Nature variations of OsNLP4 responsible for nitrogen use efficiency divergence in the two rice subspecies
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<sup>indica</sup> to nitrate response elements (NREs), amplifying transcriptional activation of nitrogen metabolism and iron homeostasis genes. Introgression of the OsNLP4<sup>indica</sup> 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<sup>indica</sup> 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<sup>indica</sup> as a cross-species genetic resource for sustainable agriculture.
Authors
- Chuanzao Mao (ORCID: https://orcid.org/0000-0001-5126-2180)
- Liangqi Sun (ORCID: https://orcid.org/0000-0001-6678-5929)
- Guangyu Wan (ORCID: https://orcid.org/0000-0001-9828-5021)
- Shigui Li (ORCID: https://orcid.org/0000-0002-7187-8123)
- Cheng‐Bin Xiang (ORCID: https://orcid.org/0000-0002-7152-1458)
- Chengcai Chu (ORCID: https://orcid.org/0000-0001-8097-6115)
- Ying Song (ORCID: https://orcid.org/0000-0001-9823-9877)
- Hongkai Wu (ORCID: https://orcid.org/0000-0001-6433-2838)
- Jie Wu (ORCID: https://orcid.org/0000-0002-7198-5797)
- Jingxian Wang (ORCID: https://orcid.org/0000-0003-4904-8892)
- Peng Qin (ORCID: https://orcid.org/0000-0001-9046-5423)
- Shimei Wang
Institutions
- South China Agricultural University (CN)
- University of Science and Technology of China (CN)
- Zhejiang A & F University (CN)
- Anhui Agricultural University (CN)
- Agriculture and Forestry University (NP)
- Sichuan Agricultural University (CN)
- Rice Research Institute (CN)
- Hefei National Center for Physical Sciences at Nanoscale (CN)
- Anhui Academy of Agricultural Sciences (CN)
- Jiyang College of Zhejiang A&F University (CN)
- Hefei Institute of Technology Innovation (CN)
- National Science Centre (PL)
- State Key Laboratory of Plant Physiology and Biochemistry
- Zhejiang University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-08-18
- DOI
- https://doi.org/10.1038/s41467-025-63109-7
- Citations
- 2
- Primary Topic
- Plant nutrient uptake and metabolism
- Type
- article
- Field-Weighted Citation Impact
- 3.50
Funders
- National Natural Science Foundation of China
- Henan University
- Anhui Agricultural University
- Nanjing Agricultural University
- Natural Science Foundation of Anhui Province
- Fundamental Research Funds for the Central Universities