1. Molecular Markers

2. Morphological Markers
Recessive in nature
Mutations - deleterious phenotype
Problems with epistasis, pleiotrophy, incomplete penetrence
Influenced by environment
Transitory phenotype
Difficult to combine

3. 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

4. Isozymes • The granddaddy of molecular markers
• Lewontin and Hubby 1966
– Amino acid substitutions shift mobility of enzyme through gel
• Folding and charge
• Still used today

6. Isozymes • Pros: – Moderately easy, well developed protocols
– Don’t need genome information
– Decades of data to tie into
• Cons:
– Low variation
– Lots of fresh tissue needed
– Many hazardous chemicals

7. Now 3 Methods of Detection
Restriction fragment length polymorphism and Southern blotting (RFLP)
Polymerase chain reaction (PCR)
Sequence information

8. Southern blotting Isolate DNA Digest DNA w/ restriction enzyme
Size fractionate DNA
Denature DNA
Blot SS DNA to membrane

9. Methodology Prepare a probe Hybridize probe with membrane Rinse
Label
Denature
Hybridize probe with membrane
Rinse
Autoradiography

17. Disadvantages: The technique is laborious Time-consuming Expensive
May use isotope

18. Hypervariable Sequences - VNTRs - Minisatellites

19. Some VNTRs detect polymorphisms at single specific loci.

20. Other VNTRs detect many bands, making them more useful for forensics.

24. Microsatellites

27. Advantages Disadvantages Initial identification,
Easy to detect via PCR
Lots of polymorphism
Co-dominant in nature
Disadvantages
Initial identification,
DNA sequence information necessary

28. Others
AFLPs
RAPDs

29. Single Nucleotide Polymorphisms (SNPs)

30. SNPs Polymorphism most used in human genomics 2/3 C → T
Coding and non-coding regions
Sequence information required
High through-put analysis

31. Nonpolymorphic Markers
Can be used for positional cloning, gene isolation
ESTs (expressed sequence tags)
STSs (sequence tagged sites)

32. Conclusions Many types of molecular markers available
Type(s) chosen for use will depend on many factors
Dominant or co-dominant, co-dominant preferable

33. 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

34. Conclusions, cont.
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.