Genome-Wide Spaced Simplex SNP Assays for Marker-Based Interspecific Germplasm Introgression and Genetic Manipulation in Cotton

Cotton is produced coast-to-coast across the United States and contributes significantly to its economy. In this presentation will discuss the development of a new resource for the cotton community, a genome-wide set of validated PCR-based SNP assays that target approximately evenly spaced regions of the genome and can distinguish upland cotton, G. hirsutum, from other tetraploid cotton species (Gossypium mustelinum, Gossypium tomentosum, Gossypium barbadense and their corresponding F1s). These SNP assays can be used individually or in low-plex combinations, and will be useful for diverse breeding and genetic research applications, e.g., backcross breeding, transmission analysis, recovery of segregates in heterozygous or hemizygous states, recombination research. Most of the SNPs are from SNPs on the CottonSNP63K array, and thus most SNP markers can be related to high-density linkage maps, QTLs and genome assemblies, too. Thus, the new assays will facilitate marker-assisted selection utilizing SNPs is one way in which beneficial genes for yield, pest resistance, and drought tolerance can be efficiently recognized and bred in to elite commercial cultivars from non-commercial species.