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^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.