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.

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)

8. Mapping Populations

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