Natural variation of OsNPF7.3 regulates alkaline tolerance by modulating ammonium uptake and redistribution in rice

Soil alkalization is one of the most severe abiotic stresses constraining rice yields. However, the genetic basis underlying alkaline tolerance of rice remains poorly understood. Here, we used genome-wide association analysis to identify OsNPF7.3 as the candidate gene for qAT4 , which is a major locus associated with alkaline tolerance at rice seedling stage. OsNPF7.3 encodes a nitrate/oligopeptide transporter and acts as a negative regulator of rice alkaline tolerance. A natural variation of 7-bp insertion/deletion in the OsNPF7.3 promoter, affecting the binding affinity of transcription factor OsDOF11, mainly contributes to differential transcriptional levels of OsNPF7.3 , and thus leads to differential alkaline tolerance between japonica and indica subspecies. OsNPF7.3 localizes to the vacuolar membrane and mediates nitrogen transport from older to younger leaves under alkaline stress. Loss of OsNPF7.3 significantly upregulated the expression of nitrogen metabolism-related genes and metabolites, suggesting its regulatory role in nitrogen allocation. Together, these findings reveal an OsDOF11- OsNPF7.3 -nitrogen metabolism regulatory module that connects nitrogen homeostasis to alkaline tolerance, providing a promising target for the development of alkaline-tolerant rice varieties.