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 and GmNPF7.5), which was associated with Cl content. GmNPF7.5 mediated Cl or nitrate (NO) uptake in a pH-dependent manner and exhibited higher permeability for Cl over NO. The suppression of GmNPF7.5 expression decreased Cl accumulation and salt damage in plants, whereas its overexpression showed the opposite effects. The elite haplotype GmNPF7.5 diminished Cl transport activity independently from NO permeability, thus enhancing soybean salt tolerance. Furthermore, the protein kinase GmPI4Kγ4 could phosphorylate GmNPF7.5, which repressed Cl uptake without affecting NO 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.