoxicity providing option of controlling broad leafed weeds.
1210 H. K. Dikshit et al.

24.10 Breeding Approaches (Conventional

and Non-conventional)

24.10.1 Conventional Breeding

The first lentil collection was made by N.I. Vavilov and his colleagues working at the
All-Union Institute of Agricultural Sciences in Leningrad, USSR, in 1920–1930.
Vavilov’s wife, Elena Barulina, led the programme on collection and characterized
the diversity of cultivated and Lens species. The collection made in Europe saved the
genetic variability. N.I. Vavilov Research Institute of Plant Industry, the first gene
bank, retains large Lens collections. At global level, lentil breeding received atten-
tion with the establishment of ICARDA at Aleppo, Syria, in 1977. Collection of
cultivated and wild species and their ex situ conservation was the top priority. The
Crop Trust supports this international collection in the form of in-perpetuity grant.
ICARDA has established gene bank, above the Arctic Circle in the Svalbard Global
Seed Vault. As the lentil demand increased, this crop entered new areas like
Australia and Canada. Breeder in these countries used both wild and cultivated
lentils to meet the challenges faced in new environment. In Canada, anthracnose
resistance from Lens ervoides was introduced in cultivated varieties.
The lentil collections of ICARDA were supplied to different National Research
Partners. These genetic resources are valuable sources of tolerance to drought, cold,
and diseases. Large numbers of lentil varieties were released for North Africa,
Middle East, and Central Asia. Bangladesh Agricultural Research Institute devel-
oped around ten short duration and high yielding varieties from ICARDA material.
The varietal improvement in lentil was initiated in 1924. Single plant selections were
made from local mixed lots. NP1, NP47 (IARI), BR25 (Bihar), L12 (Punjab), T8,
T38 (Uttar Pradesh), and B77 (West Bengal) are the earliest developed lentil pure
lines. With initiation of All India Coordinated Pulses Improvement Project in the
1960s, research work on lentil was intensified involving multidisciplinary team of
researchers. The initial emphasis was on population improvement through pure line
selection. The lentil varieties released in India till 1985 are presented in Table 24.4.
Later the focus shifted to pedigree, bulk, and single seed descent method. The
lentil varieties developed from 1985 to 2020 are presented in Table 24.5. The lentil
varieties released have poor seedling vigour and low pod set. High flower drop and
lodging besides biotic and abiotic stresses are the major bottlenecks in enhancing
productivity. Indian programme has released two biofortified varieties L 4717 and
IPL 220. L 4717 matures in less than 100 days and is the first extra-early lentil
variety of the country.
24 Lentil Breeding 1211

Table 24.4 Lentil varieties released in India up to 1985

S. no. Variety Pedigree/year of release Area of adaptation
1 Type 36 Selection from Badaun local UP, MP
1956
2 No. 26 Selection from local Bihar
germplasm 1956
3 No. 27 Selection from local Bihar
germplasm 1956
4 C 31 Selection from Sonadanger West Bengal
local 1956
5 BR 25 Selection from local Bihar, Northeastern Hill Region
germplasm 1956
6 L 9–12 Selection from local Punjab, UP, Jammu, Kashmir, Assam
germplasm 1962
7 Type 8 Selection from local UP
germplasm 1967
8 Pusa 4 Selection from indigenous Northwestern Plains, Teria Central zone
germplasm 1973
9 Pant L Selection from P 495 Assam, UP, Bihar, Punjab, NEH region
406
10 Asha Local selection from Jorhat West Bengal, assam
(B77)
11 Pant L L 9–12  T 8 UP, Bihar, MP, Punjab, Haryana,
639 Delhi, Gujarat, Maharashtra
12 LL 56 L 9–12  L 32–1 Punjab
13 Ranjan Selection from local Bengal, Punjab
germplasm/1983
14 VL Selection from Hill landrace/ UP
Masoor 1983
1
15 PL 77–2 Mutant of BR 25/1984 Eastern UP, Bihar, Bengal
16 LL 147 PL 284–67/1987 Punjab
Bold seeded varieties
1 L 4076 PL 639  PL 234 North West Plain Zone
Central Zone
2 K 75 Selection from Bundelkhand North East Plain Zone
local Central Zone
3 Sehore Selection from Sehore local Central Zone
74–3
4 Vipasha Unknown Himachal Pradesh
5 JL 1 Pure line selection from MP Madhya Pradesh
local
6 Type 8 Pure line selection from Bihar UP
local
Table 24.5 List of varieties of recent lentil released by All India Coordinated Pulses Improvement Project (1985 to 2020)
1212

Centre Year Average Days to Any other

Name of responsible for of yield maturity Reaction to major Area of relevant
S. no. variety developing Pedigree release (q/ha) (days) diseases adaptation information
1. K CSAU, Local sel. 1986 13–14 130–135 – NEPZ, CZ Foliage dark
75 (Malika) Kanpur From green; semi-
Bundelkhand spreading seeds
region grey mottled
large (2.7 g/100
seed wt)
2. LH 84–8 CCS HAU, L 9–12  JLS 1991 15–16 130–135 Resistant to rust NWPZ Plant semi-
(Sapna) Hissar 2 spreading; seeds
grey mottled
bold (2.7 g/100
seed)
3. Pant lentil 4 GBPUAandT, VPL 175  1993 16–17 135–140 Resistant to rust and NWPZ Plant semi-
Pantnagar (PL 184  P wilt spreading, dark-
288) green foliage,
small seed
4. Lens 4076 IARI, New PL 234  PL 1993 14–15 135–140 Resistant to rust NWPZ and Dark-green
Delhi 639 CZ foliage, semi-
spreading, large
seed
5. DPL IIPR, Kanpur PL 406  L 1995 15–16 135–140 Resistant to rust and NWPZ Large seeded
15 (Priya) 4076 tolerance to wilt
6. PusaVaibhav IARI, New (L 3875  P 1996 17–18 130–135 Resistant to rust NWPZ Small seed
(L 4147) Delhi 4)  PKVL
7. DPL IIPR, Kanpur JLS 1  LG 1997 17–18 130–135 Resistant to rust and NWPZ Large seed
62 (Sheri) 171 tolerance to wilt
8. JL 3 JNKVV, Land race Sel. 1999 14–15 110–115 Resistant to wilt CZ Large seed
Sehore From Sagar
H. K. Dikshit et al.
 24

9. IPL IIPR, Kanpur K 75  PL 2000 12–13 110–115 Tolerant to rust and CZ Large seed
81 (Noori) 369 wilt
10. KLS 218 CSAU, KLS 133  L 2005 13–14 120–125 Resistant to rust NEPZ Small seed
Kanpur 9362
11. HUL 57 BHU, Mutant of 2005 14–15 120–125 Resistant to rust NEPZ Small seed
Varanasi HUL 11
Lentil Breeding

12. VL 507 VPKAS, Sel. From 2006 12–13 160–170 Resistant to wilt NHZ Large seed
Almora ILL-7978
13. VL 126 Almora LL 498  LH 2006 13–14 160–170 Resistant to rust NHZ Small seed
84–8
14. IPL 406 IIPR, Kanpur DPL 35  EC 2007 17–18 125–130 Resistant to rust NWPZ Large seed
157634/382
15. WBL 77 Berhampore ILL 7723  2008 14–15 115–120 Resistant to rust NEPZ Small seed
(W.B) BLX 88176
16. Pant L 6 GBPUA & T, Pant L 4  2009 16–18 125–145 Resistant to rust Uttarakhand Small seed
Pantnagar DPL 55
17. Pant L 7 GBPUAandT, L 4076  2009 16–18 125–145 Resistant to rust Uttarakhand Large seed
Pantnagar DPL 15
18. Pant L GBPUA & T, DPL 59  2010 15–16 130–135 Moderately resistant NWPZ Small seed
8 (Pant L Pantnagar IPL 105 to rust and wilt
063)
19. IPL 316 IIPR, Kanpur Sehore 74–3 2013 14–15 110–115 Tolerance to wilt Central Large seed
 DPL 58 and rust Zone
20. RVL 11–6 RAK College, JL 3  DPL 2017 11–12 107–113 Tolerant to wilt. Central Large seed
Sehore 62 Zone
20. L 4717 (Pusa IARI, New ILL 7617  2016 12–13 96–106 Resistant to wilt and Central Extra-early type
Ageti Delhi 91,516 Ascochyta blight Zone
Masoor)
21. RKL 14–20 AU, Kota LL 1049  2018 12–15 97–104 Tolerant to drought, Central Large seed
(Kota Masoor RKL 11 high temperature Zone
1213

2)
(continued)
Table 24.5 (continued)
1214

Centre Year Average Days to Any other

Name of responsible for of yield maturity Reaction to major Area of relevant
S. no. variety developing Pedigree release (q/ha) (days) diseases adaptation information
22 L 4727 IARI, New Sehore 74–3 2018 11–15 92–128 Moderately resistant Central Suitable for
Delhi  Precoz to wilt Zone timely planting
under rainfed
conditions, large
seeded
23 IPL 220 IIPR, Kanpur (DPL 44  2018 14–18 119–122 Resistant to rust and NEPZ Suitable for
DPL 62)  Fusarium wilt normal sown
DPL 58 conditions, small
seeded
24 Kota Masoor AU, Kota KLB 339  2018 10–14 98–107 Tolerant to drought Central Suitable for
1 (RKL SL 94–09 and high Zone normal sown
607–1) temperature conditions
25 L- 4729 IARI, New SKL 259  L 2020 17–18 96–110 Moderately resistant Central Suitable for
Delhi 4147 to wilt Zone timely planting
under rainfed
conditions.
Large seeded
26 Kota Masoor AU, Kota L 4682  SL 2020 18–19 105–110 Moderately resistant Central Suitable for
3 (RKL 73–3 to wilt and tolerant Zone normal sown
605–03) to drought and high conditions.
temperature Large seeded
27 LL 1373 PAU, Ludhina IPL406  2020 15–16 125–130 Moderately resistant NWPZ Suitable for rabi
FLIP 2004- to wilt and rust season under
7L irrigated
conditions.
Large seeded
H. K. Dikshit et al.
 24

28 VL Masoor- VPKAS, DPL-15  2020 11–12 145–160 Moderately resistant NHZ Suitable under
148 Almora L-4076 to wilt and rust rainfed
conditions.
Small seeded
29 RKL 58 F AU, Kota Mutant of 2020 18–19 110–115 Resistant to rust and CZ Suitable for
3715 (Kota DPL 62 stemphylium blight, normal sowing
Lentil Breeding

Masoor 4) moderately resistant conditions (tenth

to wilt and less November)
incidence of pod
borer and aphids
1215
1216 H. K. Dikshit et al.

24.11 Genomics-Assisted Breeding

Significant achievements have been made in lentil using conventional means. For
further gains, the strengthening of conventional breeding programmes is required
with new tools and techniques. Genomics has emerged as potential tool for enhanc-
ing genetic gains in lentil.

24.11.1 Molecular Marker Development

The earliest linkage maps in lentil (Eujayl et al. 1998; Havey and Muehlbauer 1989)
were developed using RFLP/AFLP markers. RFLP markers require sound technical
skill for their development. Later PCR-based markers like random amplified poly-
morphic DNA (RAPD), sequence characterized amplified region (SCAR), and
simple sequence repeats (SSR) were developed. PCR-based markers were used
extensively in lentil breeding programmes (Gupta et al. 2016; Singh et al.
2016a, b, 2019a; Ates et al. 2016, 2018; Tsanakas et al. 2018; Mbasani-Mansi
et al. 2019; Polanco et al. 2019). Verma et al. (2014) developed genomic SSR
markers.
Following the advent of next-generation sequencing technologies, single-
nucleotide polymorphism (SNP) markers have been used in lentil to describe genetic
variation of germplasm collections and link-specific markers to phenotypic traits,
including seed quality, disease resistance, and micronutrient concentration
(Lombardi et al. 2014; Sudheesh et al. 2016; Khazaei et al. 2016, 2017, 2018).
The NGS technologies have licensed quick and cost-effective SNP mining for
mapping genes and QTLs. Now the SNP markers are preferred by breeder’s over
the PCR-based markers. Different strategies are available for identifying and
substantiating SNP markers.
Sanger sequencing technology is being utilized to resequence unigene-derived
amplicons, and the gene-based SNPs were discovered expressed sequence tags
(EST) which were converted to PCR-based markers. Sharpe et al. (2013) reported
generation of 44,879 SNPs using Illumina Genome Analyzer, and Tamel et al.
(2014) reported discovery of 50,960 SNPs for construction of linkage map in lentil.
The use of NGS platforms for transcriptome analysis (Sharpe et al. 2013; Kaur et al.
2014; Singh et al. 2019a) has generated large number of SNPs from the coding
region of lentil. These SNPs have been utilized to characterize the genetic diversity
and for development of linkage maps.

24.11.2 Molecular Markers in Lentil Improvement

Molecular markers decipher the gene networks controlling the quantitative traits, and
the molecular markers have been linked to several traits of economic importance in
different crops. The enrichment of genomic resources, development of PCR molec-
ular markers, and next-generation sequencing have increased the utilization of
24 Lentil Breeding 1217

molecular markers for crop improvement in lentil. Limited numbers of molecular

markers linked to trait of economic importance have been identified in lentil
(Table 24.6). The utilization of bi-parental populations with poor marker density
has not identified very tight association of molecular markers with QTLs/genes in
these studies.

24.12 Modernization of Crop Improvement Programme

24.12.1 Speed Breeding

Plant breeders improve productivity of crop by fast-tracking research. Conventional

breeding techniques require long time for development of improved varieties. The
reduction of generation time can accelerate the development of improved varieties.
Speed breeding is an excellent tool for rapid generation advancement utilizing
extended photoperiod (22 h). Sodium-vapour lamps (SVL) are used in glass houses
and light-emitting diodes (LED) and metal halide lighting in growth chambers
(Ghosh et al. 2018). Controlled temperature and 22-hr photoperiod reduced genera-
tion time in barley, chickpea, canola, pea, and wheat. Up to 6 generations/year have
been obtained using speed breeding. Limited reports on the use of extended photo-
period are available in lentil (Idrissi and van Damme 2018; Idrissi et al. 2019;
Mobini et al. 2016). Recently Idrissi et al. (2019) reported that efficient protocol of
extended light period to speed breeding in lentil can reduce crop duration and also
shorten the flowering time of wild types (for synchronization of flowering in
cultivated and wild for hybridization). However, there is need to optimize light
intensity, spectral composition (light-emitting diodes [LED], red, blue light) and red/
far-red light ratio for this crop.

24.13 Future Thrust Area

Lentil is grown as rainfed crop on marginal soils. The yield potential realization
depends on residual soil moisture of rainy season and rainfall during the crop season.
Climate-resilient varieties are required to stabilize the production. Thrust is required
for a number of parameters listed below:

24.13.1 Prebeeding

Lentil is grown in different agroclimatic conditions. Hybridization with Mediterra-

nean lines will introduce earliness, seedling vigour, bold seed size, and larger
secondary and tertiary branches. Using ICARDA germplasm, bold small and
large-seeded varieties have been developed. Systematic prebreeding efforts being
made at IARI, New Delhi; NBPGR, New Delhi; and IIPR, Kanpur, have led to
identification of new sources of resistance for biotic and abiotic stresses. Efforts are
1218 H. K. Dikshit et al.

Table 24.6 Molecular markers linked to desirable genes/QTLs in lentil

Phenotypic
Trait Molecular markers Mapping population variance Reference
Wilt SSR 59-2B ILL 5588(R)  L 8 Hamwieh
resistance P17m30710 692–16-1(S) RIL 3.5 et al. (2005)
RAPD marker ILL 5588(R)  L – Eujayl et al.
OPK-15900 692–16-1(S) - (2006)
OP-BH800 and F2:4 progenies and F6:
OP-DI5500 found to 8, F6:9 recombinant
be associated in the inbred line
coupling phase with
the resistance trait
Stemphylium QTL QLH4 80–81 ILL 6002(R)  ILL 46 Saha et al.
blight SSRs ME5XR10 and 5888(S) F7 RIL (2010)
resistance ME4XR16C
RAPD marker UBC
34
Rust SSR Gllc 527 PL 8 (S)  L 4149 – Dikshit et al.
resistance (R) (2016)
F2:3
Ascochyta Seven RAPD markers ILL 5588 (R)  ILL 89 Ford et al.
blight linked to the AbR1 6002(S) F2:3 (1999)
resistance gene
Three QTLs (using ILL7537 (S) / 50 Rubeena
RAPD, ISSR, and ILL6002(R) et al. (2006)
AFLP analysis) F2
QTL on LG 6 Eston(S)  PI 41 Tullu et al.
AFLP and random 320937(R) (2006)
amplified RILs
polymorphic DNA
(RAPD) markers
localized around the
resistance region
Three QTLs Northfield 34–61 Gupta et al.
(ILL5588)  Digger (2012)
(ILL5722)
F5 RILs
Two QTLS Indianhead  Digger 52 Sudheesh
Three QTLs [IH  DIG] 69 et al. (2016)
Indianhead 
Northfield [IH  NF]
Anthracnose Five QTLs with a L01-827A and IG 8.9–24.8 Bhadauria
resistance significant 72815 (L. ervoidis et al. (2017)
association with accessions)
resistance to C. lentis RIL
race 0
A major-effect QTL 200 genotypes AM 66.6–69.8% Tadesse
(qAnt1.Lc3) Panel et al. (2021)
conferring resistance
to race 1 was mapped
to lentil chromosome
3
(continued)
24 Lentil Breeding 1219

Table 24.6 (continued)

Phenotypic
Trait Molecular markers Mapping population variance Reference
Seed size One QTL Precoz  L 830 27.5 Verma et al.
F8 RILs (2015)
Seed weight One QTL Precoz  L 830 48.4 Verma et al.
F8 RILs (2015)
Three QTLs for seed Lens culinaris  -- Tahir and
weight in linkage Lens orientalis F6 Muehlbauer
groups 1, 4, and 5 RILs (1995)
Three QTLs located Lens culinaris ssp. 18.2 Fratini et al.
in linkage groups I, culinaris Medik. (2007)
III, and VI cv. “Lupa”  L. c.
Seed diameter Three QTLs located ssp. orientalis Boiss 37
in linkage groups I, (BG 16880) F2
III, and V
Seed Seed thickness QTL CDC Robin  964a- 8.4 Fedoruk
thickness were detected on all 46 et al. (2013)
LGs except LG RILs
3. The QTL that was
most stable
throughout the
different site-years
was located on LG
7, explaining an
average of 8.4% of
the variation in three
site-years
Seed Seed plumpness 50
plumpness QTLs were present on
LG 1, LG 2, and LG 4
Days to Three QTL for days Lens culinaris ssp. 90.4 Fratini et al.
flowering to flowering in culinaris Medik. (2007)
linkage groups 1, 4, cv. “Lupa”  L. c.
and 10 ssp. orientalis Boiss
(BG 16880) F2
Three significant ILL 5888  ILL 15.6–24.2 Saha et al.
QTLs were detected 6002 (2013)
with two on linkage
group 4 and one on
linkage group 13.
Single QTL was Lens culinaris – Polanco
identified for the cultivar Alpo  et al. (2019)
character flowering L. odemensis
time located on LG6 accession ILWL235
RILs
Seed QTL for cotyledon CDC Robin  964a- 23 Fedoruk
cotyledon colour locus Yc. 46 et al. (2013)
colour (Yc) LcC13114p356, RILs
located 1 cM away
(continued)
1220 H. K. Dikshit et al.

Table 24.6 (continued)

Phenotypic
Trait Molecular markers Mapping population variance Reference
Seed coat Scp locus was CDC Robin  964a- – Fedoruk
spotting mapped onto LG6 46 et al. (2013)
pattern(Scp) RILs
Plant height One QTL ILL 5888  ILL 15.3 Saha et al.
6002 (2013)
100 seed Five QTLs RILs 17.5 Saha et al.
weight (2013)
Early Quantitative trait loci Eston  PI320937 37–46 Tullu et al.
maturity affecting earliness RILS (2008)
Plant height and plant height were 31–40
identified on LG1,
LG2, LG4, LG5,
LG9, and LG12
Three QTLs for plant Lens culinaris ssp. 38.2 Fratini et al.
height in linkage culinaris Medik. (2007)
groups 1, 3, and 5 cv. “Lupa”  L. c.
Branches at Four QTLs for ssp. orientalis Boiss 91.7
first node branches at first node (BG 16880) F2
in linkage groups 3, 5,
5, and 8
Pod Three QTLs for plant 81.3
dehiscence height in linkage
groups 2, 3, and 5
Height at first Two QTLs for height 33.3
node at first node in linkage
group 1 and 5
Total no. of Two QTLs for total 54
branches number of branches
in linkage group
3 and 10
Boron Two SNP loci were Cassab  ILL2024 – Kaur et al.
tolerance found to be associated RILs (2014)
with B tolerance
through marker
regression, and a
single genomic
region was detected
in the interval
between these SNP
loci on LG4.2
Fe 21 QTL regions ILL 8006  CDC 5.9–14.0 Aldemir
concentration explaining 5.9%– Milestone et al. (2017)
14.0% of the RILs
phenotypic variation
were identified on six
linkage groups (LG1,
2, 4, 5, 6, and 7)
Three SSRs (PBALC Association mapping 9–11 Singh et al.
13, PBALC 206, and panel (2017a, b)
GLLC 563) associated
with grain Fe
concentration
(continued)
24 Lentil Breeding 1221

Table 24.6 (continued)

Phenotypic
Trait Molecular markers Mapping population variance Reference
Two SSR markers, Association mapping 17 and 6 Kumar et al.
GLLC 106 and panel (2019)
GLLC 108
Zn Four SSRs (PBALC Association mapping 14–21 Singh et al.
concentration 353, SSR 317–1, PLC panel (2017a, b)
62, and PBALC 217)
Winter One major QTL on WA8649090  20.45 Kahraman
hardiness linkage group 6 Precoz et al. (2010)
RIL
Mn 6 QTLs for Mn CDC Redberry  15.3–24.1% Ates et al.
concentration concentration ILL7502 (2018)
identified using
composite interval
mapping (CIM).
Milling Multiple QTLs for CDC Robin  946a- – Subedi et al.
quality milling traits were 46 (2018)
detected in six of RILs
seven linkage groups
(LGs). The most
stable QTLs
governing dehulling
efficiency and milling
recovery were
clustered on LGs 1, 2,
3, and 7, whereas
football recovery
QTLs were clustered
on LGs 4, 5, 6, and 7
Seed coat The Scp locus was Lens culinaris – Polanco
spotting mapped to a 3.3 Mb cultivar Alpo  et al. (2019)
Seed size region of LcChr6 L. odemensis
Ascochyta comprising accession ILWL235
blight 46 annotated genes RILs
including a candidate
gene (Lc25388)
Three QTLs were
detected for the seed
size trait in LG1,
LG5a, and LG5b,
corresponding to one
genomic location in
LcChr1 and two in
LcChr5
SNP flanking markers
of AB_NF1 in the
genes Lc28181 and
Lc25002 located in
the LcChr6
1222 H. K. Dikshit et al.

being made to map the genes utilizing the available genomic resources. Marker-
assisted selection is required to develop climate-resilient varieties.

24.13.2 Early Maturity

Earliness is required to escape terminal moisture stress in Central India and in rice
fallows of Eastern India. Among biotic stresses, wilt is important for Central India,
whereas stemphylium blight and rust for Eastern India. Tolerance to high tempera-
ture at reproductive stage and terminal soil moisture stress are of extreme impor-
tance. Herbicide tolerance will reduce the cost of manual weeding. Efforts should be
made to develop new lentil varieties for rice fallows.

24.13.3 Nutritional Dense Varieties

To address the micronutrient deficiency, micronutrient dense varieties are required.

Fe-rich lentil varieties L 4717 and IPL 220 have been released for cultivation in
Central and Eastern India, respectively. Efforts are required for reducing the phytic
acid. Enhancement of protein concentration is desired.

24.13.4 Restructuring Plant Type

Plant types ensuring higher solar light interception are required to have partitioning
of photosynthates. Mechanized harvesting is required to reduce the harvesting losses
caused by shattering and cutting the cost of harvesting and threshing. Tall, erect, and
non-lodging plants are required for mechanized harvesting.

24.13.5 Climate-Resilient Varieties

IARI, New Delhi, has developed protocols for screening for abiotic stresses. Donors
for drought, heat, salinity, and salinity have been identified. QTLs governing
tolerance to abiotic stress have been identified, and transcriptome analysis has
deciphered the mechanism involved for tolerance. Utilizing the available informa-
tion, varieties tolerant to abiotic stress can be developed utilizing genomic resources.
Phosphorus usage efficiency in lentils is being studied to produce phosphorus
absorption and utilization efficient varieties. The virulence of pathogens under
climate change requires close monitoring.
24 Lentil Breeding 1223

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Field Pea Breeding
25
A. K. Parihar, Rajesh Yadav, Amrit Lamichaney, R. K. Mishra,
Anup Chandra, D. S. Gupta, Kuldeep Tripathi, K. K. Hazra,
and G. P. Dixit

Abstract

Field pea (Pisum sativus L.) is a nutritionally dense winter season pulse crop,
consumed worldwide as food, feed and fodder and offers nutritional security to
low-income folks of various developing countries. It is an excellent source of
protein and carbohydrate in juxtaposition with vitamins, essential amino acids,
and macro- and micronutrients. In addition, it plays an important role in manage-
ment of Type 2 diabetes and body weight, blood cholesterol reduction, improves
cardiovascular health and gastrointestinal function. It is susceptible to many
biotic and abiotic stresses that seriously hinder its sustainable production. Over
the years, sincere efforts have been made toward the genetic improvement of field
pea to subsidize antinutritional components and elevate production potential. In
this book chapter, the importance of the crop, its common uses, origin, evolution,
gene pool, botanical description, floral biology, cytogenetics and molecular
cytogenetics, genetic variability for important agronomic traits, inheritance of
qualitative and quantitative traits, and brief account of genetic resources have
been illustrated. The achievement made in field pea through conventional and
nonconventional breeding approaches, that is, hybridization, distant
hybridization, and mutation breeding, have been reviewed. The current scenario
of genomics resources and marker-assisted breeding has also been deliberated.

A. K. Parihar (*) · A. Lamichaney · R. K. Mishra · A. Chandra · D. S. Gupta · K. K. Hazra ·

G. P. Dixit
ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
R. Yadav
CCS Haryana Agricultural University, Hisar, Haryana, India
K. Tripathi
Germplasm Evaluation Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi,
India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1237
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_25
1238 A. K. Parihar et al.

Moreover, the breeding objectives, major constraints, and future perspectives in

order to explore cutting-edge tools and technique for enriching field pea genomic
resources have been outlined. Furthermore, the currently existing coordinated
testing system for new entries and quality seed production has also been
described in short. Overall, to accelerate genetic gain in field pea along with
nutritional enrichment, there is urgent need of exploitation of recent advanced
tools and techniques such as transcriptomics, proteomics, metabolomics, small
RNAomics, epigenomics, interactomics, bioinformatics, genomic selection,
genome editing, and speed breeding to bolster the field pea breeding program.

Keywords
Pisum sativum · Cytogenetics · Germplasm · Breeding strategies · Breeding
objectives · Coordinated system of testing

25.1 Introduction

Field pea (Pisum sativum L.) is an imperative cool season grain legume cultivated
around the globe as food, feed, and fodder (Rubiales et al. 2019; Parihar et al.
2020a, b). Field pea with different cotyledon color, that is, yellow, green, and
orange, is an important ingredient of various culinary and confectionary stuffs
such as soup, chat, chhola, dal, stew, snacks, vegetables, and flour, while the integral
seeds are usually accepted as animal feed (Dahl et al. 2012; Singh et al. 2018;
Mahajan et al. 2018; Parihar et al. 2021a, b). Pea hay is used as fodder for animals
(Bastida Garcia et al. 2011). In terms of nutritional composition, it is an excellent
source of protein (21.2–32.9%) and carbohydrate (56–74%) in juxtaposition with
vitamins, essential amino acids, macro- and micronutrients and plays a decisive role
in nutritional security of resource poor folks (Harmankaya et al. 2010, Shivay et al.
2016, Parihar et al. 2016). Furthermore, it is a good source of arginine, valine, and
methionine (Tömösközi et al. 2001). Carbohydrates are the main constituent of pea
dry matter, which exists in variable amounts. The high amylase content in seed
results in the slow digestion of starch (Chung et al. 2009). In addition, the seed coat
and cotyledon are excellent source of dietary fiber, that is, water-insoluble and water-
soluble fiber, respectively (Guillon and Champ 2002; Tosh and Yada 2010).
In case of mineral content, field pea seed predominantly contains potassium and
phosphorus, whereas it is comparatively low in the calcium. The microelements,
especially iron, manganese, copper, cobalt, selenium, molybdenum, and zinc, are
present in substantial amount in pea seeds (Reichert and MacKenzie 1982; Savage
and Deo 1989; Sommer et al. 1994; Amarakoon et al. 2012). Additionally, field pea
has considerable amount of folate, vitamins (C, B1, B2, B3 and B6) (Dang et al.
2000; Hedges and Lister 2006). Corresponding to other pulses, it has an array of
phytochemicals: carotenoids, β-carotene, chlorophyll, and phenolic compounds
(Campos-vega et al. 2010). The carotenoids cannot be synthesized in human and
animal body; therefore, it is accessible solely from an external source (plant or an
animal) an animal (Fraser and Bramley 2004). The prevalent carotenoids in peas are
25 Field Pea Breeding 1239

xanthophylls, lutein, and zeaxanthin in addition to α and β-carotene (Hedges and

Lister 2006). A green cotyledon field pea cultivar contains 10 times higher
b-carotene concentration than yellow or orange cotyledons (Holasová et al. 2009).
Likewise, the lutein and zeaxanthin concentration in peas is many folds higher as
compared to other legumes (Hedges and Lister, 2006). The phenolic acids and
flavonoids are available in good quantity in seed coat and cotyledon, especially
pea seeds pigmented seed coat (Duenas et al. 2004; Campos-vega et al. 2010; Xu
et al. 2007). Since, the pigmentation of a seed coat is imparted by the phenolic
compounds and tannins, seeds with dark seed coat are reported to have higher
antioxidant activities (Hagerman et al. 1998; Devi et al. 2019). In addition, a
subgroup of the flavonoid category compounds, well-known as Isoflavones, also
exists in sizeable amount in peas (Hedges and Lister 2006). Saponin is a diverse
group of biologically active glycosides, which are distributed comprehensively in
the plant kingdom (Curl et al. 1985). Several saponins have been isolated in peas of
which Soyasoponin-I is predominant (Murakami et al. 2001). Being a cheaper and
rich source of protein, vitamin, minerals, and prebiotic carbohydrate particularly for
poorer consumers, it is often acknowledged as “poor man’s meat” (Amarakoon et al.
2012). The nutritionally dense field pea is a valuable international food commodity,
well equipped to cater to the daily nutritional requirements of malnourished resource
poor folks worldwide (Food and Agriculture Organization 2011). Most interestingly,
its consumption is reported to minimize the risk of occurrence of Type 2 diabetes
(Marinangeli et al. 2009; Marinangeli and Jones 2011), reduces blood cholesterol
(Ekvall et al. 2006), improves cardiovascular health (Singh et al. 2013), cancer-
combating and antioxidant properties (Kalt 2001; Kleijn et al. 2001; Boker et al.
2002; Steer 2006), body weight management, and improves gastrointestinal function
(Fernando et al. 2010; Tosh and Yada 2010; Lunde et al. 2011).

25.2 Common Uses

Field pea is used in varied ways, the tender green pods and seeds are used as
vegetables (Duke 1981), while the mature dry seed in different forms (whole, split,
flour) is used for human consumption or as animal feed (Elzebroek and Wind 2008;
Bastida Garcia et al. 2011). It is an important ingredient of various culinary and
confectionaries such as soup, chat, chhola, dal, stew, snacks, vegetables, and flour
(Dahl et al. 2012; Singh et al. 2018; Mahajan et al. 2018; Parihar et al. 2020a, b). It is
an ideal candidate crop to be used in crop rotation, as green manures, and cover
crops, since it grows fast and contributes to soil nutrient enrichment owing to its
inherent ability fixing atmospheric nitrogen (Ingels et al. 1994; Biederbeck et al.
2005; Chen et al. 2006; Clark 2007).
1240 A. K. Parihar et al.

25.3 Area, Production, and Productivity: World Scenario

Field pea or dry pea is widely cultivated across the continents, and is cultivated in
nearly 94 countries (Parihar et al. 2021a, b). The dry pea area has been oscillated
between 6.58 to 8.09 mha and production between 10.44 and 16.21 mt during 2010
to 2019 (Fig. 25.1). The leading countries in terms of production are Canada,
Russian Federation, China, India, and United States of America (Parihar et al.
2020a, b). The region-wise production scenario at global level demonstrated that
the Americas with 39.33% share hold highest contribution in total production
followed by Europe (36.98%) and Asia (18.09%). The global dry pea productivity
is currently around 2.0 tonnes per hectare. The countries having highest productivity
are Netherland (5005 kg/ha), Denmark (4463 kg/ha), Belgium (3824 kg/ha),
Germany (3486 kg/ha), and Finland (3450 kg/ha). Contrarily, in India and other
dry pea-growing countries like China, Australia, and Myanmar, productivity is quite
low than aforesaid countries, which fluctuate between 1000 and 2000 kg/ha
(FAOSTAT 2021).

25.4 Origin, Evolution, Distribution, and Gene Pools

of Field Pea

Field pea is an important member of third largest flowering plant family

(Leguminosae) and largest subfamily (papilionoideae), and tribe Fabeae. The
Leguminosae family and papilionoideae subfamily comprised of 800 and
476 genera, respectively (Doyle et al. 1997; Lavin et al. 2005; Nemecek et al.
2008; Smýkal et al. 2013; Mahajan et al. 2018). The tribe fabeae comprises of five
genera (Lathyrus, Lens, Vicia, Pisum, and Vavilovia formosa) (Smýkal et al. 2011;

Fig. 25.1 Worldwide area and production scenario of dry pea during 2010–2019
25 Field Pea Breeding 1241

Schaefer et al. 2012; Mikić et al. 2013; Warkentin et al. 2015). The genus Pisum L.,
is comprised of three species that is cultivated pea (P. Sativum subsp. sativum),
Ethiopian pea (P. abyssinicum), and P. fulvum. The cultivated pea is further classi-
fied into five subspecies (elatius, sativum, humile, arvense, and hortense) (Maxted
and Ambrose 2001; Warkentin et al. 2015; Trněný et al. 2018), of which, arvense
and hortense subspecies are considered as varieties under species sativum (Govorov
1928; Nasiri et al. 2009). All the given species could successfully generate hybrids,
though the fertility status may be constricted due to karyological and nuclear–
cytoplasmic incongruity (Ben Ze'ev and Zohary 1973; Bogdanova et al. 2015).
Based on morphological variation and wide geographical range, P. sativum/elatius
complex and the more distant P. fulvumare are considered in secondary genepool,
whereas the phylogenetically related V. formosa, a perennial mountain species,
harbored in tertiary genepool (Ben Ze'ev and Zohary 1973; Warkentin et al. 2015).
Taking into consideration the crossing potential, the genus Pisum sativum is further
grouped into following subspecies, which are recognized as varieties, that is,
P. sativum L. var. hortense (garden pea), Pisum sativum L.var. arvense (field pea),
Pisum sativum L.var.macrocarpon (whole pod edible pea), Pisum sativum L.var.
syriacum (wild form) (Gaskell 1997; Nasiri et al. 2009; Mohan et al. 2013).
The name Pisum is originated from the Greek word “pisos,” which in Rome
become Pisum and in English as peason, then pease or peasse, which later became
the universal name (Peas) (Mikicˇ 2012). Pea had penetrated in China through India
by the first century BC (Makasheva 1973). In the first century BC, pea was
mentioned by the Romans Collumela, Pliny, and Virgil (Smýkal et al. 2013). The
primary center of origin for pea is Near East and Mediterranean region where two
wild species, that is, P. fulvum and P. sativum subsp. Elatius, are still being grown.
However, the distribution of P. fulvum is constrained to the Middle East region
(Ladizinsky and Abbo 2015; Smýkal et al. 2015), whereas the wild pea (P. sativum
subsp. elatius) is distributed across the Mediterranean region with greatest diversity
in the Near East region, which is considered as the center of diversity (Smýkal et al.
2017). The upland Asiatic region of the Hindu Kush, Ethiopia, and Yemen are
considered as secondary center of diversity (Rubiales et al. 2019). Vavilov (1949)
has considered Ethiopia together with the Mediterranean countries and Central Asia
as primary centers, with Near East secondary. Moreover, pea has been cultivated
since the Fertile Crescent to today’s Russia, north and West Europe, Greece, Rome,
Persia, India, and China (Makasheva 1979; Chimwamurombe and Khulbe 2011).
The archeological evidence supported pea as one of the world oldest domesticated
grain legumes (Smýkal et al. 2018). The P. humile, which has been recently
incorporated as additional taxa, currently subsist only at secondary habitation
(Abbo et al. 2013). The literature witnessed that ssp. elatius and ssp. humile are
the progenitors of pea ssp. Sativum (Zohary and Hopf 1973; McPhee 2003). Other
species, for instance, P. jomardi, P. transcaucasicum, and P. arvense, have also been
incorporated within P. sativum (Jing et al. 2007; Zaytseva et al. 2012).
1242 A. K. Parihar et al.

