Biomedical Engineering Reference
In-Depth Information
polymorphism within this species, but the advent of better genome sequence data
has helped with the discovery of an abundance of SNP markers between cultivars.
This has cleared the way for more in-depth analysis of commercially important
agronomic traits within breeding populations.
Once SNPs are discovered, various technologies are available for large-scale
genotyping each depending on the number of SNPs needing testing and the number
of DNA samples to be assayed, as well as the budget of the program. These include
the Fluidigm, KASPar, GoldenGate, and Infinium systems [
123
]. The use of SNPs
in breeding and research will be supplanted by NGS technologies over the coming
decade. As the cost of this type of short read, high coverage analysis becomes
cheaper and the depth of sequencing increases, it will become possible to pool more
samples in a single run and analyze many individual plants. Combined with some
genome complexity reduction techniques such as restriction site-associated
sequencing (RAD-Seq) or genotype-by-sequencing (GBS) [
124
] to simplify SNP
discovery, it will be possible to discover SNPs “on the run” in the populations or
collections being studied [
123
] and without a reference genome sequence.
Bioinformatic challenges can be high, particularly in polyploid species, but they
are not insurmountable. GBS will democratize the application of genome-wide
analysis methods into non-model plants and, by simplifying SNP discovery, will
move cotton breeders toward using genomic selection (GS) techniques in their
breeding. GS is a form of MAS [
125
] that selects for the best individuals based on
genomic estimated breeding values determined from marker-trait associations.
They are derived from a training subpopulation and then applied to predict the
phenotypes of the breeding population based on their individual genotypes, but
require the assessment of large numbers of markers. Such GS strategies have been
successfully used in animals and should have value in plant breeding programs such
as cotton as the methodologies are refined and applied to our crop plants.
Integration of Biotechnology and Conventional Breeding
The increasing knowledge about the cotton genome at the structural, gene expres-
sion, and epigenetic levels, as well as the collation of the QTLs linked with fiber
quality, are contributing to fledgling “breeding by design” programs for cotton fiber
improvement based on existing SSR and some SNP markers [
126
-
128
]. Their
exploitation is still not yet widespread in mainstream commercial breeding pro-
grams and certainly not among public cotton breeders. To be successfully inte-
grated in breeding programs, there needs to be both a step change in the reliability
and relevance of particular trait-marker associations and a willingness to adopt
marker systems by breeders. This will only be achieved when there are closer ties
between the people carrying out genetic studies and the breeders who will be
applying them.
MAS in many crop species has only been used in a small number of situations
where traits are determined by a relatively few major genes and have a high value
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