Cotton breeding researchers take giant leap
This need for high-throughput marker-based capabilities in cotton motivated these researchers to establish large-scale cotton SNP development efforts, he said. They formed a consortium to develop a "cotton SNP chip" for global use by breeders, geneticists and other researchers to enhance cotton.
Internationally, the group was joined by the Commonwealth Scientific and Industrial Research Organization in Australia, the Centre for International Cooperation in Agronomic Research for Development in France, the Council of Scientific and Industrial Research Organization-National Botanical Research Institute in India. Dow AgroSciences is participating as a commercial contributor.
"The launch of the chip marks an important step forward for cotton," Stelly said. "This signals the capturing of genomic technology and our ability to put it into a platform that researchers can use to breed better cotton."
After many years of work, the international cotton community has identified large numbers of SNPs and chosen 70,000 public SNPs as "base content" to be included in every cotton SNP chip, with fully disclosed DNA sequences, he said. In addition, each chip will have capacity for "add-on content" for another 20,000 non-public SNPs, as might be desired by private industry.
Stelly said AgriLife Research worked especially close with University of California, Davis, to develop many of the SNPs in the chip.
"It was great teamwork, our lab working with that of Dr. Allen Van Deynze and his post-doctoral researcher, Dr. Hamid Ashrafi, at UC Davis. There was a lot of cross-talk in all aspects—for years," he said.
Stelly said the Texas A&M group led in development of the inter-specific SNPs, which differentiate between cultivated cottons and closely related species, and Allen's lab was the lead in developing intra-specific SNPs, which differentiate among cultivars and lines of cultivated cotton.
He explained the SNPs are basically a tool "to find your way around the genome. Breeders can use sets of these markers as tools for determining where traits of economic interest are located." For instance, a breeder trying to incorporate longer fiber length will use SNPs to do indirect selection for that trait, knowing specific SNPs are close to specific genes at different genome locations in different varieties.
"We aim to enable SNP applications that help create superior genetic combinations and foster greater and faster success by breeding programs," Stelly said. "Some of the most immediate applications will be for simply inherited traits for which plant-screening experiments are inaccurate and/or expensive, such as nematode resistance."
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