25.5 Botanical Description

Pea is an annual herbaceous plant with hollow, succulent, slender, trailing, or

climbing stems ranging from 0.3 m to 2.0 m in length with a bluish-green waxy
layer (Elzebroek and Wind 2008; Laber 2014; Parihar et al. 2014a). The plant type is
either indeterminate (often referred as tall type) or determinate (bushy or dwarf type)
(McKay et al. 1994, 2013). The leaves are alternate, pinnately compound with the
rachis terminating in a single or branched tendril and consist of large stipules at the
base, one to several pairs of oval leaflets (Yaxley et al. 2001; Pavek 2012). Several
modern cultivars have a semi-leafless or “afila” type leaf, wherein the leaflets are
transformed into additional tendrils (Parihar and Dixit 2017; Parihar et al. 2019a). In
semi-leafless types, the leaflets are replaced by tendrils with intact stipules, whereas,
in leafless types, the stipules become rudimentary and are replaced by tendrils (afila
type). The “afila” type leaves have good standing ability and are comparatively
tolerant to lodging to some extent than the leafy types owing to interlocking of
tendrils among plants (Banniza et al. 2005; Dixit and Parihar 2014; Singh and
Srivastava 2018; Parihar et al. 2019a; Dixit et al. 2014). The plants have tap root
system with high root surface area and nodules on the surface (Gupta and Parihar
2015; Rao et al. 2021). The flowers are typical papilionaceous type and
inflorescences developed in the leaf axils and consist of racemes with one to five
flowers and are highly self-pollinated (Cooper 1938).
A flower contains five green compound sepals and five white, purple or pink
petals of different sizes (Gritton 1980; Duke 1981; Majumdar 2011). The top petal is
called the “standard,” the two small petals in the middle are amalgamated together
and called the “keel” (due to their boat-like appearance), and the two shrinked
bottom petals are called the “wings” (Elzebroek and Wind, 2008). Flower color
ranges from reddish purple, white, pink, and blue (Sattell et al. 1998; MacKay 2013).
The stamens are diadelphous (9 + 1), with nine of them fused to form a staminal tube,
while the tenth is free throughout its length (Ferrandiz et al. 1999). Gynoecium is
monocarpellary and contains up to 15 ovules that is alternately attached to placenta.
Style bends at right angle to ovary with sticky stigma (Gupta and Parihar 2015). The
first flower-bearing node is characteristic of a given variety; in temperate regions, the
first flower-bearing node is reported to vary from 4 to 25 under field conditions
(Gritton 1980). The pod or fruit encapsulates about 5–10 seeds, which remains
attached to the fruit by funiculus. Pods are straight or curved, and its length may
reach up to 8–9 cm. The seed consists of an embryo, two cotyledons, and the seed
coat. The mature seeds are round, smooth or wrinkled, and can be creamy, green,
white, light brown, brown, red-orange, blue-red, dark violet to almost black, or
dotted in color (Duke 1981; Kalloo 1993; Peter and Kumar 2008). The cotyledon
colors of the mature round seed may vary from yellow, green, and red (Warkentin
et al. 2015; Rubiales et al. 2019). Its cotyledon remains buried inside the soil during
germination, characteristic of a typical hypogeal germination (Torrey and Zobel
1977).
25 Field Pea Breeding 1243

25.6 Floral Biology, Emasculation: Pollination Techniques

It is a sexually propagating crop and flowers are cleistogamous and self-pollinated,

that allows breeder to breed true breeding lines (Gill and Vear 1980; Suso et al. 2016;
Smýkal et al. 2018). However, occurrence of crosspollination (0–60%) has been
reported in pea (Kosterin and Bogdanova 2014; White 1917; Harland 1948; Myers
and Gritton 1988), which may be due to competent pistil even after anthesis
(Bogdanova and Berdnikov 2000; Kosterin and Bogdanova 2014). However, the
proportion of out-crossing reported in the commercial cultivars is less than 1.0%
(Gritton 1980; Davis 1993). Pollen grains of pea has been observed to disperse over
several hundred meters (Dostálová et al. 2005), which could be by the pollinators as
several insects belonging to Diptera, Hymenoptera, Lepidoptera, and Coleoptera are
reported to be a pollinator in pea (Saboor et al. 2016).
Anthesis and anther dehiscence in field pea occurs during morning hours between
5 and 8 AM. The stigma becomes receptive to pollen few days prior to anthesis and a
day after flower opening (Warnock and Hagedorn 1954). Pollen remains viable from
the time of anther dehisce to several days thereafter. Pollination happens 24 h before
flower opening and subsequently pollen germinates on the stigma in about 8–12 h
following fertilization (Cooper 1938; Gritton and Wierzbicka 1975; Gritton 1980;
Peter and Kumar 2008; Mohan et al. 2013). The selection of flower bud for
emasculation should be done at the stage just before anther dehiscence, which is
indicated by expansion of petals beyond sepals. In the process of emasculation, first
the sepals and standards are removed from the selected bud. Then the keel petals are
removed from the base of the bud, or slit is made in the keel to expose the stigma and
anthers using a forcep, followed by removal of ten male stamens and anthers without
touching or damaging the pistil. The following precautions must be taken during
emasculation

• The flower buds to be chosen for emasculation should be of appropriate stage:

unopened standard petal.
• To avoid damaging the pistil, the flower bud must be handled gently and disturb
the flower as little as possible.
• Confirm that no anthers are left on the pistil.

The stigma of the emasculated female flower is highly receptive during morning
hours. For pollination, male flowers about to open should be collected; the standard
and wings and keel removed to expose the pollen-rich anthers. Gently brush the
pollen onto the stigmatic surface of the emasculated flower bud. To increase the pod
setting, the old flowers and other nonpollinated flower buds should be removed after
crossing. Normally emasculation is executed in afternoon followed by pollination in
next morning. Proper cleaning of the forceps to be used for pollination should be
done by dipping them into 95% ethyl alcohol before changing pollen donor. After
pollination, proper labelling of the crossed bud should be done. Proper care must be
taken to put the pollen on the stigmatic surface, which is situated at the extreme tip of
the style, not on the hairs on the hollow side of the style, which might appear to be
1244 A. K. Parihar et al.

the suitable spot (Warnock and Hagedorn 1954). Pollen must be applied carefully to
avoid injury to the style by forcing it too far backward. Fix a tag on the pollinated
flower with date of emasculation and pollination, name of the parents (female and
male) written on or tie different color thread of about 10 cm on the peduncle of each
pollinated flower to discriminate the crossed flower.
The ease with which all forms of peas except P. fulvum can be intercrossed
provides plant breeders access to the array of variation that exists in the wild,
primitive, and cultivated forms (Davis, 1993). Some of the wild forms and cultivars
demonstrate chromosomal changes, which may cause partial sterility of hybrids
(Casey and Davies 1993). Initially, through physical mutagenesis (x-ray irradiation),
a total 13 genetic male sterile lines were developed from “Dippes gelbe Viktoria”
genotype ofPisum sativum and subsequently several studies were carried out by
many researchers (Gottschalk 1968, 1971; Gottschalk and Baquar 1971; Gottschalk
and Kaul 1974; Klein 1969). The tests of allelism of these lines revealed that nine
unique ms genes responsible for male sterility and all ms genes segregated like single
recessive genes. Interestingly, out of nine, two ms genes (ms-3 and ms-10) exhibited
reduced female fertility in addition to male sterility (Myers and Gritton 1988).
However, a spontaneous mutant plant with male sterility was noticed in “Longittee”
cultivar and, inheritance study explained that the sterile character is genetically
governed and controlled by a recessive gene (Singh and Singh 1995). However,
natural hybridization has not so far been used in pea breeding programs due to lack
of pollination control and the pollen transfer would be dependent upon insects.
In pea, nuclear–cytoplasmic incompatibility has been observed in the crosses of
wild species P. sativum subsp. elatius accession VIR 320 with cultivated forms
(Bogdanova and Berdnikov 2001; Bogdanova and Kosterin 2006, 2007;
Yadrikhinskiy and Bogdanova 2011). Further, inheritance analysis revealed that it
is governed by two complementary unlinked nuclear genes, Scs1 and Scs2. In
crosses of cultivated peas as male and wild accession (VIR320) as female the F1
was highly sterile and displays chlorophyll deficiency, reduction of leaflets, and
stipules, while the reciprocal cross produces normal hybrids. The gene Scs1is closely
linked to the PhlC gene on linkage group III, and other geneScs2 is linked to gp gene
on linkage group V (Bogdanova et al. 2009). Heterozygotes for either of the genes
Scs1 or Scs2 decrease pollen fertility about 50% and 30%, respectively, whereas in
homozygote, Scs2 reduced 20%pollen fertility. In contrast to Scs2, Scs1 allele from
the cultivated parent was shown to be both sporophyte and male gametophyte lethal
in the background of the alien cytoplasm (Bogdanova et al. 2012). Recently, the
plastid accD gene coding for the acetyl-CoA carboxylase beta subunit and the
nuclear gene bccp coding for the biotin carboxyl carrier protein of acetyl-CoA
carboxylase have been designated as candidate genes underlying nuclear–cytoplas-
mic incompatibility in peas (Bogdanova et al. 2015).
25 Field Pea Breeding 1245

25.7 Cytogenetics and Molecular Cytogenetics

Pea is a valuable model plant in genetics since the days of Gregor Johann Mendel.
Peas are diploid with a chromosome number of 2n ¼ 2x ¼ 14 (Yarnell 1962). The
standard karyotype of pea was described by Levitskii (1934) and Blixt (1959).
Contrary to the other major legumes crops such as M. truncatula and Lotus
japonicus, pea has a large genome of 4300 Mb organized in seven chromosome
pairs (2n ¼ 2x ¼ 14) (Smýkal et al. 2013; Praca-Fontes et al. 2014). Out of seven,
five are acrocentric and two with a secondary constriction corresponding to the 45S
rRNA. The chromosomes in pea are distinguishable on the basis of morphology and
can be identified with linkage groups. The chromosome and linkage group numbers
have been depicted utilizing Arabic and Roman numerals, separately such as 1 ¼ VI,
2 ¼ I, 3 ¼ V, 4 ¼ IV, 5 ¼ III, 6 ¼ II, and 7 ¼ VII (Fuchs et al. 1998; Ellis and Poyser
2002). The pea genome consists of about 37.7% GC and 30% of cytosine are
5methyl-cytosine (5meC), and 50% of 5meC contain the sequence of C(A/T)G
(Murray et al. 1978; Thompson and Murray 1980; Salinas et al. 1988).
The DNA-related studies witnessed about 75–97% of genome to be of repetitive
sequences (Flavell et al. 1974), which was further confirmed by next-generation
sequencing (NGS), which reports presence of 50–60% highly to moderately repeated
sequences (Novák et al. 2010). The grouping of sequence reads depicted that Ty3/
gypsy LTR-retrotransposons are the most important components of the pea repeats.
Ogre elements accounted 20–33% of the pea genome, while Ty1/copia and other
sorts of repeats were noticed at low proportion (Macas et al. 2007). The pea repeats
have been embraced as the important part of many studies targeting mainly on
LTR-retrotransposons (Cyclops), MITE elements (Zaba), PIGY, Angela, PDR,
Stowaway and centromeric retrotransposons (Chavanne et al. 1998; Neumann
et al. 2011). These repeats could be used as valuable markers for cytogenetic
chromosomal discrimination within its karyotype, for instance, the satellite repeat
PisTR-B the most convenient cytogenetic marker of all pea chromosomes (Smýkal
et al. 2012).

25.8 Genetic Resources Panorama at National

and International Level

The success of any crop breeding program in terms of development of high-yielding

varieties with targeted traits primarily hinged on the availability of genetic resources
and their proper exploitation. In India currently, approximately 4484 accessions of
pea are conserved in national genebank housed at ICAR-NBPGR, New Delhi, of
which about 1118 accessions are exotic, while 3366 are indigenous to India. The
Geo-referenced map illustrating the coverage of pea germplasm collections executed
across the states in India is depicted in Fig. 25.2. Around 98,000 accessions consist
of released varieties, advanced breeding lines, land races, mutants and wild species:
these are being maintained in various gene banks worldwide. Of the total collections,
wild pea accessions contribute only 2%, highest by land races (Smýkal et al. 2013;
1246 A. K. Parihar et al.

Fig. 25.2 Georeferenced map showing the distribution of pea germplasm collections in India

Warkentin et al. 2015; Rubiales et al. 2019; Parihar et al. 2020a, b). Among wild
collection, 706 accessions belong to P. fulvum, 624 to P. s. subsp. elatius, 1562 to
P. s. subsp. sativum (syn. P. humile/syriacum) and 540 to P. abyssinicum (Smýkal
et al. 2013).
National Institute for Agricultural Research, Dijon, France (8839 accessions);
Australian Temperate Field Crop Collection, Horsham (7432 accessions); N.I.
Vavilov Research Institute of Plant Industry (VIR), St. Petersburg, Russia (6790
accessions); The United State Department of Agriculture (USDA) (6827
accessions); Leibniz Institute of Plant Genetics and Crop Plant Research, Germany
(5343 accessions) and International Center for Agricultural Research in the Dry
Areas (ICARDA) (4596 accessions) are the six leading institutions, which holds
around 40% of total pea germplasm collections. However, collections of pea germ-
plasm are also available in Italy (4558 accessions), China (3837 accessions), UK
25 Field Pea Breeding 1247

Table 25.1 Major dry pea germplasm holding organizations worldwide (Source: Warkentin et al.
(2015); https://www.genesys-pgr.org/)
S. Number of
no. Name of institutions/organization accessions
1 INRA CRG Légumineuse à grosses graines, Dijon, France 8839
2 Australian Temperate Field Crop Collection, Horsham, Australia 7432
3 Plant Germplasm Introduction and Testing Research Station, Pullman, 6827
USA
4 N.I. Vavilov Research Institute of Plant Industry, St. Petersburg, Russia 6790
5 Leibniz Institute of Plant Genetics and Crop Plant Research, Gaterleben, 5343
Germany
6 International Center for Agricultural Research in the Dry Areas, Lebanon 4596
7 Istituto del Germoplasma, Bari, Italy 4558
8 ICAR-National Bureau of Plant Genetic Resources, New Delhi, India 4484
9 Institute of Crop Sciences, CAAS, China 3837
10 John Innes Centre, Norwich, UK 3562
11 Science and Advice for Scottish Agriculture, Scottish Government, UK 3298
12 Plant Breeding and Acclimatization Institute Blonie, Radziko, Polland 2896
13 NordGen, Nordic Genetic Resource Centre, Alnarp, Sweden 2849
14 Yurjev Institute of Plant Breeding, Kharkov, Ukraine 2311
15 Genetic Resources Unit, Institute of Biological, Environmental and Rural 2110
Sciences, Aberystwyth University, UK
16 National Center for Vegetable Crops Research (CNPH)/EMBRAP, 1958
Brasil
17 Junta de Castilla y León. Instituto Tecnológico Agrario de Castilla y 1772
León, Spain
18 Ethiopian Biodiversity Institute, Ethiopia 1768
19 Institutot Nacional de Investigacion y Tecnologia Agraria y Alimantaria, 1648
Spain
20 Institute of Plant Introduction and Genetic Resources, Sadovo, Bulgaria 1570
21 Centre for Applied Research of Vegetables and Special Crops, Olomouc, 1414
Czech Republic
22 AGRITEC, Research, Breeding and Services Ltd., Sumperk 1326

(3562 accessions), Poland (2896 accessions), and Bulgaria (2100). Also, countries
such as Brasil, Spain, Ethiopia, Ukraine, Czech Republic, Hungry, and the
Netherlands also conserve substantial germplasm accessions of Pisum in their
national gene banks (Smýkal et al. 2012; Warkentin et al. 2015). Detail list of
major dry pea germplasm holding at global level is given in Table 25.1. Among
the above-mentioned organizations, the Vavilov Research Institute is the oldest and
the John Innes (JI), Norwich, is having very representative and perhaps the best
studied Pisum collection with 1200 P. sativum cultivars, 600 landraces, 750 genetic
stocks, and reference lines. An estimated 20% of the world’s ex situ pea germplasm
is duplicative, and a total 59,000 of accessions are designated to be unique
(Warkentin et al. 2015; Smýkal et al. 2013).
1248 A. K. Parihar et al.

During recent times, several online portals have been developed by different
national and international organization to store and share the important information
of pea. The web portal of John Innes Centre, Norwich, UK (JIC; http://www.jic.ac.
uk/germplasm/) and the USDA (http://www.ars-grin.gov/npgs/) are the most
advanced websites involved in supply of germplasm accessions as per requisitions.
In case of wild species, Israel gene bank possesses a collection of wild relatives of
P. fulvum and P. sativum subsp. elatius var. pumilio collected from the Middle East.
To share important information of pea related to phenotypic and genotypic data sets,
there are a number of international collection web databases: for instance, European
Cooperative Program on Plant Genetic Resources (ECPGR), International Legume
Database and Information Service (ILDIS), Legume Information System (LIS),
Legume phylo-informatics database, INRA Dijon Legume genetic and genomic
resources, INRA LegumeBase, LegumeIP, Genetic Resources Information Network
(GRIN), System-wide Information Network for Genetic Resources (SINGER),
GRIN-Global, Cool Season Food Legume Database (https://
coolseasonfoodlegume.org; Washington State University), and KnowPulse (https://
knowpulse.usask.ca; University of Saskatchewan). Genesys (https://www.genesys-
pgr.org/) is an online platform where information about 21,693 pea accessions are
available, which provides information about plant genetic resources conserved in
gene banks worldwide.
So far, eight core collections have been developed in Australia, China, Czech
Republic, France, Poland, Spain, the United Kingdom, and the United States to
accelerate germplasm evaluation and their judicious utilization (Warkentin et al.
2015; Rubiales et al. 2019). The first pea core set was constructed at JIC following
Brown (1989) recommendations and consists of representatives from all the Pisum
taxon phenotyped for nine seed quality characteristics (Matthews and Ambrose
1994). Simon and Hannan (1995) developed in the USDA core collection of
P. sativum with a few P. sativum ssp. elatius based on geography and flower colour.
The USDA core was further refined to 310 accessions using 26 quantitative traits
(Coyne et al. 2005). The Spanish core is a landrace collection based on passport and
quantitative data (Martin-Sanz et al. 2011). The Polish core was developed consid-
ering diversity of type, taxon, and described genes studied using isozymes
(Swiecicki et al. 2000). Baranger et al. (2004) reported the INRA core collection
of 148 accessions wherein 43 Pisum accessions were selected based on protein and
DNA marker diversity. With further utilization of molecular data, Zong et al. (2009)
developed a core of Chinese landraces considering molecular diversity data. Smýkal
et al. (2011) proposed the use of a model-based method for the creation of a
molecular/ecogeographically diverse international pea core collection for a realistic
initiation toward phenotyping of the nonduplicative pea germplasm.
25 Field Pea Breeding 1249

25.9 Brief of Existing Genetic Variability for Agronomic

and Nutritional Parameters

Genetic variability is quintessential to increase yields and sustainable production in

the face of anticipated climatic changes. In addition, knowledge of genetic diversity
plays an important role in gene bank management and in planning experiments, as it
enables efficient sampling and utilization of germplasm through identification and
elimination of duplicates (Ghafoor et al. 2005). In order to maintain, evaluate, and
utilize germplasm efficiently and effectively, the proper investigation of the magni-
tude of genetic diversity is indispensable (Smith and Smith 1989).
Morphological characterization is the first step toward the categorization of crop
germplasm (Smith and Smith 1989; Ghafoor et al. 2003). Considerable morphologi-
cal variation is reported in pea by several research groups (Blixt 1974; Hoey et al.
1996; Kumar and Jain 2003; Sharma et al. 2003; Singh et al. 2003a, b; Parihar et al.
2014b). The significant and positive association of traits like percent emergence,
plant height, pod length, number of pods/plant, number of seeds/pod, number of
locules per pod, primary branches, number of nodes, seed set, 100-seed weight,
flowering time, days to maturity, biological yield, and harvest index with seed yield
has been reported (Singh and Singh 2006; Sardana et al. 2007; Nisar et al. 2008,
2011; Gatti et al. 2011; Basaiwala et al. 2013; Ofga and Petros 2017; Pratap et al.
2021). Also, significant morphological variation in terms of flower color, seed coat
color, cotyledon color, leaflet shape, pod shape, pod length, plant height, numbers of
pods per plant, number of seeds per pod, seed size, hilum color and seed shape,
stipule length, stipule width, intermodal length, number of nodes, seed diameter
(Ghafoor et al. 2005; Smýkal et al. 2008; Umar et al. 2014; Handerson et al. 2014). A
large number of field pea genotypes have been evaluated for major agronomic traits,
and nutritional parameters and plenty of variability was observed (Table 25.2).
Similarly, in case of nutritional value abundant amounts of variability exist in
field pea for protein, starch, minerals, and antinutritional factors (Table 25.2), that
usually is influenced by both environments and genetic factors (Ray et al. 2014;
Hood-Niefer et al. 2012; Bourgeois et al. 2011; Harmankaya, et al. 2010; Wang et al.
2008a, b). Carbohydrates are the main constituent of pea, which is available in
substantial amounts (Dahl et al. 2012). Starch content fluctuates from 27.6% to
57.23% (Tzitzikas et al. 2006; Holasová et al. 2009). Likewise, the amylose content
is reported to vary widely among varieties and mutant lines (Guillon and Champ
2002), with a mean of 27.8% of total starch (Holasová et al. 2009). However, no
effect of genotype or environment was demonstrated on the amylose content (Hood-
Niefer et al. 2012). The seed coat, hull, and cotyledon are the source of dietary fiber
in peas (Martens et al. 2017), with water-insoluble polysaccharides (mainly cellu-
lose) predominant in seed coat, while the cotyledon consists of hemicellulose,
pectin, and cellulose (Martens et al. 2017; Dahl et al. 2012; Tosh and Yada 2010;
Guillon and Champ 2002; Reichert and MacKenzie 1982).
Like other legumes, pea contains considerable amount of raffinose-family and
other galactose-containing oligosaccharides (Tosh and Yada 2010) of which
stachyose is reported to vary from 0.7% to 4.1%. (Jones et al. 1999), total
1250 A. K. Parihar et al.

Table 25.2 Genetic variation on important agronomic and seed quality traits in pea
Traits Range References
Days to 50% flower 41.00–103.00 Parihar et al. (2014b)
45–100 Handerson et al. (2014)
60–120 Rana et al. (2013)
62.08–86.08 Singh et al. (2018)
56–168 Rana et al. (2017)
55.00–73.67 Basaiwala et al. (2013)
Days to maturity 73.00–135.00 Parihar et al. (2014b)
128–212 Rana et al. (2017)
96.33–132.33 Singh et al. (2018)
81.0–121 Jha et al. (2012)
94.33–128.67 Basaiwala et al. (2013)
Plant height (cm) 13.33–209.33 Parihar et al. (2014b)
33.4–197.2 Ali et al. (2007)
47.6–175 Yadav et al. (2010)
43.20–180.40 Basaiwala et al. (2013)
14.39–245.53 Umar et al. (2014)
51.7–85.3 Annicchiarico et al. (2017)
37.9–75.3 Gatti et al. (2011)
19–117 Handerson et al. (2014)
38.66–279.8 Rana et al. (2017)
30—132 Jha et al. (2012)
30.0–132 Nisar et al. (2011)
100 seeds weight 3.03–31.6 Nisar et al. (2008)
3.2–23.27 Ali et al. (2007)
3.03–26.32 Ghafoor et al. (2005)
13.40–28.00 Handerson et al. (2014)
13.3–24.0 Gatti et al. (2011)
15.88–22.22 Jeberson et al. (2017)
15.68–23.14 Basaiwala et al. (2013)
4.26–25.65 Singh et al. (2010)
6.12–20.27 Ouafi et al. (2016)
6.2–32.3 Azmat et al. (2011)
5.6–28.9 Rana et al. (2013)
11.18–31.43 Singh et al. (2018)
2.99–47.25 Burstin et al. (2015)
Pod length (cm) 2.94–8.02 Nisar et al. (2008)
3.5–7.98 Ali et al. (2007)
2.90–12.10 Rana et al. (2017)
1.73–8.55 Umar et al. (2014)
4.66–9.99 Parihar et al. (2014b)
4.9–12.8 Azmat et al. (2011)
Pods/plant 7.67–89.00 Parihar et al. (2014b)
12.00–29.67 Basaiwala et al. (2013)
(continued)
25 Field Pea Breeding 1251

Table 25.2 (continued)

Traits Range References
8.33–53.50 Rana et al. (2017)
3.17–10.87 Jeberson et al. (2017)
3.5–195 Ali et al. (2007)
2–210. Umar et al. (2014)
8.5–18.3 Yadav et al. (2010)
11–59 Rana et al. (2013)
4.25–179.33 Ghafoor et al. (2005)
Seeds/pod 2.2–7.8 Nisar et al. (2008)
2.2–8.0 Ali et al. (2007)
2.0–8.0 Rana et al. (2017)
3.40–6.53 Parihar et al. (2014b)
3.7–5.4 Yadav et al. (2010)
4.60–10.33 Ouafi et al. (2016)
2.1–5.6 Gatti et al. (2011)
3.0–7.5 Rana et al. (2013)
3.0–9.1 Azmat et al. (2011)
3.01–6.47 Singh et al. (2018)
2.2–6.8 Ghafoor et al. (2005)
Seed yield (g/plant) 0.24–213.4 Nisar et al. (2008)
14.27–112.13 Parihar et al. (2014b)
2.28–34.42 Rana et al. (2017)
2.0–49.0 Ali et al. (2007)
8.7–17.7 Yadav et al. (2010)
7.10–19.17 Basaiwala et al. (2013)
4.15–12.82 Handerson et al. (2014)
10.1–45.6 Rana et al. (2013)
Biological yield (g/plant) 9–452.66 Nisar et al. (2008)
9–170 Ali et al. (2007)
7.20–28.00 Parihar et al. (2014b)
9.13–103.25 Ghafoor et al. (2005)
Harvest index (%) 24.75–63.87 Parihar et al. (2014b)
9.74–47.23 Ghafoor et al. (2005)
0.16–50.60 Nisar et al. (2008)
23.23–54.10 Basaiwala et al. (2013)
23.45–60.00 Singh et al. (2018)
1.81–55.71 Nisar et al. (2011)
Protein 17.5–27.8 Annicchiarico et al. (2017)
18.1–29.4 Jha et al. (2012)
21.13–27.05 Harmankaya et al. (2010)
15.8–32.1 Burstin et al. (2007)
Iron (ppm) 21.90–58.40 Harmankaya et al. (2010)
23.16–105.2 Kwon et al. (2012)
23–105 Grusak and Cakmak (2005)
(continued)
1252 A. K. Parihar et al.

Table 25.2 (continued)

Traits Range References
45–53 Amarakoon et al. (2014)
Zinc(ppm) 21.0–57.10 Harmankaya et al. (2010)
16.10–106.63 Kwon et al. (2012)
11.3–82.9 Demirbas (2018)
39.0–63.0 Amarakoon et al. (2012)

a-D-galactosides from 22.6 to 63.4 g/kg, verbascose from 0.0 to 26.7 g/kg; raffinose
from 4.1 to 10.3 g/kg, and sucrose from 11.6 to 25.4 g/kg (Vidal-Valverde et al.
2003). Most recently, Gawłowska et al. (2017) reported highest content of total
soluble carbohydrates and total RFOs in wrinkled seeds and lowest in P. fulvum. It
has also been observed that the total RFOs content was positively associated with
stachyose and verbascose. Noteworthy, all oligosaccharides contents were low in
lines having dominant alleles of pea seed genes (R, A, and I ). The recessive
mutations for these genes resulted in an increased content of RFOs. Consequently,
detection of mutant lines having very low concentrations of oligosaccharides is
prerequisite toward the development of field pea cultivars with low RFOs that
would prevent flatulence and related issues.
The protein content varied from 13.7% to 30.7% of seed dry matter (Tzitzikas
et al. 2006). Similarly, Harmankaya et al. (2010) reported noteworthy variations for
protein (21.13 to 27.05%), potassium (562.8 to 937.8 mg/100 g), phosphorus (163.4
to 374.2 mg/100 g), calcium (45.91 to 157.40 mg/100 g), magnesium (47.31 to
102.81 mg/100 g), sulfur (75.69 to 194.4 mg/100 g), iron (2.19 to 5.84 mg/100 g),
and zinc (2.10 to 5.71 mg/100 g) content. The pea proteins are predominantly
storage proteins, or globulins, and their amino acid matrix plays pivotal role in
nutritional significance (Boye et al. 2011; Bourgeois et al. 2011). Recently, number
of pea germplasm lines with more than 30% protein in the seeds have been identified
and used in breeding program (Bing 2015; Shen et al. 2016; Demirbas 2018). Pea
seed is considered as good source of several macro- and micronutrients and signifi-
cant amount of its variability has been noticed (Table 25.1). The yellow peas are
reported to have higher levels of Fe, Mg, and Mn, but lower levels of K, as compared
to green peas (Gawalko et al. 2009). The abundant variability for Fe (46–-
54 mg kg1), Zn (39–63 mg kg1), and Mg (1350–1427 mg kg1) was reported
in a multilocation evaluation (Amarakoon et al. 2012). Similarly, Kwon et al. (2012)
noticed plenty of variation for most of the micronutrients especially Fe
(23.16–105.2 ppm) and Zn (16.1–106.63 ppm) in USDA core collection. While
the Fe content of dry pea seeds is reported to vary from 45 to 58 mg/kg in
commercial cultivars (Ray et al. 2014).
Recently, Amarakoon et al. (2015) observed that the Fe concentration varied from
45 to 53 mg/kg, and reported existence of substantial concentrations of Fe promoters
like xanthophyll (17 mg/100 g), canthaxanthin (68 mg/100 g), beta-carotene
(680 mg/100 g), kestose (1433 mg/100 g), quercetin (51.7 mg/100 g), and ferulic
acid (56.1 mg/100 g). The phytic acid concentration was low (2.7–3.2 mg/g) and the
25 Field Pea Breeding 1253

phytic acid:Fe molar ratio ranged from 5.0 to 5.6. Ma et al. (2017) have registered
enormous genotypic variability for several minerals (Fe, Zn, Ca, K, and S) in a RIL
population, the iron and zinc content ranged from 37.3 to 71.2 and 30.7 to 64.9 μg/g
DW), respectively. Demirbas (2018) reported tremendous diversity for nitrogen
(22.3–66.7 g kg1), phosphorus (1.48–8.47 g kg1), potassium (6.7–18.7 g kg1),
iron (38.6–320.9 mg kg1), zinc (11.3–82.9 mg kg1), copper (10.5–50.8 mg kg1),
and manganese (10.2–37.9 mg kg1) in Turkish pea germplasm. In addition to other
micronutrients, field pea is an important dietary source of selenium and is reported to
range from 373 to 519 mg/kg (Thavarajah et al. 2010).
Pea is also rich in vitamins, particularly thiamin (B1) and folate (B9), although
limited research efforts are made so far to explore the diversity in vitamin B
concentrations in field pea (Sierra et al. 1998; Jha et al. 2015a, b). The folate content
in yellow and green seeded genotype is reported to range from 237 to 556 and 249
to 648 mg/100 g (Han and Tyler 2003), 41  55 μg/100 g, and 50  202 μg/100 g
(Gupta et al. 2013), respectively. Recently, Jha et al. (2015a, b) reported total
folate concentration to vary from 23 to 30 mg/100 g in pea, of which
5-methyltetrahydrofolate (5-MTHF) and tetrahydrofolate (THF) were the predomi-
nant forms. Significant effects of environment and cultivar were also observed for
the majority of the folates. The lutein concentration in green cotyledons ranged from
0.768 to 1.394 mg/100 g, whereas yellow cotyledon has lower amount of lutein. The
highest variation in lutein content was recorded in orange cotyledon lines. Besides,
β-carotene in green cotyledon genotypes fluctuates between 0.1 and 0.2 mg/100 g,
whereas yellow and orange cotyledon contains 10 times lower concentration of
β-carotene.
A strong positive association among lutein and chlorophyll content was obtained
(Holasová et al. 2009). Most recently, Bangar et al. (2017) reported that cotyledon
pigmentation (green and yellow) had no association with total carotenoid concentra-
tion, but β-carotene concentration was greater in green cotyledon genotypes. How-
ever, Ashokkumar et al. (2014, 2015) have reported total carotenoid to vary with
cotyledon pigmentation; the genotypes with green cotyledon had approximately
twice the amount of total carotenoids (16–21 μg g1) as compared to yellow
cotyledon (7–12 μg g1). Peas also contain various phytochemicals including
phenolic compounds, phytates, saponins, and oxalates. The prevalent phenolic
compounds in pulses are tannins, phenolic acids, and flavonoids (Campos-Vega
et al. 2010). The highest concentrations of most phenolics exist in the seed coat,
especially in dark-seeded genotypes (Campos-Vega et al. 2010; Troszynska and
Ciska 2002; Duenas et al. 2004). Likewise, Xu et al. (2007) also noticed that the
antioxidant activity is associated with seed coat color.
The results pertaining to crop wild relatives revealed that wild Pisum species and
subspecies are a source of many desirable traits, like resistance to pea weevil in
P. Fulvum (Teshome et al. 2015a, b; Clement et al. 2009; Byrne et al. 2008a, b).
Sincere efforts have been made for the transmission of powdery mildew (Fondevilla
et al. 2007b; Mishra et al. 2007) and bruchid (Byrne et al. 2008a, b; Clement et al.
2009) resistance from Pisum fulvum into cultivated pea along with the incorporation
of PSbMV and Fusarium resistances from primitive landraces (Smýkal et al. 2013;
1254 A. K. Parihar et al.

McPhee et al. 1999). The value of CWR has been demonstrated by novel dominant
gene (Er3), which was identified in Pisum fulvum conferring resistance to E. Pisi and
has been introduced successfully in adapted Pea (Sharma and Yadav 2003;
Fondevilla et al. 2008). Moreover, some P. fulvum accessions were found to show
resistance to Mycosphaerella pinodes and Orobanche crenata and subsequently
involved in crossing with cultivated pea (Fondevilla et al. 2005; Pérez-de-Luque
et al. 2005). On similar note, high level of resistance was reported in P. fulvum for
rust (Barilli et al. 2010, 2018) and ascochyta blight (Fondevilla et al. 2005; Jha et al.
2012).
Interestingly, the commercially least accepted pigmented flower and seed coat are
an outstanding sources of Aphanomyces root rot resistance (Hamon et al. 2011) and
Fusarium root rots (Weeden and Porter 2007; Grunwald et al. 2003). Most impor-
tantly, the valuable resistance for biotic and abiotic stresses can also be embraced
from Lathyrus species, which is harbored in tertiary pea gene pool (Patto et al. 2007),
preferably through the use of modern biotechnological techniques. Based on germ-
plasm characterization and evaluation for various yield attributing traits, nutritional
parameters and biotic and abiotic stress resistance potential donors have been
identified by different researchers. The details of trait specific potential donors are
given in Table 25.3.
The morphological traits are limited and most of them are multigenic, quantitative
or continuous characters, and their appearance is influenced by environmental
conditions. As a complementary approach, biochemical analysis of isozyme markers
proves its diagnostic potential in pea (Swiecicki and Wolko 1987; Swiecicki et al.
2000; Pošvec and Griga 2000; Ali et al. 2007; Smykal et al. 2008), but a limited
degree of polymorphism and potential sensitivity to environmental and developmen-
tal variation prevented its broad application. In addition to morphological and
biochemical marker, various DNA-based markers have been successfully used to
compute genetic variations among closely related pea germplasm, such as STMS
(Baranger et al. 2004; Haghnazari et al. 2005); ISSR (Lázaro and Aguinagalde
2006), SNP (Duarte et al. 2014a, b), SRAP (Esposito et al. 2007), IRAP (Smýkal
et al. 2008), RBIP (Smýkal et al. 2008), EST-SSR (Teshome et al. 2015a, b), and
SSR (Handerson et al. 2014; Negisho et al. 2017; Mohamed et al. 2019). Among
them, SSRs have gained popularity because of cost effectiveness, speed, reproduc-
ibility, and polymorphism (Snowdon and Friedt 2004). More recently, next -genera-
tion sequencing has allowed rapid SNP discovery and genotyping array
development in pea (Deulvot et al. 2010; Duarte et al. 2014a, b; Leonforte et al.
2013a; Sindhu et al. 2014).

25.10 Inheritance of Important Qualitative and Quantitative

Traits

To accelerate the success of any breeding program, the information about nature and
magnitude of gene action is mandatory (Shashikumar et al. 2010), as the selection of
suitable parent for hybridization and breeding procedure for the improvement of trait
25 Field Pea Breeding 1255

Table 25.3 Potential source for field pea improvement

Trait Germplasm/variety/wild relatives Country Reference
Earliness DDR-30 India Bhuvaneswari et al.
(2017) and Handerson
et al. (2014)
DDR 23 India Handerson et al. (2014)
IPFD 18–14, IPFD 18–16, IPFD India Parihar et al. (2021a, b
18–17, IPFD 18–11, IPFD 18–13,
IPFD 18–18, IPFD 18–19, IPFD
18–12, IPFD 18–20, IPFD 18–22
P 1613, P 73–1, P 118–1, P 1343 India Dixit and Gautam
(2015)
Spring pea Argentina Gatti et al. (2011)
Pods /plant 10,622, 11,116, 10,476, 10,479 Pakistan Ghafoor et al. (2005)
P 1541–33, P 1548–2, P 108, P 996 India Dixit and Gautam
(2015)
100-seed weight 10,603, 10,609, 10,623, 10,625, Pakistan Ghafoor et al. (2005)
11,083, 11,089
KPMR-747 India Handerson et al. (2014)
Root length and PI 261631 USA McPhee (2005)
volume
Harvest index 10,603, 10,607, 10,609, 11,052, Pakistan Ghafoor et al. (2005)
11,094, 11,100, 11,114, 10,479
Protein PS3045 (27%) Turkey Harmankaya et al.
(2010)
MI3391 (32%), CDC647–1(26%) Canada Bing (2015)
Iron content Tekirdağ2, Tokat1, Konya3, Turkey Demirbas (2018)
İzmir4, Giresun, Elazığ,
Adıyaman2
Zinc content Agassiz USA Amarakoon et al.
(2012)
PS3029–2 Turkey Harmankaya et al.
(2010)
Tekirdağ2, Konya3, Elazığ, Turkey Demirbas (2018)
Adıyaman2
Insect and pest resistance germplasm/wild relatives
Powdery mildew 9057, 9370, 9375, 10,609, 10,612, Pakistan Azmat et al. (2012)
18,293, 18,412, 19,598, 19,611,
19,616, 19,727, 19,750, 19,782,
20,126, 20,152, 20,171, It-96,
no. 267, and no. 380
Powdery mildew P. fulvum (P660–4) Spain Fondevilla et al.
(2007a, b, c)
Powdery mildew HFP4, EC598878, EC598538, India Rana et al. (2013)
EC598757, EC598704,
EC598729, EC598535,
EC598655, EC598816,
EC381866, IC278261, IC267142,
IC218988, IC208378, IC208366
(continued)
1256 A. K. Parihar et al.

