In Silico Identification of Abiotic Stress-Responsive Candidate Genes in Rice and Their Allelic Differences Between At 354 and Bg 352

Abstract

Rice (Oryza sativa L) feeds more than half of the world’s population. One of the main elements that harm yield globally is abiotic stress. Therefore, it is important to develop abiotic stress tolerant rice varieties in order to increase rice productivity and to extend the cultivation. The lack of knowledge of the genetic mechanisms underlying abiotic stress tolerance is the primary issue with the traditional breeding technique. Hence, studying genes responsible for abiotic stress mechanisms is important to accelerate breeding by molecular marker - based detection techniques. Aiming at finding the candidate genes for abiotic stress tolerance ,two rice genome sequences of At 354 and Bg 352 varieties given by National Research Council, Sri Lanka -16 -16 project were analyzed. At 354 has some abiotic stress tolerance (salt) traits and Bg 352 has some susceptible traits. Next-generation sequencing-derived genome sequences were used to identify SNPs and Indels in the At 354 and Bg 352 varieties with reference to Oryza sativa japonica group cultivar Nipponbare. The STRING Database was used to extract the most correlated genes with abiotic stress. The allelic differences among Nipponbare, At 354 and Bg 352 sequences were detected from Multiple Sequence Alignment by using the Rice Annotation Project database, UGENE software and MEGA 11 software. The mutations of the genes were validated if they were present in another germplasm in the NCBI database. Altogether 100 genes were used to examine, and 166 mutations were observed including 163 SNPs and 3 Indels while 09 genes were validated due to their presence in other rice accessions. The amino acid sequences of the validated sequences were determined by Expasy Translate tool. The Swiss model database and ProtParam tool were used to predict the protein structures and their parameters, which showed some structural differences among tested alleles. These mutant alleles further need to be assessed against abiotic stress and varietal turnover in order to use them in rice improving breeding programs to be used in abiotic stress-prone ecosystems.