SNP Genotyping Using Kaspar Assays for Screening Upland Cotton Populations Containing Germplasm Introgressed from Gossypium Diploid Species

Introgression studies require screening of larger number of individuals over several generations because of progressive decrease in the proportion of individuals carrying the desirable alien segments within the backcross progeny. Historically, introgression projects were time- consuming. Now, they can be accelerated by use of marker-assisted selection to target and retain specific alien chromosome segments during backcross breeding. This can be used to assure more comprehensive representation of desired segments or genomes in the advanced backcross generations. Marker-assisted selection in any backcross population requires markers that can be economically and accurately genotyped for large populations. We report the results of a SNP validation study through KASP assays performed for a sample set of SNP markers which were shown to be polymorphic by the CottonSNP63K Illumina SNP chip in the BC1F1 population developed in an introgression study with the A2D1 wild synthetic tetraploid. The SNP markers were selected based on their position determined by the high-density intraspecific and interspecific maps published in 2015. Once validated, this cluster file will facilitate utilization of the CottonSNP63K SNP array for high-density SNP genotyping, and subsequently for development of ad hoc simplex and lower-plex SNP assays that can be applied to large populations for marker-assisted introgression, selection and down-stream breeding.