Table 25.3 (continued)

Trait Germplasm/variety/wild relatives Country Reference
HFP 9907 B, Pant Pea 42, VL India Dixit and Gautam
Matar 42, IPFD 99–13, IPFD 1–10, (2015)
IPF 99–25, Pusa prabhat, Ambika
GPHA-9 and GPHA-19 Ethiopia Assen (2020)
Rust IPF-2014-16, KPMR-936 and India Das et al. (2019)
IPF-2014-13
PJ 207508, C 12, Wisconsin, DMR India Chaudhary and
3, Pant P 5, Pant P 8, Pant 9, HFP Naimuddin (2000) and
8711 and HUDP 15, IPFD 1–10 Dixit and Gautam
(2015)
Downey mildew Mukta, Snowpeak Australia Davidson et al. (2004)
Pea seed-borne PI 193586, PI 193835 Ethiopia Hagedorn and Gritton
mosaic virus (1973)
(PSbMV)
Salinity tolerance ATC1836 Australia Leonforte et al.
(2013a)
Pseudomonas JI0130 Spain Martín-Sanz et al.
syringae pv. Pisi (2012)
(race 6, 8)
Pseudomonas Forrimax, JI2546, PI-277852, Spain Martín-Sanz et al.
syringae pv. Pisi ZP1328, Cherokee, Corallo, (2012)
(race 8) Lincoln, JI2385, PM29, PM232,
PM33, JI1829, ZP1282, ZP0104,
ZP1301, ZP0123, ZP0168
Mycosphaerella CN 112432, CN 112441, CN Canada Jha et al. (2012)
blight 112513
(Mycosphaerella
pinodes)
P. Fulvum (P651), Radley Spain Fondevilla et al. (2005)
Stem fly P-4039, P-4107 India Vishal and Ram (2005)
(Melanagromyza
phaseoli)
Leaf miner P-4107 India Vishal and Ram (2005)
(Chromatomyia
horticola)
Pea weevil P. fulvum (ATC113) Australia Hardie et al. (1995)
(Bruchus and Byrne et al.
pisorum) (2008a, b)

of interest mainly hinged on the understanding of gene action/effects operating in a

particular breeding population (Sharma et al. 2013). The study of trait inheritance
pattern has been the major aim of myriad studies since early days (Knight 1799;
Mendel 1866). Notably, pea has been acknowledged as the original model organism
and used in the discovery of the Mendel’s laws of inheritance, which makes it the
founder of modern plant genetics (Smýkal et al. 2012). The inheritance of numerous
morphological, physiological, quality, and resistance attributes has been elaborated
25 Field Pea Breeding 1257

by several workers (Lamprecht 1948; Yarnell 1962; Blixt 1974; Kalloo and Bergh
1993; Gritton 1980; Kumar et al. 2006a, b; Amin et al. 2010). Mendel (1866) was the
first to study the inheritance of seed forms, that is round versus wrinkled and
observed it to be governed by a single gene R. Round form was dominant over
wrinkled. Due to spontaneous mutation in the wild-type, round (RR) seeded at the
beginning of seventeenth century, the wrinkled (rr) seed developed (Lamprecht
1956; Bhattacharyya et al. 1993).
Wrinkling of the seed was one of the characters used by Mendel in experiments,
which led him to formulate the laws of inheritance. This character or locus was later
named as rugosus (r) from the Latin for wrinkled or shriveled (White 1917). The
wrinkled-seed mutant (rr) arose through mutation of the gene encoding starch-
branching enzyme isoform I (SBE1) by insertion of a transposon-like element into
the coding sequence (Bhattacharyya et al. 1993). Much later, a second locus rb
causing wrinkled seeds was identified (Kooistra 1962). The rb mutation of peas
causes structural and regulatory changes in ADP glucose pyrophosphorylase from
developing embryos, but this mutation has only become available in Europe since
the 1930s (Hylton and Smith 1992; Reid and Ross 2011, Rayner et al. 2017). These
two loci are known to affect the development of embryo, and mutants at both loci
behave as single gene recessives. Despite the large number of genes that affect the
seed (Blixt 1972), very few have been identified that influence the development of
the embryo (Hedley and Wang 1987).
Recessive alleles at the r locus not only have a profound effect on the shape of the
seed but also have numerous effects at all levels of seed development. Later the role
of interaction of gene pair Aa, Rr, and Didi in determination of seed surface was
examined (Wellensiek 1943) and noticed that the gene A and a controlled indented
and smooth testa, respectively. The gene R and r was responsible for smooth and
wrinkled surface, respectively, and di gave rise to dimpling in presence of r gene.
The a and di were episatic to the smooth phenotype of R. Single recessive genes
determine flattened seed shape (com), gritty seed surface (gty), and green cotyledons
(i), while dominant gene pi along with ar and b determined black hium. Gene pair
Rr, which is responsible for seed shape, also governed the starch and amylase
content (Amin et al. 2010; Mohan et al. 2013). Round seed shape was monogenic
and dominant over wrinkled seed shape (Rastogi and Saini 1984). Recently, Rayner
et al. (2017) reported that the wrinkled-seeded phenotype is maternally determined
in JI2110 genotype, which is controlled by two genetic loci, and the extent to which
it is manifested is very sensitive to the environment.
As flowering time is associated to maturity, the investigation of inheritance
pattern of flowering is quintessential to develop the required cultivars. Mendel
(1865) reported the flowering time of hybrids to stand almost exactly between the
times of the two parents. During the early days of modern genetics, the flowering
time evoked the interest of investigators and Hansel (1954) reported flowering time
to be governed by two major genes with unspecified number of modifiers. The
polygenic system of inheritance of flowering was reported wherein lateness was
dominant to earliness and gene effects were additive (Rowlands 1964; Watts et al.
1970). Floral initiation and development in pea have been studied for many decades
1258 A. K. Parihar et al.

(Murfet and Reid 1993) and based on physiological and mutational analyses, a
model for flowering that involves both a floral inhibitor and a stimulus has been
developed (Reid et al. 1996; Weller et al. 1997b). The stimulus is specific to
flowering and is under the control of GIGAS (Beveridge and Murfet 1996). The
synthesis of the floral inhibitor is controlled by different genes (STERILE NODE,
HIGH RESPONSE, PHOTOPERIOD, DAY NEUTRAL, and EARLY) and is
strongly regulated by photoperiod (Foucher et al. 2003). Earlier reports have
identified about ten genes, that is, Lf, E, Hr, Sn, Ppd, Dne, FUN1, LV, GI, and
VEG1, involved in controlling flowering time (Murfet 1971a, 1990a, b; Murfet and
Reid 1993, Weller et al. 1997b). The Lf (late flowering) was the first major gene
identified in pea (Hoshino 1915; White 1917).
The ability to respond to photoperiod in pea requires the presence of the dominant
alleles for three complementary genes: Sn (sterile node), Dne (day neutral), and Ppd
(photoperiod response) (Murfet 1971b; King and Murfet 1985; Arumingtyas and
Murfet 1994). The genes E (early) and Hr (high response) influence expression of
the Sn Dne Ppd system during different stages of ontogeny (Murfet and Reid 1993).
So far, twenty loci pertaining to flowering time and inflorescence development have
been identified in pea. Initial work on genetic control of flowering recognized several
loci in existing variation among various cultivars of pea, whereas other loci have
been subsequently identified through characterization of induced mutants and spe-
cific mutant screens (Murfet, 1985; Weller et al. 1997a, 2009; Weller and Ortega
2015). Flowers are borne on axillary racemes in the pea and the wild type pea
cultivars usually produce two flowers per raceme; however, multiflowered types
have also been identified (Lamprecht 1947; Hole and Hardwick 1976; Gritton 1980;
Murfet and Reid 1993; Devi et al. 2018, 2021). Some reports have proposed a
polygenic control (Ibarbia and Bienz 1970; Snoad and Arthur 1973), whereas others
proposed control by two genes, Fn and Fna. The plant with FnFna produces one
flower per raceme, while Fnfna and fnFna produces two flowers, and fnfna produces
three or more flowers per raceme (Lamprecht 1947; Murfet and Reid 1993). This
trait is certainly influenced by some major flowering genes: Sn, Hr, Veg-2inc, and pim
(Maki et al. 1993; Singer and Maki 1993; Alcalde et al. 2000).
The genetic basis of the tall (Le)/dwarf (le) difference was first identified by
Mendel (1866). The Le locus is probably the best known of the internode length loci
(White 1917). The principal effect of le is to reduce the length of the upper
internodes by 40–60% by making the stem to appear in zig-zag (Blixt, 1972).
However, the Le locus is also reported to have a minor pleiotropic effect on
flowering behavior (Rasmusson 1935; Barber 1959; Marx 1975). Overall, five
major gene loci, Le/le, La/la, Cry/cryc/cry1, Na/na, and Lm/lm are known to admin-
istrate internode length in peas. Combinations of the different alleles at these loci
decide the phenotype of a plant (tall, dwarf, cryptodwarf, slender, nana, and micro).
A new phenotype cryptotall (Le la cryc Na Lm) was described in which the na mutant
was completely epistatic to the Le/le gene pair (Reid et al. 1983).
The branching is controlled by two single recessive genes, Fr and Fru
(fructicosa) in presence of each other, which are located in chromosome 3 and
4, respectively (Blixt 1968; Lamprecht 1950). The ramosus mutant rms was
25 Field Pea Breeding 1259

obtained after X-irradiation treatment (Blixt 1976). Six ramosus loci have been
identified among 16 induced, single-gene recessive, branching mutants: ram, rms-
1, rms-2, rms-3, rms-4, and rms-5. The ram mutant is characterized by profuse
branching and a large number of poorly fertile flowers. Rms1 is one of the series of
six ramosus loci in pea in which recessive mutant alleles confer increased branching
at basal and aerial vegetative nodes. The rms2, rms3, and rms4 mutants differ from
wild-type plants mainly in regard to increased lateral bud release and growth. All
mutants are responsible for the increase in number of branches (Blixt 1976;
Arumingtyas et al. 1992; Murfet and Reid 1993; Beveridge et al. 1994, 1996,
1997). In addition, most flowering and internode length genes have significant effect
on branching habit. Further, three loci have been identified that influence the angle of
growth of stem braches. The dominant alleles ASc (Ascendens) cause braches to
grow semiprostrate, the recessive ho (horizontalis) causes lateral branches to grow
horizontally, and the pro (procumbens) is said to cause stem branches to grow at first
horizontal but subsequently at approximately 45 angle (Lamprecht 1963; Murfet
and Reid 1993). In the beginning of twenty-first century a further Ramosus locus,
Rms6, with two recessive or partially recessive mutant alleles, rms6–1 and rms6–2
have been identified, which is characterized by increased branching from the basal
node (Rameau et al. 2002) and is reported to be derived from dwarf and tall cultivars,
respectively.
Generally, the stem of peas is either round or angular and hollow (Mohan et al.
2013), and rarely fascinated. Stem fasciation in peas is reported for the first time in
1597 (Święcicki 2001), and is reported to change the stem architecture along with
the physiology of flowering and maturity (Gawłowska and Święcicki 2016). It has
been shown that this character is controlled by one to four independent genes or
multiple alleles of a single locus (Scheibe, 1954; Marx and Hagedorn 1962; Blixt
1972; Lamprecht 1974; Gottschalk 1977; Święcicki 2001). The most popular was
the acceptance of two independent genes—fa in LG IV and fas in LG III responsible
for fasciated character (Lamprecht 1974; Blixt 1977). White (1917) was the first to
ascribe a gene symbol, in this case Fa for the wild-type form. Since then, another
gene for fasciation (FAS) has also been documented (Sinjushin and Gostimskii
2008). Additionally, a similar mutation type, dichotomous branching, was selected
and reported as a character governed by two polymeric genes bif1 and bif2
(Gottschalk and Wolf 1983); this alteration was associated with a fasciation of
only a few upper nodes that results in a forked stem (Gawłowska and Święcicki
2016).
The wild-type pea leaf is pinnately compound and consists of basal, foliaceous
stipules, proximal leaflets, and distal tendrils (Yaxley et al. 2001). The character of
leaves, leaflets, stipules, and tendrils are governed by single recessive gene (Amin
et al. 2010). The replacement of the tendrils in the leaf of wild type by leaflets is
controlled by a single recessive gene tendril (tl) and creates “acacia” phenotype
(de Vilmorin and Bateson 1911). On the contrary, the single recessive gene afila (af)
converted leaflets into tendrils (Kujala 1953; Goldenberg 1965). The two recessive
genes af tl altered the identity of leaf pinnae, afila (af), and acacia (tl) (Villani and
DeMason 1997, 2000). The gene stipuleless (st) reduces stipule size dramatically
1260 A. K. Parihar et al.

resulting in a narrow strap-like organ (Pellew and Sverdrup 1923; Yaxley et al.
2001). Another allele stbs (butterfly stipules) causes intermediate size of stipules
between WT and st (Apisitwanich and Swiecicki 1992). Several other genes have
been identified such as uni, unitac (uni-tacluni), and apu, which modify the form of
the leaflets or tendrils.
The gene unifoliata (uni) replaces multiple leaflets and tendrils by single leaflet.
In unitac plants, the terminal tendril is replaced by a laminate leaflet (Marx 1986,
Sharma 1972, Sharma 1981, DeMason and Schmidt 2001; Yaxley et al. 2001). In
apu (apulvinic) plants, the leaflets are produced on stalk or petiolules (Harvey 1979;
Marx 1987; Naidenova 2000). In the cochleata (coch) phenotype stipules is often
replaced by stalked leaflet, while in cochhet (heterophyllus), the stipules differ in size
and are often reduced (Rozov et al. 1992; Wellensiek 1959). There are other genes
like sil, cri, Arg, and Td that influence both the stipules and leaflets, like the sil causes
undulation in the margins of leaflet and stipule (Marx 1977); the cri mutation causes
crinkle in leaflet and stipules (Lamm 1949); the Arg causes the leaves to appear
silvery grey (Hoch et al. 1980), while the incompletely dominant gene Td causes
dent on the stipule and leaflet margins (Wellensiek 1925).
The seed coat pigmentation in peas is due to photosynthetic pigments (Chloro-
phyll, carotenoids, and xanthophylls) as well as phenolic pigments, notably
flavonoids (Marx 1977; McCallum et al. 1997). The gene responsible for cotyledon
color was designated as I by White (1917), which is reported to retain chlorophyll in
the seed. Therefore, the mature wild-type (II) seeds are yellow because of degrada-
tion of the chlorophyll, whereas the seed remains green in genotype with ii allele. In
dried field pea, the seed color is contributed by the seed coat and cotyledons. Several
other loci have been reported to affect seed senescence and color retention in pea,
notably pa, gla, and vim (Blixt 1962; Weeden and Wolko 1990). Lamprecht (1959)
suggested that seed coat and cotyledon color in dry seed of aa (white flowered) pea
genotypes are determined by the action of the genes I, o, and gla. Dribnenki (1979)
concluded that at least three genes were involved in imbibition rate, green seed coat
color, and cotyledon bleaching resistance (Blixt 1962; Lamprecht 1959; Marx 1977;
McCallum et al. 1997).
The phenotype is somewhat variable: wild-type seeds that dry out early some-
times retain green color, whereas green ii seeds can sometimes bleach (Ellis et al.
2011). It was also observed that not only cotyledon in dry seed exhibit a green color
but also senescing leaves remain green, as do detached leaves placed in the dark
(Armstead et al. 2007; Sato et al. 2007; Aubry et al. 2008). This was the result of
reduced chlorophyll breakdown during dark incubation (Sato et al. 2007). The
corresponding gene, homolog of Stay-Green (SGR), has been identified based on
candidate gene approach using knowledge from rice and Arabidopsis SGR appears
to direct chlorophyll to the degradation pathway (Armstead et al. 2007; Sato et al.
2007). Mendel noted that colored seed coats were always associated with colored
(purple) flowers. White flower in cultivated forms of pea is common but wild type
had purple flowers. On the other hand, a clear or colorless testa was always
associated with white flowers and the absence of pigmentation in the leaf axils,
suggesting that these were pleiotropic effects of a single gene. The symbol for gene
25 Field Pea Breeding 1261

that determines the accumulation of anthocyanin pigmentation throughout the plant,

most notably in flowers, is A (von Tschermak 1912; White 1917; Hellens et al.
2010).
The purple color that accumulates in the flower of wild type is due to the
anthocyanin (compounds derived from phenylalanine). The mutation in (a) gene
abolishes anthocyanin pigmentation throughout the plant (Symkal 2012). A second
locus conferring white flowers, a2, has been identified from a mutagenesis study
(Marx et al. 1989). Previous investigations in pea have suggested that the white
flower is determined by the recessive allele a (Harker et al. 1990), while the pink and
rose color flower trait is governed by gene b and ce, which is dependent on “a” for
manifestation of color (Amin et al. 2010; Mohan et al. 2013).
The color of the immature pods is controlled by gene GP (White 1917), which
imparts green (GpGp) or yellow (gpgp) color to the pods (Ellis et al. 2011). The
structural analyses revealed the role of plastids in differences such as the plastids of
yellow pod (gp) had single and paired membranes, while the plastids of green pods
(GP) were lacking grana and contained only 5% of the chlorophyll of the wild-type
green pods. However, the gp mutation did not change the chloroplasts in the
endocarp of the pods (Price et al. 1988; Reid and Ross 2011; Smýkal 2014). In
contrast to I locus where the wild-type dominant form is yellow and the recessive
mutant form is green, for the Gp locus, the wild-type dominant form is green and the
recessive mutant form is yellow. This suggests that the mutant form i represents a
failure of chlorophyll degradation, whereas the mutant form gp fails to develop a
normal chlorophyll complex in the pods (Price and Hedley 1988; Ellis et al. 2011).
The purple pod color is governed by two dominant genes puand pur (Amin et al.
2010).
The pods of wild type dehisce at maturity, scattering the seeds, whereas the pods
of cultivated types are usually nondehiscent, which is determined by Dpo (dehiscent)
and dpo (non-dehiscent) alleles (Marx 1971). Mendel (1866) referred to the form of
the ripe pod as either inflated or deeply constricted (with the pod being quite
wrinkled in appearance). Wild-type pods are inflated, with a complete layer of
sclerenchyma on the inside of the pod wall. The complementary genes P and
V interact to control formation of a tough, sclerenchymatous layer inside of the
pod wall: P V has a complete membrane, P v has patches of sclerenchyma, p V has a
band of sclerenchyma along the region near the ovule-bearing suture and recessive
mutants of both p v lack a complete layer of sclerenchyma in the endocarp of the
mature pod, and their pods are deeply constricted, because they are inflated only in
those areas where the seeds have filled (Murfet and Reid 1993).
The inflated versus constricted pod phenotype refers to the presence or absence of
a layer of lignified cells (sclerenchyma) near to the epidermis of the pod wall and is
referred to as parchment (Ellis et al. 2011). The n mutation results in a thick, fleshy
pod wall (Amin et al. 2010). Pea pods have a cord of lignified sclerenchymatous
fibers along both sutures. Two recessive mutations, that is, sin and sin-2, results in
stringless pods (Wellensiek 1971; McGee and Baggett 1992). The expression of sin-
2 is dependent on high temperature and the combination of p v n sin-2 results in a
snap pea with a pod that can be eaten even when fully inflated (Wellensiek 1971;
1262 A. K. Parihar et al.

Murfet and Reid 1993). The shape of the pod apex is controlled by the genes Bt
(blunt) and bt (pointed). The recessive gene te reduces pod breadth by 25% and allele
Te is incompletely dominant. The genes con and cp control curvature of pods in
convex and concave pattern, respectively (Amin et al. 2010; Mohan et al. 2013;
Lamprecht 1936, 1953). The twp causes twisting of the immature pod due to arrested
growth in patches of tissue (Marx 1973). The single dominant gene Np causes a
pustule-like growth on the external surface of the pod (Nuttall and Lyall 1964). The
waxiness in pod is operated by single recessive gene, like wa causes lack of wax on
pods or upper and lower surfaces of stipule and underside of leaflets, wb for pods
devoid of wax or little wax on rest of plants, and wel for no wax on any aerial parts of
the plant.
The color of different plant parts, such as foliage, flower, and seed, is also
governed by single recessive genes, like for absence of anthocyanin in plants, flower
and seed, ch-l for light yellow green plant, d for green leaf axil, pa and vm for dark
green immature seed and foliage (Amin et al. 2010; Mohan et al. 2013). The two
single recessive gene ar and def influences development of funiculus. The ar causes
reduced diameter of funiculi and def developed a funiculus that remains attached to
the seeds even after harvesting (Khangildin and Khangildin 1969; Lamichaney et al.
2021c).
The most appropriate approach to combine various desirable quantitative traits is
recombination breeding, which is completely hinged on the genetic architecture of
the traits (Cockerham 1961; Sood and Kalia 2006). Therefore, intensive efforts have
been made to understand the inheritance pattern of different traits and consequently
noticed that additive and nonadditive gene effects are instrumental in the inheritance
of various yield components (Singh and Sharma 2004; Avcı and Ceyhan 2006;
Burstin et al. 2007; Beeck et al. 2008; Ceyhan et al. 2008). In pea, grain yield is
predominantly controlled by additive gene action but nonadditive factors also play
significant role (Singh et al. 2006; Kumar et al. 2006a, b). The heritability of yield
varies widely depending on the choice of parents, the environmental conditions, and
the efficacy of field plot techniques. Various studies suggested positive association
of plant height, pods per plant, seeds per pod, seed weight with grain yield.
Therefore, selection of these traits may be more effective for breeding point of
view (Dixit and Gautam 2015; Singh et al. 2004, 2007; Sharma and Khan 1996;
Pandey and Gritton 1975; Krarup and Davis 1970). Likewise, various research
groups have accorded high heritability and genetic advance for yield-attributing
traits like pod yield/plant, plant height, number of primary branches/plant, indicating
suitability of its improvement through hybridization (Sharma et al. 1997; Singh et al.
2007). Sharma et al. (1999) demonstrated the predominant role of nonadditive gene
action for pod yield, pods/plant, grain weight, whereas additive gene action for plant
height.
High broad sense as well as narrow sense heritability was observed by different
research groups for plant height, biological yield, number of pods per plant, and
100-seed weight (Lal et al. 2011; Punia et al. 2013; Kumar et al. 2013). Similarly,
Lal et al. (2011) considering association reiterated that pod per plant and harvest
index were the most important yield components that could be used as selection
25 Field Pea Breeding 1263

indices for further improvement in field pea. Seed per pod and seed weight are the
key yield components after the pod number (Krarup and Davis 1970; Sancha and
Singh 1973; Pandey and Gritton 1975). The additive gene effects play predominant
role in the inheritance of both seed number and seed weight (Kumar 1973; Snoad
and Arthur 1974; Venkateswarlu and Singh 1982). In many reports, ovule number is
controlled by a simple, additive genetic system (Marx and Mishanec 1967; Krarup
and Davis 1970), while the seed number per pod is under control of a polygenic
system of an additive nature (Snoad and Arthur 1973). Thus, such traits can be
effectively improved by adopting standard selection procedures like pedigree and
pure line breeding methods. Singh and Singh (1990) reiterated the importance of
dominance (h) gene effect for yield/plant, pods/plant, and plant height. However,
additive, dominance, and epistatic interactions were significantly evident for this
attribute. Sharma and Rastogi (2001) recorded significant additive and dominance
gene effects for all the traits. However, duplicate type of epistasis was more
prominent for plant height and leaf area, whereas complementary type of epistais
was also recorded. The preponderance of nonadditive gene effects for plant height
and leaf area indicates that a poor gain under selection may be expected for these
traits. Dixit et al. (2006) reported that additive, dominance, and epistatic gene effects
play important role in the inheritance of these traits.
Punia et al. (2011) indicated dominance and epistatic gene interactions to play
major role in the inheritance of yield and yield-attributing traits. The additive 
additive (i) and dominance  dominance (l) digenic interactions are important as
compared to additive  dominance ( j) for seed yield and its component traits.
Duplicate-type epistasis played a bigger role than complementary epistasis. Overall,
the nonadditive types of gene action are important for most of the traits, thereby
suggesting that selection at later segregating generations could provide better results.
In another study Punia et al. (2013) reported that days to flowering, days to maturity,
pods per plant, seeds per pod, seed yield per plant, and harvest index are controlled
by more of dominant gene. Similarly, Rebica et al. (2013) noticed, nonadditive gene
effects for pods per plant, pod length, seeds per pod and seed yield per plant, but
additive gene effects for days to 50% flowering, plant height and 100-seed weight.
Kosev (2013) reported that the additive gene effects play important role in the
inheritance of seeds per pod, seed weight per plant, and seed weight whereas plant
height, first pod-bearing node, pods per plant, seeds per plant, nodes per plant, fertile
nodes per plant have an influence of nonadditive genetic interactions. Kosev (2015)
reported that epistatic gene effects controlled all traits except plant biomass and
number of fertile nodes per plant, suggesting selection in later generations for plant
biomass. The characters, such as seeds per pod, seed yield per plant, pod length, and
harvest index, showed high GCV, heritability, and genetic advance would be more
helpful in formulation of selection strategy for prediction of the gain under selection
(Lal et al. 2019). Overall to exploit all three types of gene effects (additive,
dominance, and epistatic) reciprocal recurrent selection may be adopted for devel-
oping elite population for selection of high-yielding lines in advanced generations. It
will also lead toward an increased variability in later generations for effective
1264 A. K. Parihar et al.

selection by maintaining considerable heterozygosity through mating of selected

plants in early segregating generations.
In case of biotic stresses, host plant resistance is the most appropriate, efficient,
and economic strategies. Therefore, extensive efforts have been made to understand
the inheritance of biotic stresses. Among biotic stresses, powdery mildew (Smith
et al. 1996; Kraft and Pfleger 2001), rust (Singh et al. 2015a, b; Rubiales et al. 2019),
ascochyta blight (Liu et al. 2013; Tran et al. 2014), fusarium root rot (Hamid et al.
2013; Porter et al. 2015), fusarium wilt (Sharma et al. 2010; Rubiales et al. 2015),
and common root rot (Pilet-Nayel et al. 2005; Desgroux et al. 2016) are the serious
constraints affecting field pea across the countries of the resistance to powdery
mildew and are reported to be governed by two recessive (er1 and er2) and one
dominant (Er3) gene (Heringa et al. 1969; Fondevilla et al. 2007a). A recent study
indicates that resistance provided by er1 is due to a loss of function of PsMLO1, an
MLO (Mildew Resistance Locus O) gene (Humphry et al. 2011). The gene er2
(Heringa et al. 1969) confers complete resistance that was effective in found to be
location specific (Tiwari et al. 1997; Fondevilla et al. 2006). Gene Er3 has been
recently identified in Pisum fulvum and successfully introduced into adapted Pisum
sativum material (Fondevilla et al. 2007a, 2010). Resistance toward rust is governed
by single dominant gene (Ruf) (Katiyar and Ram 1987; Tyagi and Srivastava 1999;
Vijayalakshmi et al. 2005). In addition to the reported oligogene Ruf, the polygenic
nature of gene action has also been reported for rust resistance (Singh and Ram
2001). Recently, partial dominance of single gene along with minor and 2–3 additive
genes has been reported (Singh et al. 2012).
The nature of inheritance for ascochyta blight (AB) and fusarium root rot
resistance is reported to be polygenic (Fondevilla et al. 2007b; Carrillo et al. 2014;
Jha et al. 2017; Kraft 1992). The resistance to pea enation mosaic virus and
Fusarium oxysporum f. pisi (race 1 and 2), brown root of peas, Fusarium solani
f. sp. Pisi, downy mildew, bacterial blight (race 1), and pea root rot is governed by
single dominant gene. On the contrary, resistance to pea seed-borne mosaic virus
(sbm), bean yellow mosaic virus (mo), pea mosaic virus (pmv), and bean virus is
operated by recessive gene (Mohan et al. 2013, Amin et al. 2010; Kalloo 1993). The
pod resistance for pea weevil is quantitatively controlled, whereas the seed resistance
is operated by three major recessive alleles (pwr1, pwr2, and pwr3) (Byrne et al.
2008a, b). The inheritance pattern of different biotic and abiotic stresses is briefly
given in Table 25.4. In case of abiotic stresses, heat, drought, and frost are the
important stress, which substantially affects the yield potential of field pea (Parihar
et al. 2020a, b), which are reported to be controlled quantitatively (Iglesias-Garcia
et al. 2015; Huang et al. 2017; Klein et al. 2014).
25 Field Pea Breeding 1265

Table 25.4 Inheritance pattern of biotic and abiotic stresses in filed pea
Traits Inheritance pattern References
Powdery mildew Single recessive gene er1 Heringa et al. (1969), Harland (1948),
resistance (Erysiphe Pierce (1948), Saxena et al. (1975),
pisi) Tiwari et al. (1997), Fondevilla et al.
(2006) and Humphry et al. (2011)
Single recessive gene er2 Heringa et al. (1969), Ali et al.
(1994a, b), Tiwari et al. (1997) and
Fondevilla et al. (2006)
Single dominant gene Er3 Fondevilla et al. (2007a, b, 2010),
Fondevilla et al. (2008) and Fondevilla
and Rubiales (2012)
Rust (Uromyces Single dominant gene (Ruf) Katiyar and Ram (1987), Tyagi and
viciae-fabae) Srivastava (1999) and Vijayalakshmi
et al. (2005)
Polygenic Singh and Ram (2001), Singh et al.
(2012), Rai et al. (2011) and Barilli et al.
(2018)
Ascochyta blight Polygenic Fondevilla et al. (2007b), Prioul et al.
(Mycosphaerella (2004, 2007), Xue and Warkentin (2001),
pinodes) Carrillo et al. (2014), Timmerman-
Vaughan et al. (2016) and Jha et al.
(2017)
Fusarium root rot Polygenic Lockwood (1962), Muehlbauer and Kraft
(fusarium solani (1973), Kraft (1992), Hance et al. (2004)
f. sp. pisi) and Feng et al. (2011)
Fusarium wilt Races 1, 5, and 6 (single Mcphee (2003), Hagedorn (1989),
(Fusarium dominant genes) and race McPhee et al. 1999, Bani et al. (2012,
oxysporum. f. Sp. 2 (quantitative) 2018), McPhee et al. (2012) and Rispail
pisi) and Rubiales (2014)
Common root rot Polygenic Marx et al. (1972), Pilet Nayel et al.
(Aphanomyces (2002, 2005), Hamon et al. (2011, 2013)
euteiches) and Lavaud et al. (2015)
Heat tolerance Polygenic Huang et al. (2017)
Drought tolerance Polygenic Iglesias-Garcia et al. (2015)
Frost tolerance Oligogenic and polygenic Lejeune-Henaut et al. (2008), Dumont
et al. (2009) and Klein et al. (2014)

25.11 Major Constraints of Field Pea Production at National

and International Level

Like any other crop, field pea is susceptible to many biotic and abiotic stresses that
seriously hinder its sustainable production (Parihar et al. 2020a, b). Field pea are
prone to number of diseases of which fungal diseases, powdery mildew, rust,
ascochyta blight, wilt, and root rots like are most widespread (Parihar et al. 2013;
Mahajan et al. 2018). Powdery mildew, potential of reducing seed yield by 25–80%
(Munjal et al. 1963; Singh et al. 1978; Warkentin et al. 1996; Ghafoor and McPhee
1266 A. K. Parihar et al.

2012), is caused by Erysiphe pisi, Erysiphe baeumleri, and Erysiphe trifolii

(Attanayake et al. 2010; Fondevilla and Rubiales 2012; Sun et al. 2016). Rust is
incited either by Uromyces viciae-fabae or U. pisi and causes more than 30% yield
loss (Barilli et al. 2010, 2018; Singh et al. 2015a, b). Ascochyta blight caused by a
complex of fungal species (Ascochytapisi, Peyronellaea pinodes,
Phomamedicaginis var. pinodella, Ph. koolungaand Ph. Glomerata) is the most
severe disease of field peas distributed worldwide (Bretag et al. 2006; Liu et al. 2013;
Tran et al. 2014) with a potential of reducing grain yield by 60 percent (Liu et al.
2016). Fusarium root rot, incited by Fusarium solani f. sp. pisi, may develop in both
dry and wet field conditions and reduces yield significantly under suitable
circumstances (Chang et al. 2004; Porter 2010).
Fusarium wilt is caused by Fusarium oxysporum. f. sp. Pisi, which has about
11 different races (Armstrong and Armstrong 1974; Gupta and Gupta 2019). Of
them, races 1 and 2 are widely distributed, while races 5 and 6 are scattered only in
some specific regions (Infantino et al. 2006; Bani et al. 2018). Another important
soilborne disease of pea is common root rot caused by Aphanomyces euteiches,
prevalent in USA, Europe, and Canada (Wicker et al. 2003; Pilet-Nayel et al. 2005;
Chatterton et al. 2015; Desgroux et al. 2016; Wu et al. 2018), that causes wilting of
the roots (Wu et al. 2018). Field pea crop is also damaged by a number of insect pests
like pod borer complex, seed damaging pests, leaf feeders, leaf miners, stem fly,
aphids, cut worms, etc., which appears in different stages of the crop growth period
(Sharma 2000; Yadav and Patel 2015; Yadav et al. 2019). Pod borer, Helicoverpa
armigera, a pest blessed with a diverse range of host plants, also infests field pea and
can readily adapt to new environment which is one of the reasons for its pervasive-
ness (Djihinto et al. 2012). The pest is widely distributed over Asia, Africa, the
Mediterranean region, and Oceania (EPPO 2006). The larvae of pulse pod borer
(Etiella zinckenella) feeds on seed by boring the pods. Pod damage in field pea by
pod borer complex has been reported to be 13.45–40.38% (Dahiya and Naresh
1993).
The pea weevil (Bruchus pisorum L.) is another important insect that lays their
eggs on pods and larvae bore into the pods and damaged the seed (Brindley et al.
1956). The best way to manage this pest is to develop weevil-resistant cultivars
(Clement et al. 2009). The resistant lines and non-host-like Vicia faba, Lathyrus
sativus, P. fulvum, and P. sativum ssp. syriacum holds great promise toward devel-
opment of pea weevil resistance varieties (Teshome et al. 2015a, b; Mendesil et al.
2016; Fernandez and Rubiales 2019). Bean α-amylase inhibitor has also shown
promising results in developing transgenic lines against the pest (Schroeder et al.
1995; Morton et al. 2000). The pea leaf miner, Phytomyza horticola Goureau,
taxonomically described under the family Agromyzidae of the order Diptera, is a
pest of high economic importance (Spencer 1973). It is one among the major insect
pests of pea crop (Singh et al. 1992) widely distributed over Africa, Asia, and Europe
(Crop Protection Compendium 2007). The pea leaf miner is a serious and persistent
pest of peas in northern India (Atwal et al. 1969; Bhalla and Pawar 1977; Prasad
et al. 1984). Few species of aphids do infest the field pea among which
Acyrthosiphon pisum (Bieri et al. 1983) is major one, which sucks the sap mainly
25 Field Pea Breeding 1267

from growing tender shoots, lower side of the leaves, buds, and pods, which
debilitate the plant. Ali et al. (2005) reported the field pea line “061 K-2P2/9/2” as
the most resistant genotype against this aphid. Melesse and Singh (2012)
recommended “Milky” and “Adi” cultivars and NSKE to manage pea aphid. In
case of nematodes, Heterodera species (cyst nematode), Meloidogyne sp. (root knot
nematode), Rotylenchulus species (reniform nematode), and Ditylenchus species
(stem nematode) are the important limiting factor and cause severe loss (Vovlas
et al. 2011; Lombardo et al. 2011; Leach et al. 2012; Ahmad and Prasad 2012).
In case of abiotic stresses, extremities of temperature (low and high), moisture
(drought and flood), and salinity have becomes major concern in sustainable pro-
duction of dry pea (Guilioni et al. 2003; Karatas et al. 2012; Sadras et al. 2012; Liu
et al. 2019; Rubiales et al. 2019; Lamichaney et al. 2021a). This crop has relatively
low heat tolerance compared to other cool-season legumes like chickpea and lentil
(Siddique 1999), and so very often, the production starts to decline when the
maximum day-time air temperature during flowering exceeds 25  C (Guilioni
et al. 2003; Sadras et al. 2012). Several studies have addressed the impact of high
temperature on crop growth, physiology, and yields of field pea across the different
agroregions (Sadras et al. 2013; Liu et al. 2019; Jiang et al. 2019; Mohapatra et al.
2020). Most recently, Lamichaney et al. (2021a) observed reduction in the seed yield
(24–60%), seed germination (4–8%), seed set (7–14%), and 100-seed weight
(6–16%) under elevated ambient temperature during vegetative and reproductive
stages. Frost stress is another major abiotic stress causing significant problem at
vegetative and reproductive stage (Shafiq et al. 2012; Liu et al. 2017). Drought or
water stress is a critical environmental constraint that declines quality and quantity of
the produce (Ali et al. 1994a, b). The reduction in grain yield by 25% due to moisture
stress is reported under field conditions (Sánchez et al. 1998).

25.12 Breeding Progress/Varietal Development

Grain yield improvement is indispensable and continued objective for field pea
breeding program along with improvement in plant type, earliness, and resistance/
tolerance to multiple biotic and abiotic stresses, like diseases, insect pests, plant
parasites ((broomrape), drought, heat, frost, and salinity. Breeding for resistance/
tolerance against such stresses has been core objectives for field pea breeders in
order to increase and stabilize grain yields. In recent years, efforts have been made
toward development of biofortified genotypes especially for protein, iron, and zinc
(Parihar et al. 2021a, b). To attain above targets, concentrated efforts have been
made in field pea using different breeding approaches, which in detail are elaborated.

