Detection of Large-Scale Single Nucleotide Polymorphisms (SNP) Using Genotyping-by-Sequencing in Upland Cotton (Gossypium hirsutum L.)

Polyploidy combined with narrow genetic base with a very little sequence divergence between At and Dt sub-genome have hindered the identification of polymorphic genetic markers and their utilization in improving this important crop. Genotyping by sequencing (GBS) has been proven to identify single nucleotide polymorphism (SNP) markers effectively and rapidly. A study was conducted to discover a large set of polymorphic SNPs with broad applicability to the cultivated cotton germplasm using 11 diverse cultivars and their random-mated recombinant inbred progeny via GBS. Two different GBS methodologies were used by Data2Bio, LLC, and the Institute for Genome Diversity, at Cornell University, to identify 4441 and 1176 polymorphic SNPs with minor allele frequency of ≥0.1, respectively. We further filtered the SNPs and aligned their sequences to the diploid Gossypium raimondii reference genome. We were able to use homeologous SNPs to assign 1071 SNP loci to the At sub-genome and 1223 to the Dt sub-genome. These filtered SNPs were located in genic regions about twice as frequently as expected by chance. We tested 111 of the SNPs in 154 diverse Upland cotton lines which confirmed the utility of the SNP markers developed in such approach. Not only were the SNPs identified in the 11 cultivars present in the 154 cotton lines, no two cultivars had identical SNP genotypes. We conclude that GBS can be easily used to discover SNPs in Upland cotton which can be converted to functional genotypic assays for use in breeding and genetic studies.