Molecular Markers 2005

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.