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

Zhiqi Ma, Yuhang Ming, Jinlong Li, Honglin Li, Haozhen Wang, Xiaoyang Zhu, Yawen Xu, Yong Zhao, Qianfeng Hu, Ruiqi Liu, Yinghua Pan, Danting Li, Wensheng Wang, Jianlong Xu, Xingming Sun, Jinjie Li, Hongliang Zhang, Zichao Li and Zhanying Zhang ()
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Zhiqi Ma: China Agricultural University
Yuhang Ming: China Agricultural University
Jinlong Li: China Agricultural University
Honglin Li: China Agricultural University
Haozhen Wang: China Agricultural University
Xiaoyang Zhu: China Agricultural University
Yawen Xu: China Agricultural University
Yong Zhao: China Agricultural University
Qianfeng Hu: China Agricultural University
Ruiqi Liu: China Agricultural University
Yinghua Pan: Rice Research Institute of Guangxi Academy of Agricultural Sciences
Danting Li: Rice Research Institute of Guangxi Academy of Agricultural Sciences
Wensheng Wang: Chinese Academy of Agricultural Sciences
Jianlong Xu: Chinese Academy of Agricultural Sciences
Xingming Sun: China Agricultural University
Jinjie Li: China Agricultural University
Hongliang Zhang: China Agricultural University
Zichao Li: China Agricultural University
Zhanying Zhang: China Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Grain number per panicle 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 GRAIN NUMBER PER PANICLE 3 (GNP3) as a regulator of GNP through genome-wide association study (GWAS) combined with map-based cloning. GNP3 encodes a MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 22 (OsMKKK22) that phosphorylates S-adenosyl-L-methionine synthetase 1 (SAMS1), triggering its degradation to suppress ethylene biosynthesis. Ethylene overaccumulation in gnp3−1 mutants reduces grain number, while GNP3 overexpression enhances 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 grain number. 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.

Date: 2025
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DOI: 10.1038/s41467-025-61326-8

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