LAUSR

Summary The sodium cation (Na+) is the predominant cation with deleterious effects on crops in salt‐affected agricultural areas. Salt tolerance of crop can be improved by increasing shoot Na+ exclusion. Therefore, it is crucial to identify and use genetic variants of various crops that promote shoot Na+ exclusion. Here, we show that a HKT1 family gene ZmNC3 (Zea mays L. Na + Content 3; designated ZmHKT1;2) confers natural variability in shoot‐Na+ accumulation and salt tolerance in maize. ZmHKT1;2 encodes a Na+‐preferential transporter localized in the plasma membrane, which mediates shoot Na+ exclusion, likely by withdrawing Na+ from the root xylem flow. A naturally occurring nonsynonymous SNP (SNP947‐G) increases the Na+ transport activity of ZmHKT1;2, promoting shoot Na+ exclusion and salt tolerance in maize. SNP947‐G first occurred in the wild grass teosinte (at a allele frequency of 43%) and has become a minor allele in the maize population (allele frequency 6.1%), suggesting that SNP947‐G is derived from teosinte and that the genomic region flanking SNP947 likely has undergone selection during domestication or post‐domestication dispersal of maize. Moreover, we demonstrate that introgression of the SNP947‐G ZmHKT1;2 allele into elite maize germplasms reduces shoot Na+ content by up to 80% and promotes salt tolerance. Taken together, ZmNC3/ZmHKT1;2 was identified as an important QTL promoting shoot Na+ exclusion, and its favourable allele provides an effective tool for developing salt‐tolerant maize varieties.