A Large Exonic Insertion in the Rice DEP2 Gene Creates a Novel Allelic Mutant srt with Increased Grain Number per Panicle and Short, Round Grains

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.