SG12 regulates grain size by affecting cell proliferation in rice

The grain size of rice (Oryza sativa) plays a pivotal role in determining yield. It is crucial to explore the genes related to grain size and analyze their molecular mechanisms to enhance rice yield further. This study identified a small-grain mutant small grain 12 (sg12), from the ethyl methanesulfonate-induced mutant library of Shuhui 498, a backbone parent of heavy-panicle hybrid rice. We found that sg12 rice mutant exhibits a decrease in grain size and 1000-grain weight, but an increase in grain number per panicle. Genetic analysis indicated that the small grain of sg12 is controlled by a pair of semi-dominant genes. Furthermore, cytological analysis showed that the number of longitudinal cells in the spikelet hull of sg12 decreased, indicating that SG12 regulates grain size by affecting cell proliferation. In this study, we also identified a candidate gene of SG12 as OsPPKL3, which encodes a putative protein phosphatase with Kelch-like repeat domains. A single-nucleotide polymorphism substitution (G/A) occurred in the conserved Kelch domain of OsPPKL3 in the sg12, resulting in the mutation of the 176th amino acid from Ala to Thr, and this amino acid substitution led to significant differences in the three-dimensional structure of the OsPPKL3 protein. Finally, genetic analysis indicated that OsPPKL3 regulates grain size independent of Oryza sativa BRI1-associated receptor kinase 1 (OsBAK1) and Oryza sativa Brassinosteroid-signaling kinase 2 (OsBSK2). Overall, this study identified a new allelic mutant of OsPPKL3, clarified the cytological basis of OsPPKL3 regulating grain size, and emphasized the crucial role of the 176th amino acid in the Kelch domain of OsPPKL3 for its biological function. Our results provided important resources for further studying the molecular mechanisms of OsPPKL3 regulating grain size in rice. Small grain 12 (sg12) is a new gain-of-function allele mutant of OsPPKL3. SG12/OsPPKL3 regulates grain size by affecting cell proliferation. A single-nucleotide polymorphism (SNP) substitution (G/A) in the conserved Kelch domain of OsPPKL3 affected the protein structure of OsPPKL3. OsPPKL3 regulates grain size independent of Oryza sativa BRI1-associated receptor kinase 1 (OsBAK1) and Oryza sativa Brassinosteroid-signaling kinase 2 (OsBSK2). Our results provided important resources for further studying the molecular mechanisms of OsPPKL3. The grain size of rice plays a pivotal role in determining yield. It is crucial to explore the genes related to grain size and analyze their molecular mechanisms to enhance rice yield further. This study identified a small-grain mutant small grain 12 (sg12), and the small grain of sg12 is controlled by a pair of semi-dominant genes. Cytological analysis showed that SG12 regulates grain size by affecting cell proliferation. We also identified a candidate gene of SG12 as OsPPKL3, which encodes a putative protein phosphatase with Kelch-like repeat domains. A single-nucleotide polymorphism substitution (G/A) occurred in the conserved Kelch domain of OsPPKL3 in the sg12, resulting in the mutation of the 176th amino acid from Ala to Thr, and this amino acid substitution led to significant differences in the three-dimensional structure of the OsPPKL3 protein. Our results provided important resources for further studying the molecular mechanisms of OsPPKL3 regulating grain size in rice.