Results of the CottonSNP63K Array and Future Directions

The Cotton SNP Chip Consortium organized the development of an Infinium Array that was released February 2014.  Drawing from lists of prospective SNPs from research teams in 5 continents, but primarily TAMUS, UC Davis, and CSIRO, 70,000 putative SNPs were chosen for the Array largely on the basis of prior evidence of convertibility to experimental assays and Infinium design scores.  Contributions from diverse sources also provided the samples used for cluster file development, mapping and diversity analysis represented much of the global G. hirsutum germplasm; they also included representatives of several other species.  The CottonSNP63K array includes ~63,000 1-bead SNP assays, and will be a resource that will be used globally by public and private breeders, geneticists, and other researchers to enhance cotton genetic analysis, breeding, genome sequence assembly and many other uses. To assist the cotton community, a cluster file has been developed for the 45,104 intra-specific SNPs and the 17,954 inter-specific SNPs included in the fixed content of the array which will allow for automated genotyping. Two high-density genetic maps for one intra-specific and one inter-specific F2 mapping population have been generated containing a total of 22,829 SNPs. Here we report on the findings using the developed cluster file including high-density linkage maps and utilization possibilities for future analyses.