Understanding the cross-talk of major abiotic-stress-responsive genes in rice: A computational biology approach

Abstract

This study aims to identify key abiotic-stress-responsive genes in Oryza sativa and investigate their expression profiles, protein–protein interactions, and co-expression patterns to better understand the molecular mechanisms underlying stress response in rice. The ultimate goal is to employ these findings in the development of gene-based molecular markers to breed rice cultivars with enhanced resistance to challenging environmental conditions. A total of 14 abiotic-stress-responsive genes in O. sativa were identified through literature mining. These genes were analyzed for their chromosomal distribution, transcript length, CDS length, and translated amino acid length. Pairwise similarity matrix, phylogenetic analysis, and protein–protein interaction networks were employed to understand the evolutionary relationships and functional interactions among these genes. Expression profiles of six key genes (AOX1a, AOX1b, ALDH2a, ALDH2b, OsNAC6, OsDHN1) were investigated using the electronic fluorescent pictogram (eFP) program. KEGG pathway analysis and co-expression studies were also conducted to further understand the roles of these genes in abiotic stress response pathways. The 14 abiotic-stress-responsive genes were distributed across different chromosomes of O. sativa, suggesting the presence of interconnected cascades regulating abiotic-stress-response. Phylogenetic analysis revealed four clusters of genes, indicating their potential shared ancestry. Protein-protein interaction analysis identified three prominent clusters of interactions, with the strongest interactions occurring among Aldh2a, Aldh2b, OS07T0188800-01, and OsJ_04113 in one cluster, and between AOX1a and AOX1b in another cluster. Expression profiles of the six key genes varied across different stages of the rice life cycle. KEGG pathway analysis showed that ALDH2a and ALDH2b participated in almost all pathways except propanoate metabolism.The study demonstrated that the six key genes play significant regulatory roles in abiotic stress responses in O. sativa. The expression profiles, phylogenetic analysis, protein–protein interactions, and gene co-expression studies revealed interconnected cascades and cross-talk in response mechanisms of these genes. These findings can be employed to develop gene-based molecular markers for breeding rice cultivars with enhanced resistance to abiotic stresses, and contribute to the successful application of computational biology in plant breeding towards sustainable development goal.