25.12.1 Accomplishment Through Conventional Breeding

The overall improvement in productivity of dry pea has been mainly achieved
through conventional breeding for tailoring plant type (lodging resistance and
1268 A. K. Parihar et al.

plant height), resistances to key biotic (powdery mildew, rust, ascochyta blight, etc.),
and abiotic (heat, drought and cold) stresses (Rubiales et al. 2019). In field pea, plant
stature has dramatically been changed from tall and high biomass to dwarf type.
Earlier, maximum cultivars were of tall type with high biomass, which caused severe
lodging problems that leads to disease induction (Donald and Hamblin 1983).
Concentrated efforts were made to incorporate the dwarf gene (le-1), resulting in
modern dwarf plant type varieties. The dwarf gene resulted due to developmental
mutation that shortened the internode length by reducing 3β-hydoxylation of GA20
to GA1 (Ingram et al. 1984; Ross et al. 1989; Martin et al. 1997). An analogous
experience was earlier exploited in wheat and rice during Green Revolution period,
which has association with gibberellin (GA) pathway (Martin et al. 1997). The short
internode length also improved the standing ability significantly (Burstin et al.
2007). Inspite of the incorporation of dwarfing traits, the pea plant still lodged due
to high biomass (Amelin et al. 1991). Therefore, to reduce lodging, an alternative
tactic, that is, development of “semi-leafless” pea cultivars using “afila” leaf type,
was used, which is considered to be a greatest accomplishment in pea breeding
(Amelin et al. 1991; Duparque 1996).
The semi-leafless plant type considerably improved standing ability of pea
genotypes, which ultimately condensed grain yield losses (Wang et al. 2002;
Banniza et al. 2005, Singh and Srivastava 2015). The crop with better standing
ability resulted in proper aeration and reduced humidity, which otherwise remained
very high in lodged crop and was very favorable for the development of various
diseases like Ascochyta blight (Banniza et al. 2005). The first commercial semi-
leafless (afila) variety was “Solara” developed in 1970s in Europe. The “semi-
leafless” cultivars are accountable for about 95%, 80%, and 30% of the total dry
pea production in Canada, European Union, and Russia, respectively (Tayeh et al.
2015a, b, c, d). An interesting achievement has been made through trait pyramiding
for lodging resistance and reduced pod shattering and consequently the first broadly
adapted semi-dwarf cultivar “Kaspa” has been developed, which dominated produc-
tion across southern Australia (Leonforte et al. 2006; Warkentin et al. 2015).
In last 20 years, a large number of varieties were developed with semi-leafless
trait, which helped in enhancement of production of dry pea in India (Dixit and
Parihar 2014; Dixit et al. 2014; Gupta and Parihar 2015; Parihar and Dixit 2017;
Parihar et al. 2019a). In India, dwarfing and afila plant type has been extensively
used in pea breeding programs and both the traits were successfully transferred in
conventional cultivars through hybridization, which ultimately enhanced productiv-
ity. The dwarf varieties are more responsive to fertilizers, irrigation, and could be
densely planted. In India, the first dwarf and semi-leafless variety HFP 4 (Aparna)
was developed in 1988. Toward the end of the twentieth century, a dwarf and
landmark variety Malviya matar-15 (HUDP-15) was developed, which is derived
from the three way cross (PG 3/S 143)/FC 1, which also showed resistance against
powdery mildew and rust (Dixit et al. 2014).
In central part of India and in rice fallows, a short cropping window is available,
which however is prone to terminal drought and heat stresses. In such conditions,
extra early varieties are the best alternative that matures before the onset of terminal
25 Field Pea Breeding 1269

stresses, and also the field remains available for timely planting of subsequent crops
(Dixit et al. 2014). Therefore, breeding efforts were made to reduce the duration of
crop, resulting in the development of short duration (100–105 days) high-yielding
dwarf varieties like DDR 23, DDR 27, IPFD 99–13, IPFD 11–5, and IPFD 2014–2
(Anonymous 2021). However, there lies scope for further reduction in the duration
of field pea crop as Parihar et al. (2021a, b), have identified lines with extra earliness
(<100 days), which could be utilized as donor in future breeding program to develop
extra early and high-yielding varieties.
In addition to plant type, the productivity of dry pea is limited largely by different
biotic and abiotic stresses. The powdery mildew remains a severe bottleneck in dry
pea production in most of the pea-growing ecologies (Tayeh et al. 2015a, b, c, d; Sun
et al. 2019; Parihar et al. 2020a, b). Considering these facts, with extensive breeding
efforts, the PM resistance was first noticed in the landrace “Huancabamba,” which is
genetically operated by a single recessive geneer1 (Harland 1948). Further, many
resistant accessions were identified over the period and subsequently characterized
their gene(s) for resistance to E. pisi. Hitherto, three genes er1, er2, and Er3 were
reported for PM resistance, of which er1, er2 are recessive and Er 3 is dominant Er3
(Heringa et al. 1969; Fondevilla et al. 2007c; Parihar et al. 2013). Among these
genes, er1 provides resistant in maximum accessions followed by er2, which
operates only in few accessions, whereas Er3 has been recently identified in
P. fulvum, a wild relative (Tiwari et al. 1997, Fondevilla et al. 2007a, b, c; Fondevilla
and Rubiales 2012). Ascochyta blight (AB) is another serious disease of field pea
distributed worldwide (Li et al. 2011; Tran et al. 2014; Rubiales et al. 2019). Till
date, none of the cultivated pea could exhibit complete resistance against
AB. However, few genotypes were identified with low to moderate level of resis-
tance in cultivated pea (Kraft et al. 1998; Zhang et al. 2006). Interestingly,
accessions of wild relatives, that is, P. fulvum, P. sativum ssp. Elatius, and
P. sativum ssp. Syriacum, have demonstrated high level of resistance and have
been utilized for resistance breeding (Fondevilla et al. 2005; Jha et al. 2012, 2016;
Sindhu et al. 2014).
Fusarium root rot is another major limiting factor in dry pea production
(Grunwald et al. 2003; Hamid et al. 2013; Porter et al. 2015) and till date source
for its complete resistance is not reported, while some sources for partial tolerance
have been found (Gretenkort and Helsper 1993; Hwang et al. 1995; Grunwald et al.
2003; Porter et al. 2015). Interestingly, the accessions with pigmented flower are
associated with enhanced resistance to root rot (Kraft 1975; Grunwald et al. 2003).
Fusarium wilt is a serious production threat worldwide and causes huge loss in dry
pea production (McClendon et al. 2002; Sharma et al. 2010; Rubiales et al. 2015;
Aslam et al. 2019). The resistance accessions for race 1 and 2 have been reported by
McPhee et al. (1999) in pea core collection. Common root rot (CRR) (caused by
Aphanomyces euteiches) is yet another serious disease of pea. The accessions
showing partial resistance to CRR have been reported (Kraft 2000; Kraft and
Coffman 2000; Pilet Nayel et al. 2007; Conner et al. 2013), which have been used
in breeding programs to develop breeding lines (Roux-Duparque et al. 2004;
Moussart et al. 2007) and various experimental populations (Pilet Nayel et al.
1270 A. K. Parihar et al.

2002, 2005; Hamon et al. 2011, 2013; McGee et al. 2012; Lavaud et al. 2015).
However, breeding for tolerance to CRR always remains complicated owing to
polygenic nature and other associated unwanted traits (Mark et al. 1972; Pilet
Nayel et al. 2002). Thus, deployment of modern technologies in regular breeding
program is essential to accelerate breeding for CRR-resistant varieties.
Rust, incited either by Uromyces viciae-fabae or U. pisi, is also an important
disease scattered in all pea-growing countries (Barilli et al. 2010, 2018; Rubiales
et al. 2011; Singh et al. 2015a, b). Dedicated efforts have been deployed toward
screening of germplasm for rust, but unfortunately, so far, none of the genotypes has
shown complete resistance (Gupta 1990; Anil-Kumar et al. 1994). However, numer-
ous genotypes have been identified with partial resistance for rust (Vijayalakshmi
et al. 2005; Chand et al. 2006; Kushwaha et al. 2006; Barilli et al. 2009). The
reported partial resistance sources have been inculcated in pea breeding and devel-
oped some high-yielding and partial rust-resistant varieties such as HUDP
15, Prakash, Swati, Aman, Pant P 42, IPF 5–19, IPFD 11–5, IPFD 12–2, and
IPFD 9–2.
In case of abiotic stresses, high ambient temperature of more than 25  C during
pea life cycle is reported to negatively affect its production owing to reduced plant
growth, flowering nodes, pods per plant, seed set (%), vegetative and reproductive
phase, seed weight, and pollen viability (Sadras et al. 2012; Bueckert et al. 2015;
Jiang et al. 2015, 2018; Lamichaney et al. 2021a). Considering traits like membrane
stability index, plant height, biomass, seed yield, and harvest index, few genotypes
were identified showing resistance to high temperature stress (Vijaylaxmi 2013).
Lamichaney et al. (2021a) reported that terminal heat stress not only reduced seed
yield but also seed quality in terms of its planting value and also identified few
promising genotypes considering mean performance and stability for yield and
germination efficiency. Drought is an imperative environmental limitation that
reduces quality and quantity of the produce (Boyer 1982; Ali et al. 1994a, b;
Sánchez et al. 1998). In general, the ability of plants to combat with moisture stress
is judged through its yield potential in a specific environment. There are primarily
three ways, that is, escape, avoidance, and tolerance of crops to sustain in moisture-
restricted conditions (Turner et al. 2001). The mentioned strategies can be used to
develop genotypes that would perform well under limited water conditions. The
avoidance via escape approach is primarily considering earliness in case of flowering
and maturity and as a result, it has become the preferred approach for breeders. But
early flowering–early maturing crops cannot respond well under normal moisture
conditions and shows a significant reduction in the yield (Khan et al. 1996).
Therefore, early vigor and flowering and good pod setting are important criteria
for development of genotypes with drought tolerance (Khan et al. 1996; Turner et al.
2001). Currently, selection pressure is targeted toward high yield potential with
earliness and prolonged flowering duration for development of drought resistance
genotypes. The drought avoidance is mainly hinged on delayed water loss by various
means of, for example, stomatal conductance, leaf area and any nontranspirational
water loss from leaves. Due to reduced leaf area, the semi-leafless type has many
advantages in water-deficit situations (Rodríguez-Maribona et al. 1990; Alvino and
25 Field Pea Breeding 1271

Leone 1993; Sánchez et al. 2001). The elevated ABA content was also used as a
scale for selection of drought-tolerant genotypes in 1980s and successfully adopted
in maize and wheat but only in restricted environments (Read et al. 1991). The
correlation between growth and osmotic adjustment and turgor maintenance has
been observed at seedlings stage in induced water stress condition. The turgor
maintenance at the early stages of development could be used to identify drought-
tolerant genotypes (Sanchez et al. 2004). So far, limited study has been conducted to
address the inheritance pattern of adaptation to drought in pea; however, the drought
adaptation in pea is reported to be quantitative and also identified the genomic
regions controlling the trait (Iglesias-Garcia et al. 2015).
Frost stress is one of the major abiotic stresses causing significant problem at
vegetative and reproductive stage in pea (Shafiq et al. 2012; Liu et al. 2017).
Genotypic variation was noticed for frost tolerance in dry pea at seedling (Bourion
et al. 2003), vegetative (Lejeune-Henaut et al. 2008), and reproductive stage (Shafiq
et al. 2012). Interestingly, few varieties of pea with winter hardiness are found,
which are capable of adapting in a wide range of temperature from 8 to 12  C
(Homer and Sahin 2016). The genotypes belonging to winter production regions
recorded better cold tolerance as compared to genotypes from spring production
regions (Zhang et al. 2016). Efforts were made to incorporate the delayed flowering
locus Hr, resulting into initiation of flowering after passage of main winter freezing
periods may improve the cold tolerance (Lejeune-Henaut et al. 2008, Avia et al.
2013; Dhillon et al. 2010). Liu et al. (2017) have identified a number of accessions
tolerant to frost based on their ability to survive. These winter-hardy accessions will
play a vital role in breeding of winter-hardy pea cultivar.
The root parasitic weed Orobanche crenata is widely distributed in the Mediter-
ranean region and the Middle East and severely affects dry pea production (Rubiales
and Fernández-Aparicio 2012). Some levels of resistance were recognized, which is
operated by quantitative gene action (Rubiales et al. 2005) and has been successfully
transferred to cultivated pea by crossing and selection, resulting in the release of the
first resistant cultivars (Rubiales et al. 2009; Fondevilla et al. 2017; Rubiales 2018).
Very restricted attempts have been employed toward resistance to insect pest in pea.
However, some level of resistance for pea weevil infestation has been found in the
cultivated pea and wild relatives (Clement et al. 2002; Teshome et al. 2015a, b;
Aznar-Fernández et al. 2018) and successfully transferred into cultivated pea
(Clement et al. 2009; Aryamanesh et al. 2012). Likewise, few sources of intermedi-
ate resistance against aphid have been reported (Aznar-Fernández and Rubiales
2018). Achievements are in premature stage of exploitation in case of salinity,
boron toxicity, and iron deficiency. However, some landrace with improved stress
tolerance has been identified in case of boron toxicity (Bagheri et al. 1994; Paull
et al. 1992), salinity (Leonforte et al. 2013a) and iron deficiency (Kabir et al. 2012).
Quality attributes of peas cultivated for dry seed have been focused primarily on
the visual appearance of the seed, that is, uniformity and intensity of seed color as
well as shape. Mainly two types of field pea, that is, seed with yellow and green
cotyledons are available in market, of which green seeded dominates the market
especially in Canada (Ubayasena et al. 2010). To get highest market grade, green pea
1272 A. K. Parihar et al.

seeds should be naturally green in color with less than 2% bleached seeds. Conse-
quently, cotyledon bleaching during seed maturation or seed storage is a critical
factor that determines the value of green pea (Holden 1965; McCallum et al. 1997;
Cheng et al. 2004). Bleaching is reported to have negative effect on seed germination
and early seedling vigor (Maguire et al. 1973; Loria 1979). Thus, the improvement in
bleaching resistance has been an objective of pea breeding worldwide. Sincere
efforts have been made to understand the genetics of bleaching and quantitative
inheritance, transgressive segregation, and moderately high heritability were
observed for seed color, shape, and surface dimpling (Ubayasena et al. 2010,
2011). However, due to dearth of information regarding inheritance of this trait,
accurate phenotypic characterization and effects of the environment on the trait have
slowed down efforts to deliver improved cultivars.
During recent years, greater attention is being given to improve the nutritional
composition of the pea due to its importance in food and feed. In field pea, restricted
attempts have been invested to screen the existing released varieties and germplasm
for various nutritional parameters. However, ample amount of genetic variability
was noticed for Fe, Zn, and Mg (Gawalko et al. 2009; Amarakoon et al. 2012).
Notably, numerous promising genotypes with high iron and zinc content have been
identified and being used in conventional breeding for development of high-yielding
nutritionally rich genotype and development of mapping populations (Parihar et al.
2021a, b). The nutritional quality upscaling may be done by selection of locality
specific genotypes and their judicious deployment in conventional breeding for
developing location specific biofortified varieties. In addition to the enhancement
of seed micronutrient status, the bioavailability of micronutrients could be improved
by reducing antinutritional compounds, for instance, phytate, and escalating levels of
absorption-promoting compounds, such as xanthophyll, ascorbate, and betacarotene
(Hurrell and Egli 2010; Lockyer et al. 2018). The genotype, environment, and their
interactions affect the concentration of phytate phosphorus, inorganic phosphorus,
and concentration of iron (Delgerjav 2012; Warkentin et al. 2012; Shunmugam
et al. 2015). The high carotenoid concentration is part of a biofortification strategy
and substantial variability has been reported, higher in seeds with green cotyledon
(Ashokkumar et al. 2014). The genotypic and environmental significantly influenced
carotenoid content, the amount of which is higher in cotyledon followed by the
embryo axis and seed coat (Liu et al. 2015a, b).
In India, rigorous attempts have been made and numbers of high-yielding
varieties with dwarf/tall plant type, resistance to powdery mildew, and rust have
been developed. For example, in tall category, IPF 99–25 (Adarsh), IPF 5–19
(Aman), IPF 4–9, IPF 16–13, TRCP-9, TRCP 8, Pant Pea 243, VL-42, Pant P-42,
and Ambika have been developed during last 20 years. Similarly, in dwarf class
varieties such as IPFD 99–13 (Vikas), IPFD 1–10 (Prakash), IPFD 10–12, HFP
9907B, Pant P-74, SKNP 04–09, HFP 529, HFP 715 and Pant P 250, IPFD 12–2,
IPFD 11–5, IPFD 2014–2, IPFD 9–2, IPFD 6–3, IPF 16–13, IPFD 12–8, IPFD 13–2
have been developed (Parihar and Dixit 2017; Dixit et al. 2017, Parihar et al.
2019a, b, 2020a, b, 2021a, b; Anonymous 2021).
25 Field Pea Breeding 1273

25.12.2 Distant Hybridization

Crop wild relatives (CWRs) are extensively recognized as a valuable resource for
crop improvement, because they are reservoir of genetically important traits due to
their wider adaptation to a diverse range of habitats (McCouch et al. 2013;
Dempewolf et al. 2014; Smýkal et al. 2017). Currently, main focus of any breeding
program is development of high-yielding and climate-resilient genotypes with
resistance to prevailing disease and pest. As the genetic variability in domesticated
pea has reported to be low, recently attention is being given to prebreeding to induce
and increase the variation for further genetic enhancement (Sharma et al. 2013). In
case of pea, approximately 98,000 accessions of pea germplasm are available
worldwide, of which, only a small proportion (less than 1%) represent wild pea
(Smýkal et al. 2013). The genetic diversity of cultivated pea germplasm has been
extensively studied during recent past (Jing et al. 2010; Smýkal et al. 2011, 2013;
Holdsworth et al. 2017); however, a limited number of wild peas have been
evaluated (Kosterin and Bogdanova 2008; Polans and Moreno 2009; Jing et al.
2010; Holdsworth et al. 2017).
Wild pea forms have large potential to be used as a donor of several
agronomically important traits such as P. fulvum, which has resistant toward the
pea weevil (Clement et al. 2002, 2009; Byrne et al. 2008a, b; Aryamanesh et al.
2012, 2014), rust (Barilli et al. 2009, 2010), powdery mildew (Fondevilla et al.
2007b) and ascochyta blight (Fondevilla et al. 2005; Carrillo et al. 2013). Notably,
P. sativum subsp. elatius also showed resistance for pea weevil (Berdnikov et al.
1992). In addition, some of the wild forms of the cultivated pea (P. sativum subsp.
elatius) showed resistance against nematode Heterodera goettigniana (Vito and
Perrino 1978), broomrape Orobanche crenata (Valderrama et al. 2004), powdery
mildew (Tiwari et al. 1997; Fondevilla et al. 2007a, 2008, 2011a, b; Fondevilla and
Rubiales 2012; Cobos et al. 2018), rust (Barilli et al. 2010, 2018), Fusarium wilt
(McPhee et al. 1999; Hance et al. 2004), PSbMV virus (Konečná et al. 2014), and
white mold (Porter et al. 2009). Likewise, accession AWP 442 (P. elatius) and AWP
600, AWP 601 ((P. fulvum) have been identified, which show complete resistance
against pulse beetle (Callosobruchus chinensis L.), could be used in breeding
programs for development of resistant cultivars (Esen et al. 2019).
To enhance seed protein quality, a double null mutant for the two closely linked
genes encoding TI1 and TI2 seed protease inhibitors has been identified in Pisum
elatius. This mutant has extremely low seed protease inhibitor activity and intro-
gression of the mutation into cultivated germplasm has been achieved (Clemente
et al. 2015). The CWR, for instance, P. fulvum and P. sativum subsp. Elatius, are
recognized as promising genetic resources for abiotic stress tolerance including
drought and temperature extremities (Ali et al. 1994a, b; Coyne et al. 2011; Naim-
Feil et al. 2017).
The use of natural pea diversity from CWR in pea breeding is hampered by
reproductive barriers existing not only between different species but even within
P. sativum. However, interspecific crosses have been attempted between the
cultivated pea (Pisum sativum) and wild relatives such as P. elatius, P. humile and
1274 A. K. Parihar et al.

P. fulvum, and observed that P. elatius and P. humile are conspecific with P. sativum.
Due to chromosomal incompatibility between P. fulvum and P. sativum, hybrid seed
could not be produced (Ben Ze'ev and Zohary 1973; Smartt 1984; Errico et al. 1996),
while fertile hybrids seed can be produced when P. fulvum serves as male parents
(Ben Ze'ev and Zohary 1973; Muehlbauer and Kaiser 1994). Later, intergeneric and
interspecific crosses of P. sativum  L. sativus and P. sativum  P. fulvum, respec-
tively, have been attempted, which recorded strong cross-incompatibility. Con-
versely, the interspecific crosses successfully produced hybrid without bridging
cross, which has also been confirmed through different in vitro techniques such as
flow cytometry, isoenzymes, molecular approaches, and GISH (Campbell 1997;
Ochatt et al. 2004). Advanced introgressed populations using P. fulvum as pollen
donor with pea weevil resistance have also been developed (Fondevilla et al.
2007a, b, c; Byrne 2005). The P. fulvum accession ATC113 (PI 595933) has been
successfully crossed with P. sativum and produced interspecific pea weevil-resistant
lines (Byrne 2005; Byrne et al. 2008a, b). The introgression of pea weevil resistance
into cultivated field pea was further demonstrated in advanced backcross lines of the
original population (Aryamanesh et al. 2012). Therefore, an interspecific
hybridization approach has potential for developing pea cultivars with resistance
to pea weevil.
Unfortunately, the nuclear–cytoplasmic incompatibility has been displayed in
crosses of P sativum subsp. elatius accession VIR320 when used as a cytoplasm
donor with most of the cultivated P. sativum representatives. The produced hybrids
were sterile with chlorophyll deficiency, chlorophyll variegation, and reduced
leaflets and stipules (Bogdanova and Berdnikov 2001). Analysis of plastid DNA
markers showed that the incompatibility is mainly owing to improper functioning of
plastids rather than mitochondria (Bogdanova and Kosterin 2006, 2007). The
nuclear–cytoplasmic incompatibility is operated by two unlinked nuclear genes
Scs1 and Scs2 and located on LG III and LG V, respectively (Bogdanova et al.
2009). Some progress has been made in the introgression of genes for resistance
from P. fulvum into the genome of the cultural species (Fondevilla et al. 2010).
When wild pea VIR320 was used as cytoplasm donor, the Scs1 allele from the
cultivated pea is gametophyte lethal and sporophyte recessive lethal. The Scs2 allele
from the cultivated pea reduced male gametophyte viability. In homozygous situa-
tion, Scs2 from cultivated parent bring nuclear–cytoplasmic inconsistency and
reduced pollen fertility by 20%, while in heterozygous condition for either of the
genes Scs1 and Scs2 had subsidized pollen fertility by 50 and 30%, respectively.
Genetic mapping demonstrated that the gene Scs1 has flanking marker located at
2.5 cM on LG III and Scs2 gene has flanking markers positioned at varied distance
from cross to cross in the range of 2.0–15.1 cM on LG V (Bogdanova et al. 2012).
Interestingly, the different wild peas differ in hybrid sterility in reciprocal crosses
with cultivated pea depending on alleles of a nuclear “speciation gene” involved in
nuclear–cytoplasmic compatibility (Bogdanova et al. 2014). Bogdanova et al. (2015)
reported that the nuclear–cytoplasmic conflict is associated with nuclear and plastid
candidate genes acetyl-CoA carboxylase beta subunit.
25 Field Pea Breeding 1275

In recent past, Bobkov and Selikhova (2017) had successfully made interspecific
crosses between P. sativum  P. fulvum, while the crosses P. fulvum  P. sativum
resulted in the formation of seeds with unfilled embryos. The hybrid nature of
P. fulvum  P. sativum plants was confirmed using biochemical and morphological
markers. Kosterin et al. (2019) shed light on reproductive compatibility of P. fulvum
in both directions with P. abyssinicum, P. sativum L. subsp. elatius and P. sativum
L. subsp. sativum. They noticed that the cross ability with P. fulvum as the female
parent was very poor, but at least some viable seeds were obtained in all crosses. The
sum of evidence available suggests that P. fulvum does not differ from P. sativum by
reciprocal translocations. Most recently, the presence of identified cultivated
isoforms of storage proteins in all studied lines of BC2F5 interspecific hybrids of
P. sativum  P. fulvum indicated the possibility of using the P. fulvum in pea
breeding program (Bobkov et al. 2020). The realistic exploitation of CWR of peas
is hindered by inadequate knowledge of their diversity (Kosterin 2016). Therefore,
there is urgent need of investment of more intensive efforts to study the useful traits
of CWRs and their diversity in natural habitats, which is currently being vanished
because of transformation and degradation of plant communities because of direct
and indirect human influence. Most importantly, the interspecific hybridization leads
to the transfer of both desirable and undesirable genes. Thus, during transfer of genes
of interest, utmost care should be taken to stop the transfer of worthless genes. The
backcross with cultivars and elite breeding lines encourage the selective introgres-
sion of valuable genes. These tactics for transferring desirable alleles are not
exclusive, and there are good predictions for their joint use.

25.12.3 Mutation Breeding

Mutation breeding being cheaper, fast, and robust approach has great promise
toward creation of quantitative and qualitative variability in crop plants, which
along with hybridization leads to creation of new genetic variation that is crucial
for the genetic improvement as well as evolution of crops (Sharma and Sharma 2004;
Solanki et al. 2011). In plant breeding programs, physical and chemical mutagens
have been successfully applied for the development of new varieties with enhanced
traits. Till now, more than 3200 mutant varieties have officially been released for
commercial use in more than 210 plant species from over 70 countries (FAO/IAEA
Mutant Varieties Database). The mutation studies in pea were mainly concerned
with spontaneous mutations initially, but subsequently shifted toward induced
mutations. In field pea, limited efforts have been invested in mutation breeding as
compared to other pulse crops. Nevertheless, several biologically interesting mutants
in pea have been released as variety with improvements including increased yield,
lodging resistance (afila leaf trait), larger seeds, increased protein content, modified
maturity, disease, and insect pest resistance and less toxic compounds (Jaranowski
and Micke 1985; Micke 1988, 1993; Micke et al. 1985, 1990; Gottschalk 1991;
Naidenova and Vassilevska-Ivanova 2004a, b; Vassilevska-Ivanova and Naidenova
2006).
1276 A. K. Parihar et al.

So far, more than 30 varieties of pea have been developed through exploitation of
mutation breeding. The highest number of varieties through mutation breeding has
been developed in Poland followed by Russian Federation. In addition, few mutants
with super-nodulation and nonnodulation have also been reported. So far, natural
variation and induced mutation have identified 50 symbiotic regulatory genes in pea
(Tsyganov and Tsyganova 2020). Of which, many pea mutants have been
characterized at the morphological level (Borisov et al. 1992; Markwei and LaRue
1992; Postma et al. 1990; Sagan et al. 1993, 1994; Tsyganov et al. 1999) and a block
at a specific stage of nodule development has been delineated (Voroshilova et al.
2001). Two powdery mildew-resistant mutant, that is, S(er1mut1) and F(er1mut2),
have been induced from Solara and Frilene cultivars, respectively, with
ethylnitrosourea (Leitão et al. 1998; Pereira et al. 2001). The further genetic analysis
of the novel PMR mutant lines showed that both resistances are inherited as
monogenic recessive traits (Pereira and Leitão 2010). Vassilevska-Ivanova and
Naidenova (2006) estimated stability and adaptability of waxbloom and waxless
pea (Pisum sativum L.) mutant lines. The investigated mutants demonstrated diverse
response to environments, thus suggesting development of targeted breeding pro-
gram. Recently, Singh et al. (2015) irradiated two cultivars of field pea viz. HFP-4
and Rachna with different doses of gamma-rays, wherein a considerable amount of
genetic variability and heritability recorded for all the traits in both cultivars, which
can be exploited through selection. Mutagenesis is also a promising means to
identify novel genes and their functional regulations.
The mutants are also playing crucial role in development of various genomic
tools such as fast neutron and TILLING populations that have been developed for
reverse genetics approaches (Dalmais et al. 2008; Ambrose et al. 2008; Wang et al.
2008a, b; Le Signor et al. 2009a, b). A fast neutron (FN)-mutagenized population
was developed in pea using recombinant inbred line, JI 2822 as a parent, to facilitate
the identification and isolation of genes underlying the trait (Hofer et al. 2009;
Domoney et al. 2013). To develop a Pisum sativum TILLING platform, an EMS
mutagenized library of 8000 M2 families derived from the cultivar “Terese” was
used (Rameau et al. 1997; Triques et al. 2007). A sufficiently large TILLING
population has been developed from the genotype “Cameor” and subsequently the
characterization data have been stored in an online database, that is, UTILLdb,
which provides phenotypic as well as sequence information regarding mutant
genes in public domain. At present, the population size is 4817 lines: 1840 lines
have been characterized for phenotypes and 464 mutations have been identified
(Ambrose et al. 2008; Dalmais et al. 2008).
Unlike traditional screening methods, TILLING focuses on identification of
mutation within gene of interest and subsequent linking of those mutations to a
specific phenotype. Though this technique is only feasible when a gene correlated to
the trait of interest is well known and the gene sequence is available (Sikora et al.
2011). The major pea mutant collections institutions are as follows: John Innes
Collection, Norwich, UK (575 accessions); IPGR collection, Plovdiv, Bulgaria
(122 accessions); a targeted-induced local lesions in genomes (TILLING) popula-
tion of 4817 lines (1840 described by phenotype), and 93 symbiotic mutants for
25 Field Pea Breeding 1277

26 genes involved in nitrogen fixation (Duc et al. 1994; Duc and Sagan 1996;
Ambrose et al. 2008; Le Signor et al. 2009a, b). In addition, fast neutron produced
deletion mutant resources (around 3000 lines) are available for pea, which have been
used in identification of several developmental genes (Ambrose et al. 2008; Le
Signor et al. 2009a, b, Jacobs et al. 2010; Smýkal et al. 2012). In addition,
mutagenesis approach needs to embrace PCR-based screening techniques and
mapping techniques (NGS techniques) for the characterization of mutant lines as
well as for the mapping of causal mutations. Furthermore, new approaches such as
mapping by mutation (MutMap), mutant chromosome sequencing (MutChromSeq),
exon capture, whole genome sequencing, MutRen-Seq, and different tilling
approaches need to be used for the detection of induced mutation.

25.13 Breeding Objectives

The main objectives or goals of any crop breeding program are to increase the
production of crop with sustainability. The major breeding objectives in field pea are
elaborated below:

25.13.1 High Grain Yield

Improvement in grain yield and its stability are considered as key goals in most of the
plant breeding programs. Yield is a cumulative effect of many yield attributes such
as number of pods per plants, numbers of seeds per pods, pod length, productive
nodes per plants, biomass, and seed weight. Therefore, in addition to high grain
yield, the above-mentioned yield attributes need adequate attention.

25.13.2 Short Duration or Earliness

Development of extra early and high-yielding cultivars would allow expansion of

field pea toward new niches with short season and prone to terminal stresses like rice
fallows (Parihar et al. 2021a, b). In addition, such type of varieties will very well fit
in different cropping systems, ultimately increasing per unit time and area
productivity.

25.13.3 Resistance to Biotic Stresses

The productivity of dry pea is negatively influenced by a large number of biotic

stresses including fungal, viral, bacterial pathogens causing diseases and various
insect pests and nematodes. Of them, powdery mildew, rust, root rots, wilt, and
ascochyta blight are the important fungal diseases affecting field pea across the globe
(Mahajan et al. 2018, Parihar et al. 2020a, b) and need continuous attention for
1278 A. K. Parihar et al.

further improvement. In case of insect pest pea weevil, aphids and leaf miner are the
serious menace; therefore, resistance and tolerant varieties are the need of the hour.

25.13.4 Resistance to Abiotic Stresses

Temperature extremities (low and high), drought, and frost are the major limiting
factors in pea production (Parihar et al. 2020a, b). Therefore, intensive efforts need
to be made for identification of resistance and tolerant genotypes and their judicious
utilization in regular breeding program.

25.13.5 Biofortified Genotypes

To combat the hidden hunger among the resource poor vegetarian populations of
developing and underdeveloped nations, cultivar with high iron, zinc, and protein
needs to be developed (Parihar et al. 2021a, b). The use of pea seeds in human and
animal nutrition is limited by the presence of antinutritive substances: for example,
trypsin inhibitors, raffinose family of oligosaccharides and phenolic compounds
(Dvorak et al. 2005; Parihar et al. 2016; Gawłowska et al. 2017). Therefore,
reduction of such antinutritional compounds would increase the acceptance of this
crop among consumers.

25.13.6 Mechanical Harvesting Amenable Genotypes or Lodging

Resistance

Owing to the succulent and hollow stem, field pea lodged at maturity. Therefore,
breeding for erect type genotypes has remain a key objective in pea breeding
programs (Zhang et al. 2006), which could also help in mechanized harvesting in
addition to reduction in disease pressure (Smitchger et al. 2020).

25.13.7 Seed Quality Improvement

Visual appearance of seed is one of the most imperative determinants of market

value of the harvested crop. Seed coat color, seed shape, and seed dimpling are the
major components of visual seed quality and are considered as important breeding
objectives (Ubayasena et al. 2011). Therefore, development of varieties having a
potential of resisting the weather damage caused by unfavorable weather variables
during maturity is the need of an hour to harvest a seed with good physical
appearance.
25 Field Pea Breeding 1279

25.14 Brief of Available Genetic and Genomic Resources

Pea genome is comprised of 7 pairs of chromosomes with haploid size (1C) of

4.45 GB and of which about 50–60% is of high to moderate repetitive sequences
with preponderance of Ty3/gypsy family (Novák et al. 2010; Dolezel and Greilhuber
2010; Praca-Fontes et al. 2014; Gali et al. 2018). Unquestionably, the big genome
size and high transposable elements have played decisive role in impediment of the
development and availability of genomic tools in pea as opposed to other major food
legumes (Kreplak et al. 2019). In recent past, considerable improvement has been
made in molecular marker development, which to a great extent facilitated diversity
analysis, genetic mapping, QTL analyses, and marker-assisted breeding. Several
types of markers like morphological, isozymes, RFLP, AFLP, RAPD, SCAR, SSR,
IRAP, RBIP, ESTs, and more recently, high-throughput parallel genotyping have
been developed and deployed in genetic studies and improvement of pea (Blixt
1972; Hall et al. 1997; Aubert et al. 2006; Weeden and Marx 1987; Timmerman
et al. 1994; Tiwari et al. 1993, 1998; Irzykowska et al. 2001; Laucou et al. 1998;
Gilpin et al. 1997; Weeden and Boone 1999; Timmerman-Vaughan et al. 2000; Ford
et al. 2002; Janila and Sharma 2004; Ek et al. 2005; Konovalov et al. 2005; Smýkal
et al. 2008; Katoch et al. 2010; Deulvot et al. 2010; Bordat et al. 2011; Kaur et al.
2012; Mishra et al. 2012; Teshome et al. 2015a, b). Genomic and EST-based SSRs
were extensively used for studying genetic diversity and building different genetic
maps (Mishra et al. 2012; Sun et al. 2014; Tayeh et al. 2015b).
There is a long history of genetic mapping studies in pea. In 1912, the first genetic
linkage map of pea was reported, and the first genetic map was constructed in 1925
with six-linkage group (Wellensiek 1925). Lamprecht (1948) developed a full map
with 7 LGs using 37 morphological markers (Rozov et al. 1999). The plenty of
genetic markers, such as AFLP (Vos et al. 1995), RAPD (Laucou et al. 1998),
retrotransposon (Flavell et al. 1998; Pearce et al. 2000), or EST based (Gilpin et al.
1997), has paved the way toward the development of moderate density linkage
maps. The availability of common markers has permitted the integration of the
maps derived from different crosses and a consensus map was synthesized from an
RIL population, by positioning classical mutants, isozymes, RFLP, RAPD, EST,
SSR, and STSM markers on the Pisum genetic map (Gilpin et al. 1997; Weeden et al.
1998). On similar note, pea consensus linkage maps were generated using three RIL
populations (Hall et al. 1997). Later, a composite genetic map of 1430 cM (Haldane)
was built using 239 microsatellite markers in three RIL populations (Loridon et al.
2005), which has been deployed to localize numerous QTLs for disease resistance as
well as quality and morphology traits.
Over the years, several linkage maps have been generated using F2 populations
(Dirlewanger et al. 1994; Timmerman-Vaughan et al. 1996, 2005; Hunter et al.
2001; Sun et al. 2014; Timmerman-Vaughan et al. 2004; Barilli et al. 2010) and RIL
populations (Pilet Nayel et al. 2002; Hamon et al. 2013; Krajewski et al. 2012; Tayeh
et al. 2015a; Bourgeois et al. 2011; Bourion et al. 2010). More recently, a number of
functional maps composed of genes of known function have been developed by
many researchers (Deulvot et al. 2010; Bordat et al. 2011; De Caire et al. 2012;
1280 A. K. Parihar et al.

