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Summary  Salt stress has detrimental effects on crop growth and yield, and the area of salt‐affected land is increasing. Soybean is a major source of vegetable protein, oil and feed, but considered as a salt‐sensitive crop. Cultivated soybean ( Glycine max ) is domesticated from wild soybean ( G. soja ) but lost considerable amount of genetic diversity during the artificial selection. Therefore, it is important to exploit the gene pool of wild soybean. In this study, we identified 34 salt‐tolerant accessions from wild soybean germplasm and found that a 7‐bp insertion/deletion (InDel) in the promoter of  GsERD15B  (early responsive to dehydration 15B) significantly affects the salt tolerance of soybean.  GsERD15B  encodes a protein with transcriptional activation function and contains a PAM2 domain to mediate its interaction with poly(A)‐binding (PAB) proteins. The 7‐bp deletion in  GsERD15B  promoter enhanced the salt tolerance of soybean, with increased up‐regulation of  GsERD15B , two  GmPAB  genes, the known stress‐related genes including  GmABI1 ,  GmABI2 ,  GmbZIP1 ,  GmP5CS ,  GmCAT4 ,  GmPIP1:6 ,  GmMYB84  and  GmSOS1  in response to salt stress. We propose that natural variation in  GsERD15B  promoter affects soybean salt tolerance, and overexpression of  GsERD15B  enhanced salt tolerance probably by increasing the expression levels of genes related to ABA‐signalling, proline content, catalase peroxidase, dehydration response and cation transport.

Natural variation in the promoter of GsERD15B affects salt tolerance in soybean