A natural variation in SlSCaBP8 promoter contributes to the loss of saline–alkaline tolerance during tomato improvement

Abstract Saline–alkaline stress is a worldwide problem that threatens the growth and yield of crops. However, how crops adapt to saline–alkaline stress remains less studied. Here we show that saline–alkaline tolerance was compromised during tomato domestication and improvement, and a natural variation in the promoter of SlSCaBP8, an EF-hand Ca2+ binding protein, contributed to the loss of saline–alkaline tolerance during tomato improvement. The biochemical and genetic data showed that SlSCaBP8 is a positive regulator of saline–alkaline tolerance in tomato. The introgression line Pi-75, derived from a cross between wild Solanum pimpinellifolium LA1589 and cultivar E6203, containing the SlSCaBP8LA1589 locus, showed stronger saline–alkaline tolerance than E6203. Pi-75 and LA1589 also showed enhanced saline–alkaline-induced SlSCaBP8 expression than that of E6203. By sequence analysis, a natural variation was found in the promoter of SlSCaBP8 and the accessions with the wild haplotype showed enhanced saline–alkaline tolerance compared with the cultivar haplotype. Our studies clarify the mechanism of saline–alkaline tolerance conferred by SlSCaBP8 and provide an important natural variation in the promoter of SlSCaBP8 for tomato breeding.