A phosphorylation-regulated NPF transporter determines salt tolerance by mediating chloride uptake in soybean plants.

Chloride (Cl^-) ions cause major damage to crops in saline soils. Understanding the key factors that influence Cl^- uptake and translocation will aid the breeding of more salt-tolerant crops. Here, using genome-wide association study and transcriptomic analysis, we identified a NITRATE TRANSPORTER 1 (NRT1)/PEPTIDE TRANSPORTER family (NPF) protein, GmNPF7.5, as the dominant gene locus influencing Cl^- homeostasis in soybean (Glycine max). A natural SNP variation resulted in two haplotypes (GmNPF7.5^HapA and GmNPF7.5^HapB), which was associated with Cl^- content. GmNPF7.5^HapA mediated Cl^- or nitrate (NO₃^-) uptake in a pH-dependent manner and exhibited higher permeability for Cl^- over NO₃^-. The suppression of GmNPF7.5^HapA expression decreased Cl^- accumulation and salt damage in plants, whereas its overexpression showed the opposite effects. The elite haplotype GmNPF7.5^HapB diminished Cl^- transport activity independently from NO₃^- permeability, thus enhancing soybean salt tolerance. Furthermore, the protein kinase GmPI4Kγ4 could phosphorylate GmNPF7.5, which repressed Cl^- uptake without affecting NO₃^- permeability. Our findings define a regulatory mechanism for Cl^- control under NaCl stress, providing a strategy for the improvement of salt tolerance in soybean plants.