Agriculture Reference
In-Depth Information
Sample
Phenotyping
Genotyping
Population
structure
LD
decay
Association
assessment
Fig. 2.2.
A
flow-through chart for association mapping considering population structure.
observe in a study population the better the resolution we will have in
our study. The population should be diverse but not compartmentalized
or highly structured. In some cases, we can choose related species, but
most studies are conducted with individuals of the same species.
Genotypes should have different evolutionary histories, different geo-
graphical origins, and be phenotypically diverse. The use of a collection
of individuals, such as those derived from wild populations, germplasm
collections, or subsets of breeding germplasm, will ensure the simulta-
neous evaluation of several alleles at each locus (Rafalski 2010).
Zhu et al. (2008) identi
five types of plant populations that are
common and could be useful for AM: (i) a sample with subtle population
structure and family relatedness (ideal), (ii) multifamily sample,
(iii) sample with population structure, (iv) sample with population
structure and family relationships, and (v) sample with severe popula-
tion structure and family relationships (nonideal). Many of the popula-
tions in plant species will be of the fourth type where population or
family structure must be corrected for (Zhu et al. 2008). Since mapping
resolution is a function of LD decay, it is crucial that researchers choose a
diverse set of germplasm that exploits the recombination events that
have occurred in the history of the species of interest (Myles et al. 2009).
ed
B. Population Genotyping
Two genotyping methods, candidate gene analysis and genome-wide
analysis scans (GWAS), or a combination of both, can be used for AM
studies. The selection of an approach determines the amount of markers
