Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number
Rice grain yield is primarily determined by three key agronomic traits: panicle number, grain number per panicle, and grain weight (GW). However, the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs. Notably, compared with GW, brown rice weight...
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Elsevier
2025-07-01
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| Series: | Rice Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672630825000733 |
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| author | Lin Zhou Hong Jiang Long Huang Ziang Li Zhonghao Yao Linhan Li Kangwei Ji Yijie Li Haijuan Tang Jinping Cheng Yongmei Bao Ji Huang Hongsheng Zhang Sunlu Chen |
| author_facet | Lin Zhou Hong Jiang Long Huang Ziang Li Zhonghao Yao Linhan Li Kangwei Ji Yijie Li Haijuan Tang Jinping Cheng Yongmei Bao Ji Huang Hongsheng Zhang Sunlu Chen |
| author_sort | Lin Zhou |
| collection | DOAJ |
| description | Rice grain yield is primarily determined by three key agronomic traits: panicle number, grain number per panicle, and grain weight (GW). However, the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs. Notably, compared with GW, brown rice weight (BRW) provides a more direct metric associated with actual grain yield potential. In this study, we conducted a two-year replicated genome-wide association study to elucidate the genetic architecture of BRW and identify new loci regulating GW. Among seven consistently detected loci across experimental replicates, four were not co-localized with previously reported genes associated with BRW or GW traits. BRW1.1, one of the four newly identified loci, was found to encode a novel RNA-binding protein. Functional characterization revealed that BRW1.1 acts as a negative regulator of BRW, potentially through modulating mRNA translation processes. Intriguingly, through integrated analysis of mutant phenotypes and haplotype variations, we demonstrated that BRW1.1 mediates the physiological tradeoff between GW and panicle number. This study not only delineates the genetic determinants of BRW but also identifies BRW1.1 as a promising molecular target for breaking the yield component tradeoff in precision rice breeding. |
| format | Article |
| id | doaj-art-057dceb6b1874a1c85dda71c43a8701b |
| institution | Kabale University |
| issn | 1672-6308 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Rice Science |
| spelling | doaj-art-057dceb6b1874a1c85dda71c43a8701b2025-08-20T05:06:07ZengElsevierRice Science1672-63082025-07-0132452553610.1016/j.rsci.2025.06.002Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle NumberLin Zhou0Hong Jiang1Long Huang2Ziang Li3Zhonghao Yao4Linhan Li5Kangwei Ji6Yijie Li7Haijuan Tang8Jinping Cheng9Yongmei Bao10Ji Huang11Hongsheng Zhang12Sunlu Chen13Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaSanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaCorresponding author.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaCorresponding author.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 211800, ChinaRice grain yield is primarily determined by three key agronomic traits: panicle number, grain number per panicle, and grain weight (GW). However, the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs. Notably, compared with GW, brown rice weight (BRW) provides a more direct metric associated with actual grain yield potential. In this study, we conducted a two-year replicated genome-wide association study to elucidate the genetic architecture of BRW and identify new loci regulating GW. Among seven consistently detected loci across experimental replicates, four were not co-localized with previously reported genes associated with BRW or GW traits. BRW1.1, one of the four newly identified loci, was found to encode a novel RNA-binding protein. Functional characterization revealed that BRW1.1 acts as a negative regulator of BRW, potentially through modulating mRNA translation processes. Intriguingly, through integrated analysis of mutant phenotypes and haplotype variations, we demonstrated that BRW1.1 mediates the physiological tradeoff between GW and panicle number. This study not only delineates the genetic determinants of BRW but also identifies BRW1.1 as a promising molecular target for breaking the yield component tradeoff in precision rice breeding.http://www.sciencedirect.com/science/article/pii/S1672630825000733genome-wide association studybrown rice weightRNA-binding proteintradeoffgrain weightpanicle number |
| spellingShingle | Lin Zhou Hong Jiang Long Huang Ziang Li Zhonghao Yao Linhan Li Kangwei Ji Yijie Li Haijuan Tang Jinping Cheng Yongmei Bao Ji Huang Hongsheng Zhang Sunlu Chen Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number Rice Science genome-wide association study brown rice weight RNA-binding protein tradeoff grain weight panicle number |
| title | Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number |
| title_full | Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number |
| title_fullStr | Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number |
| title_full_unstemmed | Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number |
| title_short | Genome-Wide Association Study of Brown Rice Weight Identifies an RNA-Binding Protein Antagonistically Regulating Grain Weight and Panicle Number |
| title_sort | genome wide association study of brown rice weight identifies an rna binding protein antagonistically regulating grain weight and panicle number |
| topic | genome-wide association study brown rice weight RNA-binding protein tradeoff grain weight panicle number |
| url | http://www.sciencedirect.com/science/article/pii/S1672630825000733 |
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