molecular markers. morphological markers recessive in nature recessive in nature mutations -...
TRANSCRIPT
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
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
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
Now 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
Disadvantages Initial identification, DNA sequence information
necessary
Others
AFLPs RAPDs
Single Nucleotide Polymorphisms (SNPs)
SNPs
Polymorphism most used in human genomics
2/3 C → T Coding and non-coding regions Sequence information required High through-put analysis
Nonpolymorphic Markers
Can be used for positional cloning, gene isolation
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
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.