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Molecular Markers 2005

This document discusses and compares different types of molecular markers and genetic mapping techniques. It outlines the characteristics of ideal molecular markers and describes three main methods for detecting markers: restriction fragment length polymorphism (RFLP), polymerase chain reaction (PCR), and sequence information. Southern blotting, microsatellites, and single nucleotide polymorphisms (SNPs) are highlighted as important marker techniques. The conclusion emphasizes that the best markers depend on the specific research goals and that molecular markers are generally preferable to morphological traits for genetic mapping.

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248 views31 pages

Molecular Markers 2005

This document discusses and compares different types of molecular markers and genetic mapping techniques. It outlines the characteristics of ideal molecular markers and describes three main methods for detecting markers: restriction fragment length polymorphism (RFLP), polymerase chain reaction (PCR), and sequence information. Southern blotting, microsatellites, and single nucleotide polymorphisms (SNPs) are highlighted as important marker techniques. The conclusion emphasizes that the best markers depend on the specific research goals and that molecular markers are generally preferable to morphological traits for genetic mapping.

Uploaded by

sweene0455
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPT, PDF, TXT or read online on Scribd
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Molecular Markers

Morphological Markers
• Recessive in nature
• Mutations - deleterious phenotype
• Problems with epistasis, pleiotrophy,
incomplete penetrence
• Influenced by environment
• Transitory phenotype
• Difficult to combine
Characteristics of Ideal Polymorphic
Markers
• Co-dominant expression
• Nondestructive assay
• Complete penetrance
• Early onset of phenotypic expression
• High polymorphism
• Random distribution throughout the
genome
• Assay can be automated
3 Methods of Detection
• Restriction fragment length
polymorphism and Southern
blotting (RFLP)
• Polymerase chain reaction
(PCR)
• Sequence information
Southern blotting
• Isolate DNA
• Digest DNA w/ restriction enzyme
• Size fractionate DNA
• Denature DNA
• Blot SS DNA to membrane
Methodology
• Prepare a probe
– Label
– Denature
• Hybridize probe with membrane
• Rinse
• Autoradiography
Disadvantages:
• The technique is laborious
• Time-consuming
• Expensive
• May use isotope
Hypervariable Sequences -
VNTRs - Minisatellites
Some VNTRs detect
polymorphisms at single
specific loci.
Other VNTRs detect many bands,
making them more useful for
forensics.
Microsatellites
• Advantages
– Easy to detect via PCR
– Lots of polymorphism
– Co-dominant in nature

• Disadvantage
– Initial identification,DNA
sequence information necessary
Others

• AFLPs
• RAPDs
Single Nucleotide Polymorphisms
(SNPs)
SNPs
• 2/3 C → T
• Coding and non-coding regions
• Sequence information required
• High through-put analysis
Nonpolymorphic Markers
• ESTs (expressed sequence tags)
• STSs (sequence tagged sites)
Conclusions
• Many types of molecular markers
available
• Type(s) chosen for use will depend on
many factors
• Dominant or co-dominant, co-dominant
preferable
Conclusions, cont.
• Now, markers where there is sequence
information are preferred to anonymous
markers, for sharing, PCR
• Polymorphism is necessary for genetic
mapping, not for physical mapping
Conclusion

All molecular markers are not equal.


None is ideal. Some are better for
some purposes than others.
However, all are generally preferable
to morphological markers for
mapping.

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