Agriculture Reference
In-Depth Information
resistance to drought or salt stress and to N deficiency; or resistance to disease
caused by a host of prokaryotic and eukaryotic pathogens, from microbes to insects
and nematodes.
Candidate Gene Association and Genome-Wide Association
Studies
An explanation of how association mapping refers to the analysis of statistical
association between genotypes (usually individual SNPs or SNP haplotypes, deter-
mined in a collection of individuals), and the phenotypes (traits) of the same
individuals is undertaken here. Until recently, genetic mapping was usually done
in purpose-created populations, such as progeny of parents chosen on the basis of
the difference between them for the trait(s) of interest, or in defined pedigrees
(families) (Rafalski
2010
). By contrast, genetic association mapping involves using
a collection of individuals, such as those derived from wild populations, germplasm
collections or subsets of breeding germplasm. Consequently, at each locus several
alleles may be simultaneously evaluated for association in a diverse population,
while only two alleles segregate in any biparental population. Two association
mapping methodologies are in use: Candidate Gene Association and Whole
Genome Scan, also called Genome-Wide Association Study. In the candidate
gene approach, the hypothesis that there is a correlation between DNA polymor-
phisms in gene A and the trait of interest is tested. For example, it is possible to test
if in a diverse germplasm collection there is a correlation between DNA sequence
alleles of phytoene synthase (or any other gene involved in carotenoid biosynthesis)
and carotenoid content of seeds (Palaisa et al.
2003
; Pozniak et al.
2007
). This
approach assumes good understanding of the biochemistry and genetics of the trait,
but many genes may escape attention. Therefore, in the absence of detailed knowl-
edge of the biochemical pathway of interest, including regulatory genes, whole
genome scan (described below) is a better choice (Rafalski
2010
). Genome scan
involves testing most of the segments of the genome for association by genotyping
densely distributed genetic marker loci over all chromosomes. The simple hypoth-
esis that one of the genetic loci being considered is either causal for the trait or in
linkage disequilibrium (LD, defined as association between genetic loci) with the
causal locus is under consideration. The choice of population for association
mapping, and of the appropriate marker density, are crucial decisions. One of the
sources of false positives in association mapping is population structure. Complex
population structure could be expected in crop species that were subject to a severe
domestication bottlenecks followed by breeders
selection. Pronounced differences
in the germplasm used in different regions of the world and maturity-related sets of
allele frequencies for many genes may also be expected. Examples include the
division of maize germplasm into heterotic groups (Reif et al.
2005
) and a severe
post-domestication bottleneck associated with adoption of soybean in North
'
