Gene associated SNP discovery in fine quality Indian Gossypium barbadense cotton through whole genome resequencing

The present study deals with the resequencing of cultivars, Suvin and BCS-23-18-7 belonging to Gossypium barbadense which are distinctly differing in fiber qualities and seed cotton yield using Illumina Hiseq2500 sequencer. A total of 2,604,107 single nucleotide polymorphism (SNP) and 592,364 insertion and deletions (INDELs) were identified when compared with G. barbadense reference genome. Among the 14,075 preferentially expressed genes of agronomically important traits of cotton, we have identified 33,637 markers in the genic regions. Comparing between the variants of Suvin and BCS-23-18-7, among the 4,929 preferentially expressed genes in fiber, only 1,128 genes have 2,453 variants and of these 1,512 variants are non-synonymous types, leading to change at the protein level. In order to validate the presence of these markers in the expressed genes could tag the expression and/or phenotypic variation bought by alleles of Suvin/BCS-23-18-7, among 51 fiber elongation genes, ten genes that had high effect SNPs were utilized for real-time PCR, which showed an extended period of expression up to 15 days post-anthesis (DPA) in Suvin. Hence, utilization of such markers for the construction of SNP array / linkage maps would provide greater value to quantitative trait loci (QTL) mapping instead of random genomic markers.