Plant architecture, one of the key factors that determine grain yield in rice, is mainly affected by components such as plant height, tiller number, and panicle morphology. For this paper, we obtained a multi-tillering and lazy mutant from a japonica rice cultivar, Wuyunjing 7 (WYJ7), via treatment with a heavy ion beam. Compared to WYJ7, the mutant showed a significant increase in tiller angle, tiller number, number of primary and secondary branches, and number of grains; however, the plant height and grain thickness of the mutant was significantly decreased. Phenotypic analysis of the F₁ hybrids revealed that the multi-tillering and lazy mutant phenotypes were regulated by a recessive gene. The segregation ratio of 1׃3 of the mutant phenotype and the wild-type plant in the F₂ population indicated that the former was controlled by a single gene named Multi-Tillering and Lazy 1 (MTL1). Bulked segregant analysis was performed using the individual plants with extremely typical tiller angles in the F₂ population. The MTL1 gene was initially mapped within a region of 5.58–17.64 Mb on chromosome 11. By using the F₂ segregated population for fine mapping, the MTL1 gene was ultimately fine mapped within the range of 66.67 kb on chromosome 11. The analysis of genes in this region revealed the presence of the previously identified LAZY1 (LA1) gene. Genomic PCR amplification and semi-quantitative RT-PCR assays showed that the LA1 gene could not be amplified and was not expressed, thus indicating that the MTL1 gene might be identical to the LA1 gene. This study suggests that the multi-tillering and lazy mutant phenotypes might be caused by the deletion of LA1 function. This finding can guide further investigations on the functional mechanisms of the LA1 gene, thus enriching the theoretical knowledge of plant architecture in relation to rice.

Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development.

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.

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.

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.

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.