Agriculture Reference
In-Depth Information
dicotyledenous crops, the number of markers used in the cotton study
was a limitation based only on a few hundred SSRmarkers. Likewise, the
AM study by Simko et al. (2009) was limited in SNPmarkers available for
lettuce evaluations. In canola, mapped AFLP markers have been used to
increase genome coverage for the identi
cation of associations with
quality traits (Honsdorf et al. 2010).
Many more markers have been developed in model species such as
Arabidopsis
. In one recent GWA study with
Arabidopsis
, up to 107
phenotypes were analyzed (Atwell et al. 2010). In interspeci
c crosses,
Zhang et al. (2011) used gene expression levels in the heterogeneous F
1
population to identify trait
gene associations for 59 phenotypes. The
new approach of creating a MAGIC population for GWA has also been
applied to
Arabidopsis
using 19 founder genotypes and 1,260 SNP
markers (Kover et al. 2009). Speci
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c traits of interest in CG studies of
this species have been the genetic architecture of shoot branching, where
36 loci were evaluated in a panel of 96 accessions and compared with
QTL analysis, where epistatic interactions were suggestions to interfere
with the detection of trait
gene associations (Ehrenreich et al. 2007).
Glucosinolate secondary metabolites were the subject of an extensive
GWA study by Chan et al. (2010). Other species of dicotyledenous
plants, even those with recent genome sequencing, still have a limitation
in the number and availability of molecular markers needed for AM.
Overall, the association studies in dicotyledenous plants have used
notably fewer markers than those studies in the cereals due to technol-
ogy gap between these two clades. One exception was the use of 677 SNP
markers in an association study for sugar beet (Würschum et al. 2011).
However, sugar beet is an industrial dicot crop that has received more
private investment than many other dicot crops. The concept of an
orphan crop may no longer be truly applicable to most well-known
species but the funding needed for AM studies has often been unattain-
able for more minor crops or ones that, despite their worldwide impor-
tance, have a much smaller research community. The new approach of
creating NAM or MAGIC populations for dicotyledenous crops other
than
Arabidopsis
is just the beginning.
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V. SOFTWARE FOR DATA ANALYSIS
A. Population Structure Determination
There are several computer programs developed for population structure
determination. These software programswere developed to determine the
