Integrative analysis of coding and non-coding RNAs in rice reveals conserved molecular response signatures to heat, drought, and salt stresses.

Abiotic stresses such as heat, drought, and salinity significantly impact rice cultivation by affecting its yield and quality. Identifying molecular candidates that confer resistance or tolerance to these stresses is crucial. This study identifies unique and overlapping molecular signatures mediated by coding and non-coding RNAs during heat, drought, and salt stresses in rice. It uses RNA-Seq data from 66 rice samples, including those treated with heat, drought, and salt stresses, to identify both unique and shared differentially expressed mRNAs and long non-coding RNAs (lncRNAs). Analyses reveal key regulatory hubs in transcriptional networks, particularly the ERF, DOF, and MYB family transcription factors, which are central to abiotic stress responses. Stress-specific competing endogenous RNA networks reveal conserved regulatory elements that coordinate these responses. Overlap analysis identifies 637 shared mRNAs and 76 lncRNAs among the three stresses. These findings enhance our understanding of the molecular mechanisms underlying stress resilience in rice and provide a foundation for developing stress-resistant cultivars.