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.

An exploration and understanding of cultivar adaptability to specific environmental conditions are critical in rice breeding. This study aimed to compare the agro-morphological data of 36 japonica rice cultivars (Oryza sativa L.) from Chinese rice accessions grown under two different environments (Fengyang and Hexian) and to identify important genes associated with key traits in the cultivars. Higher significant differences were observed between Fengyang and Hexian in traits like, grain width, grain length, yield per plot, plant height, and tiller number with cultivars grown in Hexian having the greatest values. This revealed that the environment in Hexian favored these traits, and most cultivars performed better in Hexian than in Fengyang. Correlation analysis also showed strong positive correlations between tiller number and yield per plot in both environments, indicating the influence of tiller number on rice yield potential. The PCR analysis showed the amplification of DEP1, Ghd7, Wx, Chalk5, COLD1, DST, Xa13, and Bph6 in most japonica cultivars, indicating presence of these genes in the cultivars. This study suggests that differences in agronomic performance between the cultivars grown in Fengyang and Hexian might be caused by differences in environmental conditions. This finding could be valuable for future breeding of high-yielding and climate-resilient cultivars.

A exploration and understanding of cultivar adaptability to specific environmental conditions are critical in rice breeding. This study aimed to compare the agro-morphological data of 36 japonica rice cultivars (Oryza sativa L.) from Chinese rice accessions grown under two different environments (Fengyang and Hexian) and to identify important genes associated with key traits in the cultivars. Higher significant differences were observed between Fengyang and Hexian in traits like, grain width, grain length, yield per plot, plant height, and tiller number with cultivars grown in Hexian having the greatest values. This revealed that the environment in Hexian favored these traits, and most cultivars performed better in Hexian than in Fengyang. Correlation analysis also showed strong positive correlations between tiller number and yield per plot in both environments, indicating the influence of tiller number on rice yield potential. The PCR analysis showed the amplification of DEP1, Ghd7, Wx, Chalk5, COLD1, DST, Xa13, and Bph6 in most japonica cultivars, indicating presence of these genes in the cultivars. This study suggests that differences in agronomic performance between the cultivars grown in Fengyang and Hexian might be caused by differences in environmental conditions. This finding could be valuable for future breeding of high-yielding and climate-resilient cultivars.

Rice, as a globally vital food crop, is frequently threatened by flooding, which adversely affects its growth and yield. The most immediate and prominent influence of waterlogging or submergence induced by flooding on rice is hypoxia (reduced oxygen availability) or anoxia (absence of oxygen) stress and the consequent energy deficiency. Rice has evolved specific acclimation strategies to counteract or alleviate flooding stress, including leaf gas film (LGF) formation, adventitious root (AR) emergence, aerenchyma formation, radial oxygen loss (ROL) barrier development, and the stunted or elongated growth of coleoptiles or internodes, all of which serve to secure oxygen supply and maintain energy homeostasis for sustaining survival. These adaptive traits and strategies are governed by the regulatory genes involved in the reprogramming of energy and carbohydrate metabolism, the accumulation and scavenging of reactive oxygen species (ROS), and the programmed cell death (PCD) process, as well as the phytohormone biosynthesis and signaling pathways. To facilitate a comprehensive understanding of the submergence response and tolerance and the intricate regulatory mechanisms in rice, this review integrates the impacts of flooding on the growth and development, the strategies employed to adapt to submergence, the physiological and biochemical characteristics, the phytohormonal signaling and crosstalk, and the molecular mechanistic framework of rice subjected to submergence stress. It also highlights the importance of key superior genes for flooding-tolerance, flooding-tolerant germplasms, and molecular breeding technologies in developing submergence-tolerant rice varieties. By aligning these advances, this review provides valuable insights into and guidance for improving resilience to submergence stress and enhancing crop production under constantly changing climate conditions.