Measuring Diversity in Gossypium hirsutum Using the CottonSNP63K Array

A CottonSNP63K array and accompanying cluster file has been developed and includes 45,104 intra-specific SNPs and 17,954 inter-specific SNPs for automated genotyping of cotton (Gossypium spp.) samples.  Development of the cluster file included genotyping of 1,156 samples, a subset of which were identified as improved or wild G. hirsutum.  In our diversity study of 402 Gossypium samples genotyped with the CottonSNP63K array, over half (38,822) of the SNPs were polymorphic.  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 improved cultivars of G. hirsutum.  The polymorphism profiles and distribution results have significant implications for breeding and utilizing the CottonSNP63K array in the US and worldwide.