Molecular Markers. Morphological Markers Recessive in nature Recessive in nature Mutations -...

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Molecular Markers

Transcript of Molecular Markers. Morphological Markers Recessive in nature Recessive in nature Mutations -...

Page 1: Molecular Markers. Morphological Markers Recessive in nature Recessive in nature Mutations - deleterious phenotype Mutations - deleterious phenotype Problems.

Molecular Markers

Page 2: Molecular Markers. Morphological Markers Recessive in nature Recessive in nature Mutations - deleterious phenotype Mutations - deleterious phenotype Problems.

Morphological Markers

Recessive in nature Mutations - deleterious phenotype Problems with epistasis, pleiotrophy,

incomplete penetrence Influenced by environment Transitory phenotype Difficult to combine

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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

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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

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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

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Now 3 Methods of Detection

Restriction fragment length polymorphism and Southern blotting (RFLP)

Polymerase chain reaction (PCR)

Sequence information

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Southern blotting

Isolate DNA Digest DNA w/ restriction

enzyme Size fractionate DNA Denature DNA Blot SS DNA to membrane

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Methodology

Prepare a probe Label Denature

Hybridize probe with membrane

Rinse Autoradiography

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Disadvantages:

The technique is laborious

Time-consuming Expensive May use isotope

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Hypervariable Sequences - VNTRs - Minisatellites

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Some VNTRs detect polymorphisms at single specific loci.

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

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Microsatellites

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Advantages Easy to detect via PCR Lots of polymorphism Co-dominant in nature

Disadvantages Initial identification, DNA sequence information

necessary

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Others

AFLPs RAPDs

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Single Nucleotide Polymorphisms (SNPs)

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SNPs

Polymorphism most used in human genomics

2/3 C → T Coding and non-coding regions Sequence information required High through-put analysis

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Nonpolymorphic Markers

Can be used for positional cloning, gene isolation

ESTs (expressed sequence tags) STSs (sequence tagged sites)

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Conclusions

Many types of molecular markers available

Type(s) chosen for use will depend on many factors

Dominant or co-dominant, co-dominant preferable

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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

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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.


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