Agriculture Reference
In-Depth Information
for association. For candidate gene association analyses, markers should
be chosen based on their location in the genome based on previous QTL
studies or on the function of the genes involved in either biochemical or
regulatory pathways that lead to
final trait variation. This methodology
implies good understanding of the biochemistry and genetics of the trait,
with the risk that many genes can be inadvertently left out of the analysis
due to lack of knowledge or inappropriate hypotheses. Given low
variability in many crop genomes, a haplotype sequencing approach
in blocks in and around the candidate gene is needed.
Meanwhile, GWA involves testing for association using markers that
represent most of the segments of the genome. This requires genotyping
the population individuals with densely distributed genetic marker loci
covering all of the chromosomes (Rafalski 2010). The selection of
markers is important for both methodologies. The growing
of
high-throughput SNP markers has helped to make association genetics
and especially GWA analysis possible. The availability of markers and
the low costs of high-throughput molecular markers or next-generation
sequencing are the keys to realizing the potential of association genetics
in crops.
Next-generation sequencing methods provide an extraordinary gen-
otyping capacity for model and nonmodel organism provided there is a
reference genome sequence for the species. This technology produces
read lengths from 72 to 400 bp based on sequencing of single DNA
molecules. Complete or draft genome sequences are now available for a
large number of plant species, such as apple,
Arabidopsis
,banana,
barley, cacao, grape, maize,
Medicago
, poplar tree, potato, rice, straw-
berry, soybean, sorghum, watermelon, and wheat (Brunner et al. 2004;
Schnable et al. 2009; Ingvarsson and Street 2010; Schmutz et al.
2010; Velasco et al. 2010; Argout et al. 2011; PGSC 2011; Shulaev
et al. 2011; Brenchley et al. 2012; D
“
boom
”
'
Hont et al. 2012; IBGSC 2012; Guo
et al. 2013).
Although various sorts of markers such as ampli
ed fragment length
polymorphism (AFLP), cleaved ampli
ed polymorphisms CAPS, diver-
sity array technology (DArT), restriction fragment length polymorphism
(RFLP), and simple sequence repeats (SSR) can be used in association
studies, some sort of SNP marker genotyping is generally needed for
GWA analyses. SNP markers are favored given the accuracy and random
distribution of this type of marker. SNP identi
cation can be done in a
small group of individuals, with the selected SNPs having a high
minimum allele frequency than scored in a greater number of genotypes
from the species. This reduces the randomness and monomorphism of
some SNP markers that are simply left out of the analysis. Yet, this
