All_SNPs.vcf

Salinity is a major abiotic constraint for rice farming. Although rice is sensitive to salt stress, tremendous natural variability in world germplasm provides opportunity for both basic and applied research to improve its adaptation under saline environment. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt susceptible (Bengal, Cocodrie, and IR64) rice genotypes were analyzed to provide genetic insights into salt tolerance mechanisms through discovery of DNA polymorphisms and their consequences. The frequency and density of SNPs and InDels was highest in pairs involving Bengal followed by Cocodrie and IR64. Analysis of DNA polymorphisms between salt tolerant and salt susceptible genotypes revealed 2347 nonsynonymous SNPs and 51 frameshift mutations. The integrated analysis of genome-wide polymorphism data with QTL mapping and expression profiling resulted in identification of 396 and 573 differentially expressed genes with large effect variants, which were involved in ion transport, oxidative stress tolerance, signal transduction, stress response, and transcriptional regulation. Overall, the complexity in salt tolerance was clearly apparent due to involvement of genes associated with multiple salt tolerance mechanisms. This study, however, provided a useful genomic resource on salt stress related genes and their variants to design salt tolerant rice varieties.