Agriculture Reference
In-Depth Information
marker density and lower genotyping costs. To
improve QTL analysis, map densities must be
adequate across the genome and the markers must
be rich in polymorphism, such as SSRs. Further,
the technical aspects of increased genotyping
throughput along with accurate, reliable allele
sizing for robust loci would greatly improve our
ability to make genetic maps and perform QTL
analysis. Capillary electrophoresis and microar-
ray-based genotyping are having a signifi cant
infl uence on genotyping and this will continue in
the future, enabling laboratories to share technical
information developed from a common genotyp-
ing platform.
Quantitative trait locus analysis itself is largely
a statistical exercise combining genotype and phe-
notype data and has seen less dramatic change
over time, but software applications continue to
be improved for wheat researchers. One can spec-
ulate that QTL analysis will play an important
role in future wheat genome analysis, since the
genome is large and whole-genome sequencing
for gene identifi cation is still immature. The trend
will continue for using QTLs as a starting point
to fi ne-map traits or genes of interest in wheat,
leading to gene cloning and perfect markers for
wheat breeders.
The development of association mapping strat-
egies is just beginning. Again, marker density
in specifi c chromosome regions is sometimes
suffi cient, but whole-genome analysis will likely
require 2,500-3,000 robust markers across the
genome. This is where SNPs or single-feature
polymorphism (microarray-based polymor-
phisms) can improve marker densities and facili-
tate association mapping.
Field performance and end-use quality testing
of wheat breeding materials will continue to be
the ultimate evaluation methods in the develop-
ment of new wheat cultivars. Nevertheless, the
use of molecular markers to test and select for
qualitative traits is an accepted practice among
wheat breeders. Thus, there is an ongoing need
to develop markers for important breeding traits,
both qualitative and quantitative. Marker devel-
opment and deployment will likely become
increasingly “a breeder responsibility,” moving
from the genetics laboratory to the screening lab
which will be part of the breeding program. It will
be imperative for future wheat breeders to be
well-versed in molecular approaches to wheat
cultivar development.
Fortunately, new advances in DNA technology
are facilitating marker development and deploy-
ment. Robotics-based liquid handling systems
and capillary electrophoresis technologies permit
high-throughput DNA extraction and marker
screening so that entire breeding populations can
be screened for the trait(s) of interest. As more
and more DNA markers are developed using the
same marker technologies (i.e., microsatellites),
multiplexing of markers for different genes of the
same trait or for multiple traits in the same screen
will be facilitated.
Cloning of candidate genes for the traits of
interest will continue to permit the development
of the “perfect markers,” which is required to
maximize the effectiveness and effi ciency of
marker-assisted breeding. The fi ne-mapping of
genes that control a signifi cant proportion of the
phenotypic variability of quantitatively inherited
traits has begun, and this effort will need to con-
tinue so that marker-assisted breeding can be
effectively applied to quantitatively inherited
traits.
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