An Overview of Diversity in US and Global Cotton Using the CottonSNP63K Array.

A CottonSNP63K array and accompanying 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 allows for automated genotyping of cotton (Gossypium spp.) samples.  Development of the cluster file included genotyping of 1,156 samples, a subset of which were inbred lines of cultivated varieties and wild accessions.  Our diversity study was based on 402 Gossypium samples genotyped with the CottonSNP63K array.  Over half (38,822) of the SNPs were polymorphic in this dataset.  The SNPs separated G. hirsutum samples from other tetraploids and diploids, and distinguished between wild and improved types within G. hirsutum. Here we report the first diversity analysis with large numbers of SNP markers over a wide range of cotton germplasm, particularly within cultivated G. hirsutum. The polymorphism profiles and distribution results have significant implications for breeding and utilizing the CottonSNP63K array in the US and worldwide.