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 the saline-alkaline tolerance was compromised during tomato domestication and improvement, and a natural variation in promoter of SlSCaBP8, an EF-hand Ca2+ binding protein, contributes 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 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 promoter of SlSCaBP8 for tomato breeding.

Chromosome-level genome assembly of Solanum pimpinellifolium

“…Particularly, the well-established introgression line population from cross of S. lycopersicum cv. E6203 and LA1589 represents one of the widest crosses and serves as an important source for scientists and breeders 27 . Although the draft genome assembly of this accession was published 10 years ago 28 , a chromosome-level genome sequence has not yet been published, and thus the vast majority of sequence variations are poorly characterized and their impact on important traits are largely hidden.…”