Zeqi Zhao, Chengwei Yang, Xiaoke Shang, Mengdi Li, Xiaoyang Su, J H Liu, Chunlong Li
ABSTRACT Salt stress and nitrogen utilisation efficiency (NUE) represent critical constraints affecting worldwide crop productivity. While nitrate transporter proteins (NPFs) have been implicated in saline chloride (Cl − ) ion transport, the mechanistic linkage between chloride stress and NUE remains poorly understood. Through comparative transcriptomic profiling of Citrus trifoliata , we identified CtrNPF2.1 as a dual‐responsive gene significantly upregulated in root tissues under both chloride salt and high nitrate conditions. The CtrNPF2.1 protein is localized to the vacuole membrane and highly expressed in root cortical cells. Transport functional characterisation combined with transgenic phenotypic analyses established that CtrNPF2.1 mediates dual transport mechanisms: facilitating vacuolar Cl − compartmentalisation while enabling nitrate efflux. This coordinated process enhances cellular ion detoxification and promotes nitrate redistribution for optimal root development under saline conditions. Molecular investigations further uncovered that CtrNAC019 transcriptionally regulates CtrNPF2.1 expression through direct binding to its promoter, forming a chloride/nitrate‐responsive regulatory module. Notably, physiological validation reveals coordinated responses in which nitrate supplementation mitigates chloride toxicity while chloride availability enhances nitrogen utilisation in trifoliate orange, which may be explained by the CtrNAC019‐CtrNPF2.1 expression regulation module. These results provide new insights into vacuolar chloride sequestration and nitrate efflux by CtrNAC019‐CtrNPF2.1 under saline and high‐nitrate conditions, offering a promising strategy for breeding salt‐resilient and resource‐efficient crops.