Biomedical Engineering Reference
In-Depth Information
[
129
]. In cotton, markers are reportedly only being used for introgression of
existing GM insect and herbicide tolerance traits or novel sources of nematode
resistance and mostly in private companies. Recent advances in high-throughput
genotyping and high-throughput sequencing are shifting the pendulum back in
favor of using DNA markers in breeding. A number of the larger maize and soybean
breeding companies have already started down this route and have adopted a
nondestructive seed-based screening strategy to apply markers. “Seed chippers”
[
130
] help automate the process of removing a small portion of seed, extracting
DNA and running panels of SNP markers in a high-throughput manner. Cotton is
likely to be more difficult as the seeds contain secondary chemicals that inhibit
common molecular biology reactions. Seed-based screening will be essential in any
large-scale GS program as it would be impractical to plant extremely large
populations just to find the small numbers of plants to be kept that may contain
the required large number of favorable alleles. If the correct genotypes can be
identified from dried seed, then only small numbers of individuals would need to be
planted out for phenotypic evaluation.
The availability of the new SNP genotyping technologies should begin to
address the issues of the low numbers of markers and high costs associated with
MAS in cotton genetics and breeding. Public SNP discovery efforts in cotton are
well under way [
131
], and a public release of a high-density SNP chip was launched
at the end of 2013 by the Illumina Company. The availability of hundreds of
thousands of SNPs on these chip platforms should allow the use of association
mapping on big collections of genotypes or breeding lines representing a broad
genetic base to discover trait-marker associations quicker and at much higher
resolution than has been possible in traditional biparental populations and SSR
markers. The rapid and widespread adoption of GM traits for insect and herbicide
tolerance in cotton has, out of necessity, begun to change breeder attitudes about the
value and the practicability of DNA markers as plant breeding tools. GM insect and
herbicide traits are mostly single traits that need to be combined in various
combinations depending on market demands. Each trait segregates independently,
but must be stacked together in the best available genetic backgrounds. They are
generally first introduced in poorly adapted backgrounds that must be backcrossed
into elite material suited to each region where they are to be deployed, or even later
when they are already in elite material, they must be continually reincorporated into
any new conventional germplasm as it is developed. A new cultivar with better fiber
quality or disease tolerance, for example, is not going to achieve widespread
adoption unless it also incorporates the current advantages of existing GM cultivars
on the market. DNA diagnostic markers (both trait-specific and event-specific) have
been developed for all released GM traits because of their utility in breeding and as
a regulatory requirement for being able to detect any traits that might contaminate
non-GM cotton seed or products (reviewed in [
132
]). These diagnostics are in
essence a “perfect marker” for the genomic region containing the GM trait and
are treated just like a marker would for a QTL. Breeding GM traits are similar in
many ways to breeding with a small number of QTLs using MAS or marker-
assisted backcrossing (MABC). If DNA has already been prepared to screen
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