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

Abstract 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 (NO 3 − ) uptake in a pH-dependent manner and exhibited higher permeability for Cl − over NO 3 − . 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 NO 3 − permeability, thus enhancing soybean salt tolerance. Furthermore, the protein kinase GmPI4Kγ4 could phosphorylate GmNPF7.5, which repressed Cl − uptake without affecting NO 3 − 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.