Identification of SNP-Allelic Polymorphism Based Changes in Two Salt Responsive Proteins, Na+ H+ ANTIPORTER 4 and GLUTAREDOXIN 24 Between Two Rice Varieties

Abstract

Rice is identified as a salinity vulnerable crop. To avoid the salinity stress problem, advanced steps have been taken, including developing novel plant sources with genetic variation associated with stress tolerance. Therefore, developing salt-tolerant varieties by combining different salt-tolerant mechanisms is a long-term solution to withstand salinity stress. Subsequently, single nucleotide polymorphisms (SNPs) are largely utilized in crop improvement including rice. This study was focused on analyzing the SNP variations discovered in two key salt responsive genes: Na+ H+ antiporter 4 (OsNHX4) and Glutaredoxin 24 (OsGRX24). The OsNHX4 and OsGRX24 gene sequences of At354 and Bg352 were retrieved from the Next Generation Sequencing derived whole genomes of two rice varieties. The gene sequences were aligned along with the Nipponbare reference gene sequences and the SNP variants present in the coding regions were identified. The amino acid sequences of each gene were obtained and their physiochemical parameters and protein structures were predicted. Results showed that OsNHX4 had 4 and 9 SNPs in At354 and Bg352 while OsGRX24 had 3 and 5 SNPs in At354 and Bg352 respectively. The secondary protein structure of OsNHX4 in Bg352 was modified due to an amino acid residue substitution, causing an alpha-helix to beta-sheet transition. In OsGRX24 of Bg352, two different alpha-helix regions were affected due to amino acid substitutions. Consequently, it could be speculated that these amino acid differences between the two varieties might be one of the causal factors for their phenotypic differences in salinity responsiveness.