ASSOCIATION MAPPING WITH TASSEL. Presenter: VG SHOBHANA PhD Student CPMB. Genomics Effective tools Identify genes in pathways Alleles of agronomic traits Quite challenging ASSOCIATION MAPPING - high resolution
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VG SHOBHANAPhD Student
Identify genes in pathways
Alleles of agronomic traits Quite challenging
- high resolution
- to evaluate wide range of alelles rapidly
Co- inheritance of neighbouring DNA variants (in both).
Only few chances for recombination to occur.
Low resolution of map.
Recombination is the main force of elimination of linkage.
Recombination events occur over many generations.
Eliminated linkage between a mutated gene.
Only very close markers are in LD with the mutated gene.
Differences: Linkage and Association
that occur in a locus and the phenotypes (physical
forms or traits) that they produce.
Limitations of using natural populations:
linkage analysis is possible.
achieve a high resolution map.
Successfully in humans - no large mapping families.
LD between two loci in natural populations - affected by all the recombination events.
Have happened since the two alleles appeared in some individuals of the population.
LD declines as the number of generations increases, so that in old populations.
LD is limited to small distances.
This is desirable!!
Since a marker very close to a mutation responsible for a disease makes it easier to reach the mutated gene.
-- LD measures the closeness of the genetic association between markers and a particular trait.
-- May be used to identify markers in close proximity to the gene(s) responsible for the trait.
100 genotypes from each cluster – no closely related lines.
One line from one taxon only.
Has to be as diverse it could be – Extensive recombination history.
50 - 150 markers in a non random mated population – Good statistical power!!
Modest number of SSRs
large numbers of SNPs,
AFLP may provide a good compromise
Across 2-3 seasons in replicationsMaterials
(http://www.codoncode.com/) - to assess sequence quality and contig (join) sequences
Population Structure: STRUCTURE (http://pritch.bsd.uchicago.edu)
- (http://pritch.bsd.uchicago.edu) - for testing association of binary traits across structured populations
SAS (http://www.sas.com) carries out a wide range of statistics useful for association analysis.
Trait Analysis by aSSociation, Evolution and Linkage