Natural variation in the promoter of qRBG1/OsBZR5 underlies enhanced rice yield

Seed size, a key determinant of rice yield, is regulated by brassinosteroid (BR); however, the BR pathway in rice has not been fully elucidated. Here, we report the cloning and characterization of the quantitative trait locus Rice Big Grain 1 ( qRBG1 ) from single-segment substitution line Z499. Our data show that qRBG1 Z is an unselected rare promoter variation that reduces qRBG1 expression to increase cell number and size, resulting in larger grains, whereas qRBG1 overexpression causes smaller grains in recipient Nipponbare. We demonstrate that qRBG1 encodes a non-canonical BES1 (Bri1-EMS-Suppressor1)/BZR1(Brassinazole-Resistant1) family member, OsBZR5, that regulates grain size upon phosphorylation by OsGSK2 (GSK3-like Kinase2) and binding to D2 ( DWARF2 ) and OFP1 ( Ovate-Family-Protein1 ) promoters. qRBG1 interacts with OsBZR1 to synergistically repress D2 , and to antagonistically mediate OFP1 for grain size. Our results reveal a regulatory network controlling grain size via OsGSK2–qRBG1–OsBZR1–D2–OFP1 module, providing a target for improving rice yield. A rare variation in the promoter of qRBG1/OsBZR5 is associated with larger rice grains. OsBZR5 is found to negatively regulate grain size in rice, a biological role opposite to other OsBZR members. A regulatory module of OsGSK2–qRBG1–OsBZR1–D2–OFP1 is further revealed.