Hamon et al. 2013; Sindhu et al. 2014; Duarte et al. 2014a, b; Sudheesh et al. 2014).
Consensus maps have been built in order to offer higher mapping resolution and
better genome coverage. SNP markers are being preferred by researchers because of
their profuse frequency, ease of scoring, and approachable to high-throughput
genotyping (Desgroux et al. 2018; Gali et al. 2018; Aznar-Fernández et al. 2020).
Numerous SNPs marker have been identified considering sequencing data from
4 (Hamon et al. 2013; Leonforte et al. 2013b; Duarte et al. 2014a, b), 5 (Sindhu
et al. 2014), 6 (Bordat et al. 2011), 8 (Duarte et al. 2014a, b), and 12 (Tayeh et al.
2015a) populations.
Illumina GoldenGate (Deulvot et al. 2010; Leonforte et al. 2013b; Duarte et al.
2014a, b; Sindhu et al. 2014), Infinium (Tayeh et al. 2015a), and Sequenom
MassARRAY (Cheng et al. 2015) platforms have been adopted for SNP genotyping.
The availability of next-generation sequencing permitted detection of thousands of
SNPs across the genome, as established by polymorphism studies and genetic map
construction. Recently, by employing Illumina Infinium genotyping array, a consen-
sus map was developed, which provides insights into the structure and organization
of the pea genome built using 12 RIL populations (Tayeh et al. 2015a). A total of
12,802 transcript-derived SNP markers were positioned on a 15,079-marker high-
density, high-resolution consensus map. So far, in total around 58 genetic maps have
been constructed using different F2 or RIL populations (Pandey et al. 2021). The
developed individual and consensus genetic maps are valuable genomic tools to
strengthen pea as a model for genetics and physiology and accelerate breeding.
Most recently, a new online pea marker database (PMD, www.peamarker.
arriam.ru) platform has been developed to hoard/maintain valuable genomic
resources including different types of pea gene based markers (Kulaeva et al.
2017). The PMD ver.1 (PMD1) included information for 2484 genic markers
(Duarte et al. 2014a, b; Sindhu et al. 2014), while an updated version, PMD2,
comprised information of 15,944 markers with advanced attributes (Tayeh et al.
2013, 2015a). Most recently, the whole-genome sequencing data have been pro-
duced, which facilitate detection of additional 92,457 SNPs from the pea genome
(Duarte et al. 2014a, b; Boutet et al. 2016). In addition, 1000 SNP markers have been
transformed to competitive allele-specific PCR (KASP) markers to develop KASP
assays for ease of genotyping (Boutet et al. 2016). The SLAF-BSA and DArTseq
approaches have been used and identified 12,213 and 14,880 SNP markers, respec-
tively (Zheng et al. 2018; Aznar-Fernández et al. 2020).
The important genomic information accessible through different programs has
encouraged the pea community to make speedy progress toward targeted and
efficient molecular breeding. The genomics approaches, for example, fast neutron
and TILLING method, have been utilized for reverse genetics studies. The fast
neutron and TILLING induces deletion and point mutations, respectively, in geno-
mic DNA targets. The pea cultivar “Cameor” (Dalmais et al. 2008) and the germ-
plasm accession “JI 2822” (Domoney et al. 2013) have been treated to build up
TILLING populations. The TILLING populations online database platform, that is,
UTILLdb (http://urgv.evry.inra.fr/UTILLdb) sharing phenotypic information in
25 Field Pea Breeding 1281

addition to gene sequence of mutant genes (Wang et al. 2008a, b; Dalmais et al.
2008; Zhuang et al. 2012; Domoney et al. 2013; Moreau et al. 2018).
In addition, the bacterial artificial chromosomes (BACs) library is normally used
to produce and gather large and steady genomic clones for large genome size crops
(Yu 2011). The pea cultivar “Cameor” has been used to build up a BAC library for
physical mapping, genome sequencing, positional cloning, and analysis of gene
structure and function (Gali et al. 2019). Another BAC library developed from a
multidisease-resistant line, that is, PI 269818, which has been used for the isolation
and recognition of Fusarium wilt resistance genes (Coyne et al. 2007). The avail-
ability of pea chloroplast genome sequence could be very crucial in transgenic and
evolutionary applications (Smýkal et al. 2012). In 2019, the first chromosome-level
reference genome assembly of pea variety cv. “Cameor” has been generated using
complementary approaches (Illumina short-read sequences, PacBio RSII sequences
and BAC library). The reference genome assembly representing approximately 88%
of the estimated pea genome size (~ 4.45 Gb). The genome assembly holds 44,756
annotated genes with an average gene length of 2784 bp and an average exon length
of 308.5 bp. The annotation also identified 2225,175 repetitive elements
representing ~83% of the genome, most of which are transposable elements
(Kreplak et al. 2019). This reference sequence holds great promise for accurate
and in depth configuration of the pea genome and faster detection of the trait specific
genes to accelerate the genomic tools development which ultimately will speed up
the crop improvement program.
The transcriptome assemblies of pea are not only helpful in probing specific
genes but also play a critical role in creation of high-density genetic maps. Initially,
transcriptomic analysis was performed through microarray or RNA sequencing
(RNA-Seq) technology during P. pinodes infection in pea, thereby 346 differentially
regulated genes were identified, which were involved in various metabolism and
processes (Fondevilla et al. 2011a, b). Another EST-based microarray analysis in
pea recognized changed gene expressions related to oxidative stress and cell death
during seed aging (Chen et al. 2013). NGS approach arises as a powerful tool for
transcriptome analysis non-model species at reasonable cost. DeepSuperSAGE
genome wide transcriptional profiling was carried out to recognize pea genes
associated with resistance to P. pinodes. In totality, 17,561 UniTags were detected,
of them, 509 UniTags expression were significantly altered in infected versus
non-infected plants (Fondevilla et al. 2014). By using Massive Analysis of cDNA
Ends (MACE), positional and expressional candidate genes were identified for
resistance to P. pinodes in pea (Winter et al. 2016). Franssen et al. (2011) developed
a comprehensive gene expression atlas of pea by sequencing of above-ground organs
of pea cultivar “Little Marvel.” Similarly, transcriptome sequencing was performed
using multiple tissues of the field pea genotypes Kaspa and Parafield that vary in
terms of seed and plant morphological characteristics (Sudheesh et al. 2015).
Alves-Carvalho et al. (2015) also performed transcriptome analysis using various
plant tissues harvested at different growth stages planted under distinct nitrogen
levels. Liu et al. (2015a, b) sequenced seed RNA libraries for one vegetable and one
grain pea cultivar, from which 459 and 801 differentially expressed genes have been
1282 A. K. Parihar et al.

discovered at the early and late seed maturation stages, respectively. By RNA
sequencing of below-ground organs of pea-like nodules and root tips using an
Illumina GAIIx system, followed by de novo transcriptome assembly using the
Trinity program obtained about 58,000 and 37,000 contigs from “Nodules” and
“Root Tips” assemblies, respectively (Zhukov et al. 2015). In further analysis,
approximately 13,000 nodule-specific contigs have been found, which were
known as plant-protein-coding sequences, of them, 581 sequences possessed full
CDSs and considered as novel nodule-specific transcripts of pea. RNA sequencing
time series analyses was performed using frost-tolerant (Cv. Champagne) and frost-
sensitive (cv. Térèse) under low temperature and control condition, which led to
identification of 4981 differentially expressed genes (Bahrman et al. 2019). These
assemblies play instrumental role in the identification of markers and loci associated
with their traits of interest (Kulaeva et al. 2017). Transcriptome analysis provides
extensive information regarding genes expressions and has been uploaded to the
NCBI database platform, and it facilitates users to execute BLAST searching and to
study gene polymorphism.

25.15 Marker-Assisted Breeding (MAB)

Availability of closely linked molecular markers or QTLs with the target traits is the
prerequisite for MAB. Remarkably, the deployment of molecular markers in plant
breeding accelerates the generation of new varieties by helping plant breeders in
early selection of desirable individuals using at least one pair of markers flanking a
single target gene/QTL (Tayeh et al. 2015a). A number of genes/QTLs responsible
for the genetic regulation of yield attributes, seed protein, and biotic and abiotic
stress tolerance are available, which have been elaborated by Pandey et al. (2021).
Genome-wide association (GWA) mapping has recently emerged as an important
method to refine the genetic basis of polygenic resistance to plant diseases, which are
being used in integrated strategies for durable crop protection (Desgroux et al. 2018).
Specific markers associated with major genes have been developed for use in
breeding, particularly for trypsin inhibitors (Page et al. 2002; Duc et al. 2004),
flowering (Weller and Ortega 2015), and resistance powdery mildew (Reddy et al.
2015; Cobos et al. 2018), pea enation and seed-borne mosaic virus (Scegura 2017;
Grimm and Porter 2020), fusarium wilt (Kwon et al. 2013; Jiang 2013) or QTLs such
as lodging resistance (Zhang et al. 2006), rust (Singh et al. 2015a, b; Barilli et al.
2018), Ascochyta blight (Carrillo et al. 2014; Jha et al. 2015a, b; Jha et al. 2017),
Fusarium root rot (Feng et al. 2011; Coyne et al. 2019) and common root rot (Lavaud
et al. 2015; Desgroux et al. 2016) are available for MAB. Recently, marker-assisted
backcrossing (MABC) has been used successfully for the introgression of QTLs for
Aphanomyces root rot resistance (Hamon et al. 2013) into several recipient lines
(Lavaud et al. 2015).
Most recently, the MABC approach has also been deployed for the introgression
of three frost tolerance QTLs (Lejeune-Henaut et al. 2008). Several QTLs associated
with visual quality traits, including seed coat color, seed shape, and seed dimpling,
25 Field Pea Breeding 1283

have been detected; however, these are highly influenced by environmental

conditions (Taran et al. 2003; Ubayasena et al. 2011). Some of the researchers
have explained the genetic basis of the iron content in seeds and identified genetic
markers and QTL to aid in breeding programmes (Kwon et al. 2012; Diapari et al.
2015; Ma et al. 2017; Gali et al. 2018). Monogenic inheritance of phytic acid-
phosphorus (PA-P) concentration has been proposed, which is located with a QTL
linked to iron bioavailability (Shunmugam et al. 2015), consequently allowing the
development of DNA markers, which facilitates simultaneous selection for low
phytate and high iron bioavailability in MAS. In recent past, QTLs for the different
macro- and micronutrients, that is, boron, calcium, iron, potassium, magnesium,
manganese, molybdenum, phosphorus, sulfur, and zinc as well as for seed weight,
have been identified (Ma et al. 2017).
The genome-wide SNPs and the genetic linkage map permitted QTL identifica-
tion for seed mineral nutrients that will serve as important resources to enable MAS
for nutritional quality traits in pea-breeding programs. More recently, a high-density
linkage map has been developed to map the various seed quality-related traits such as
seed shape, seed dimpling, seed weight, grain yield, seed fiber, iron, selenium, and
zinc concentrations (Gali et al. 2018). Likewise, Cheng et al. (2015) detected SNPs
marker associated with calcium and magnesium concentration. Bangar et al. (2017)
detected QTLs for iron concentration, which collectively demonstrated 51% of the
phenotypic variance. Recently, Huang et al. (2017) developed a genetic linkage map
and reported ten QTLs of which five were associated to flowering traits and yield
component traits. Iglesias-Garcia et al. (2015) identified ten quantitative trait loci
QTLs associated with the drought tolerance-related traits and accounted 9–33% of
the phenotypic variation. The SSR marker associated with the drought adaptation
QTLs could be useful for MAS in drought adaptation breeding programs. Lejeune-
Henaut et al. (2008) reported six QTL region confirming oligogenic determinism of
frost tolerance in pea with a major QTL located in the vicinity of the Hr locus. Hr is a
gene controlling plant response to photoperiod (Weller et al. 2012). By using
marker-trait association, out of 672 accessions, sixteen accessions were identified
as frost tolerant (Liu et al. 2017). So far limited efforts have been made in MAB, but
these reports have proved the usefulness of MAS and MABC in pea improvement.
The availability of the reference genome will provide more opportunities to find out
the genes of breeding interest and to understand the genetic background at a genome-
level by deploying molecular markers amenable for high-throughput genotyping.

25.16 Coordinated System of Testing

The coordinated research program of field pea in India is being executed under the
umbrella of AICRP on MULLaRP (Mungbean, Urdbean, Lentil, Lathyrus, Rajmash
and Pea), which was established in 1995 and administered by the Indian Council of
Agricultural Research (ICAR). The AICRP on MULLaRP has a large network of
cooperating centers, covering major pulse-growing states of the country. These
centers are involved in carrying out activities and strategic research in the area of
1284 A. K. Parihar et al.

Fig. 25.3 Flow chart for testing entries under the AICRP on MULLaRP

crop improvement, production, and protection. The testing of entries for grain yield
is being conducted as per revised guidelines for testing of varieties (Tandon et al.
2015) under All India Coordinated Research Project, wherein the proposed entries
are tested in initial varietal trial (IVTs), advanced varietal trial-I (AVT-I), and
advanced varietal trial-II (AVT-II) at multiple locations in different zones, that is,
NHZ, NEPZ, NWPZ, and CZ (Fig. 25.3).
The IVTs trials are formulated with the new candidate entries submitted by
cooperating breeders/institutions including zonal and national checks. The total
number of test entries should be optimum according to experimental design so that
trial may be implemented with more precision. At least three check varieties
consisting of national, zonal, and local check shall be used continuously for three
years for proper comparison with the test entries. The seeds of candidate entries and
checks must be genetically pure and true-to-type and should fulfil minimum seed
certification standards. The experimental design, plot size, and number of
replications shall be finalized in the Annual Group Meet considering the experience
gained from the precedent trials to condense experimental error. The plot size and
number of replications should be harmonized at all the test locations/zone/ecology.
Besides, sufficient scope for date of planting, seed rate, sowing depth, plant geome-
try, nutrient and water management, weed, insect-pests, and disease management
shall be given in the technical program and that should be supplied to all the test
locations well in time. The testing centers must be recognized in the workshop and
that could be ICAR Institutes/SAUs/Main or Regional Research Centres/Zonal
Research Centres/State Govt. centres, where a multidisciplinary team of scientists
exists with adequate operational amenities to perform coordinated trials as per the
25 Field Pea Breeding 1285

guidelines. All the trials shall be monitored carefully by a team of scientists deputed
by the Project Director/Coordinator. The team shall visit the testing locations
preferably during flowering to maturity time and record comments on the quality
of the trials conductance as per the specified norms, and remark on the reliability of
data likely to be produced.
Moreover, observations should be noted on the agronomic character such as days
to flowering and maturity, plant height, reaction to major diseases and insect-pests,
easily measurable grain quality attributes such as color, weight and appearance, etc.
The details of traits on which data shall be recorded should be decided during
workshop. The data received at the coordination cell shall be crucially ascertained
to make a verdict on appropriateness of data for further statistical processing
considering the recommendations of the monitoring team. The point of view of the
zonal coordinator/concerned breeder, variation from the specified range of sowing
date, specified crop management practices for the trial, for example, fertilizer doses,
irrigation levels, etc., and any other serious error in conducting trial/data recording/
reporting should be considered properly before any final decision. The advancement
of candidate entries from IVT to AVT would be firmly on the basis of overall
performance/merit of the test entries and benchmarks finalizes in workshop.
AVT-I shall be constructed independently for each recognized agroecological zone
for the entries promoted from the IVT on the basis of the criteria specified, the repeat
entries from the previous year’s AVT-I along with the check varieties as per
workshop approval.
In AVT-I plot size should be larger than IVT to generate more rational estimates
of the yield performance and to subsidize any possible errors of measurements
inherent in small plots. The testing location shall be much more than IVT trials in
a given zone. Data on disease and insect-pest resistance and other ancillary
characters shall be recorded only at the locations where desirable amenities available
as specified in the workshop. Data on quality parameters including biochemical and
processing properties shall be produced from certain sites in specified laboratories as
per workshop recommendation. The promotion of AVT-1 entries must be done
primarily based on grain yield superiority with consideration of other specified
characters, that is, biotic and abiotic stress tolerance/resistance, quality traits, etc.
All the package and practices adopted under the IVT and AVT-I stage shall be
followed at AVT-II stage also. The entries, which demonstrated desired superiority
over the best check in AVT-II stage, their identification proposal is invited by project
coordinator for deliberation in varietal identification committee (VIC). The VIC after
detailed deliberation recommends the best entry for release and notification to central
subcommittee on crop standard notification and release of varieties for cultivation in
specific zones. After notification by Gazette of India, the varieties enter into seed
production chain: breeder seed, foundation seed, and certified seed.
1286 A. K. Parihar et al.

25.17 Seed Production and Seed Standards

Quality seed is the most critical agricultural input having a potential of increasing
yield by about 15–20%. Quality seed production differs from commercial grain crop
production in several aspects. Special operations, precautions, and operations are
needed to deploy to produce seed of optimum quality. Proper selection of seed
production site is important in producing quality seed of field pea. Generally, it is
recommended to undertake seed production in the same climatic area or zone for
which the variety has been bred, developed, tested, and recommended. It is very
important to ensure that the irrigation facilities are available in seed production site.
The land to be used for seed production of field pea shall be free of volunteer plants.
Ensure that in the preceding season either different crop or same variety of field pea
was grown to avoid mixture, and avoid taking seed production of field pea if in the
preceding season different variety of field pea was grown. Quality seed production
and maintenance of quality of a seed is a sequential process that starts from timely
sowing, which leads to timely flowering, pollination, successful fertilization, seed
development, and adequate accumulation of storage reserve in seed till maturity,
harvesting at physiological maturity, threshing, drying to optimum moisture levels,
seed processing, and its storage at adequate condition (Fig. 25.4).
Climatic variables like temperature, rainfall, relative humidity, carbondioxide
concentration, etc., prevailing during crop growth stage and subsequently during

Fig. 25.4 Steps in quality seed production

25 Field Pea Breeding 1287

storage affects the quality of seed (Maity et al. 2016; Lamichaney et al. 2018;
Lamichaney and Maity 2021). Timely sowing is must to produce high-quality
seed in field pea. Lamichaney et al. (2021a) have reported significant reduction in
seed set, 100-seed weight and germination of field pea when planted late, which was
attributed to high temperature-mediated reduction in reproductive period (forced
maturity), which resulted in improper development of seed. Likewise, rainfall and
elevated concentration of carbondioxide during crop growth period is reported to
reduce seed quality in legumes (Lamichaney et al. 2018, 2021b, c). Therefore,
precaution in each and every step is quintessential for producing and maintaining
the quality of a seed. Field pea being self-pollinated, a minimum isolation distance of
5 and 10 m is essential for certified and foundation seed production, respectively,
from the fields of other varieties or same variety not confirming to varietal purity
requirement of Indian Minimum Seed Certification Standards (Trivedi and
Gunasekaran 2013). A minimum of two inspections are required to be made, the
first before flowering and the second at flowering and podding stage (Trivedi and
Gunasekaran 2013). The main objective of field inspections is to verify the factors,
which can affect the genetic purity of the seed and to take the corrective measures.
During preflowering inspections, the requirements on the isolation distance and
land conditions are checked and to undertake roguing if any type of off-types are
present. While inspections during flowering and fruiting stage are done to further
check the occurrence of off-types based on flower and pod character and to remove
them. During flowering, daily inspections should be done to identify the not true to
type plants and to remove such off-types. A final rouging must be carried out during
maturity to eliminate any chance of contamination. The field pea crop should be
harvested when 90% of the pods turn brown, either by stationery threshers or
manually. Bleaching, discoloration of green seed to lighter green or yellow due to
loss or degradation of chlorophyll is reported to considerably reduce the quality of
seed, which could occur before as well as after harvesting (McDonald et al. 2019).
Bleaching before harvesting can occur due to intermittent rainfall and dry condition
occurring during physiological maturity (McCallum et al. 1997; Cheng et al. 2004),
and may lead to reduced germination and loss of seed vigour (Fenner 1985).
Therefore, delayed harvesting should be avoided as it increases the risk of bleaching
especially in green seeded cultivars (French 2016). Unfavorable storage conditions
such as high temperature, high relative humidity, or light intensity could cause
bleaching after harvesting (Ubayasena et al. 2013).
After threshing, the seeds should be dried to about 9% moisture before processing
and storage. The maximum permitted percentage of off-types at the final inspection
is 0.10% and 0.20% for foundation and certified seed production plots, respectively.
Pure seed in field pea refers to any seed with a portion of seed coat attached, or a
piece of seed but larger than one half the original size with a portion of the seed coat
attached, seeds with cotyledon broken apart yet are held together within a seed coat
(ISTA 2016). The minimum proportion of such pure seeds should be 98% for
foundation as well as certified seed. However, seeds and its pieces without seed
coat are considered as inert matter. Also, separated cotyledons are considered as inert
matter irrespective of whether the radicle-plumule axis and/or more than half of the
1288 A. K. Parihar et al.

Table 25.5 Field pea quality seed production standards as per Indian Minimum Seed Certification
Standards
Standards for each class
Factor Foundation seed Certified seed
Pure seed (minimum) 98.0% 98.0%
Inert matter (maximum) 2.0% 2.0%
Other crop seeds (maximum) None 5/kg
Weed seeds (maximum) None None
Other distinguishable varieties (maximum) 5/kg 10/kg
Germination including hard seeds (minimum) 75.0% 75.0%
Moisture (maximum) 9.0% 9.0%
For vapor proof containers (maximum) 8.0% 8.0%

seed coat are attached. Inert matter also includes the dust particles, muds, stones, and
any part of seed not included as pure seeds (ISTA 2016). The maximum permissible
limit of inert matter is 2% for both foundation and certified seed. In foundation as
well as certified seed, not a single weed seed is permitted seed. Likewise, the
maximum permissible limit of other crop seed is 0 and 5 per kg for foundation
and certified seed, respectively (Table 25.5).

25.18 Conclusions and Future Perspective

Despite the substantial efforts, the dry pea productivity in many countries such as
India, China, Australia, and Myanmar is still low. In addition, the production is
constantly declining in countries like USA, Finland, Brazil, Ireland, Belgium,
Pakistan, and Netherland, which is a serious concern and needs concentrated
research and developmental efforts to reverse the trend. The yield gain in Canada
is 2.0% and is superior to the yield gain in any other crops worldwide, which reveals
investment made in pea breeding over the years (Rubiales et al. 2019) and it should
be replicated in other countries also. Interestingly, across the countries the breeding
objective is mainly focused on few traits like tendril (afila), dwarf plant type, and
powdery mildew resistance, which led to narrow down the genetic base; hence, there
is urgent need of involvement of diverse parents in regular breeding program to
expand the genetic base (Dixit et al. 2014). Development of high-yielding varieties
possessing multiple stresses resistance remains the main objective. Very limited
usage of dry pea in terms of direct consumption prevails, therefore, proper value-
addition and novel ways to use the grain or its by-products must be developed, if the
popularity of this crop has to increase. Another important aspect of pea breeding is to
develop multipurpose cultivars (food-feed-fodder).
There is no doubt that in addition to its use as protein source, the demand for
cattle/poultry feeds and fodder will increase manifold in coming years particularly in
developing nations. Noteworthy, existing abundant natural genetic variation for
macro- and micronutrient and RFOs needs to be exploited for development of
25 Field Pea Breeding 1289

biofortified cultivars. In case of genomic resources, pea has made significant prog-
ress during recent past with several major/minor genes or QTLs identified governing
important traits. However, there is a need of large-scale high-throughput screening
of germplasm and subsequent identification of associated genes/QTLs for various
targeted traits. Besides, the introgression of these resistant sources in good agro-
nomic background should be done by employing marker-assisted selection. The
large number of biparental populations, the individual and consensus genetic maps,
the dense arrays of genetic markers, the high-throughput SNP genotyping tools, the
BAC libraries, the TILLING population, reference genome, proteomics,
metabolomics, epigenomics, bioinformatics, transcriptomics, genomic selection,
and genome editing approaches are available, which need to be embraced in regular
breeding program to accelerate the genetic gain in dry pea. Most fascinatingly, the
amalgamation of omics approaches with speed breeding will further speed up the
breeding cycle.

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Lathyrus Breeding
26
A. K. Parihar, S. Barpete, Arpita Das, Amrit Lamichaney,
and Sanjeev Gupta

Abstract

Grass pea (Lathyrus sativus L.) is a climate-resilient nutrient-dense crop that

offers food and nutritional security to many low-income communities of different
underdeveloped regions of the world including South Asia, Sub-Saharan Africa
and Mediterranean region. It is recognized to have a good source of protein,
healthy fatty acids, vitamins and micronutrients, notwithstanding, the stigma of
neurotoxin (ODAP) associated with grass pea that cause irremediable neurologi-
cal disorder in humans and animals. Interestingly, it is the only known dietary
source of L-homoarginine a non-proteinogenic amino acid which has admirable
medicinal properties. It has better tolerance to different biotic and abiotic stresses
as compared to other pulse crops. Over the years, sincere efforts are made towards
the genetic improvement of grass pea to subsidize ODAP content and elevate
production potential. In this book chapter, the economic importance of the crop,
its origin, domestication, evolution, botanical description and floral biology have
been illustrated. The accomplishment made in grass pea improvement through
conventional and non-conventional breeding approaches, that is selection,
hybridization, pre-breeding and distant hybridization along with application of
mutation breeding have been reviewed. The current status of genomics resources

A. K. Parihar (*) · A. Lamichaney

ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
S. Barpete
International Centre for Agricultural Research in the Dry Areas (ICARDA), Amlaha, Sehore,
Madhya Pradesh, India
A. Das
Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, India
S. Gupta
Crop Science Division, ICAR, Krishi Bhawan, New Delhi, India

# The Author(s), under exclusive licence to Springer Nature Singapore Pte 1323
Ltd. 2022
D. K. Yadava et al. (eds.), Fundamentals of Field Crop Breeding,
https://doi.org/10.1007/978-981-16-9257-4_26
1324 A. K. Parihar et al.

and marker-assisted breeding has also been deliberated. Moreover, the breeding
objectives, major constraints and future thrust areas toward exploring cutting-
edge tools and technique for enriching grass pea genomic resources have been
outlined. Furthermore, the existing coordinated testing system for new entries and
quality seed production has also been reviewed in brief. Overall, to accelerate
genetic gain in grass pea along with low ODAP embracement, urgent need is
being felt to explore recent advanced tools and techniques such as
transcriptomics, proteomics, metabolomics, small RNAomics, epigenomics,
interactomics, bioinformatics and genome editing to strengthen the grass pea
breeding programme towards its transformation from orphan to main stream crop.

Keywords

Breeding objectives · Genetic resources · Grass pea · Pre-breeding · Trait genetics

26.1 Introduction

Grass pea (Lathyrus sativus L.) is the climate-resilient nutritious cool-season legume
crop grown for food, feed and fodder (Almeida et al. 2015a, b, c; Rizvi et al. 2016;
Lambein et al. 2019). It is an ancient crop which has been cultivated for more than
8000 years owing to its tolerance towards drought, flooding, salinity, problematic
soils along with its ability of nitrogen fixation (Girma and Korbu 2012; Vaz Patto
and Rubiales 2014a, b; Dixit et al. 2016; Sarkar et al. 2019; Gupta et al. 2021). Given
traits endorsed it as an “insurance crop” that can perform exceptionally well under
marginal lands with low input and ensure economic, social and nutritional security to
the resource poor farmers’ of developing nations in the face of changing climate
(Hillocks and Maruthi 2012; Vaz Patto and Rubiales 2014a, b; Sarkar et al. 2019;
Mahapatra et al. 2020). Among the Lathyrus species, grass pea is the most cultivated
one predominantly grown for food, feed and fodder in India, Bangladesh, Nepal,
Pakistan and Ethiopia (Kumar et al. 2013; Dixit et al. 2016; Lambein et al. 2019).
The grass pea has various “common” names in different countries: for example
Chickling pea, Indian vetch (United Kingdom and North America), Almorta, Titos
(Spain), Khesari, Teora, Lakhdi, Lakh, Batura (India), Alverjas (Venezuela), Gilban
(Sudan), sabberi, Guaya (Ethiopia), Matri, mattra (Pakistan), Gesette (France), san
lee dow (China), Saatplatterbse (Germany), chicharo (Portugal) and Pisello bretonne
(Italy) (Skiba et al. 2007; Caminero Saldaña and Grajal Martín 2009; Hillocks and
Maruthi 2012; Rizvi et al. 2016; Al-Snafi 2019). Broadly grass pea may be classified
into two groups: one from the Indian sub-continent and second from the Mediterra-
nean group with higher yield potential (Hanbury et al. 1999; Girma and Korbu 2012;
Hillocks and Maruthi 2012). This crop is regarded as a perfect candidate crop of rice
fallows of South East Asia where it holds immense potential by thriving well on
residual soil moisture and provides additional income to the farming folks (Dixit
et al. 2016; Maji et al. 2019).
26 Lathyrus Breeding 1325

Table 26.1 Nutritional composition of grass pea

Constituents Amount References
Calories 362.3 kcal/kg Rahman et al. (1974) and Majumdar (2011)
Protein 17.7–49.3% Sammour et al. (2007a, b), Pastor-Cavada et al. (2011) and
Barpete et al. (2012a, b)
Fat 2.7% Rahman et al. (1974)
Carbohydrates 51.8–72.91% Tamburino et al. (2012) and Al-Snafi (2019)
Starch 32–52.3% Urga et al. (1995) and Al-Snafi (2019)
Total lipid 1.67–2.0% Buchanan (1904) and Tamburino et al. (2012)
Fatty acids 16–53.69% Grela et al. (2010) and Tamburino et al. (2012)
(saturated)
Fatty acids 45.7–66.7% Grela et al. (2010)
(unsaturated)
Iron (mg) 41.1–94.8 ppm Grela et al. (2010, 2012) and Gupta et al. (2021)
Zinc (mg) 15–54.7 ppm Hanbury et al. (2000), Urga et al. (2005), Grela et al. (2010)
and Gupta et al. (2021)
Homoarginine 7.49 to Sacristán et al. (2015)
12.44 mg/g
ODAP 0.02–2.50% Abd El Moneim et al. (2001), Fikre et al. (2008), Xiong
et al. (2015) and Barpete et al. (2021a, b)

In term of nutritious profile (Table 26.1), it is acknowledged as the cheapest

source of protein in the daily diets of millions of vegetarian folks unable to have
non-vegetarian product for balanced diet. The protein amount oscillated from 17.7 to
49.0% which is superior to almost other pulse crops (Sammour et al. 2007a, b;
Pastor-Cavada et al. 2011). The grass pea protein is constituted of albumins
(14–26%), globulins (53–66%), glutelins (15%) and prolamins (5–6%) (Duke
1981; Chandna and Matta 1994). The protein of grass pea contains 17 essential
amino acids in sufficient amount especially lysine at higher level than other legumes
or cereals crops (Yang and Zhang 2005). Among other essential amino acids, the
most abundant are leucine, phenylalanine, threonine and valine, whereas, likely to
other legumes it is deficient in sulphur-containing amino acids, that is, methionine,
cysteine and tryptophan (Yan et al. 2006; Mahler-Slasky and Kislev 2010; Pastor-
Cavada et al. 2011). Phosphorus and calcium content in grass pea ranges from 380.4
to 511.6 mg/100 g and 131.6 to 200.1 mg/100 g, respectively (Urga et al. 1995)
which can easily meet the daily recommended intake of 500 mg/day of phosphorus
and 800 mg/day of calcium for children of 4–8 years old (Yates et al. 1998; Teshager
2019). Seeds of grass pea are rich in potassium with a value ranging from 8.3 to
10.8 g/kg in dry matter.
The average copper, zinc, iron and manganese levels in grass pea are 5.1, 44.1,
62.1 and 23.7 mg/kg in dry matter, respectively. The tannin content ranges between
2.76 and 5.62 g/kg in dry matter (Grela et al. 2010). Although the lipid content in this
legume is below 2% (Buchanan 1904) with nutritionally valuable well-balanced
fatty acids constitution where major proportions of palmitic and linoleic acids and
smaller quantities of oleic, linolenic and arachidonic acids improve its nutraceuticals
1326 A. K. Parihar et al.

value (Hanbury et al. 2000; Chinnasamy et al. 2005; Pastor-Cavada et al. 2009;
Grela et al. 2010). Therefore, grass pea is much appropriate for human consumption
owing to excellent quality of fatty acid with 58% polyunsaturated fatty acid wherein
linoleic acid (18:2) accounted for 51% and linolenic acid (18:3) for 6.4% (Grela et al.
2010). Grass pea is a good source of almost all essential vitamins for health viz.,
retinol, β-carotene, thiamine, riboflavin, niacin, pantothene, pyridoxine, folic acid
and ascorbic acid (Arslan 2017). Most importantly, grass pea is much appropriate for
human consumption owing to excellent quality of fatty acid with 58% polyunsatu-
rated fatty acid wherein linoleic acid (18:2) accounted for 51% and linolenic acid
(18:3) for 6.4% (Grela et al. 2010). Grela and Günther (1995) reported 40 IU and
7 mg of vitamin E and tocopherol content per kg of seeds, respectively. The measure
of energy level in grass pea is similar to those for many other common feed grain
legumes (Hanbury et al. 2000). Furthermore, it also showed the highest concentra-
tion of flavonoids and antioxidants (Sarmento et al. 2015).
Grass pea seed is a coffer of many compounds that can contribute to physical
health and fitness of humans. For example it is the only acknowledged dietetic
source of L-homoarginine amino acid which is one of the first strange non-protein
amino acids (Rao et al. 1963; Bell 1962) with nutraceutical properties (Lambein
2000; Rao 2011; Singh and Rao 2013; Llorent-Martínez et al. 2017) and plays
instrumental role in cardiovascular disease treatments (Rao 2011; Singh and Rao
2013; van Wyk et al. 2016). It also helps in combating the repercussion of hypoxia
associated with cancer tumour development (Ke and Costa 2006; Jammulamadaka
et al. 2011). Therefore, as nutraceutical, grass pea is regarded as an excellent
example of a potential “functional food” (Singh and Rao 2013; Llorent-Martínez
et al. 2017). Although arginine is the usual substrate for nitric oxide synthase (NOS),
homoarginine also provides an alternative substrate. Thus, a daily dietary intake of L-
homoarginine through small quantities of grass pea may be valuable for human
health and deserves further investigation (Rao 2011). Moreover, one additional
potential beneficial application of grass pea seeds is to ameliorate diabetic
symptoms, as they have glycosyl phosphatidyl inositol with insulin-mimetic activity
(Pañeda et al. 2001).
In addition, condensed polyphenols are present in grass pea seeds which have
positive correlation with seed coat colour (Deshpande and Campbell 1992). Total
phenolics in grass pea ranged from 868 to 2059 mg/kg dry matter. Condensed
tannins in grass pea ranged from 0.89 to 5.18 g/kg dry matter. Grass pea seeds
with darker seed coat colour contained higher levels of condensed tannins (Wang
et al. 1998; Talukdar 2012a, b, c). In addition, high level of trypsin inhibitor has also
been recorded in grass pea and trypsin inhibitor activity (TIA) values vary from
15.53 to 18.99 TIU/mg. Total phenolic contents ranged from 1.88 to 7.12 mg/g
extract and 20.3 to 70.3 mg/100 g seeds (Rybinski et al. 2018; Al-Snafi 2019).
However, grass pea is also defamed due to neurotoxin, that is β-ODAP (β-N-
oxalyl-l-α,β-diaminopropionic acid) which caused lathyrism, a neurodegenerative
ailment in humans and domestic animals owing to its overconsumption under
extreme food crisis (Lambein and Kuo 2009; Vaz Patto and Rubiales 2014a, b).
The term “lathyrism” was coined by Cantani of Naples in 1873 (Barrow et al. 1974).
26 Lathyrus Breeding 1327

This disease is more prominent when grass pea was taken as core ingredient of daily
diet at least 30% of the caloric ingestion for at least a period of 3–4 months (Kumar
1998). To further challenge the bad reputation of grass pea owing to its metabolite
β-ODAP, a Chinese group has obtained a patent for the use of β-ODAP as a
haemostatic agent during surgery (Lan et al. 2013). β-ODAP is also present in the
longevity-promoting Panax ginseng root (Kuo et al. 2003) that under the name
Dencichin is known for its haemorrhage-stopping property and thrombopoiesis
treatment (Ding et al. 2018). In China, it is even supplemented in some toothpaste
brands and used as an herbal medicine to avoid bleeding. Most fascinatingly,
β-ODAP has also been described as a multi-functional plant metabolite which
adds a new dimension to explore its potential in the treatment of Alzheimer’s
disease, hypoxia and long-term potential of neurons essential for memory (Singh
and Rao 2013). Recent investigations have revealed that β-ODAP induces wound
healing and can be considered as a natural wound curative agent (Sharma et al.
2018). An increasing number of therapeutic applications derived from grass pea may
be developed in the coming years. This existing variability for different nutritional
traits will be useful to the breeders for further utilization in grass pea improvement.

26.2 Common Uses of Grass Pea Worldwide

In India, Pakistan, Bangladesh and Nepal, the most common use of grass pea is as
split seeds (dhal) and flour (besan) (Al-Snafi 2019). The besan is used to prepare
many traditional food items including pakoras, piazu, chapati, dhal, vadi, dhokla
and sweets (Pandey and Kashyap 1995; Campbell 1997; Kumar 1998; Asthana and
Dixit 1998). The use of grass pea as leafy vegetable, green pods, green seeds as
snacks or as cooked vegetable is also common in many countries (Peña-Chocarro
and Peña 1999; Almeida et al. 2015a, b, c. In Ethiopia, grass pea is eaten in different
ways such as boiled seed (nifro), bread (kitta), roasted grains (Kollo), flour (Shiro)
and sauce (wott) (Tekle-Hainamot et al. 1995; Campbell 1997). In China, it is used
as animal feed and as a supplement in food processing (Zhou and Arora 1995).
Young grass pea plants are used as fodder for cattle or for grazing in many countries
(Kumar 1998). As fodder, the plants can be eaten green or as hay (Duke 1981; Tekle-
Haimanot et al. 1993; Ahsan et al. 2010). Notably, in Bangladesh, the grass pea seed
oil is also used to cure scabies, eczema and allergy (Al-Snafi 2019).
Moreover, the other species of genus Lathyrus, that is L. cicera and L. ochrus are
also cultivated for food and fodder purposes in Iran, Iraq, Syria, Jordan, Greece,
Cyprus and Turkey (Saxena et al. 1993; Kumar et al. 2013). Some other species like
L. clymenum and L. hirsutus are cultivated as minor forage crops in Greece and
Southern United States (Sarker et al. 2001). A few species are valued as ornamental
plants, especially L. odoratus (sweet pea), L. sylvestris and L. latifolius in the
modern world (Campbell 1997). Recently, the novel biological properties, that is
antioxidant, enzyme inhibitory, cytotoxic effects and phytochemical profiles of
selected Lathyrus species, that is L. czeczottianus and L. nissolia, have been noticed
(Llorent-Martínez et al. 2017). Consequently, both the species hold great promise to
1328 A. K. Parihar et al.

be utilized in designing of new phytopharmaceutical and nutraceutical formulations.

