A Cluster File for Automated Genotyping of Cottons Containing Germplasm from Gossypium Diploid Species on the CottonSNP63K

Diploid cotton species are a recognized source of novel genes and traits with potential agronomic benefits. Molecular marker technologies play increasingly significant roles in facilitating and expediting the transfer of germplasm, genes, and traits through introgression. SNP arrays based on Illumina Infinium assays are a go-to tool for quick-turnaround genotyping. However, the speed and ease of use depends on “cluster files” that statistically describe the “behavior” of each SNP across relevant germplasm, and thereby enable automated computer-based genotype calling. The CottonSNP63K Chip released in early 2014 includes 63K potential SNP assays relative to Upland cotton, Gossypium hirsutum (L.). A cluster file was developed to enable automated genotype calling of intraspecific and interspecific germplasm involving natural “tetraploid” AD-genome species (2n=52). Not surprisingly, genetic types containing germplasm from diploid species proved to be recalcitrant to automatic genotype calls using the aforementioned cluster. We report here progress toward a cluster file for populations of introgression lines containing A2 and D1 Gossypium diploid species germplasm; it also has potential applicability to other diploid genomes. Using GenomeStudio^TM and the previously developed AD-genome cluster file, we examined each SNP across the diploid-based sample population; for any SNP that exhibited an atypical graphical distribution, we manually adjusted the software cluster definitions. The resulting cluster file can be used to report putative genotypes and segregation ratios specific for populations that are derived in introgression studies involving these diploids and perhaps others. It will expedite and facilitate marker assisted analysis and selection of diploid-derived traits.