Agriculture Reference
In-Depth Information
high-density haplotype map of the NAM parental lines has been pub-
lished recently and these data make mapping new traits possible in this
population. NAM is an interesting approach that combines efforts to
obtain high-resolution genetic mapping with the capture of wide diver-
sity and detection of epistatic interactions (Beló and Luck 2010; Rafalski
2010). This approach of joint linkage
LD mapping can be an alternative
approach to overcome some of the inherent limitations of both linkage
and LD methods (Lu et al. 2010).
MAGIC is a different population type in which an intercrossed map-
ping population is created from multiple founder lines, typically in a
self-pollinating species, such as wheat, using eight genotypes combined
in double-cross hybrids that are crossed with each other. The resulting
hybrid is then selfed using single-seed descent until recombinant inbred
lines are developed (Cavanagh et al. 2008). As with NAM, the diversity
involved in the different crosses for MAGIC populations enhances
mapping resolution. This type of population is currently in construction
for a range of plants and established for
Arabidopsis
(Kover et al. 2009)
and wheat (Huang et al. 2012).
The principal aim of these alternative or complementary methods of
association genetics is to improve precision with which QTL can be
mapped. It is important to consider that these are alternatives that are
valid for crops that do not suffer from inbreeding depression. But if the
crop suffers from inbreeding depression, it is better to stay with AM or
combinations of simple crosses and associations. Finally, less-well
constructed or more poorly characterized populations from a typical
breeding program can also be used for a new type of AM that is reiterative
and model based, namely genomic selection (GS) or genome-wide
selection (GWS). This will be the topic of the next section because of
its potential in crop breeding.
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VII. GENOME-WIDE SELECTION AND GENOMIC SELECTION
Most breeding programs are based on elite germplasm that is recom-
bined carefully with the hope of incremental improvements in yield and
other traits. Most breeding programs do not use the landraces favored for
AM studies, the biparental and unselected inbred lines of RIL popula-
tions, or the
finely structured populations favored for NAM and MAGIC
studies. Plant breeders are generally conservative in their use of exotic
germplasm, while geneticists relish the attempt to dissect such genetic
stocks. Therefore, plant breeders often feel that there is a dichotomy
between genetic studies (i.e., association genetics) and
“
real breeding.
”
