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.