Towards a Cluster File for Automated Genotyping of Germplasm Introgressed from Gossypium Diploids

A Cotton SNP Chip based on Illumina Infinium assays was released in early 2014, and includes both intra-specific (50,000) and interspecific (20,000) potential SNP assays relative to Upland cotton, Gossypium hirsutum (L.). Some of the interspecific SNPs targeted diploid relatives of the secondary gene pool.  We will report on the development of a customized cluster file for Gossypium diploid genomes. While a cluster file has been developed by the Cotton SNP Chip Consortium for tetraploids, samples from diploids and involving diploid germplasm behave distinctly different and require a different cluster file.  Using the GenomeStudio software by Illumina, we screened the SNPs and manually adjusted for any anomalous graphical results. Distributions and ratios for specific families and populations can be used to guide further classification refinements.  The file will also denote markers whose behavior does not conform to the norms specific to diploids. Once completed, the cluster file can be used to report putative genotypes and segregation ratios specific for diploids.