Natural variation in GNP3 determines grain number and grain yield in rice

Grain number per panicle (GNP) critically determines rice yield. Although many underlying genes have been reported, yet the molecular mechanisms linking ethylene to panicle development remain unclear. Here, we identify GNP3 as a key regulator of GNP through genome-wide association combined with map-based cloning. GNP3 encodes a mitogen-activated protein kinase kinase kinase that phosphorylates S-adenosyl-L-methionine synthetase 1 (SAMS1), triggering its degradation to suppress ethylene biosynthesis. Ethylene overaccumulation in gnp3-1 mutants reduced GNP, while GNP3 overexpression enhanced panicle branching and grain yield by lowering ethylene levels. We demonstrate that a natural haplotype GNP3Hap-Tprevalent in indica subspecies strengthens GNP3-SAMS1 interaction, accelerating SAMS1 degradation and improving GNP. Furthermore, overexpressing GNP3 increases grain yield by approximately 20% in field plot conditions. Our findings unveil a MAPK-ethylene regulatory module and highlight GNP3Hap-T as a valuable genetic resource for breeding high-yield rice.