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Genome-wide identification of DNA polymorphism in salt-tolerant and sensitive rice genotypes using double digest RADseq


 Salt-tolerant rice varietal development is necessary and the best approach to enhance crop productivity in areas with high salinity. To identify the genetic variation in stress-related genes in salt-tolerant genotypes, we carried out genotyping by sequencing (GBS) of seven rice lines with contrasting responses to salinity stress, including FL478 as a tolerant variety and IR64 as a sensitive check. The GBS reduces genomic complexity and enables us to obtain many SNP markers in the genome. A total of 7,980,092 high-quality single-end reads of 94 bp each were generated, and approximately 83% of the reads mapped to the rice reference genome (Nipponbare). We identified a total of 80,159 SNPs and 6,403 InDels among the seven rice genotypes. Forty-two percent of these SNPs were identified from the genic regions, and further, 27% were observed in the coding areas out of these genic SNPs. We used bioinformatics analysis to identify functional SNPs in the genes that changed the functions of proteins. We found variations between tolerant and sensitive genotypes by comparing the identified SNPs in coding regions. We found that 566 of the SNPs identified in the coding regions were non-synonymous (nsSNPs), affecting proteins. We identified 116 abiotic stress-related genes that contained 138 nsSNPs (between FL478 and IR64) in coding regions, thus directly affecting the proteins. Analysis indicated that these genes might contribute to the salt stress phenotype in rice varieties and the identified nsSNP markers that were useful to distinguish tolerant and sensitive genotypes. Our results revealed that the identified SNPs could be used as an essential source of genomic variability for improving and developing saline tolerant genotypes.