Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies
Abstract Nitrogen use efficiency (NUE), a critical determinant of crop productivity and agricultural sustainability, varies significantly between indica and japonica subspecies. Here, we identify three coding-region SNPs in OsNLP4 underlying this divergence. These SNPs enhance the binding affinity o...
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-63109-7 |
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| author | Jie Wu Ying Song Guangyu Wan Liangqi Sun Jingxian Wang Hongkai Wu Shimei Wang Chuanzao Mao Peng Qin Shigui Li Chengcai Chu Chengbin Xiang |
| author_facet | Jie Wu Ying Song Guangyu Wan Liangqi Sun Jingxian Wang Hongkai Wu Shimei Wang Chuanzao Mao Peng Qin Shigui Li Chengcai Chu Chengbin Xiang |
| author_sort | Jie Wu |
| collection | DOAJ |
| description | Abstract Nitrogen use efficiency (NUE), a critical determinant of crop productivity and agricultural sustainability, varies significantly between indica and japonica subspecies. Here, we identify three coding-region SNPs in OsNLP4 underlying this divergence. These SNPs enhance the binding affinity of OsNLP4 indica to nitrate response elements (NREs), amplifying transcriptional activation of nitrogen metabolism and iron homeostasis genes. Introgression of the OsNLP4 indica allele into elite japonica cultivar XS134 increases both grain yield and NUE by 12–25% across multi-location field trials under varying nitrogen regimes. Heterologous expression in Arabidopsis increases shoot biomass by 23%, demonstrating possible conservation of function in dicots. Mechanistically, the indica allele’s stronger NRE-binding capacity synergistically modulates downstream pathways. Furthermore, combining OsNLP4 indica with balanced nitrogen-iron fertilization boosts NUE by 30–32%. Our findings resolve a critical genetic basis of indica-japonica NUE divergence, provide a validated strategy for improving yield and NUE of commercial japonica varieties, and highlight OsNLP4 indica as a cross-species genetic resource for sustainable agriculture. |
| format | Article |
| id | doaj-art-7f24760d668f4daeb65fcfa716df0008 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
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| series | Nature Communications |
| spelling | doaj-art-7f24760d668f4daeb65fcfa716df00082025-08-24T11:38:17ZengNature PortfolioNature Communications2041-17232025-08-0116111110.1038/s41467-025-63109-7Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspeciesJie Wu0Ying Song1Guangyu Wan2Liangqi Sun3Jingxian Wang4Hongkai Wu5Shimei Wang6Chuanzao Mao7Peng Qin8Shigui Li9Chengcai Chu10Chengbin Xiang11Division of Life Sciences and Medicine; Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics; University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of SciencesDivision of Life Sciences and Medicine; Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics; University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of SciencesDivision of Life Sciences and Medicine; Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics; University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of SciencesDivision of Life Sciences and Medicine; Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics; University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of SciencesDivision of Life Sciences and Medicine; Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics; University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of SciencesZhejiang Agricultural and Forestry University, LinganRice Research Institute, Anhui Academy of Agricultural SciencesState Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang UniversityRice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural UniversityRice Research Institute, State Key Laboratory of Hybrid Rice, Sichuan Agricultural UniversityGuangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, and Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural UniversityDivision of Life Sciences and Medicine; Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics; University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of SciencesAbstract Nitrogen use efficiency (NUE), a critical determinant of crop productivity and agricultural sustainability, varies significantly between indica and japonica subspecies. Here, we identify three coding-region SNPs in OsNLP4 underlying this divergence. These SNPs enhance the binding affinity of OsNLP4 indica to nitrate response elements (NREs), amplifying transcriptional activation of nitrogen metabolism and iron homeostasis genes. Introgression of the OsNLP4 indica allele into elite japonica cultivar XS134 increases both grain yield and NUE by 12–25% across multi-location field trials under varying nitrogen regimes. Heterologous expression in Arabidopsis increases shoot biomass by 23%, demonstrating possible conservation of function in dicots. Mechanistically, the indica allele’s stronger NRE-binding capacity synergistically modulates downstream pathways. Furthermore, combining OsNLP4 indica with balanced nitrogen-iron fertilization boosts NUE by 30–32%. Our findings resolve a critical genetic basis of indica-japonica NUE divergence, provide a validated strategy for improving yield and NUE of commercial japonica varieties, and highlight OsNLP4 indica as a cross-species genetic resource for sustainable agriculture.https://doi.org/10.1038/s41467-025-63109-7 |
| spellingShingle | Jie Wu Ying Song Guangyu Wan Liangqi Sun Jingxian Wang Hongkai Wu Shimei Wang Chuanzao Mao Peng Qin Shigui Li Chengcai Chu Chengbin Xiang Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies Nature Communications |
| title | Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies |
| title_full | Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies |
| title_fullStr | Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies |
| title_full_unstemmed | Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies |
| title_short | Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies |
| title_sort | nature variations of osnlp4 responsible for nitrogen use efficiency divergence in the two rice subspecies |
| url | https://doi.org/10.1038/s41467-025-63109-7 |
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