Other Lathyrus species namely L. cicera, L. ochrus, L. clymenum, L. latifolius
L. sylvestris and L. tingitanus are cultivated for both forage or grain purposes
(Campbell 1997; IPGRI 2000).

26.3 Origin, Evolution, Distribution and Gene Pools

of Grass Pea

Grass pea belongs to the genus Lathyrus consisting of 187 species (Vaz Patto and
Rubiales 2014a, b; Sarkar et al. 2019) within the Fabaceae family (syn.
Leguminosae), sub-family Faboideae (syn. Papilionoideae) and tribe Fabeae (syn.
Vicieae) (Allkin et al. 1986; Wojciechowski et al. 2004; Kenicer et al. 2005; Smýkal
et al. 2011; Schaefer et al. 2012). This genus has been grouped into 13 sections
(Orobus, Lathyrostylis, Lathyrus, Orobon, Pratensis, Aphaca, Clymenum,
Orobastrum, Viciopsis, Linearicarpus, Nissolia, Neurolobus and Notolathyrus)
based on morphological and molecular phylogenetic studies (Kupicha 1983; Croft
et al. 1999; Kenicer et al. 2005, 2009). However, studies of the chloroplast DNA of
42 Lathyrus species (Asmussen and Liston 1998) and AFLP analysis of 18 species
(Badr et al. 2002) suggested that reclassification of some species to different sections
may be required (Skiba et al. 2007). It is scattered throughout the temperate regions
of the Northern Hemisphere with 52 species in Europe, 30 species in North America,
78 species in Asia and 24 species extending into tropical East Africa and 24species
into temperate South America (Kupicha 1983; Allkin et al. 1985; Goyder 1986; Badr
2006). In India, Lathyrus species is distributed throughout the country and cultivated
from 1200–3000 m altitude (Gautam et al. 1998).
The name Lathyrus is originated from the Greek word “la thyros” that indicates at
something exhilarating, referring to the aphrodisiacal qualities credited to grass pea
(Loudon et al. 1855). The most probable centre of origin is the eastern Mediterranean
or Fertile Crescent, around 6000 before present (BP). This has been supported by
archaeological evidences and recent phylogenetic reports (Kislev 1989; Schaefer
et al. 2012) that contradicted the hypothesis of Smartt (1984) wherein the centre of
origin was mentioned in Southwest or Central Asia. It is being mainly cultivated in
India, Bangladesh, Pakistan, Nepal, Ethiopia, China and in many countries of
Europe, the Middle East and Northern Africa (Vaz Patto et al. 2006a; Yan et al.
2006; Dixit et al. 2016). The archaeological facts witnessed that grass pea has a long
history of domestication and seeds of Lathyrus species had been found in Turkey and
Iraq in the form of collected or cultivated stuff (Lambein et al. 2019). Grass pea
cultivation started around 6000 BC and might have been the first crop domesticated
in Europe (Kislev 1989). Similarly, seeds from 2500 BC were identified in the oldest
excavation in India (Kislev 1989) and also in the Balkan in 8000 BC. According to
Vavilov (1951) Lathyrus has two centres of origins: one was the Central Asiatic
Centre which includes northwest India, Afghanistan, the Republics of Tajikistan and
Uzbekistan and western Tian-Shan, whereas the second was the Abyssinian Centre
(Campbell 1997).
26 Lathyrus Breeding 1329

In general, Lathyrus species are classified into five groups considering taxonomy
and morphology attributes namely Aphaca, Nissolia, Clymenum, Cicerula and
Lathyrus (Asmussen and Liston 1998; Kenicer et al. 2005). Of which, first four
species are annual, whereas Lathyrus species are mostly perennial type (Asmussen
and Liston 1998; Bässler 1966; Kupicha 1983). The Lathyrus species has been
grouped into primary, secondary and tertiary gene pools based on the cross-
compatibility (Jackson and Yunus 1984; Yunus and Jackson 1991; Heywood et al.
2007; Kumar et al. 2013). The cultivated and wild races of L. sativus are part of
primary gene pool (Heywood et al. 2007; Rizvi et al. 2016) that is classified into
gene pool 1A in which white flowered and white seeded varieties are included, while
gene pool 1B includes blue flowered and small speckled seeded varieties (Townsend
and Guest 1974; Smartt 1984; Jackson and Yunus 1984). The primary gene pool of
Lathyrus mainly included only one species L. sativus which have limited cultivars
and landraces. Thus, further improvement through conventional breeding
completely hinged on exploitation and utilization of other distant wild relatives
(Yunus and Jackson 1991).
According to Heywood et al. (2007), a total of 10 species belongs to secondary
gene pool, namely L. cicera, L. amphicarpus, L. chrysanthus, L. gorgoni,
L. marmoratus, L. pseudocicera, L. blepharicarpus, L. chloranthus,
L. hierosolymitanus and L. Hirsutus. However, very limited information is available
regarding cross-compatibility of these species with the cultivated L. sativus. How-
ever, Heywood et al. (2007) further reported that some of the species such as
L. chrysanthus, L. gorgoni, L. marmoratus and L. pseudocicera belonging to
secondary gene pool is compatible with L. sativus, but only ovules were produced.
Other species (Lathyrus sp.) which are included in the tertiary gene pool can be
exploited for crop improvement activities with the help of modern biotechnological
approaches, like embryo rescue techniques etc., for transferring desirable genes from
tertiary gene pool to cultivated background.
Few attempts have been made to introduce novel genes through inter-specific
hybridization between Lathyrus spp. and other crop wild relatives (CWR). Because
there is huge potential in some of the species particularly ornamental L. odoratus for
some exclusive traits like flower coloration and disease resistance that can be
transferred into cultivated L. sativus if crosses can be made successfully (Gurung
and Pang 2013). Numerous attempts were made to cross L. sativus with a range of
Lathyrus spp. using embryo rescue technique (Addis and Narayan 2000). The
progenitor of L. sativus (primary gene pool) is still unknown; however, according
to the Jackson and Yunus (1984), L. cicera is morphologically and cytogenetically
nearest to the cultivated species and it is the most probably qualifying candidate for
progenitor of L. sativus (Hopf 1986). This small-seeded Lathyrus species is gener-
ally cultivated in the countries from Greece to Iran and Transcaucasia. In this area,
carbonized Lathyrus seeds had been recovered from a number of ancient sites, going
as far east as India. Recently, Kumar et al. (2013) reported that some of Mediterra-
nean species namely L. cicera, L. marmoratus, L. blepharicarpus and L.
Pseudocicera have been recognized as candidates for progenitor of L. sativus
based on the morphological synteny with cultigens. Among the other economically
1330 A. K. Parihar et al.

Table 26.2 Grass pea genetic resources available at different institutions/organizations worldwide
No. of
S. no. Institute name with address accessions
1 International Center for Agricultural Research in Dry Areas (ICARDA), 4184
Morocco
2 Conservatoire Botanique National des Pyrénées et de Midi-Pyrénées 4477
(CBNPMP), France
3 National Bureau of Plant Genetic Resources (NBPGR) in India, New 2619
Delhi, India
4 Plant Genetic Resource Centre (PGRC), Bangladesh Agricultural 1841
Research Institute (BARI), Bangladesh
5 Royal Botanic Gardens Kew, UK 1115
6 ARS-GRIN Pullman, ARS Ft Collins, Boyce Thompson Arboretum, 949
Arizona, ARS National Arboretum, Washington, DC, USA
7 National Genebank, Beijing, China 704
8 Instituto Nacional de Investigación Agraria (INIA), Chile 1424
9 Ustymivka Experimental Station of Plant Production, Ukraine 1215
10 N.I. Vavilov All-Russian Scientifc Research Institute of Plant Industry, 1207
Russian Federation
11 Australian Grains Genebank Australia 1020
12 Plant Gene Resources of Canada (PGRC) Canada 840
13 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 515
Germany
14 Centro de Recursos Fitogenéticos (CRF) Institutonacional de 429
Investigación y Tecnología Agraria y Alimentaria (INIA), Spain
15 ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India 450
16 IGKV, Raipur 1964
17 International Center for Agricultural Research in Dry Areas (ICARDA), 400
India
18 Institute of Biodiversity Conservation (IBC), Addis Ababa, Ethiopia 586
Sources: Girma and Korbu (2012), Vaz Patto and Rubiales (2014a, b), Almeida et al. (2015a, b, c),
Sarkar et al. (2019) and Anonymous (2020)

important legume crops, Pisum sativum is considered as the closest to grass pea,
followed by lentil (Lens culinaris), faba bean (Vicia faba L.), barrel medic
(Medicago truncatula Gaertn.), chickpea (Cicer arietinum L.) and Lotus
corniculatus L. (Asmussen and Liston 1998; Ellison et al. 2006; Wojciechowski
et al. 2004). CWRs are the arsenals of many important traits; therefore, they play a
pivotal role towards genetic enhancement of the grass pea (Table 26.2). Neverthe-
less, extra-terrestrial gene transfer is rarely attempted in grass pea, notwithstanding
the successful setting of viable seeds in inter-specific hybridization between
L. sativus with L. cicera and L. amphicarpus (Khawaja 1988; Yunus 1990; Davies
1957, 1958; Addis and Narayan 2000).
On the contrary, some other CWRs can develop pods which remain devoid of
viable seeds (Yamamoto et al. 1989; Yunus 1990; Kearney 1993). Interest in inter-
specific hybridization in the Lathyrus genus was shown Burpee (1916) in sweet pea
26 Lathyrus Breeding 1331

(L. odoratus). Inter-specific hybridization between other species in the genus

Lathyrus had been attempted by many researchers since the report of the successful
crossing of L. hirsutus
L. odoratus by Barker (1916). Initially, distant
hybridization involving L. sativus was successful when L. cicera was crossed with
L. sativus (Lwin 1956); however, these crosses remain unsuccessful in subsequent
attempts (Davies 1958; Khawaja 1988). Later on, many studies reported successful
inter-specific hybridization in the genus Lathyrus using different species namely
L. sylvestris, L. latifolius, L. articulates, L. ochrus, L. clymenus, L. annuus,
L. hierosolymilanus, L. cicera, L. marmoratus, L. blepharicarpus,
L. pseudocicera, L. gorgoni, L. marmoratus, L. blepharicarpus, L. odoratus,
L. belinenesis, L. hirsutus, L. rotundifolius and L. tuberosus in specific combinations
(Marsden-Jones 1919; Davies 1957, 1958; Trankovskij 1962; Khawaja 1988;
Yamamoto et al. 1989; Kearney 1993; Hammett et al. 1994, 1996).
However, sincere efforts have been made to exploit secondary gene pool
resources in L. odoratus to obtain new pigmentations and fragrance by successful
crossing with L. hirsutus, L. chlorantus (Khawaja 1988) and L. belinensis (Hammett
et al. 1994). Based on the crossing ability, chromosomal behaviour and setting of
viable seed in the hybrids, novel gene transfer for crop improvement in L. sativus is
attainable through L. cicera and L. amphicarpus which are easily crossable species
with cultivated one. For other species of Lathyrus which are not producing viable
hybrids can be utilized through biotechnology-based tools and techniques (Ochatt
et al. 2001; Barpete et al. 2009, 2017, 2020a, 2021a, b).

26.4 Botanical Description

It is a herbaceous annual winter season crop which may achieve a height of about
1.5–1.7 m (Smartt 1984; Campbell 1997). It has slender, glabrous, ribbed, quadran-
gular, branched stem with a straggling or climbing habit, it mounts with the help of
tendril instead of twining (Campbell 1997). Grass pea has noticeable leaf like,
triangular to ovate shape stipules with basal attachment to petiole (Majumdar
2011). It has well-developed taproot system in which rootlets are prolonged and
sheltered by small, cylindrical, branched nodules which usually bunched together in
dense groups (Parihar and Gupta 2016). Grass pea can develop lateral roots and
aerenchyma, which minimize oxygen use, aid oxygen transfer from shoot to root and
remove harmful by-products during environmental stresses like flood (Zhou et al.
2016). The leaves are pinnate, terminates in 3–5 tendrils and consist of one or two
leaflets which are cuneate at the base and acuminate at the top (Fig. 26.1a). The
flowers are axillary, solitary and may be bright blue, reddish purple, red and pink
with white keel (Fig. 26.1b, c).
The ten stamens are arranged in diadelphous (9 + 1) pattern with elliptoid and
yellow anthers. Ovary is sessile, thin and pubescent with 5–8 ovules and style
bearded below the stigma. Stigma is glandular-papillate and spatulate. The pods
are oblong, flat, straight or slightly curved ending in a beak (Fig. 26.1d) and have
three to five angled and wedge-shaped seeds, ranging in colour from creamish,
1332 A. K. Parihar et al.

Fig. 26.1 Lathyrus sativus L. botanical description, (a) leaves and tendrils pattern of different
accessions of grass pea, (b and c) flower color and keel color variation in grass pea, (d) grass pea
pods are oblong, flat, straight or slightly curved ending in a beak, (e) different seed shapes with
variable hilum pattern

yellow, brown grey, or light grey and occasionally spotted or mottled (Fig. 26.1e).
The hilum is elliptic, and cotyledons are yellow to pinkish yellow (Fig. 26.1e). The
seed germination is hypogeal type (Campbell 1997; Skiba et al. 2007; Parihar and
Gupta 2016). Based on seed size, grass pea is classified into to two groups: small
seeded (5.0–7.02 g/100 seed weight) and large seeded (7.15–15.92 g/100 seed
weight) (Watt 1980). The small seeded is known as lakhodi or choti teora is
primarily cultivated in Chhattisgarh area and large seeded known as lakh or badi
teora is commonly grown in Nagpur and Bhandara district in India (Majumdar
2011).
26 Lathyrus Breeding 1333

26.5 Floral Biology, Emasculation: Pollination Techniques

Grass pea is principally self-pollinated, although some outcrossing has also been
reported in this species (Mehta and Santha 1996), which is reliant on environmental
or genetical factors. The average outcrossing rate ranged between 2.2% and 27.8%;
however, the rate of outcrossing is varied significantly between grass pea genotypes
(Rahman et al. 1995; Chowdhury and Slinkard 1997). The amount of outcrossing is
27.8% for blue, 19.4% for pink, and 9.8% for the white flowered genotypes (Rahman
et al. 1995). Bees are presumed to be the predominant pollinator of grass pea
(Rahman et al. 1995; Chowdhury and Slinkard 1997). According to cytological
and karyotype research in Lathyrus genus, all known annual species and most
perennial species of Lathyrus are diploid with 2n ¼ 14 chromosomes (Barpete
et al. 2012b; Hao et al. 2017). Some aneuploid as well as polyploid species are
also reported among the Lathyrus genus viz., L. palustris (2n ¼ 6x ¼ 42, hexaploid)
and L. venosus, (2n ¼ 4x ¼ 28, tetraploid) (Narayan and Durrant 1983; Talukdar and
Biswas 2008). Grass pea has attractive flower colour like blue, pink, red, white or
various combinations. The blue-flowered ecotypes are found in South-East Asia and
the South Asia with high outcrossing rate (Polignano et al. 2005a, b; Kumar et al.
2013), whereas, white flower types with less outcrossing are generally common in
Mediterranean region (Smartt 1984).
Normally, in any grass-pea-breeding programmes, the crossing programme is
executed under controlled condition in the greenhouse or under net house for
avoiding possible outcrossing through bee or other pollinators. At the outset, the
flowers are emasculated by removal of the anthers in the late bud stage. In the next
morning, the styles are fertilized with pollen from desired parents plant as soon as
possible following dehiscence of the anthers. Emasculation and pollination are long-
lasting practices in crossing programme of grass pea which results in a sufficient
number of successful cross seeds as several seeds normally develop in a single
pollination attempt. The male sterility was first reported by Srivastava and
Somayajulu (1981) wherein they noticed that some plants have reduced stamens
and the anthers did not produce viable pollen. Quader (1987) revealed the existence
of both cytoplasmic and genetic male sterility with the presence of both single and
double restorer genes.

26.6 Cytogenetics and Molecular Cytogenetics

The available literature indicated Corti (1931) as the pioneer to discover chromo-
some number in L. sativus L. who illustrated the presence of 2n ¼ 14 chromosomes
in the somatic complement. Cytological and karyotype examination demonstrated
that the L. sativus chromosome number is 2n ¼ 2x ¼ 14 throughout the genus and
most of the species are diploid with rare exceptions of polyploidy (Battistin and
Fernandez 1994; Campbell 1997; Schifino-Wittmann 2000; Seijo and Fernandez
2001; Talukdar 2009a, b, c, d; Barpete et al. 2012b; Hao et al. 2017). Only three
perennial species contain more than 14 somatic chromosomes of which L. pratensis
1334 A. K. Parihar et al.

and L. venosus are tetraploid with 2n ¼ 4x ¼ 28 and L. palustris is hexaploid with

2n ¼ 6x ¼ 42. However, stability in chromosome number in L. sativus was noticed,
but substantial variations in size and morphology of chromosome have performed an
important role in the evolution of diploid Lathyrus species (Narayan and Durrant
1983; Yamamoto et al. 1984; Klamt and Schifino-Wittmann 2000; Schifino-
Wittmann 2001; Sammour 1991). From an evolutionary viewpoint, the variation
in genome size is harmonious with morphological variation as well as with the life
cycle (Badr 2006). The change in chromosome size is linked with 2C nuclear DNA
amount variations (Ceccarelli et al. 2010). The deviation in chromosome size is often
due to amplification or deletion of a chromatin section during species diversification.
Moreover, intra- and inter-specific fluctuation in chromosome size indicates
noticeable difference in the quantity of DNA that affect complement size and a
high percentage of DNA is moderately repetitive (Talukdar and Biswas 2008). In
addition, Ali et al. (2000) exhibited that the karyotype surveillance supported well
the phylogenetic relationships among Lathyrus species that harboured into different
sections as proposed by Kupicha (1983). However, other studies demonstrated the
inter-specific karyotype variations that allow species characterizations (Battistin and
Fernandez 1994; Shahiquzzaman and Kabir 1994). Such type of inconsistency in
karyotype (L. odoratus L. and L. sativus L.) was also identified at the intra-specific
level (Murray et al. 1992b). Intra-specific variability in the position and number of
secondary constrictions was observed in L. nervosus and L. pubescens (Klamt and
Schifino-Wittmann 2000). Some cultivars of L. sativus also exhibited satellites
chromosomes that varied between 1 and 2 pairs (Ghasem et al. 2011; Barpete
et al. 2012b).
Several studies have been conducted for the phylogenic relationships among
different Lathyrus species including cytological traits karyotype analysis, chromo-
some banding and in situ hybridization (Battistin and Fernandez 1994; Murray et al.
1992a; Schifino-Wittman et al. 1994; Unal et al. 1995; Klamt and Schifino-
Wittmann 2000; Ali et al. 2000; Ali and Osman 2020; ). Aneuploid and polyploid
plants are also reported within Lathyrus species that showed the same basic chromo-
some number (Talukdar and Biswas 2008). In addition, a complete set of seven
different primary trisomics has an extra chromosome (2n + 1 ¼ 15) and has been
successfully isolated and cytogenetically characterized (Talukdar and Biswas 2007).
Subsequently, seven different types of tetrasomics were also isolated and
characterized in the advanced selfed generations of these primary trisomics
(2n + 1; 2n ¼ 15) obtained earlier in diploid (2n ¼ 14) grass pea (L sativus L.).
The extra chromosomes were noticed either in bivalent or in trivalent-univalent or in
quadrivalent form at metaphase-I (Talukdar 2008). The Trisomics and tetrasomics
developed tailored segregation ratios for marker genes on the extra chromosomes.
These ratios can be used to place genes on chromosomes and to create linkage
groups (Khush 1973). The cytological examination of the F1 hybrids attempted
between L. amphicarpus
L. sativus, L. amphicarpus
L. cicera and
L. odoratus
L. chloranthus was carried out by Khawaja (1988) which showed
50–70% chromosome homology and pollen fertility in consistency with the meiotic
pairing (Campbell 1997).
26 Lathyrus Breeding 1335

26.7 Genetic Resources Panorama

Breeding efforts towards genetic improvement of any cultivated plant species mainly
rely on the precise identification and characterization of the germplasm resources of
the crop and the study of its evolution (Yunus and Jackson 1991). The comprehen-
sive knowledge of its closest and distant relatives and geographical origins (Schaefer
et al. 2012) are quintessential to accelerate any breeding process which has been
already elaborated in previous sections. The most economical and significant
Lathyrus species which is being cultivated commercially comes under the section
Lathyrus comprising L. sativus, L. cicera and L. odoratus. However, in comparison
to other crops, very limited efforts have been made throughout the world towards the
genetic improvement of these species. The success of breeding programme relies on
availability and access of suitable genetic resources. During recent years, the con-
servation of Lathyrus genetic resources engrossed more attention owing to the
potential role of this climate-resilient species under current climate changing
circumstances (Kumar et al. 2013, 2020). Coordinated global efforts to bring
together and conserve Lathyrus crop species have been started in the last decades
of twentieth century, with the establishment of a “Lathyrus Genetic Resources
Network” (Mathur et al. 1998).
Grass pea was enlisted in conservation programme with other major food
legumes in multi-lateral platforms that developed to ensure access and benefit
sharing under the International Treaty on Plant Genetic Resources for Food and
Agriculture (ITPGRFA) (FAO 2009). On similar note, another programme was
developed by the Global Crop Diversity Trust (GCDT) in the collaboration of
International Centre for Agricultural Research in the Dry Areas (ICARDA) with
the intention for long-term conservation strategy of L. sativus, L. cicera and
L. ochrus (GCDT 2009). Some large collections of cultivated and wild Lathyrus
species have already been assembled and are being maintained in ex situ (gene
banks) and in situ (natural habitats) circumstances by different institutes/
organizations in worldwide. The largest Lathyrus gene bank is available at the
Conservatoire Botanique National des Pyrenees et de Midi-Pyrenees (CBNPMP)
in France with a total of 4477 accessions: 53% belongs to L. sativus and 18% to
L. cicera.
The second leading institute is International Center for Agricultural Research in
Dry Areas (ICARDA) which holds nearly 4200 accessions at its research centre in
Morocco which comprised of L. sativus and L. cicera (Vaz Patto and Rubiales
2014a, b; Sarkar et al. 2019). The third widest collection of Lathyrus species is
also held under the European Cooperative Program on Crop Genetic Resources,
hosted by Bioversity International in Rome, which hold over 4000 accessions
(Hillocks and Maruthi 2012). The ICAR-National Bureau of Plant Genetic
Resources (NBPGR) in India holds about 2600 accessions (3% wild types and
85% cultivated type), of them 98% are L. sativus and 0.04% are L. cicera. Another
leading institute is Plant Genetic Resource Centre (PGRC) of Bangladesh Agricul-
tural Research Institute (BARI) having all the accessions of cultivated type (Vaz
Patto and Rubiales 2014a, b). Among European countries, Germany, Hungary and
1336 A. K. Parihar et al.

Table 26.3 Wild species with various desirable traits

Species name Traits References
L. tingitanus Toxin-free gene Zhou and Arora (1995) and Kumar et al.
(2011)
L. ochrus, Resistance to broomrape Sillero et al. (2005), Fernández-Aparicio
L. clymenum et al. (2009, 2012), Fernández-Aparicio
L. cicero and Rubiales (2010) and Linke et al.
(1993)
L. cicero Low ODAP content, earliness Hanbury et al. (2000), Abd El Moneim
and cold tolerance et al. (2001), Kumar et al. (2011), Granati
et al. (2003), Vioque et al. (2009) and
Abd EI Moneim and Cocks (1993)
L. cicero Pseudomonas syringae Martín-Sanz et al. (2012)
L. latifolius Meloidogyne hapla (root knot Rumbaugh and Griffin (1992)
L. sylvestris nematode)
L. hirsutus
L. czeczottianus Antioxidant abilities with the Llorent-Martínez et al. (2017)
highest concentration of
phenolics
L. nissolia Enzymatic inhibitory effects Llorent-Martínez et al. (2017)
against cholinesterase, amylase
and glucosidase
L. cicera, Zero or low-ODAP (0.01% or Campbell (1997) and Kumar et al. (2013)
L. less)
amphicarpus,
L. ochrus
L. ochrus, Ascochyta blight resistance Gurung et al. (2002) and Skiba et al.
L. clymenum (2004a)
L. cicera, Pod borer resistance Mathur et al. (1998)
L. odoratus

Spain hold collection with 300–500 accessions. The largest collection of Lathyrus in
Africa is in Ethiopia with 96 accessions (Hillocks and Maruthi 2012). In addition, as
a backup, a total of 2134 grass pea accessions from 44 countries have been deposited
at the Svalbard Global Seed Vault (Almeida et al. 2015a, b, c). There are also other
organizations at global level where small collections of grass pea germplasm are
available as enlisted in Table 26.3.
Besides, the aforementioned ex situ collections, in situ preservation is also
recommended for long-term conservation. In situ conservation means active and
long-term conservation of genetic diversity of natural wild populations within
defined areas (Maxted et al. 1997). However, there has been very limited effort
invested to conserve Lathyrus diversity in situ; consequently, native populations are
susceptible to genetic erosion or even extinction (Maxted and Bennett 2001). A
multi-gene pool approach has been used by Maxted et al. (2012) for several legume
genera including Lathyrus. This involved the collation of 61,081 unique
geo-referenced Lathyrus records collected between 1884 and 2008. These conserved
26 Lathyrus Breeding 1337

germplasm accessions represent a huge repertoire of genetic diversity and preserve a

wide range of interested agro-morphological traits such as earliness, plant architec-
tural traits, disease and pest tolerance, as well as low ODAP content (Almeida et al.
2015a, b, c). Sincere efforts have been directed for characterization of diversity in
Lathyrus germplasm, as for ODAP content (Fikre et al. 2008; Grela et al. 2012;
Kumar et al. 2011), phenology and yield (Grela et al. 2012; Mera 2010), parasitic
weed resistance (Fernández-Aparicio et al. 2012), disease resistance (Gurung et al.
2002; Vaz Patto et al. 2006a; Vaz Patto and Rubiales 2009) or quality traits (Granati
et al. 2003). Characterization and judicious exploitation of existing diversity through
high-throughput phenotyping and genotyping studies will uncover novel alleles that
can be used to improve this underutilized crop.

26.8 Brief of Genetic Variability and Potential Donors

In spite of several advantages, limited attempts have been made towards the
improvement of grass pea owing to the presence of neurotoxin (ODAP). The grass
pea farmers are still cultivating traditional cultivars which contain high ODAP and
susceptible to biotic and abiotic stresses, therefore ultimately gaining low yield. The
basic requirement of any breeding programme is genetic diversity which ultimately
plays decisive role in adaptability and survival of a species (Hamrick and Godt
1989). The estimation of genetic diversity is based on morphological (qualitative &
quantitative), cytological, biochemical and molecular parameters which are helpful
for the measurement of variation; however, quantitative traits are highly influenced
by both environmental and genetic factors. Therefore, they might not provide actual
estimation of germplasm variability (Brown and Marshall 1995). A considerable
level of variability for pods per plant, grain yield and 100-seed weight was reported
by Vedna Kumari and Mehra (1989) in grass pea.
A wide range of variability for days to flowering, days to maturity, pod length,
seeds per pod, seed weight and grain yield has been observed (Hanbury et al. 1995;
Sarwar et al. 1995a, b). In another study, Mehra et al. (1995) evaluated exotic
germplasm accessions belonging to France, Bangladesh, Ethiopia, Cyprus,
Afghanistan, Germany and noticed ample variability for branches per plant and
pod length. Likewise, Yadav (1995) reported large range of variation for days to
flowering, days to maturity, plant height, pods per plant and seeds per pod in local
germplasm accessions of Nepal. Robertson and Abd El-Moneim (1996)
characterized 1082 accession of 30 species for various phenological and agronomic
traits and noticed plenty of variation in days to flower, seed weight and seeds per pod
for L. cicera and days to flower for L. ochrus. Asthana and Dixit (1998) reported
enormous variability for plant height, number of primary branches, pods per plant,
seeds per pod, 100-seed weight and grain yield in a set of germplasm. Syouf (1995)
stated that Lathyrus species were among the most promising in terms of forage yield;
however, the highest-yielding forage species was L. ochrus.
Further, remarkable variations for morphological traits, that is leaf length, flower
colour, podding structure, seed size and colour, grain yield, ODAP and protein, have
1338 A. K. Parihar et al.

been reported in germplasm of L. sativus and L. cicera (Kaul et al. 1982; Jackson and
Yunus 1984; Kumari et al. 1995; Grela et al. 2010). Number of grass pea genotypes
evaluated for plant height, number of branches per plant, pods per plant, pod length,
day to 50% flowering, days to maturity, seeds per pod, biological yield, 100 seed
weight, flower colour, nutritional value and anti-nutritional (ODAP) concentration
(Dutta et al. 1982; Deshpande and Campbell 1992; Pandey et al. 1995a, b; Campbell
1997; Tarade et al. 2007). The diversity study and cluster analysis in set of >350
germplasm reflects that ample amount of genetic variation existed for seed yield and
other yield components (Parihar et al. 2013). In another study, Parihar et al. (2015)
reported enormous variability for individual traits like days to flowering (60–96),
days to maturity (117–142), plant height (22–89 cm), seeds per pods (2–5), primary
branches (4–15) and pods per plant (13–100). Parihar et al. (2015) identified some
trait-specific genotypes such as BioR 202 (higher yield/plant, pods/plant and
biological yield); EC20034, JBT 29/83 and RSR/SSC-1/12 (higher yield/plant and
harvest index); ET48116 (high yield/plant, no. of pods/plant). These lines may be
useful in future grass pea breeding programme for developing better segregants.
Based on seed size, grass pea is grouped into three classes: large seeded (lakh
type) originated from the Mediterranean region (Syria, Turkey, Italy, Spain),
medium seeded from northern France and Germany and the smallest seeded
(Lakhori type) belonging to the South Asian and Polish cultivars (Hanbury et al.
1995). A range of 3.45 to 22.59 g/100 seeds have been reported in Canada by
Robertson and Abd El-Moneim (1995). Hammer et al. (1989) indicated that the large
seeded grass pea genotypes from South Italy having a larger vegetative canopy with
exceptionally high 100 seed weight. The small-seeded grass pea genotypes are
prevalent in South Asian and South East Asian countries (Barpete 2015). Radwan
Safaa et al. (2013) reported a reasonable genetic variability for the evaluated traits for
18 accessions of L. inconspicuous and found possibility of genetic improvement
through simple selection for those traits. The blue-flowered ecotypes are found in
South-East Asia and the South Asia (Polignano et al. 2005b; Kumar et al. 2013),
whereas white flowered types are generally reported from Mediterranean region
ecotypes (Smartt 1984).
High variability of ODAP content was recorded for both inter-specific and intra-
specific levels in Lathyrus (Sammour et al. 2007a). In the beginning of last decades,
Barpete et al. (2012a) observed high genetic variation in total seed protein and
weight. Apart from this, some of the available Lathyrus germplasm having attractive
yield traits such as single node double flower or pods (L900239 and L920278) and
more than 30 g/100-seed weight (LS-2026, LS-8, LS-97 and Quila-blanco), these
traits can be further utilized for grass pea improvement programme (Campbell and
Briggs 1987; Ulloa and Mera 2010). Promising genotypes for harvest Index like Bio
R-202, Bio L-203, Bio R-231 and Bio L-208 were also identified (Gautam et al.
1998). Some wild relatives namely L. cicera, L. amphicarpus and L. ochrus species
have been identified with zero or low-ODAP (0.01% or less) gene that can be
utilized for development of toxin free Lathyrus varieties (Campbell 1997; Kumar
et al. 2013).
The variation for biotic and abiotic stresses has also been recorded in grass pea
and consequently, identified genotypes (RLK-1, RLK-281, RLK-617, RPL-26,
26 Lathyrus Breeding 1339

RLK-273-1, RLK-273-3, JRL-6 and JRL-41) possessing resistance to powdery

mildew (Erysiphe pisi syn. E. polygoni) (Asthana and Dixit 1998; Pandey et al.
1997; Lal et al. 1985). Some CWRs such as L. ochrus, L. clymenumand and
L. aphaca also demonstrated resistance to powdery mildew (Gurung et al. 2002;
Pandey et al. 1995a, b). Therefore, serious efforts need to be made to utilize these
available sources to incorporate powdery mildew resistance gene into high-yielding
and stable genotypes (Campbell 1997; Vaz-Patto et al. 2004; Dixit et al. 2016).
Downy mildew (Peronospora lathyri-palustris) is another serious disease in South
Asia owing to suitable climatic conditions for the development of this pathogen (Lal
et al. 1985). Some resistance grass pea accessions (RLS-1, RLS-2, JRS-115, JRL-43,
and JRL-16) for downey mildew have been reported in India (Lal et al. 1985;
Narsinghani and Kumar 1979). Ascochyta blight (Mycosphaerella pinodes) is also
important disease and resistance reaction for this has been recorded in ATC 80878
accession of L. sativus and in wild species L. ochrus and L. clymenum (Gurung et al.
2002; Skiba et al. 2004b).
Downy mildew and ascochyta blight resistance sources (Sel. 553, 555, 563, 529,
504) were also identified by Robertson and Abd El-Moneim (1998). This may be one
of the most necessary and advantageous traits to transfer in cultivated legume crop.
Similar to grass pea, ascochyta blight is a serious impediment in case of field pea
production and complete resistance to the fungal infection has not been observed
(Skiba et al. 2004a). Rust is one of the devastating diseases of grass pea in the
Ethiopia and Spain (Campbell 1997; Vaz Patto and Rubiales 2009). So far, complete
resistance to rust pathogens (Uromyces pisi) is not recorded in L. sativus although
few grass pea lines, namely, BG-15744 and BG-23505, have been found to be
partially resistant against rust (Vaz Patto and Rubiales 2009, 2014a, b). The rust-
resistant genes hold great promise not only for grass pea but also for lentil, chickpea
and field pea improvement. Grass pea is more susceptible to Orobanche or broom-
rape (Orobanche crenata), and none of the grass pea genotypes demonstrated
resistance reaction (Sillero et al. 2005).
Nevertheless, some other Lathyrus species, particularly L. clymenum and
L. ochrus, were detected as highly resistant to Orobanche (Linke et al. 1993;
Sillero et al. 2005). In case of insect pest, thrips (Caliothrips indicus) is a serious
nuisance to grass pea; however, tolerance to thrips was registered in some Indian
accessions (RLK-1, RLK-281, RLK-617, RPL-26, RLK-273-1, RLK-273-3, JRL-6
and JRL-41) (Asthana and Dixit 1998; Pandey et al. 1997; Lal et al. 1985). The
aforementioned thrips-tolerant accessions can be further utilized for grass pea
improvement program. Cyst nematodes (Heterodera ciceri) and root knot nematode
(Meloidogyne artiella) also cause substantial damage in grass pea but partially
resistance lines for cyst nematode (IFLA347) were identified in L. sativus germ-
plasm at ICARDA (Di Vito et al. 2001) and resistance reaction for root knot
nematode were noticed in Lathyrus wild species such as L. latifolius, L. sylvestris,
and L. hirsutus (Rumbaugh and Griffin 1992).
The initial work for exploration of genetic variability for ODAP was started in
1966 in India (Lal et al. 1985). In 1970, more than 1500 samples were screened for
ODAP and found few lines containing low (0.15–0.3%) ODAP (Jeswani et al.
1340 A. K. Parihar et al.

1970). Likewise, 1000 samples were screened for ODAP content at IARI, New
Delhi during 1971 wherein ODAP varied from 0.2 to 2.56% (Leakey 1979).
Similarly, Asthana and Dixit (1998) reported low ODAP donors like Bio R
202, Bio L 212, Bio L 203, Bio R 231, Bio L 208, P 94–3, P 28, L5 8246 and Bio
I 222. In comparison to L. sativus, the ODAP concentration in L. cicera and L.
gorgoni is lower among the CWRs (Hanbury et al. 1999; Kumar et al. 2013).
Assessment of ODAP in different species of Lathyrus indicated that none of the
species are free from ODAP (Aletor et al. 1994; Hanbury et al. 1999; Siddique et al.
1996). It was observed that grass pea genotypes from South East Asia and Ethiopia
are having high ODAP (0.7–2.4%) in comparison to the germplasm collected from
Mediterranean region (0.02–1.2%) (Abd-El-Moneim et al. 2000).
Overall L. cicera was found to have consistently low ODAP content (0.07%) and
L. ochrus with high ODAP content (1.35%) (Eichinger et al. 2000; Kumar et al.
2011). The ODAP and protein analyses of different populations at Ethiopia also
revealed the presence of variability (Tadesse and Bekele 2004). The ample
variability demonstrated for seed weight, protein and ODAP content that ranged
from 40.50 to 79.23 g, 25.05% to 33.95% and 0.32% to 2.02%, respectively
(Mondal and Puteh 2014). Srivastava et al. (2015) observed variation for ODAP in
different genotypes of Lathyrus which was in the range of 0.46 to 1.14 mg/g. Gupta
et al. (2018) measured neurotoxin content in a set of grass pea accessions originated
in Bangladesh which ranged from 0.13 to 0.57%. The content of the anti-nutritional
factor β-ODAP varied from 0.21% to 0.55% with a mean value of 0.36% in a panel
of 50 grass pea accessions collected from different geographic locations of Ethiopia
(Shiferaw and Porceddu 2018). Recently, a total of 702 accession of grass pea was
screened for ODAP and protein content and new promising sources (ILG468,
ILG1934, ILG1950 and ILG1951) were identified for low seed ODAP content and
for high protein content (ILG311, ILG670, ILG688, ILG691 and ILG708)
(Rajendran et al. 2019). The judicious utilization of available Lathyrus germplasm
holds great promise toward improvement of grass pea cultivars in coming future.

