a genetic map was constructed using F2 population derived from a cross between a wild germplasm of C. olitorius L. (J009) and the variety Guangfengchangguo (GFG), including 4839 SNP markers. Using the genetic map, we identified major and minor QTLs involved in salt tolerance. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.