Meta-analysis of RNA-seq data of soybean under heat, water, and drought stresses

Climate change is a key driver of abiotic stress, i.e., heat, water, and drought, in plants, particularly impacting soybean production. Understanding the molecular processes that underlie soybean responses to these stresses is crucial for developing tolerance. Here, we investigated soybean stress response by analyzing RNA-seq meta-data, focusing on drought, heat, and water stress. A total of 73 paired datasets were analyzed based on HN-ratio [Treated (H), Control (N)] and HN-score to identify differentially expressed genes, followed by functional annotation and motif analysis. The analysis identified 398, 332, and 322 up-regulated genes, and 453, 301, and 455 down-regulated genes in response to drought, heat, and water stresses, respectively. Of these, six down-regulated genes were common between drought and heat, six between heat and water, while four between drought and water stress. Whereas, among the up-regulated genes, 14 were common between drought and water stress, 10 between drought stress and heat stress, and 2 genes between heat and water. The down-regulated genes were associated with nicotianamine synthase activity and metal chelation (drought), protein phosphate inhibitor activity (heat), and photosynthesis and fructose metabolism (water). Up-regulated genes were enriched for flavin mononucleotide binding and isoflavonoid biosynthesis (water), protein complex oligomerization, protein self-association, and response to hydrogen peroxide (heat). Common stress-responsive genes and their domains were connected to pathways like glutathione and nitrogen metabolism. The study also identified several uncharacterized genes with potential roles in stress response. This meta-analysis provides a valuable resource for selecting candidate genes for genome-editing targeted at improving soybean's abiotic stress tolerance.