26.9 Inheritance of Qualitative and Quantitative Traits

The efficiency of any breeding programme depends on the availability of informa-

tion about nature and magnitude of gene action, which is utmost to accelerate its
success (Shashikumar et al. 2010). The genes may display additive, dominance
and/or interaction effects. In case of grass pea, very limited efforts have been
made to understand the nature of gene action of complex traits such as yield and
its contributing traits (Parihar et al. 2016). During 1970s, Dahiya and Jeswani (1974)
found that non-additive gene action was predominant for pods/plant, 100-seed
weight, seeds/pod and grain yield/plant. Kumari et al. (1993) had reported that
four genes were responsible for flower pigmentation. A study was also done to
understand the genetics of flower colour and its relation with ODAP content. The
results revealed that both monogenic and digenic segregation was noted.
26 Lathyrus Breeding 1341

The gene action for yield and its components was studied in grass pea by Dixit
(1998a, b) and revealed that additive and non-additive gene effects were involved in
the expression of number of primary branches, pods per plant and grain yield per
plant. Plant height was predominantly under the control of dominance gene effect.
Earlier few researchers have reported high heritability for seed yield and other traits
such as 100 seed weight, seeds/plant, seeds/pod and pods/plant (Kumari
et al.1995; Kumar and Dubey 1996). Parihar et al. (2015) reported that the seed/
pod, pod length, pod width, 100-seed weight and seed yield/plant are governed by
non-additive gene action. In another study, Parihar et al. (2016) inferred that yield
and its contributing traits exhibited all three types of gene actions, that is additive,
dominant and epistasis. In such situation, recombination breeding could be
exploited, followed by selection delayed to later generations.
There are several reports regarding the inheritance pattern of ODAP content in
seed of grass pea from qualitative to quantitative inheritance (Nerkar 1972; Dahiya
and Jeswani 1974; Gowda and Kaul 1982; Dahiya 1986; Quader et al. 1987; Briggs
and Campbell 1990; Tiwari and Campbell 1996). Certain reports are there about the
presence of modifying genes (Quader 1985) and presence of maternal inheritance
(Quader et al. 1987; Tiwari and Campbell 1996). Biosynthetic pathways studies by
Malathi et al. (1967) and Lambein et al. (1990) revealed that at least two enzymes
were involved in the synthesis of the neurotoxin. This also suggested that more than
one gene controls ODAP synthesis (Quader et al. 1987). However, Dahiya and
Jeswani (1974) reported for the first time that low ODAP content is controlled by
non-additive gene action. Nevertheless, later on predominance of additive and
additive
additive gene effects for ODAP becomes familiar (Briggs and Campbell
1990; Mehra et al. 1993; Pandey et al. 2000; Sharma et al. 1997; Tiwari and
Campbell 1996). Dahiya (1986) reported high ODAP content in white/cream seeded
varieties but later on Pandey et al. (2000) contradicted with him and reported wide
variation for ODAP content in white
blue and blue
red flowered F2 populations.
Hanbury et al. (1995) found positive correlation between seed size and vigour. The
narrow sense heritability of the ODAP indicates effectiveness of selection in early
generations for accumulation of favourable alleles in the direction of selection
(Nerkar 1972; Quader et al. 1987).
The negative association of ODAP content with days to maturity and seed yield
was noticed (Sharma et al. 2000; Tadesse and Bekele 2003). Interestingly, the
correlation between ODAP concentration and seed weight was reported either to
be positive (Hanbury et al. 1995; Siddique et al. 1996), negative (Hanbury et al.
1999) and no correlation (Kumari and Prasad 2005). Other studies also pointed out
no relationship between ODAP content and other agronomic traits (Pandey et al.
1997), suggesting that selection for high yield and low ODAP can simultaneously be
practiced for grass pea improvement. A recent study discovered that the biosynthesis
of ODAP involves more than two genes, with dominant alleles predominating
(Tripathy et al. 2015). The genotype
environment interaction plays crucial role
in the inheritance of ODAP content in grass pea (Nerkar 1972; Quader 1985;
Ramanujam et al. 1980; Chen et al. 1992; Dixit et al. 1997; Tadesse 2003; Jiao
et al. 2011; Tripathy et al. 2015). Mondal and Puteh (2014) observed significant
1342 A. K. Parihar et al.

positive correlation between seed size and protein content but negative association
between seed size and ODAP content.
Therefore, it may be feasible to develop low neurotoxin varieties by selecting
bold seed size following hybridization of bold seeded and low neurotoxin types with
those having small seeds and high neurotoxin. Significantly negative correlation
between protein and β-ODAP content under different cooking methods for grass pea
germplasm was also recorded (Barpete et al. 2021a, b). This suggested that improve-
ment in protein content may indirectly reduce the β-ODAP concentration in grass
pea seed through breeding efforts. Although limited sincere efforts have been made
till date to identify the biosynthetic pathway and discover the putative genes
associated with ODAP biosynthesis. It has been noticed that ODAP is generally
present in all plant parts; however, the concentration remains high in leaf and
embryo during vegetative and reproductive stages, respectively (Barpete 2015).
The variation in seed ODAP concentration of genotypes results due to variation in
net accumulation of ODAP in leaves and pods during vegetative and early reproduc-
tive phase (Xiong et al. 2015). In a recent report, it is noticed that nutritional
deficiencies of cysteine and methionine may exaggerate the neurotoxicity of
ODAP which advocated that ODAP biosynthesis is allied with nitrogen and sulphur
metabolism (Xu et al. 2017).

26.10 Major Constraints of Grass Pea Promotion at National

and International Level

The prime stalemate in grass pea improvement both nationally and internationally is
the existence of neurotoxin (β-ODAP) which is popularly known as b-N-oxalyl-
amino-L-alanine (BOAA) that is responsible for irrevocable neurological mayhem in
humans and animals if grass pea seeds are consumed constantly as more than 25%
part of daily diet for 3–4 months (Vaz Patto et al. 2006a, b; Lambein and Kuo 2009;
Vaz Patto and Rubiales 2014a, b; Dixit et al. 2016; Lambein et al. 2019). Conse-
quently, it has been banned especially in all states of India except Chhattisgarh,
Maharashtra and West Bengal (Dixit et al. 2008). However, sincere efforts have been
made worldwide and a number of low ODAP and high-yielding varieties were
released (Table 26.4), although the general acceptance of these varieties among
the farmers is miserable due to lack of knowledge. Therefore, there is urgent need of
intensive efforts for removal of this stigma from grass pea by demonstrating the
potential of these technologies through on-farm trials. In addition, grass pea is being
grown primarily on marginal land with minimum input under rain-fed conditions
(Dixit et al. 2016) which ultimately lead to low yield potential.
However, in addition to variety of agronomic limitations, grass pea is also
exposed to a number of biotic stresses to some extent: powdery mildew, rust,
downy mildew, ascochyta blight, fusarium wilt, broomrape and thrips cause sizeable
yield reduction under favourable environmental conditions (Campbell 1997,
Robertson and Abd El-Moneim 1996; Gurung et al. 2002; Vaz Patto et al. 2006b;
Barilli et al. 2011, 2012; Talukdar 2013; Abdallah et al. 2021; Sampaio et al. 2021).
 26

Table 26.4 Improved varieties of grass pea recommended for cultivation in different countries
Name of
S. no. variety Developing institution Country Brief description References
1 Ratan IARI, New Delhi India This variety was isolated from Somaclonal variation of Anonymous (2020), Dixit
(Bio L 212) Pusa-24 during 1997. It has yield potential of et al. (2016), Vaz Patto and
1500–1600 kg/ha and matures in 110–115 days. The Rubiales (2014a, b), Kumar
variety has low ODAP content (0.7%), large seed size et al. (2011), ICAR (2009)
Lathyrus Breeding

and blue colour flower. This variety recommended for and Abd El Moneim et al.
cultivation in north eastern plain zone and central zone (2001)
2 Prateek IGKV, Raipur India This elite genotype developed by hybridization of Dixit et al. (2016), Vaz
LS-8246
A 60 following pedigree method and Patto and Rubiales
released in 2006. This variety has low ODAP (2014a, b), Kumar et al.
(0.076%) with high protein (25.83%) content. It (2011), ICAR (2009) and
matures in 110–115 days and has tolerance toward Abd El Moneim et al.
downy mildew, thrips and pod borers and resistance to (2001)
powdery mildew. The plant height varied between http://igau.edu.in/pdf/
45 and 70 cm and flowers colour is blue. This variety CropTechnologies.pdf.
recommended for rain-fed and utera cultivation and as Accessed 19 Jun 2021
irrigated crop in rabi late sowing of entire Chhattisgarh
and MP
3 Mahateowda IGKV, Raipur India This variety evolved through pedigree method from a ICAR (2009), Abd El
(RLS 4595) cross Ratan
JRL-II and released in 2008 for Moneim et al. (2001),
cultivation in Chhattisgarh. This variety has pink Kumar et al. (2011), Vaz
coloured flowers and could be easily identified from Patto and Rubiales
the land races as well as earlier released varieties. The (2014a, b) and Dixit et al.
yield potential of this variety is 1000–1400 kg/ha (2016); http://igau.edu.in/
coupled with low ODAP content (0.07–0.08%) and pdf/CropTechnologies.pdf
medium maturity duration (90–100 days). Suitable for
rain-fed and utera cultivation and as irrigated crop in
rabi late sowing of entire Chhattisgarh and Madhya
Pradesh. Also suitable for medium to heavy soils
(continued)
1343
Table 26.4 (continued)
1344

Name of
S. no. variety Developing institution Country Brief description References
4 BidhanKhesari- BCKV, Kalyani, West India This elite genotypes is developed through selection ICAR (2009)
1 Bengal and has low ODAP and high yield potential
5 Nirmal – India This genotype is also developed by selection method Asthana and Dixit (1998)
and released in 1980 for cultivation. It has low ODAP and Sarkar et al. (2003)
(0.2%) and high yield potential
6 BARI Khasari- Bangladesh Agriculture Bangladesh This is tall type variety (70 cm) developed by Malek et al. (1996), Malek
1 Research Institute hybridization between P-24
local and released in (1998), Abd El Moneim
(BARI), Gazipur, 1995. It has large deep blue flower with larger seed et al. (2001), Kumar et al.
Bangladesh size (1000 SW 48–52 g). It contains ODAP content (2011) and Vaz Patto and
0.0137 m/g (0.04%) with average grain yield of Rubiales (2014a, b); http://
1720 kg/ha and matures in 125–130 days. It is tolerant dhcrop.bsmrau.net/.
to drought and salinity and also tolerant to powdery Accessed 26 Jun 2021
and downy mildew disease
7 BARI Khasari- Bangladesh Agriculture Bangladesh This is a low ODAP variety (0.06%) developed from http://dhcrop.bsmrau.net/.
2 Research Institute local materials and released in 1996. It has plant stature Accessed 26 Jun 2021;
(BARI), Gazipur, of 55–60 cm and blue colour flower with light grey Malek et al. (1996), Malek
Bangladesh color seed. It matures in 125–130 days and gives (1998), Abd El Moneim
1727 kg/ha grain yield. It has tolerance to drought and et al. (2001), Kumar et al.
salinity with 24–26% protein content (2011) and Vaz Patto and
Rubiales (2014a, b)
8 BARI Khasari- Bangladesh Agriculture Bangladesh This variety is developed from lines developed http://dhcrop.bsmrau.net.
3 Research Institute through hybridization at ICARDA; of which one Accessed 26 Jun 2021;
(BARI), Gazipur, superior fixed line, i.e. Sel-190 line was released as Rizvi et al. (2016)
Bangladesh BARI Khasari-3 in 2011. This high-yielding variety
(1800–2000 kg/ha) with plant height 62–65 cm, pod
no 35–38, 1000 grain weight 53–58 g, ODAP 0.04%,
crop duration 120–125 days. This variety is cultivated
as rely crop with Aman rice and also cultivated
individual crop
A. K. Parihar et al.
 26

9 BARI Khasari- Bangladesh Agriculture Bangladesh This variety was developed from ICARDA low ODAP http://dhcrop.bsmrau.net.
4 Research Institute materials and released as BARI Khesari-4 in 2013. Accessed 26 Jun 2021;
(BARI), Gazipur, This variety has large leaflet, white flower and white Sarkar et al. (2019)
Bangladesh, Pulse colour seeds with 1000 grain weight 70 g. this variety
Research Centre, Ishurdi, matures in 118–117 days with yield potential of
Pabna 720–1080 kg/ha. Besides, it also has tolerance to
powdery mildew disease
Lathyrus Breeding

10 BARI Khasari- Bangladesh Agriculture Bangladesh This variety released in 2018 with high yield and low http://dhcrop.bsmrau.net.
5 Research Institute ODAP content (0.04%). It has average yield of Accessed 26 Jun 2021;
(BARI), Gazipur, 1480–1700 kg/ha plant height (60–70), high biomass Sarkar et al. (2019)
Bangladesh, Pulse and matures in 121–125 days. The flowers are large
Research Centre, Ishurdi, and dark blue. The seeds are large in size with
Pabna smoothness and gray in color. This variety is also
tolerant to rot and downy mildew
11 BINA Khesari Bangladesh Institute of Bangladesh This variety was developed through mutation and Abd El Moneim et al.
1 Nuclear Agriculture released in 2001. This is high-yielding variety (2001), Kumar et al. (2011),
(BINA), Mymensingh, (1900–2400 kg/ha) having low BOAA content (less Vaz Patto and Rubiales
Bangladesh than 0.2%). It has black spotted seed coat and medium (2014a, b) and Rizvi et al.
tall plant stature. This variety 100-seed weight is 7.9 g (2016)
and matures in 110 days
12 Wasie ICARDA Ethiopia This elite genotypes developed by hybridization using ICARDA (2006, 2007),
SC5
PGRC 46071(OLAT-LS-LS-B2). It has low Abd El Moneim et al.
ODAP (0.08%) and yield potential of 1673 kg/ha with (2001), Kumar et al. (2011),
8.6 g 100-seed weight. It is semi-erect type with blue Vaz Patto and Rubiales
flower colour and has resistance to powdery mildew (2014a, b), Almeida et al.
(2015a, b, c) and Rizvi et al.
(2016)
(continued)
1345
Table 26.4 (continued)
1346

Name of
S. no. variety Developing institution Country Brief description References
13 Ali-Bar ICARDA Kazakhstan It is developed by selection from germplasm line ICARDA (2006, 2007),
(IFLLS 554). It has yield potential of 1200 kg/ha in the Abd El Moneim et al.
dry areas with 250–300 mm precipitation. The ODAP (2001), Kumar et al. (2011),
content is 0.01% and matures in 156 days. It is a high Vaz Patto and Rubiales
biomass, white seeded and drought-tolerant variety (2014a, b), Almeida et al.
(2015a, b, c) and Rizvi et al.
(2016)
14 Pusa 24 IARI, New Delhi India This variety developed through selection from Mehra et al. (1995), Abd El
germplasm and released in 1974. It has ODAP content Moneim et al. (2001),
0.2–0.3% and yield potential of 1655 kg/ha. It has blue Kumar et al. (2011), ICAR
colour flower, grey seeds and matures in 125–130 days (2009), Dixit et al. (2016)
and Rizvi et al. (2016)
15 LS8246 – Canada This variety developed through selection from Pusa Campbell and Briggs
24. It has 0.03% ODAP content and high yield (1987), Kumar et al. (2011)
potential of 2050 kg/ha. It has 100-seed weight 9.3 g and Rizvi et al. (2016)
and maturity period ranges from 110 to 130 days. It is
suitable for fodder and feed purpose
16 AC Greenfix – Canada This is high nitrogen-fixation variety Krause and Krause (2003)
17 Luanco-INIA – Chile This elite genotype developed through selection from Mera et al. (2003), Kumar
LS0027. It has less than 0.18% ODAP content with et al. (2011) and Rizvi et al.
yield potential of more than 4000 kg/ha. It is a tall type (2016)
(150 cm) and white seeded variety with large seed size
18 Jumbo-INIA – Chile It is a large seeded variety developed through selection Mera et al. (2003)
19 Quila-Blanco – Chile This genotype developed by direct selection and Campbell et al. (1994) and
released in 1983. It has high yield potential and large Ulloa and Mera (2010)
white seed, uniform maturity, protein content of 24.3%
A. K. Parihar et al.
 26

20 Ceora CLIMA, WA Australia This is Australia’s first Lathyrus cultivar and released Siddique et al. (2006),
in 2004. This variety was developed by hybridization Gupta et al. (2021) and
between K33
8604. It has low ODAP content and Kumar et al. (2021)
ranges between 0.04 and 0.09% and high protein
content (30%). It is a semi-erect, early to medium
duration variety with 500–1800 kg/ha yields potential.
It is also suitable for forage and green manure. It has
Lathyrus Breeding

tolerance to water logging, drought, disease and insect

resistant. It has white flowers with dark blue flecking in
the centre. Its grain is angular in shape with a greyed
orange colored seed coat and a yellow cotyledon
21 Chalus CLIMA, WA Australia Chalus is a Syrian line released in 1998. It is slightly Hanbury and Siddique
early maturing and has low ODAP levels of below (2000), Hanbury and
0.09%. This variety is developed by selection from Hughes (2003), Kumar et al.
IFLA 1279 line of L. cicera. It has less than 0.1% (2011), Vaz Patto and
ODAP content and 6.6 g 100-seed weight. It is an early Rubiales (2014a, b) and
to medium duration variety with good protein (26.5%) Rizvi et al. (2016); https://
content grdc.com.au/
22 Lath-BC – Australia This variety was commercialized in 1997 and the first https://grdc.com.au/Grain_
variety available in Australia. It has red flowers, brown Legume Handbook.PDF
to green seed coat and bright yellow seed color. Seed
size is comparatively small (100 seed wt of 6 g) and
ODAP levels are 0.13%
23 CLIMA pink CLIMA, Australia Nepal This variety was introduced in Nepal by CLIMA, Yadav (1996), Neupane and
Australia. This variety has yield potential of 1550 kg/ Tiwari (2005), Kumar et al.
ha with 9.0 g 100-seed weight. It has pink flowers and (2011), Rizvi et al. (2016),
matures in 132 days. The ODAP content is less than Neupane et al. (2017) and
0.04% Sarkar et al. (2019)
(continued)
1347
Table 26.4 (continued)
1348

Name of
S. no. variety Developing institution Country Brief description References
24 19A CLIMA, Australia Nepal This variety is developed by direct selection and Yadav (1996), Neupane and
introduced in Nepal by CLIMA Australia. It has Tiwari (2005), Kumar et al.
average yield potential of 1075 kg/ha with 10.0 g (2011), Gharti et al. (2014),
100-seed weight. It is blue flower colour variety and Rizvi et al. (2016), Neupane
matures in 131 days et al. (2017) and Sarkar
et al. (2019)
25 20B CLIMA, Australia Nepal This variety is developed using selection and Yadav (1996), Neupane and
introduced in Nepal by CLIMA, Australia. It has Tiwari (2005), Kumar et al.
average yield potential of 750 kg/ha with 11.0 g (2011), Gharti et al. (2014),
100-seed weight. It is blue flower colour variety and Rizvi et al. (2016), Neupane
matures in 132 days et al. (2017) and Sarkar
et al. (2019)
26 BARI-2 CLIMA, Australia Nepal This variety introduced in Nepal by CLIMA, Neupane and Tiwari (2005),
Australia. It has yield potential of 1000 kg/ha and Kumar et al. (2011), Gharti
10.0 g 100-seed weight. It is blue flower colour variety et al. (2014), Rizvi et al.
mature in 135 days (2016) and Neupane et al.
(2017)
27 CLIMA-2 CLIMA, Australia Nepal This variety was introduced in Nepal by CLIMA Neupane and Tiwari (2005)
Australia and Neupane et al. (2017)
28 Derek – Poland This variety is developed by selection frosm Der. It has Kumar et al. (2011), Rizvi
average yield potential of 1920 kg/ha with 11.5 g et al. (2016), Milczak et al.
100-seed weight and mature in 115 days. It is semi- (2001) and Sarkar et al.
erect and white seeded variety (2019)
29 Krab – Poland This variety is developed through selection from Kra. Kumar et al. (2011), Rizvi
It has average yield potential of 2280 kg/ha with 19.3 g et al. (2016), Milczak et al.
100-seed weight and mature in 109 days. It is semi- (2001) and Sarkar et al.
erect and white seeded variety (2019)
A. K. Parihar et al.
 26

30 Strandja – Bulgaria This variety developed through local selection. It is Campbell and Briggs
high-yielding variety with more than 2.5 t/ha (1987), Kumar et al. (2011)
productivity and 17.0 g 100-seed weight. It has and Sarkar et al. (2019)
medium plant stature and early maturity duration
(90 days)
31 Italian – Pakistan Low ODAP variety Kumar et al. (2013)
Lathyrus Breeding

32 Poltavskaya – Russia It is developed by mutation (EMS 0.01%) and has low Kumar et al. (2013)
ODAP content
33 Studenica – Serbia This variety was developed by pedigree method from Lambein and Kuo (2009),
hybrid populations of polish cultivars and Serbian Mikic et al. (2011) and
landraces. It has high grain and forage yield. The crude Kumar et al. (2021)
protein content in forage and grain dry matter is 208 g/
kg and 281 g/kg, respectively
34 Sitnica – Serbia This variety was developed through pedigree method Lambein and Kuo (2009),
from hybrid populations of Polish cultivars and Mikic et al. (2011) and
Serbian landraces. It has high grain and forage yield. Kumar et al. (2021)
The crude protein content in forage and grain dry
matter is 233 g/kg and 286 g/kg, respectively
35 Jaboulah – Lebanon Jaboulah variety is derived from Lathyrus cicera Kumar et al. (2021)
germplasm of ICARDA and released in Lebanon
during 1997. The variety is developed through
ICARDA low ODAP material (IFLLC-492). This
variety has broad leaflets with copper red flower color
with brown and small seed size. It has high forage
yield and low in ODAP content (0.1%). The variety
has high yield potential and drought tolerant
36 IFLLO 185 – Jordan The variety (IFLLO-185) is selected for forage Kumar et al. (2021)
purpose from ICARDA material and released during
1994 in Jorden. It has high forage yield with medium
to late duration variety with good protein content. It
has also high yield and resistant to Orobanche
1349

(continued)
Table 26.4 (continued)
1350

Name of
S. no. variety Developing institution Country Brief description References
37 Gurbuz-2001 – Turkey This variety was commercialized in 2002 and the first Kumar et al. (2021)
cultivated variety available in Turkey. This variety was
selected and developed from ICARDA low ODAP
materials (IFLVN-794) and released as Gurbuz-1 in
2002. This variety has large leaflet, blue flower and
brown seed coat color with 100 grain weight 12.10 g.
this variety matures in 145–155 days and yielded
between 1250 and 1350 kg/ha in Mediterranean type
environments
A. K. Parihar et al.
26 Lathyrus Breeding 1351

Among the abiotic factors, drought, waterlogging, salinity and temperature

extremities affect quantity and quality of seeds (Campbell 1997; Herwig 2001;
Kumar and Tripathi 2007; Palta et al. 2007, 2012; Polignano et al. 2009, Gusmao
et al. 2012; Jiang et al. 2013; Tsegay and Andargie 2018). Scarcity of quality seed of
improved and higher-yielding varieties, low acceptance rate of novel crop produc-
tion technologies, minimum application of fertilizer are some of the other factors that
negatively affect grass pea production (Pandey et al. 1996). Notwithstanding, it has
been recommended that the application of micronutrients to deficient soils could be a
lucrative approach to enhance grass pea production but farmers seldom take up such
practices (Baghel et al. 1995; Mehta 1997). Furthermore, the inadequate transfer of
improved technologies remains another constraint.

26.11 Breeding Progress/Varietal Development

As compared to other pulse crops, grass pea has always been ignored in terms of
genetic research; however, it has been grown as a pulse crop for over 8000 years
(Smartt 1984; Rahman et al. 1995). The reasons for being ignored as a pulse crop
might be due to the presence of neurotoxin (ODAP) and primarily being used as a
fodder. The selection criteria imposed on forage crops are opposite of grain crops in
several ways. Therefore, it is recommended that the development of a more compact
growth habit, coupled with some increase in seed size and eradication of the
neurotoxin, could convert grass pea into one of the great value crops in the semi-
arid areas of the developing nations (Campbell 1997).
Many programmes currently are addressing with several aspects of grass pea
improvement simultaneously such as low ODAP content, nutritional quality, resil-
ience to biotic and abiotic stresses, nitrogen fixation, food, fodder and forage
production to ensure food security in harsh environments, low input livestock feed
and a cover crop for soil conservation (Hillocks and Maruthi 2012). There are
various old schools (conventional) and new schools (non-conventional) breeding
approaches that have been used for genetic enhancement of grass pea over the years.
In case of conventional approaches, several methods such as selection, introduction,
hybridization and mutation breeding have been used (Dixit et al. 2016). In this
section, we will elaborate and narrate the different breeding strategies and
accomplishments made for genetic improvement of grass pea during last five
decades.

26.11.1 Conventional Approaches

Albeit, the abundant reward grass pea hold but comparatively very modest attempt
has been made towards its improvement due to the disgrace of ODAP (Vaz Patto
et al. 2006a, b). However, most of the initial progress and around 50% varieties
(Table 26.4) with low ODAP have been developed by direct selection from
landraces and lines (Vaz Patto et al. 2006a, b). The traditional breeding approaches
1352 A. K. Parihar et al.

intend primarily on hybridization of pre-selected trait specific genotypes and subse-

quently screening and evaluation of the ensuing progenies for targeted trait. To trim
down ODAP content, low ODAP genotypes were crossed with high seed yield
material with good agronomic potential in conventional breeding (Campbell
1997). The high seed yield potential has been a selection criterion for most crop
improvement programmes. Conversely, on some of the yield components, that is
double podding or increased seeds per pod lesser efforts were invested.
The high biomass yield of grass pea is also important and has acknowledged more
attention during the recent past decades (Campbell 1997; Abd El Moneim et al.
2001; Vaz Patto et al. 2006b). This is a very important area due to the large potential
of this crop for forage and straw in the North African and South Asian regions
(Campbell 1997). Moreover, superfluous parameters, for instance, prostrate and
indeterminate plant growth habit, prolonged duration and pod shattering (Rybinski
2003), are being addressed by numerous breeding programmes. As stated earlier, at
the outset most of the grass pea varieties were developed through selection from
accessible germplasm and landraces. Indeed, the grass pea advancement programme
taken place in three different phases during last 80 years. The first phase
(1940–1960) of grass pea improvement primarily focussed on grain yield improve-
ment through congregation of local landraces and isolation of superior single plants
progenies for high yield and delivered several high-yielding varieties (BR13, LC76,
T2–12, No.91, No. 11 and B-19) pertinent for cultivation in Madhya Pradesh and
West Bengal (Gautam et al. 1998; Dixit et al. 2016). The second phase (1974–1990s)
was devoted for the development of high-yielding varieties along with low β-ODAP
content (0.2%) for upland conditions (Gautam et al. 1998).
Consequently, improvement programme was initiated by different countries like
India in 1966 (Lal et al. 1986), Canada in 1967 (Campbell 1988), Bangladesh in
1980 (Kaul and Islam 1981) and Nepal in 1986 (Yadav and Prasad 1993). Conse-
quently, numbers of improved varieties (Table 26.4) possessing β-ODAP content
less than 0.1% were emanated as the product of different national and international
breeding programmes (Abd El Moneim et al. 2001; Kumar et al. 2011, 2013; Dixit
et al. 2016 ; Lambein et al. 2019). The first variety which had low ODAP content in
seed (0.2%) was the Indian landmark variety “Pusa-24” and it was selected from a
field in 1966 from Bihar. This variety was released in 1973–1974 particularly for
upland cultivation where it was widely accepted (Dahiya and Jeswani 1974; Lal et al.
1985; Campbell and Briggs 1987; Jain et al. 1974; Mehra et al. 1995). Afterwards,
“Pusa-24” variety has been used as the base parent in a number of other low ODAP
varieties in India and elsewhere. For example, in Canada, LS82046 was selected
from “Pusa 24,” with low ODAP (0.03%) level in seed (Campbell and Briggs 1987).
However, the value/concentration of ODAP may vary in different environments,
but genotype has much stronger effect (Hanbury et al. 1999). Succeeding research
work led to the development of varieties suitable for upland (LSD1, LSD2) and rice
fallow (LSD3, LSD6, Pusa-305, and Selection 1276) with low ODAP contents
(0.15–0.20%). Especially, the LSD series was developed by selection from P-24
during 1978 (Gautam et al. 1998; Sethi et al. 1987). Notably, the intense efforts for
grass pea improvement have been amplified after the development of low ODAP
26 Lathyrus Breeding 1353

genotypes (Campbell et al. 1994; Hanbury et al. 1999). Similarly, in Chile, grass pea
cultivar “Quila-blanco” was developed having synchronous maturity and bold white
seeds coupled with good protein concentration during 1983 by selection from the
local heterogeneous population (Campbell et al. 1994). Meanwhile, various attempts
have also been made to establish association between easily observable characters
and ODAP for ease of selection, but it remains unsuccessful owing to polygenic
inheritance of ODAP which is highly influenced by genotype, environment and their
interactions (Kaul et al. 1982; Tiwari and Campbell 1996; Hanbury et al. 1999).
During past five decades (1940–1990), the prime breeding objectives were to
develop high-yielding varieties with low ODAP in grass pea and inadequate efforts
were made towards the development of biotic and abiotic stresses resistance
varieties. Therefore, in third phase (1990s onwards), the major objectives were
good yield, low ODAP and tolerance to powdery mildew and thrips. To accomplish
these objectives, conventional breeding programmes of grass pea were initiated in
several countries, including Australia (Hanbury et al. 1995; McCutchan 2003),
Bangladesh (Malek 1998; Rahman et al. 2001), Canada (Campbell and Briggs
1987), China (Yang and Zhang 2005), Ethiopia (Tadesse and Bekele 2003; Tadesse
2003), India (Pandey et al. 1996; Sharma et al. 2000; Santha and Mehta 2001), Nepal
(Yadav 1996) and Syria (Abd-El-Moneim et al. 2000, 2001; Kumar et al. 2011,
2020), Poland (Grela et al. 2010), Italy (Granati et al. 2003), USA (Krause and
Krause 2003) and Chile (Mera et al. 2003).
In some of the countries mentioned above, the lathyrus breeding programmes
are still functioning, though in much smaller scale as compared to other major
legume crops (Vaz Patto et al. 2011). Germplasm (accessions) with low ODAP
have many undesirable agronomic traits such as late flowering, low yield and
susceptibility to biotic and abiotic stresses. In order to combine low ODAP with
high yield, appropriate phenology and stress tolerance, breeding programs were
initiated (Abd-El-Moneim et al. 2000; Addis and Narayan 2000; Crino et al. 2004;
Hanbury et al. 2000; Robertson and Abd El-Moneim 1997; Vaz Patto et al.
2006a, b). Several improved varieties and lines were developed that combined low
β-ODAP (<0.1%) with high-yield potential (up to 1.5 tons/ha) and resistance to a
variety of biotic and abiotic stresses (Kumar et al. 2013; Dixit et al. 2016). In
addition to productivity and adaptability owing to the episode of lathyrism in
mankind, major breeding programmes are fundamentally intended for low ODAP
content. This has now led to the development of several L. sativus or L. cicera
varieties with low ODAP content and other desirable characters (Hanbury and
Siddique 2000; Mera et al. 2003; Siddique et al. 2006; Kumar et al. 2011; Almeida
et al. 2015a, b, c).
For example, in India, following elite lines BioR-202, BioL-203, BioL-212,
BioR-231, and BioL-208 had enhanced yield and high harvest index. Of them,
BioL-212 was identified and released as “Ratan” in 1997 for cultivation in the
North East Plain Zone (NEPZ) and Central Zone (CZ) in India (Gautam et al.
1998; Pandey et al. 1998; Santha et al. 1998). Later, two varieties viz., “Prateek”
(LS8246
A-60) and Mahateora (BioL-212
JRL-2) were developed using
hybridization which have very low ODAP content (<0.1%) with 1.5 t/ha grain
1354 A. K. Parihar et al.

yield (Kumar et al. 2013; Dixit et al. 2016). Similarly, in Bangladesh, two
(Barikhesari-1 and Barikhesari-2) high-yielding, low ODAP (<0.29%) varieties
were developed during 1995–1996 by hybridization (Malek et al. 1996; Rahman
et al. 2001). Likewise, in Australia, one variety, that is Ceora with low ODAP levels
(0.04–0.09%), was developed which is a derivative of a conventional cross between
K33 belonging to Pakistan and 8604 (0.05% ODAP) from Bangladesh (Hanbury
et al. 1995; Siddique et al. 2006). Another variety “Chalus” was developed through
selection from IFLA1279 and has high protein (26.5%) and low ODAP (0.09%)
content (Hanbury and Siddique 2000). On similar note, in Chile a variety namely
“Luanco-INIA” with white colour bold seeded (30–35 g/100 seed weight) was
developed through selection from germplasm accession “LS 0027” (Mera et al.
2003). Overall, most of varieties are developed by direct selection method followed
by hybridization, mutation and tissue culture.

26.11.2 Pre-Breeding and Distant Hybridization

To broaden the genetic base of crop, the introgression of desirable alleles from
outside the primary gene pool is needed through opting pre-breeding and distant
hybridization. Although inter-generic hybridization is tedious, there have been
several successful instances of the development of inter-specific and wide crosses
with Lathyrus (Dixit et al. 2016). There have been successful inter-specific crosses
between grass pea and other Lathyrus spp. particularly L. pseudocicera. Embryo
rescue has increased the range of species in successful inter-specific crosses (Addis
and Narayan 2000). The results of inter-specific hybridization in grass pea suggest
that the identification and transfer of desirable traits from exotic and wild germplasm
offer many opportunities for especially for development of low ODAP genotypes
that particularly for crossable species including L. cicera and L. amphicarpus
(Davies 1957; Khawaja 1988; Yunus 1990; Yunus and Jackson 1991).
Crosses have also been made with other CWRs such as L. chrysanthus,
L. gorgoni, L. marmoratus and L. pseudocicera (Heywood et al. 2007), but only
ovules were produced. Successful inter-specific hybrids between different species in
specific combination were also made and pods were obtained as mentioned earlier
(Davies 1958; Trankovskij 1962; Yunus 1990; Kearney 1993; Hammett et al. 1994,
1996; Kumar et al. 2011). The appraisal of wild Lathyrus spp. for ODAP content has
clearly witnessed that the lowest ODAP amount has been noticed in L. cicera,
followed by L. sativus and Lathyrus ochrus (Aletor et al. 1994; Siddique et al.
1996; Hanbury et al. 1999; Kumar et al. 2013). The toxin-free gene recognized in
L. tingitanus could be used to develop varieties with low levels of toxin (Zhou and
Arora 1995). In addition, wild species including L. ochrus, L. clymenum (Sillero
et al. 2005) and L. cicera (Hanbury et al. 1999; Fernández-Aparicio et al. 2009;
Fernández-Aparicio and Rubiales 2010; Robertson and Abd El-Moneim 1998) are
resistant to broomrape that is not available in the cultivated gene pool.
Besides its low ODAP content, L. cicera may be used as a promising source of
other important agronomic traits such as earliness and cold tolerance (Robertson and
26 Lathyrus Breeding 1355

Fig. 26.2 In vitro regeneration of Lathyrus sativus L., (a) in vitro cultured of epicotyl explant,
(b and c) callus-derived shoot induction from epicotyl explant, (d) root induction on callus-derived
shoots, (e and f) acclimatization and hardening of in vitro regenerated grass pea explants

Abd El-Moneim 1998). Most importantly, the Lathyrus gene pool holds great
promise being a source of resistance to important diseases of legumes such as
ascochyta blight (Mycosphaerella pinodes), downy mildew (Peronospora lathyri-
palustris) and powdery mildew (Erisyphe spp.) (Gurung et al. 2002). Therefore, the
variation noticed in the Lathyrus wild species offers considerable potential for
improvement of grass pea and other related legume species through pre-breeding.
However, to overcome strong reproductive barriers among different species, various
modern techniques such as biotechnological tools (Barpete et al. 2014a, 2020a,
2021b), including tissue culture (Fig. 26.2), somaclonal variation (Barpete et al.
2014b, 2020b) and protoplast fusion, may also need to be utilized (Ochatt et al.
2001; Piwowarczyk and Pindel 2015; Tripathy et al. 2016). Therefore, reliable and
reproducible protocols are prerequisite for successful genetic transformation (Barik
et al. 2005; Barpete et al. 2016, 2017).

26.11.3 Mutation Breeding

During recent years, being a climate resilience crop, the demand and importance of
this crop has increased. The grass pea improvement is impeded owing to its narrow
genetic base which resulted due to self-pollination and inter-specific incompatibility
1356 A. K. Parihar et al.

