Genome-wide SNP Development and Validation for Intraspecific SNPs in Upland Cotton

SNP-based genetic analysis, manipulation and improvement of Upland cotton (Gossypium hirsutum) is limited by the lack of large numbers of SNPs. Streamlined large scale genomic analysis is presently limited by the modest numbers of intraspecific SNPs available. SNP development via NGS assemblies from normalized transcriptome was quite successful for wild species, but less so for intraspecific SNPs. Limited intraspecific polymorphism exists between lines and cultivars, and when combined with conservation of exon sequences, the yields of SNPs were relatively low and insufficient in number. In order to determine the applicability of current intraspecific SNPs, identified loci need to be screened against a large number of diverse undomesticated and improved lines. The KASPar assay of Kbiosciences was used to assess a large sample of Gossypium hirsutum lines.  Here we report on the results of screening existing intraspecific SNPs on a large population of upland cotton.