Transcriptome Analysis of Submergence Stress in Rice Provides Insights into the Molecular Mechanism of Rice Response to Flooding and the Roles of OsEXPB3 Under Submergence

Abstract

This study aims to compare the transcriptional responses of japonica and indica rice genotypes with contrasting submergence tolerance and to functionally validate the role of OsEXPB3. Flooding is a major abiotic stress limiting stable rice production, and different genotypes show substantial variation in submergence tolerance. However, the transcriptional and molecular regulatory mechanisms underlying subspecies-specific responses remain poorly understood. Here, RNA-seq analysis of japonica and indica accessions with contrasting tolerance levels was performed to construct molecular response networks and identify key tolerance-related genes. Comparative analysis revealed that both subspecies activate biological processes such as stimulus response, redox homeostasis, carbon metabolism, and hormone signaling under submergence. In the analyzed japonica genotypes, plants relied more on integrated hormone-regulated signaling, whereas in the analyzed indica genotypes, metabolic homeostasis was more prominent. Among the identified genes, OsEXPB3, a β-expansin gene, was consistently upregulated in tolerant accessions, whereas osexpb3 mutants displayed suppressed coleoptile and seedling elongation and reduced tolerance. Hormone profiling revealed a 0.1–0.3-fold increase in ethylene (ETH) and a 50–70% reduction in gibberellin (GA) in mutants after submergence. Defense-related hormones, including jasmonic acid (JA) and salicylic acid (SA), were initially higher but declined markedly under stress conditions. Given that the OsEXPB3 promoter contains multiple ETH-, GA-, ABA-, JA- and SA-responsive cis-elements, we propose that OsEXPB3 may coordinate the balance between growth- and defense-related hormones to mediate adaptive responses to flooding. This study reveals conserved and divergent molecular responses between subspecies and suggests that OsEXPB3 may contribute to submergence tolerance in rice, although its regulatory role requires further validation.