Shoot transcriptome and co-expression network analysis of African rice cultivars identify drought-tolerance hub genes and growth stage-dependent trade-offs

Abstract

Drought is a major abiotic stress limiting rice growth and productivity, posing a considerable threat to global food security. Understanding the molecular mechanisms that regulate plant responses to water deficit is critical for developing drought-tolerant rice varieties. While most breeding programmes evaluate drought responses at the adult or reproductive stages, early developmental responses remain understudied. Here, we compared the responses of young rice plants from previously characterized drought-tolerant (APO and CRI-Enapa) and drought-sensitive (ART132-35-1-1-B-B and CRI-Amankwatia) rice varieties. We applied a transcriptome-based weighted gene co-expression network analysis using WGCNA to identify key regulatory genes and pathways associated with drought response in rice. Comprehensive transcriptional profiling after 30 days of drought stress revealed that APO showed extensive transcriptional reprogramming with 96.63% and 97.32% uniquely differentially expressed genes (DEGs) compared to CRI-Enapa and ART132-35-1-1-B-B, respectively. Module-trait relationship analysis identified several modules significantly associated with shoot fresh weight and root fresh weight under drought stress and control condition, with the turquoise and blue modules showing the strongest correlations. Within these, 30 genes exhibited exceptionally high connectivity, suggesting potential central roles in the regulatory network. Notably, S-acyltransferase ( BGIOSGA023969 ) and NAD(P)-binding Rossmann-fold protein ( BGIOSGA038191 ) showed the highest correlation with the shoot and root fresh weight. Functional enrichment analyses of APO and hub genes revealed that most of the DEGs were associated with phytohormone signalling, transcription factors, carbohydrate metabolism and drought response genes, suggesting their key role in drought tolerance mechanisms. These transcriptional units may not only serve as potential targets for functional validation but also function as molecular markers for drought tolerance at the early-developmental stages, which is critical for successful crop establishment in stressful paddy environments.