Association mapping
- 1. ASSOCIATION MAPPING T. Nivethitha , GPB
- 2. 4 Cycles of intermating and selection – 15 years Extensive phenotyping and value judgement
- 3. Association Mapping & Advantages ‟Association genetics‟ or ‟association studies,” or ‟linkage disequilibrium mapping” Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level. Natural population surveyed to determine MTA using LD.
- 4. Approaches • On the basis of distance between two loci • By analyzing linkage disequilibrium between marker and target gene in natural population. LD refers to nonrandom association of alleles at different loci. LD can occur between more distant sites or sites located in different chromosomes LD is difference between the observed gametic frequencies of haplotypes and the expected gametic haplotype frequencies under linkage equilibrium . D = PAB − PAPB = (PAB.Pab − PAb.PaB)
- 5. …A..T.. 2 …A..C.. 2 …G..T.. 2 …G..C.. 2 …A..T.. 4 …A..C.. 0 …G..T.. 4 …G..C.. 0 Linkage Equilibrium Linkage disequilibrium Significantly differs from expected 1:1:1:1 ratio
- 6. Estimation of LD AB - 4/8 = 0.5 ab - 3/8 = 0.375 aB - 1/8 = 0.125 Frequencies Lewontin, 1964 D = PAB-PA.PB = 0.5-0.5*0.625 = 0.1875 Again if we calculate for “Ab” D = PAb -PA.Pb = 0.0-0.5*0.375 = -0.1875 D = PAB.Pab - PAb.PaB = 0.5*0.375 – 0*0.125 = 0.1875 Standardised estimates D’ and r2
- 7. • LD mapping detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. • Offers greater precision in QTL location than family-based linkage analysis • More efficient marker-assisted selection, facilitate gene discovery. • Does not require family or pedigree information , can be applied to a range of experimental and non experimental populations. • Care must be taken during analysis to control for the increased rate of false positive results arising. (Mackay and Powell, 2007)
- 9. Advantages of Natural population Any panmictic population. Samples from natural /breeding and synthetic population Random sample or core set of germplasm . Superior QTL from elite germplasm directly used for MAS.
- 10. NAM First developed in Maize, Common founder – B73. Higher power than AM panel, the controlled crosses for NAM minimize population structure and familial relatedness. Frequency of rare alleles increases. Uses both historical LD and recombinant LD. BC NAM & DH NAM – also developed.
- 11. MAGIC Population development includes many rounds of recombination . - QTL precision & Resolution Can be used directly or indirectly for varietal development. Common Wheat and Rice.
- 12. Approaches-GWAS
- 13. Population Structure Relatedness IBS (Identical By State)-Two individual carrying the same allele but not from common ancestry. IBD (Identical By Descend)- Two individual carrying the same allele and they have a common ancestry
- 14. Procedure