Agriculture Reference
In-Depth Information
still distant, the ultimate objective of this research includes the full
description of the susceptibility architecture of major biomedical traits
and translation of the
findings into clinical practice.
The use of association genetics in plants started about 10 years ago,
with a recent increase in the amount of research funding dedicated to
this approach (Xu and Crouch 2008). Previously, most trait analyses
were done exclusively by linkage mapping, with thousands of articles of
this nature published in many different journals and species. Interest in
the dissection of quantitative traits has characterized studies in plants
and especially crop species. QTL are those loci that control or are part of
the control of complex traits like yield. Efforts have been made to
improve the amount and quality of information to locate QTL and
here is where association genetics can sometimes improve the resolution
and the number of alleles and loci associated with agronomic traits as
compared with mapping assays. The development of large numbers of
molecular markers and the decrease in their cost has made association
genetics a good methodology for analyzing QTL, especially for unknown
regions of the genome.
There are two kinds of AM approaches: one is the GWA approach and
an alternative is the candidate gene (CG) approach. The
first one requires
a large amount of well-distributed molecular markers; while the second
requires a detailed genetic and biochemical understanding of the trait.
Therefore, GWA is usually applied to more complex traits such as seed
size or host plant resistance and CG analysis to simpler traits of known
biochemical pathways such as oil content or vitamin accumulation.
GWA can also be applied to various complex breeding populations, such
as those derived from recurrent selection, long-term pedigrees, or mul-
tiple crosses
—
a theme to which we will return to at the end of this
chapter.
A. Principles of Association Genetics and Association Mapping
Association genetics or AM is based on linkage disequilibrium LD map-
ping. This term refers to the analysis of statistical association between
genotypic marker alleles (molecular markers of different types, including
single-nucleotide polymorphism (SNP) haplotypes) determined in a
group of materials or individuals and the phenotype under study for
the same individuals (Rafalski 2010). It detects and locates QTL based on
the signi
cance of the association between mapped genetic markers and
traits (Mackay and Powell 2006). The basis of this type of study is LD that
exploits the phenotypic and genetic variation present across a population
