Natural variation in GNP3 determines grain number and grain yield in rice
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 as...
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61326-8 |
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| author | 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 Zhanying Zhang |
| author_facet | 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 Zhanying Zhang |
| author_sort | Zhiqi Ma |
| collection | DOAJ |
| description | 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 GNP3 Hap-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 GNP3 Hap-T as a valuable genetic resource for breeding high-yield rice. |
| format | Article |
| id | doaj-art-4a14a44b7d7349b8b3ee6bf5d776f817 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-4a14a44b7d7349b8b3ee6bf5d776f8172025-08-20T03:37:37ZengNature PortfolioNature Communications2041-17232025-07-0116111610.1038/s41467-025-61326-8Natural variation in GNP3 determines grain number and grain yield in riceZhiqi Ma0Yuhang Ming1Jinlong Li2Honglin Li3Haozhen Wang4Xiaoyang Zhu5Yawen Xu6Yong Zhao7Qianfeng Hu8Ruiqi Liu9Yinghua Pan10Danting Li11Wensheng Wang12Jianlong Xu13Xingming Sun14Jinjie Li15Hongliang Zhang16Zichao Li17Zhanying Zhang18Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityState Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute of Guangxi Academy of Agricultural SciencesGuangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute of Guangxi Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural UniversityAbstract 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 GNP3 Hap-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 GNP3 Hap-T as a valuable genetic resource for breeding high-yield rice.https://doi.org/10.1038/s41467-025-61326-8 |
| spellingShingle | 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 Zhanying Zhang Natural variation in GNP3 determines grain number and grain yield in rice Nature Communications |
| title | Natural variation in GNP3 determines grain number and grain yield in rice |
| title_full | Natural variation in GNP3 determines grain number and grain yield in rice |
| title_fullStr | Natural variation in GNP3 determines grain number and grain yield in rice |
| title_full_unstemmed | Natural variation in GNP3 determines grain number and grain yield in rice |
| title_short | Natural variation in GNP3 determines grain number and grain yield in rice |
| title_sort | natural variation in gnp3 determines grain number and grain yield in rice |
| url | https://doi.org/10.1038/s41467-025-61326-8 |
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