Transcriptomic Analyses and Weighted Gene Co-Expression Network Analysis (WGCNA) Identify Key Drought-Responsive Genes in Rice Roots (Oryza sativa L.) Under PEG Treatment

Rice depends on its root system to perceive drought, a major environmental constraint that leads to severe yield losses worldwide. To dissect the underlying molecular basis, we conducted a comparative analysis of drought-sensitive (WAB) and drought-tolerant (IR65) rice genotypes that exhibited divergent drought tolerance at the seedling stage. After exposure to 15% PEG6000 (−0.4 MPa) for two days, the shoot and root architectural traits of IR65 were better than those of WAB seedlings. Measurements of physio-biochemical parameters (SOD, CAT, POD, APX, H2O2, and proline) suggest that IR65 seedling roots exhibit greater ROS scavenging and osmotic adjustment capacity than WAB, aligning with tolerance to PEG-induced water deficiency. Transcriptomic assessments of roots identified 802 commonly differentially expressed genes (DEGs) during the drought time course (12, 24, and 48 h) in WAB and IR65. They were clustered into eight groups based on their expression profiles and mainly enriched in phytohormone signaling, protein phosphorylation, and transcription factors. Using weighted gene co-expression network analysis (WGCNA), nine significant modules were identified based on n = 382 of the DEGs. A total of 12 DEGs up-regulated in IR65 were distributed in five modules, and five of them were selected for rapid functional validation through in vivo yeast expression. The results showed that transgenic yeasts were tolerant to simulated drought conditions (135 mM PEG3350), indicating that these genes would be potential targets for rice improvement in drought tolerance in the future.