A Cotton SNP Chip Derived from International Consortium-Based Collaborations

Date: Monday, January 13, 2014
Room: Grand Exhibit Hall
Amanda M. Hulse-Kemp , Texas A&M University, College Station, TX
Cotton SNP Chip Consortium , TAMUS, UC Davis, CSIRO, CIRAD, CSIR-NBRI, USDA-ARS, CI
An international collaborative effort has led to development of a SNP Chip for Cotton (Gossypium hirsutum L.).  The Chip will use Illumina Infinium genotyping assays in a BeadArray Panel that allows genotyping of 90,000 attempted bead types.  Of these, 70,000 are comprised of public SNPs, i.e. “Base Content”, while the remaining 20,000 attempted bead types are available for “Add-On Content”, typically non-public applications.  The Consortium effort has included nearly all previously published SNPs, and some sets of SNP data sets now in-press.  All others have been deposited into NCBI's dbSNP.  As diversity is low among agronomically elite cottons, the overall pool of SNPs is necessarily large and the Base Content will primarily target intra-specific Gossypium hirsutum SNPs, which will strongly support global conventional breeding efforts.  The interspecific SNPs are designed primarily to target germplasm of G. barbadense, G. tomentosum, G. mustelinum, G. armourianum, and G. longicalyx, but some SNPs will be applicable to genomes of other species, e.g., A- or D-genome species.  The inter-specific targeted SNPs are all developed relative to G. hirsutum and primarily are devoted to the other 52-chromosome species. The inter-specific SNPs will greatly facilitate introgression breeding and various types of research involving the AD species, i.e., the "primary gene pool".  The SNP Chip is a resource that will be used globally by public and private breeders, geneticists, and other researchers to enhance cotton genetic analysis, breeding, genome sequence assembly and many other uses.