ARS | Publication request: Collaborative development of SNPs for cotton research, introgression, MAS and breeding

Submitted to: National Cotton Council Beltwide Cotton Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 6, 2012
Publication Date: N/A

Technical Abstract: Extensive use of genome-wide analyses requires that molecular markers be highly abundant, informative and, once developed, extremely cost-effective to use, such as single-nucleotide polymorphisms (SNPs). The efforts toward development of cotton SNPs have been few and small-scale. The novel cotton fiber ESTs from a few Gossypium species were developed from normalized non-clonal cDNA libraries. They were deep-sequenced by the best high-throughput sequencing technology, 454 and Illumina. The protocols and parameters were established to identify 10,000s of putative SNP markers relative to Upland cotton, for inter-cultivar SNPs, as well as interspecific SNPs relative to another tetraploid species, G. barbadense, and a diploid species G. longicalyx. The Kaspar Assay from Kbiosciences was used to assess putative SNPs by screening TM-1, 3-79, F1 euploid and hypoaneuploid cytogenetic stocks, radiation hybrids and certain 2x and 4x wild species. As part of the informatic pipeline development, more than 1,253 SNPs were tested. Putative SNPs (G. hirsutum vs. G. barbadense) are currently being validated by linkage mapping. To contend with the extreme complexity of the cotton genome, which exhibits diploid, tetraploid and even octaploid-like features, we are using cytogenetic stocks, linkage mapping and radiation hybrid mapping as independent assessments of structure. SNP maps will be used to associate valuable complex traits, such as fiber characteristics, disease resistance, improved yield potential and stress tolerance, with specific markers and render them amenable to marker-assisted selection (MAS). We solicit other researchers and breeders to inquire about screening SNPs against their parents and population samples for possible deployment in association and MAS.