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.

DENSE AND ERECT PANICLE 2 (DEP2) is a key pleiotropic gene regulating panicle architecture and grain shape in rice. To explore its favorable allelic variations, a stably inherited mutant with short, round and thick grains (srt) was identified in this study using the Japonica rice variety ‘Zhonghua 11’ (ZH11) as the genetic background. Compared with ZH11, srt exhibited reduced plant height and a shorter panicle length but significantly increased numbers of primary branches, secondary branches, and grains per panicle. The mutant grains showed decreased length, increased width, and thickness, ultimately leading to reductions in both thousand-grain weight and grain yield per plant. Cytological analysis revealed that both the longitudinal and transverse dimensions of hull cells in srt were significantly enlarged, while the number of longitudinal cells per unit length decreased. This suggests that srt remodels grain shape by altering the balance between cell division and expansion. Genetic analysis indicated that the phenotype is controlled by a single recessive gene. Map-based cloning and whole-genome resequencing localized the target gene to chromosome 7 and confirmed that srt is the DEP2 gene. Sequence analysis revealed the presence of a large fragment insertion of approximately 87 kb entirely within the seventh exon region of the DEP2 gene in srt. However, unlike most reported DEP2 mutants, in which the numbers of primary branches, secondary branches, and grains per panicle showed no significant difference from the wild type, the srt mutant exhibited a significant increase in all these traits. This unique phenotypic combination expands the understanding of the functional diversity of this gene. This study provides new genetic material for further elucidating the molecular mechanisms by which DEP2 regulates panicle development and for molecular design breeding of rice grain shape.

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.