(Nerkar 1976; Singh and Chaturvedi 1997). Consequently, mutation breeding has
been embraced as improvement strategy, since it has been regarded as an ultimate
way of creating new genetic variation. It can be a valuable supplement to conven-
tional plant breeding to create additional genetic variability that may be utilized by
the plant breeder in the development of desired cultivars for specific purposes
(Campbell et al. 1994). In case of grass pea, the chemical mutagens such as EMS
(ethyl methane sulphonate) and NMU (N-nitroso-N-methyl urea) are more efficient
than radiation in the production of chlorophyll mutations (Nerkar 1976). Neverthe-
less, different genotypic responses have been noticed when exposed to gamma
irradiation (Prasad and Das 1980b). Likewise, the mutagenic effectiveness is in the
order of NMU, EMS and gamma rays and efficiency in vice versa (Singh and
Chaturvedi 1997). A wide range of morphological mutations have been noticed
which affects growth habit, maturity, branching, stem shape, leaf size, stipule shape,
flower color and structure, pod size, seed size and seed coat colour (Nerkar 1976;
Prasad and Das 1980a; Waghmare et al. 2001; Rybinski 2003; Talukdar and Biswas
2006; Biswas 2007; Talukdar 2009a, b).
Corresponding to morphological changes, chromosomal changes including
translocations were induced in grass pea by mutagenesis (Biswas and Biswas
1997; Talukdar 2009a). Mutants with enhanced salt tolerance have been developed
which led to an increase in the activities of antioxidants such as superoxide
dismutase and ascorbate peroxidase (Talukdar 2011a, b). Mutagenesis approach
has also been utilized to create additional genetic variability to develop zero/low
ODAP varieties (Talukdar 2009a). Mutagenic treatments have also created
noticeable biochemical changes in grass pea, most of them have been reported to
contribute directly or indirectly to plant defence system. For instance, a glutathione
(GSH)-deficient mutant (gshl-1) was isolated from gamma-ray-treated M2 progeny
of the genotype BioL-212 and this mutant demonstrated greater sensitivity to
cadmium (Talukdar 2012c). Conversely, improved tolerance to salt and metal
toxicity was obtained through induced mutagenesis (Talukdar 2011b, 2013).
One such mutant, dwf1, registered an increase in foliar GSH content and normal
growth under cadmium stress (Talukdar et al. 2001; Talukdar 2010). Likewise, an
EMS-induced mutant, rlfL-1, was characterized that portrayed increased rate of cell
division and cell growth. Some other mutants like gshl-1, an ascorbate (AsA)-
deficient mutant (asfL-1) and a GSH-overproducing mutant have been examined
to ascertain the role of arsenic on wilt tolerance (Talukdar 2013). On the similar note,
physical mutagenesis developed an asfL-1 mutant having only 42% leaf and 20%
root ascorbate content compared to the base material. The results pointed towards the
possible incidence of a reorganization event involving antioxidant defence machin-
ery in asfL-1 that efficiently mitigated the adverse effect of ascorbate deficiency and
permitted survival under salt-stress conditions (Talukdar 2012a). Furthermore, two
flavonoid-deficient mutants, namely, fldL-1 and fldL-2, were produced by EMS
mutagenesis wherein leaf flavonoid content was reduced up to 20% relative to
CWRs (Talukdar 2012b).
By mutation breeding using EMS (0.01%) and gamma rays (250 Gy), two
varieties such as “Poltavskaya” in Russia and “Bina Khesari 1” in Bangladesh
26 Lathyrus Breeding 1357

were developed, respectively (Kumar et al. 2011, 2013). In vitro culture has also
been used to induce somaclonal variation (Ochatt et al. 2002; Roy et al. 1993;
Zambre et al. 2002; Barpete et al. 2014a, 2020b). Induced mutagenesis and
somaclonal variation created new variability that offers great opportunities to
breeders for the selection of lines with traits of interest. Recently, Tripathy et al.
(2014) observed somaclones with variation in flower colour, seed colour, leaflet
length and breadth, foliage and pod pigmentation which may be used as genetic
markers in breeding. Besides, variants with broad leaf, dwarf height, long pod, large
seed, short duration and synchronous maturity are agronomically desirable. Notably,
a large seeded somaclone NGOG 5 recovered with high seed yield and low neuro-
toxin content (ODAP) that can be used as a desirable candidate for future breeding
programmes. Notably, dwarf mutants with erect and determinate growth habit, and
various leaflet and tendril mutants (Talukdar 2009a, b, c, d), provide an opportunity
to restructure the present plant type of grass pea, which is dominated by traits such as
prostrate and indeterminate growth habit, weak and tall stature and lodging type
(Rybinski 2003). In field pea, the dwarf leafless plant type has better standing ability
and is amenable to machine harvesting owing to conversion of leaflets into tendrils,
thus development of similar plant type in lathyrus could aid in escalating its produc-
tivity (Ali and Kumar 2009; Snoad 1974).

26.12 Breeding Objectives

The prime objectives of any crop breeding programme are to accelerate production
potential with sustainability of this potential by developing resistance against dis-
ease, pest and unfavourable environments. For grass pea, major breeding objectives
can be summarized as follows:

26.12.1 Low ODAP Content (<0.1%)

Sincere efforts have been made across the globe and numbers of varieties have been
developed as mentioned in Table 26.4. Although the ODAP content is still an
important goal of most of the current grass pea breeding programmes and needs
continuous efforts to accelerated development of low- or near-zero-level ODAP
genotypes.

26.12.2 High Grain Yield

The mean yield potential of most of the released varieties is in the range of 1.0–2.0 t/
ha, except for some of the varieties (Table 26.4). Hence, yield increment up to
2.5–3.0 t/ha should be the selection criterion for most of the crop improvement
programmes. In addition, some of the other yield attributes that affect yield such as
double podding or increased seeds per pod need sufficient attention. While
1358 A. K. Parihar et al.

improving yield and adaptation to the environment, emphasis is also given to ensure
that the palatability, intake and other nutritive values of grain are acceptable.

26.12.3 High Biomass

In many parts of the world, there is a shortage of feed and fodder for livestock and
this is especially true for many arid regions where grass pea is being grown. In many
cases, the value of the fodder equals or exceeds that of the grain produced (Campbell
1997). The high biomass yield of grass pea is also important and has received more
attention during the recent decades (Abd El Moneim et al. 2001; Campbell 1997;
Vaz Patto et al. 2006b). This is a very important area due to the large potential of this
crop for forage and straw in the North African and South Asian regions (Campbell
1997). Moreover, negative breeding for undesirable traits such as prostrate plant
habit, indeterminate growth, late maturity and pod shattering should be handled by
several breeding programmes (Rybinski 2003). At the same time as improving
biomass and adaptation to the environment, emphasis also should be given to ensure
that the palatability, intake and other nutritive values of herbage, hay and straw are
acceptable.

26.12.4 Resistance to Biotic Stresses

Grass pea is mainly exposed to following biotic stresses like powdery mildew
(Erysiphe pisi), rust (Uromyces fabae), downy mildew (Peronospora lathyri-
palustris), ascochyta blight (Mycosphaerella pinodes), fusarium wilt, broomrape
(Orobanche crenata Forsk.) and thrips (Caliothrips indicus) which causes consider-
able yield penalty under congenial environments (Campbell 1997; Robertson and
Abd El-Moneim 1996; Gurung et al. 2002; Vaz Patto et al. 2006b; Barilli et al. 2011,
2012; Talukdar 2013; Abdallah et al. 2021; Sampaio et al. 2021). However, efforts
have been made and some of the improved varieties developed and genotypes
identified for tolerance to prevailing biotic stresses. Actually, this crop is being
cultivated mainly by resources poor farmers under poor management with no
chemical control for diseases and pests. Hence, continuous efforts with more
intensity are required to develop varieties resistant to prevalent biotic stresses.

26.12.5 Resistance to Abiotic Stresses

Grass pea has comparatively better tolerance to drought, flooding, salinity, tempera-
ture extremities (high and low) and problematic soils than other pulse crops (Dixit
et al. 2016; Sarkar et al. 2019). In case of abiotic stress resistance screening, the
scarcity of methodologies to identify resistant genotypes has hampered the proper
exploitation in breeding of grass pea and subsequent understanding of the
mechanisms underlying resistance to environmental injuries is also lacking.
26 Lathyrus Breeding 1359

However, the effects of drought and salt stress on different morphological and
physiological traits have been ascertained and several L. sativus salt- and drought-
resistant genotypes have been reported (Talukdar 2011a, b; Silvestre et al. 2014).

26.12.6 Bio-Fortified Genotypes

In addition to low ODAP to combat the hidden hunger among the resource poor
vegetarian populations of developing nation’s particularly Asia and Africa where
grass pea is prominently grown, cultivars with high iron, zinc and methionine need
to be developed. Henceforth, there is an urgent need to develop grass pea cultivars
having high iron and zinc with lesser amount of anti-nutritional factors that may
promote this underutilized and neglected crop to mitigate micronutrient malnutrition
of the underprivileged communities.

26.12.7 Mechanical Harvesting Amenable Genotypes

In future, scarcity of farm/agricultural labour is anticipated that will lead to increase

in the cost of cultivation which creates the necessities of developing grass pea
varieties suitable for mechanical harvesting. For mechanical harvesting, genotype
should have more ground clearance with lodging resistance.

26.13 Genomics-Enabled Improvement

Genomics provides various tools and techniques to tackle the emerging challenge of
escalating grain yield, quality and stability of production in the face of anticipated
climate changes (Kole et al. 2015). The application of DNA markers has proved
successful to facilitate marker-aided selection (MAS) for crop improvement. The
further advancement in plant genomics by developing functional DNA marker at
large scale offers additional resources to get better understandings of crop diversity
at species and gene levels that ultimately assists in acceleration of the pace of genetic
improvement (Muthamilarasan et al. 2013, 2014). The following section
summarizes the current scenario of genomic resources in grass pea and their possible
utilization in marker-assisted/genomic-assisted breeding.

26.13.1 Genomics Resources Panorama

This crop could not make much advancement using conventional breeding in the
past, and very fewer attempts have been made in molecular biology due to scarcity of
reliable molecular markers representing the entire genome (Yang et al. 2014).
Indeed, Lathyrus is lagging behind in case of genomic resources as compared to
other pulses crops. To date, three linkage maps have been developed for any
1360 A. K. Parihar et al.

Lathyrus species using molecular markers (Chowdhury and Slinkard 1999; Skiba
et al. 2004a; Santos et al. 2018). One of them was developed by using 11 RAPD
markers, 1 isozyme marker and flower colour (Chowdhury and Slinkard 1999). The
another maps were constructed using 47 RAPDs, 7 cross-amplified pea microsatel-
lite simple sequence repeats (SSR) markers and 13 cleaved amplified polymorphic
sequence (CAPS) markers (Skiba et al. 2004a). This map was used to conduct
quantitative trait loci QTL analysis to evaluate a backcross population for resistance
to ascochyta blight. However, no candidate genes were identified at that time for
these resistance QTLs that hamper their use in precision breeding (Vaz Patto et al.
2006b). However, these two linkage maps have not been sufficiently saturated with
markers and offered many gaps and short linkage groups; therefore, these could not
be aligned and compared with linkage maps of other legume species (Vaz Patto et al.
2006b; Almeida et al. 2015a, b, c).
During recent decades, genetic diversity in grass pea has been delineated by
various molecular markers such as RFLP (restriction fragment length
polymorphism), RAPD (random amplified polymorphic DNA) and AFLP (amplified
fragment length polymorphism) (Croft et al. 1999; Hanada and Hirai 2000;
Chtourou-Ghorbel et al. 2001; Barik et al. 2007; Tavoletti et al. 2007; Nosrati
et al. 2012). The existing taxonomic categorization of Lathyrus has supported
using internal transcribed spacer (ITS), nuclear ribosomal and chloroplast
(cp) sequence-specific DNA markers (Kenicer et al. 2005). Generally EST-SSR
marker system has a high degree of conservation and can be transferred among
species, but the numbers of ESTs for L. sativus (178) and L. cicera (126) are very
limited as compared to ESTs (8702) available for L. odoratus (Dixit et al. 2016;
Lambein et al. 2019). A set of SSR markers including 20 SSRs was developed using
an in silico survey (Lioi et al. 2011). The cross-species and cross-genus amplification
of molecular markers system facilitates comparative genomic mapping by providing
an alternative for the development of new molecular markers for orphan species
(Gutierrez et al. 2005). For instance a large number of molecular markers from
Medicago truncatula, garden pea, lentil, lupine, and faba bean were shown to be
transferable to L. cicera and L. sativus for their future applications in mapping and
diversity studies (Zhu et al. 2005; Chandra 2011; Almeida et al. 2014a).
Genomic and EST microsatellites were the most commonly attempted cross-
species amplification marker systems in Lathyrus. Some of these marker systems,
like microsatellites being co-dominant markers, have an additional advantage for
linkage map development (Vaz Patto et al. 2011). In four diverse accessions of
Lathyrus which belongs to different species, that is L. sativus, L. cicera, L. ochrus,
L. tingitanus) and P. sativum seven SSRs were validated (Lioi and Galasso 2013).
The genotyping of 176 accessions with EST-SSRs developed two subpopulations
using a model-based population structure analysis wherein authors predicted gene
flow among the accessions across the geographical regions in India (Soren et al.
2015). During last decades, different groups used EST-SSR for diversity analysis in
different set of genotypes (Shiferaw et al. 2012; Sun et al. 2012; Gupta et al. 2018;
Arslan et al. 2020). Ponnaiah et al. (2011) have developed seven Lathyrus-specific
EST–SSR markers. Ghorbel et al. (2014) employed an Inter-Simple Sequence
26 Lathyrus Breeding 1361

Repeats (ISSRs) technique to assess genetic diversity and relationships of seven

Mediterranean species of the Lathyrus belonging to different sections: Lathyrus,
Clymenum, Nissolia and Aphaca.
Cleaved amplified polymorphic sequence (CAPS) and derived-CAPS (dCAPS)
marker were also developed for utilization in Lathyrus (Almeida et al. 2014a, b).
Most recently, in silico mining of nucleotide sequences recognized 203 SSRs, of
which 150 markers were screened and only 60 markers were amplified 75 alleles
with polymorphic information content (PIC) of 0.45 (Soren et al. 2020). The genetic
diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed
using ten SSR markers (Aci et al. 2020) and subsequent population structure
demonstrated that Lathyrus accessions were divided into three populations regard-
less of their geographic origin. These results are mostly in conformity with the
morphological classification of these species (Kupicha 1983) as well as other DNA-
marker-based classifications such as RAPD (Croft et al. 1999), RFLP (Chtourou-
Ghorbel et al. 2002a, b), ISSR (Belaid et al. 2006) and SSR (Wang et al. 2015).
SSRs and EST-SSRs have specifically been selected by breeders because of their
polymorphic character and co-dominant inheritance, as well as the large number of
alleles per locus and abundant in distribution throughout the genome (Gupta et al.
2018; Varshney et al. 2005). These markers allowed the use of Lathyrus as a source
of interesting traits for other related species and vice versa; the availability of number
of molecular markers for Lathyrus species, in particular for L. cicera and L. sativus,
has been increased during recent decade. These markers will be useful for molecular
plant breeding in the future.
Genetic mapping and QTLs analysis, by means of bi-parental or association
mapping (AM) populations, have accelerated the untangling of genetic control of
targeted traits which eventually led to MAS, QTL, and AM studies or direct
calculation and further genomic selection (GS) (Kulwal et al. 2011). Earlier, AM
and GS were hampered due to restricted coverage of genome by available markers.
But during recent decade, the next-generation sequencing (NGS) technologies have
become popular on its success of sequencing DNA at exceptional speed, thus
enabling remarkable scientific achievements and novel biological applications
(Mardis 2008; Schuster 2008; Kole et al. 2015). The application of NGS platforms
in Lathyrus to generate large-scale SSR-enriched sequence data and to develop SSR
markers will facilitate the construction of high-resolution maps for positional clon-
ing and QTL mapping (Yang et al. 2014; Wang et al. 2015).
In recent past, Yang et al. (2014) developed 50,144 non-redundant SSR primers,
of which 288 were randomly selected for validation among 24 accessions comprised
of 23 L. sativus and one L. cicera accession. Of them only 74 primers showed
polymorphic pattern and remaining were either monomorphic or could not be
amplified. The large number of SSR markers developed in this study would make
a significant contribution to genomics-enabled improvement of grass pea. Of them
30 high-throughput SSRs were further employed to analyse 266 Lathyrus accessions
and 17 relatives from Africa, Europe, Asia and ICARDA (Wang et al. 2015). The
population structure analysis delineated the possibility of gene flow between the
European and African accessions, which was further supported by unweighted pair
1362 A. K. Parihar et al.

group method with arithmetic mean (UPGMA)-based cluster analysis and principal
component analysis (PCA).
The RNA-Seq technology has been used to design 200 EST-SSR markers, of
which 40 markers were validated and only 62.5% marker registered polymorphism
between two accessions. Furthermore, they identified 2634 contigs containing SNP
(Almeida et al. 2014a, b). The first high-throughput transcriptome assemblies were
generated by the RNA-sequencing technology in grass pea genotypes to unravel the
molecular mechanisms underlying pre-haustorial rust resistance (Almeida et al.
2014b). This study generated a large number of new gene-based molecular tools:
ESTs, EST-SSRs, and single nucleotide polymorphism (SNP) based markers. These
markers will be instrumental for future work on high-throughput mapping for
uncovering the genetic basis of disease resistance in L. sativus and, eventually,
comparative mapping with other legume species.
Later, by coupling high-throughput sequencing (Illumina) technology with serial
analysis of gene expression (SAGE) analyses, a set of differentially expressed genes
was identified in the leaves of L. sativus in response to ascochyta lathyri inoculation
(Almeida et al. 2015a, b, c). Likewise, Hao et al. (2017) conducted RNA-sequencing
based transcriptome analysis using Illumina NextSeqTM500 platform and obtained
570 million quality-filtered and trimmed cDNA sequence reads with total length of
over 82 billion bp. Approximately two million contigs and 142,053 transcripts were
assembled from RNA-Seq data, which resulted in 27,431 unigenes; of these
unigenes, 3204 EST-SSR primers were designed, 284 of which were randomly
chosen for validation. Of these validated unigenes, 87 EST-SSR primers produced
polymorphic amplicons among 43 grass pea accessions selected from different
geographical locations. Meanwhile, 146,406 SNPs were screened and 50 SNP loci
were randomly chosen for the competitive allele-specific PCR (KASP) validation.
Finally, 42 SNP loci were successfully transformed to KASP markers. However, the
detection of sufficient number of molecular markers and construction of highly
statured genetic linkage map in grass pea is lagging as compared to the other legume
crop, which is the prerequisite for localizing the position of the genes/QTLs in the
genome that will certainly facilitate MAS programme.

26.13.2 Marker-Assisted Breeding

To perform MAS, the fundamental requirement is availability of closely linked

molecular markers with the trait of interest. The DNA markers in addition to
assessing the level of genetic diversity in phylogenetic studies have also been used
in plant breeding (Vaz Patto et al. 2006a, b). Markers are being used as necessary
tools to find out the number, position and individual effects of genes/QTLs
controlling traits of interest by linkage mapping and QTL analysis (Campbell et al.
1994). Most importantly, the application of molecular markers in plant breeding
hastens the generation of new varieties by helping plant breeders in early selection of
desirable individuals based on genetic architecture rather than external appearance
(Tanksley et al. 1989; Almeida et al. 2015a, b, c). In addition, markers could
26 Lathyrus Breeding 1363

establish the association of phenotypic characters with the genomic loci accountable
for them, which could make easy gene transfer to appropriate agronomic back-
ground. So far, different types of molecular markers as given in previous section
such as RFLP, RAPD, SCAR, AFLP, SRAP and EST-SSR have been used for
diversity study in grass pea (Chtourou-Ghorbel et al. 2001; Hanada and Hirai 2003;
Marghali et al. 2016; Nosrati et al. 2012; Tavoletti and Iommarini 2007; Lioi et al.
2011; Ponnaiah et al. 2011; Shiferaw et al. 2012; Sun et al. 2012; Lioi and Galasso
2013; Soren et al. 2015; Gupta et al. 2018; Arslan et al. 2020).
The number of molecular markers available for Lathyrus species, in particular for
L. cicera and L. sativus, has increased in recent decade (Chandra 2011; Lioi et al.
2011; Shiferaw et al. 2012; Almeida et al. 2014a; Soren et al. 2020). So far limited
efforts have been made for establishment of marker trait association in grass pea. In
first decades of twenty-first century, only one attempt was made for QTL analysis in
a backcross population for ascochyta blight resistance. However, none of the
candidate genes were found associated with these resistance QTLs at that time
which hampered their use in precision breeding (Vaz Patto et al. 2006b). Later,
with the development of high-throughput and dense genotyping, association
mapping has taken advantage over bi-parental population by generations of more
recombination in short time span (Morrell et al. 2012; Cobb 2013). In addition, NGS
platforms generated large-scale SSR-enriched sequence data and enabling mining of
SSR markers (Yang et al. 2014; Wang et al. 2015) which will facilitate the construc-
tion of high-resolution maps for positional cloning and QTL mapping. Most
recently, in grass pea, significant marker–trait association was developed with six
markers (Soren et al. 2020).
Although first linkage map of L. cicera has been constructed using part of the
developed markers in a RIL population. This map covered 724.2 cM (mapping
interval of 2.4 cM) with 7 major and 2 minor linkage groups. This study provides a
large new set of genic polymorphic molecular markers with potential for mapping
rust resistances in this robust species and its most closely related species L. sativus
(Santos et al. 2018). It also represents the first step towards genomics-assisted
precision breeding in L. cicera. Overall, there is an urgent need to develop a more
comprehensive genetic map for grass pea, with identification of valuable genes and
QTLs for MAS and with the possibility of alignment with other species in a
comparative mapping approach. Further development of this approach will facilitate
the transfer of resistance to diseases such as downy mildew and rusts and selection of
superior plants at the seedling stage, through MAS. Linkage maps, gene cloning and
MAS will hasten the introgression of novel genes for such traits as disease resistance,
low ODAP and increased methionine, to develop germplasm which can be used to
improve locally adapted cultivars.
1364 A. K. Parihar et al.

26.14 Modernization of Crop Improvement Programme

To accelerate genetic gain in grass pea, there is urgent need of modernization of

ongoing improvement programme by further embracement with advanced tools and
techniques. As briefed in previous section substantial number of molecular markers
have been used for deciphering genetic diversity in grass pea (Chtourou-Ghorbel
et al. 2001; Marghali et al. 2016; Nosrati et al. 2012; Tavoletti and Iommarini 2007;
Lioi et al. 2011; Ponnaiah et al. 2011; Shiferaw et al. 2012; Sun et al. 2012; Lioi and
Galasso 2013; Soren et al. 2015; Gupta et al. 2018; Arslan et al. 2020). The recent
adoption of NGS has facilitated the development of considerable numbers of SSRs,
SNPs and transcriptome assemblies in grass pea (Yang et al. 2014; Almeida et al.
2014a, b; Hao et al. 2017; Santos et al. 2018). Discovery of novel genes/alleles for
trait of interest needs to be executed via genotyping-by-sequencing (GBS)
approaches (Kole et al. 2015). Correspondingly, genome-wide association studies
(GWAS) could be used to recognize the genomic regions controlling traits of interest
by performing marker trait association’s analysis in diverse collection of germplasms
that are genotyped and phenotyped for traits of interest.
NGS coupled with GWAS increases the mapping resolution for precise position-
ing of genes/alleles/QTL linked to the targeted traits (Ma et al. 2012; Liu et al. 2013;
Varshney et al. 2014) which is still lacking in grass pea. The genome sequencing of
crop is essential for understanding biochemical and physiological processes that
discover plant traits and their behaviour towards external environmental extremities
(Gedil et al. 2015). The rapid advancement in genome sequencing technologies
(Barba et al. 2014) has resulted in unprecedented increase of genomic information
which eventually increased opportunities to apply this resources into crop improve-
ment programme, for example through the development of genome-wide marker
assays (Rius et al. 2015; Nybom et al. 2014). The draft genome sequencing of grass
pea has been recently available, but unfortunately, so far, no significant development
has been made on grass pea genome editing to tackle any abiotic or biotic stresses
and quality aspects (Emmrich et al. 2020; Kumar et al. 2020). In the rapidly
changing scenery of life science technologies, a number of new tools have emerged,
particularly for deciphering gene function and metabolic pathways including
transcriptomics, proteomics, metabolomics, small RNAomics, epigenomics,
interactomics and bioinformatics (Gedil et al. 2015).
It is important to adopt the above-mentioned tools and techniques for the better
understanding of biological processes which are the key factors for enhancing
productivity and quality of grass pea. Recently with the advancement of
NGS-based technologies, transcriptomic-based studies have also been initiated in
grass pea (Yang et al. 2014; Almeida et al. 2015a, b, c; Chapman 2015; Tan et al.
2017; Xu et al. 2018; Rathi et al. 2019). Transcriptome profiling has been employed
for extrication of grass pea–U. pisi interaction to discover the putative biochemical
pathways and transcripts governing resistance (Almeida et al. 2014a). Similar use of
transcriptomic studies has been made in grass pea differing in aschochyta blight
resistance reaction for identification of putative proteins/pathways controlling its
resistance (Almeida et al. 2015a, b, c). The biosynthesis pathway of β-ODAP is still
26 Lathyrus Breeding 1365

in ambiguity in grass pea; therefore, a transcriptome analysis was conducted to

ascertain the genes and pathways controlling β-ODAP synthesis during different
growth stages and concluded that the cysteine synthase genes influenced β-ODAP
accumulation and were coregulated with primary metabolism (Xu et al. 2018). So,
far only one transcriptome study has been done in grass pea pertaining to abiotic
stress tolerance and some transcripts concerning drought tolerance have been
detected (Rathi et al. 2019).
A recent study on grass pea identified several miRNAs associated with drought
tolerance. Of which, 8 miRNAs were upregulated under drought stress while
12 known miRNAs were down-regulated under drought condition (Bhat et al.
2020). In this study, a number of novel miRNAs have also been identified. Further
studies are needed to functionally characterize different miRNAs available in grass
pea involved in various stress signalling and development of transgenic plants to
combat abiotic stresses through functional genomics approach. In conjunction with
the genomic and transcriptomic progress, proteomic research has also been exploited
in grass pea. By using proteomic, 100 protein spots through two-dimensional gel
electrophoresis were identified, which were at least two times differentially
expressed when exposed to independent treatment of salt stress, cold stress and
abscisic acid treatment for 36 h compared to control plants (Chattopadhyay et al.
2011). The small interfering RNA (siRNA)-mediated gene silencing and virus-
induced gene silencing (VIGS) also dictate the gene expression solitary at post-
transcriptional level (Unver and Budak 2009; Kasai et al. 2011; Banerjee et al. 2017;
Lee et al. 2017). However, in L. odorata, Phytoene desaturase (PDS) gene was
silenced using VIGS approach, but this has not been replicated in other Lathyrus sp.
(Grønlund et al. 2008).
Gene regulation through siRNA or miRNA often leads to other effects also,
hence, to get rid of that genome-editing technologies are acquiring noteworthy
attention to specifically deregulate a targeted gene (Zhang et al. 2015). Generally,
three approaches of genome editing are popular among the researchers, namely, zinc
finger nuclease (ZFN), transcription activator like effector nuclease (TALEN) and
clustered regularly interspaced short palindromic repeats (CRISPR-cas9) mediated
approaches having potential merits and demerits of each one of them (Zhang et al.
2020). Some other reverse genetic approaches such as TILLING (Targeting Induced
Local Lesions IN Genomes) and Eco-TILLING which detects induced mutation and
natural mutation, respectively, need to be explored properly (McCallum et al. 2000;
Comai et al. 2004). However, sincere efforts have been initiated at John Innes
Centre, Norwich, Norfolk, England, for studying EMS mutagenized populations
for searching low ODAP mutant (Emmrich 2017).
Grass pea hold great promise as a good candidate for both TILLING and
Eco-TILLING as the genomic resources are meagre as well as it is recalcitrant in
nature during genetic transformation. The development of transgenic in grass pea
through Agrobacterium-mediated transformation and particle bombardment showed
great promise after regeneration of complete plants via tissue culture (Gharyal and
Maheshwari 1980; Malik et al. 1993; Roy et al. 1991, 1992; Zambre et al. 2002;
Kumar et al. 2011; Barpete et al. 2016, 2021a, b). To replicate the success of other
1366 A. K. Parihar et al.

major crops into grass pea, suitable regeneration and transformation protocol need to
be optimized (Barpete et al. 2017, 2020a, b). Sincere efforts have been devoted for
optimization of regeneration protocol in tissues culture by using shoot tips, stem, leaf
as well as root, seed and epicotyl explants and meristematic tissue (Zambre et al.
2002; Barik et al. 2005; Barpete et al. 2014a, b, 2021a, b).
The transformation was attempted through Agrobacterium-mediated and biolistic
gene gun (Barna and Mehta 1995; Barik et al. 2005). Moreover, in L. maritimus
Agrobacterium rhizogenes-mediated transformation and subsequently somatic
embryogenesis was also reported (Jiangbo and Jingfen 2002). So far, based on
available literature very few attempts were made towards grass pea transformation.
Hence, urgently intensive efforts are needed for the optimization of genetic transfor-
mation protocol in grass pea and successful generation of transgenic lines of reduced
ODAP content as well as improved abiotic stress tolerance. Recent advances in
molecular biology, biochemical pathways and metabolic change offer scope to
produce genetically bio-fortified grass pea to increase its nutritional value (Kumar
et al. 2011; Gupta et al. 2021).

26.15 Coordinated System of Testing

Before the establishment of All India Co-ordinated Pulses Improvement Project

(AICPIP) in 1967, the research efforts toward grass pea improvement have remained
isolated at individual level. The AICPIP provided an opportunity to access the
improved materials to pulse breeders and to test their improved breeding lines
over multi-locations across the country. Later on this crop was brought under the
compass of separate All India Coordinated Research Project (AICRP) on MULLaRP
(Mungbean, Urdbean, Lentil, Lathyrus, Rajmash and Pea) which got operational in
November 1995. The coordinated research programme of grass pea in India is
carried out through the aegis of AICRP on MULLaRP administered by the Indian
Council of Agricultural Research (ICAR). The AICRP on MULLaRP has a large
network of 28 AICRP centres covering major pulse-growing states of the country.
These centres pursue activities and strategic research in the area of crop improve-
ment, production and protection. Besides, AICRP on MULLaRP also coordinates
the nucleus and breeder seed production to meet out the demand of quality seed in
the country.
Recently, Tandon et al. (2015) revised the guidelines for testing of varieties under
All India Coordinated Research Project, in which the proposed entries are being
tested consecutively for 3 years in three trials, that is Initial varietal trials (IVTs),
advanced varietal trials-I (AVT-I) and advanced varietal trials-II (AVT-II) at multi-
location in different zones (Figs. 26.3 and 26.4).
The IVTs are constituted with the new entries proposed by cooperating breeders/
institutions along with the specified number of check varieties. The total number of
test entries including checks should not be more so that appropriate experimental
design may be implemented without any compromise. A minimum of three check
varieties, comprising of national, zonal and local check, shall be used and remain
26 Lathyrus Breeding 1367

Fig. 26.3 Grass pea AICRP field trials in central zone (a) and north-eastern plain zone (b)

unchanged for a minimum period of 3 years to enable comparison with the same test
entries. The seed of candidate entries and checks must be genetically pure, true-to-
type and meet the requirements of minimum seed certification standards. The
experimental design, plot size and number of replications shall be decided in the
Annual Group Meet on the basis of the experience gained from the past trials over
years, to reduce experimental error. The plot size and number of replications should
be homogeneous at all the test locations/zone/ecology. In addition, proper scope for
date of sowing, seed rate, depth of sowing, plant geometry, fertilizer, irrigation,
weed, insect-pests and disease management, etc. shall be mentioned in the technical
programme and supplied at all the test locations.
The test centres shall be identified in the workshop and that could be ICAR
Institutes/SAUs/Main or Regional Research Centres/Zonal Research Centres/State
Govt. centres, where a multi-disciplinary team of scientists is available with enough
operational facilities to carry out coordinated trials as per the instructions. All the
trials shall be monitored meticulously by a team of scientists constituted by the
Project Director/Coordinator. The team shall visit the testing locations during
flowering to maturity time and record observations on the quality of the trials
conducted and on the management as per the specified norms, and comment on
the reliability of data likely to be generated. Additionally, observations should be
recorded on the agronomic character like days to flowering and maturity, plant
height, lodging, thresh ability; response to important diseases and insect-pests; easily
measurable grain quality attributes such as colour, weight, appearance etc. The
details of characters on which data shall be recorded should be specified by the
workshop. All the data that is received at the coordination cell shall be crucially
examined to make a decision on suitability of data for further statistical processing
based on the recommendations of the monitoring team. Suggestions by the zonal
coordinator/concerned breeder, deviation from the specified range of sowing date,
specified crop management practices for the trial such as fertilizer doses, irrigation
1368 A. K. Parihar et al.

Fig. 26.4 Coordinates system for testing of new entries of grass pea in India

levels and any other severe error in conducting of trial/data recording/reporting

should be considered aptly.
The promotion of entries from IVT to AVT would be strictly based on the overall
performance/merit of the test entries and criterias finalized in workshop. AVT-I shall
be constituted separately for each recognized agro-ecological zone by the entries
promoted from the IVT on the basis of the criteria specified, the repeat entries from
the previous year’s AVT-I and the check varieties as per workshop recommendation.
The number of entries in AVT-1 should normally not exceed 20. Higher number
may be considered under exceptional cases with the approval of house (committee)
26 Lathyrus Breeding 1369

during workshop. In AVT-I, plot size should be larger than IVT to make more
realistic estimates of the yield performance and to reduce inadequacies/errors of
measurements inherent in small plots. The number of trial sites shall be much more
than IVT trials in a given zone. Data on disease and insect-pest resistance and other
ancillary characters shall be recorded only at the centres where facilities exist as
specified in the workshop. Data on quality parameters including biochemical and
processing properties shall be generated from selected sites in specified laboratories
as per workshop recommendation.
The promotion of AVT-1 entries may be done mainly based on grain yield
superiority with consideration of other specified characters. All the practices
specified under the IVT and AVT-I stage shall be followed at AVT-II stage also.
The entries which showed desired superiority over the best check in AVT-II stage
will be selected and the identification proposal of that genotype is invited by project
coordinator to put in varietal identification committee (VIC). The VIC after thorough
discussions recommends the best entry for release and notification to central
sub-committee on crop standard notification and release of varieties. After notifica-
tion, the varieties enter into seed production chain: breeder seed, foundation seed and
certified seed.

26.16 Seed Production and Seed Standards

A number of grass pea improved varieties have been released from various breeding
programmes as already described in the previous section. In any plant species if
outcrossing frequency rate is up to 30%, exceptional efforts are required for
maintaining the purity of cultivars (Rahman et al. 1995; Chowdhury and Slinkard
1999; Almeida et al. 2015a, b, c). The outcrossing percentage is less in white
flowered cultivars in comparison to blue, pink and crimson colour (Kiyoshi et al.
1985; Rahman et al. 1995). The proper isolation distance during seed production is
essential to maintain genetic purity and phenological features of the developed
cultivars. Land to be used for seed production of grass pea shall be free of volunteer
plants. To maintain the genetic purity of the seed considering reported out-crossing,
the existing minimum isolation distance, that is 5 m and 10 m for certified and
foundation seed production, respectively, from the fields of other varieties for
certification, need to be revisited. A minimum of two inspections are required to
be made, the first before flowering and the second at flowering and fruit stage
(Trivedi and Gunasekaran 2013).
The main objective of field inspections is to verify the factors which can affect the
genetic purity of the seed and to take the corrective measures. During pre-flowering
inspections, the requirements on the isolation distance and land conditions are
checked and to undertake roguing if any off-types plants are present. At flowering
and fruiting stage, inspection must be done to further check the occurrence of
off-types based on flower colour and pod character and to subsequently remove
them. During flowering, daily inspections should be done to identify the not true to
type plants and to remove such off-types. A final rouging must be carried out during
1370 A. K. Parihar et al.

Table 26.5 Grass pea seed standards as per Indian Minimum Seed Certification Standards
Standards for each class
Factor Foundation seed Certified seed
Pure seed (minimum) 98.0% 98.0%
Inert matter (maximum) 2.0% 2.0%
Other crop seeds (maximum) 5/kg 10/kg
Weed seeds (maximum) 5/kg 10/kg
Other distinguishable varieties (maximum) 10/kg 20/kg
Germination including hard seeds (minimum) 75.0% 75.0%
Moisture (maximum) 9.0% 9.0%
For vapour proof containers (maximum) 8.0% 8.0%
Source: ISTA (2016)

maturity to eliminate any chance of contamination. The maximum permitted per-

centage of off-types at the final inspection is 0.10% and 0.20% for foundation and
certified seed production plots, respectively (ISTA 2016).
The minimum proportion of such pure seeds should be 98% for foundation as
well as certified seed. However, seeds and its pieces without seed coat are considered
as inert matter. Also, separated cotyledons are considered as inert matter irrespective
of whether the radicle-plumule axis and/or more than half of the seed coat are
attached. Inert matter also includes the dust particles, muds, stones and any part of
seed not included as pure seeds (ISTA 2016). The maximum permissible limit of
inert matter is 2% for both foundation and certified seed. Likewise, the maximum
permissible limit of other crop seed and weed seed is 5 and 10 per kg for foundation
and certified seed, respectively (Table 26.5).

26.17 Future Thrust Areas

To promote or exploit the potential of grass pea to ensure nutritional security of

resource poor people of developing countries and sustainable pulses production, the
quintessential step in coming years is the development of grass pea as a safe crop for
human and animal consumption with low level ODAP (<0.1%) content. Further, for
judicious utilization of available genetic resources in international and national gene
banks, a comprehensive characterization needs to be undertaken using high-
throughput phenotyping. In case of genomic resources, grass pea is still under-
researched as compared to other pulses crops; therefore, intensive efforts should
be made using recent molecular tools and techniques to create ample genomic
resources. The delineation of inheritance pattern of economically important traits
and a dense linkage map of Lathyrus species needs to be developed. To speed up
functional genomics studies, development of various mapping populations including
RILs, NILs, TILLING and MAGIC populations is considered necessary for trait–
marker association and gene inactivation/deletion studies.
26 Lathyrus Breeding 1371

To accelerate genetic gain, further research on different Lathyrus species using

genetic, cytogenetic techniques, inter-specific hybridization and advanced molecular
approaches needs to be undertaken. Overall, there is urgent need to develop
low-toxin and high-yielding varieties with resistance to various biotic and abiotic
stresses and rapid delivery of that to farmers. For horizontal extension of grass pea
particularly in Utera system of India, the development of high-yielding genotypes
with earliness, deep root system, small seed size, erect plant habit and medium plant
height is urgently required. In addition, other Lathyrus species also need to be
explored for their suitability in different cropping systems. Intensive efforts may
be placed to develop genotypes with medium maturity, higher biomass, bold seed
and input responsiveness for irrigated areas with high yield potential that can be used
as dual purpose.
The draft genome sequence of grass pea has been recently published and further
progress in that will pave the way toward genomics-enabled breeding. Advanced
tools and techniques, such as transcriptomics, proteomics, metabolomics, small
RNAomics, epigenomics, interactomics, bioinformatics and genome editing, may
be embraced to strengthen the grass pea improvement programme. Till date, the
exact physiological and molecular mechanisms controlling ODAP content in grass
pea remains uncharted that need urgent attention. National and International level
collaborative research efforts are imperative to bring the grass pea crop in main-
stream legume crop.

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