Unveiling the molecular mechanisms of drought stress tolerance in rice (Oryza sativa L.) using computational approaches

The devastating impact of drought on rice yield as a serious problem has been demanding an enormous effort to develop drought tolerant rice varieties. To start with, one of the major challenges in this regard is identifying the genes and pathways associated with drought tolerance for effectively governing the factor in rice. In the present study, a variety of computational biology techniques including Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene network analysis were applied on putative candidate drought-tolerant genes (previously identified via microarray analysis) to decipher the biological processes and pathways by which tolerant genotype copes with drought stress. In terms of biological process, GO enrichment analysis revealed the significance of developmental process, signaling, reproduction, cell death, small molecule metabolic process, oxidation reduction, secondary metabolic process, and response to stimulus. In addition, the majority of uniquely upregulated genes were strongly associated with “response to stimulus”. Significantly, from the point of view of molecular function ontology, the uniquely upregulated genes were enriched in serine-type endopeptidase inhibitor activity (5 genes). Utilizing KEGG pathway enrichment analysis underscored glutathione metabolism as a critical pathway in tolerant genotype imposed on drought stress. Also, network analysis highlighted UvrD helicase as the central gene. According to the results, the tolerance of tolerant genotype seems to be related to high antioxidant and DNA repair systems efficiencies. This study provides a potent approach for uncovering the crucial genes and pathways that may be contributing to drought tolerance.