association mapping

1. Association Mapping
PLINK Software

2. Association Mapping
“Association analysis, also known as LD mapping or
association mapping, is a population-based survey used to
identify trait-marker relationships based on linkage
disequilibrium”
(Flint-Garcia et al. 2003)

3. Linkage Disequilibrium
• nonrandom association of alleles at different loci.
• LD can occur between more distant sites or sites located in
different chromosomes
• LD was firstly described by Jennings in 1917
• Quantification of LD developed by Lewtonin in 1964
• AM is actually an application of LD

4. Pros
• AM offers three main advantages over linkage mapping:
– Mapping resolution, allele number and time saving in
establishing a marker-trait association and its application
in a breeding program (Flint-Garcia et al., 2003).
• availability of broader genetic variations with wider
background for marker-trait correlations
• no need for the development of expensive and tedious
biparental populations

5. Cons
 Complicated or unknown patterns of LD
 The complexity and mode of gene action of the trait of
interest.
 sample size and experimental design.
 Rare alleles cannot be detected with good confidence, unless
the effect is very large.