Metabolomics‐driven gene mining and genetic improvement of tolerance to salt‐induced osmotic stress in maize

Abstract

• The farmland of the world’s main corn‐producing area is increasingly affected by salt stress. Therefore, the breeding of salt‐tolerant cultivars is necessary for the long‐term sustainability of global corn production. • Previous studies have shown that natural maize varieties displayed large diversity of salt tolerance, however, the genetic variants underlying such diversity remains poorly discovered and applied, especially those mediating the tolerance to salt‐induced osmotic stress (SIOS). Here we report a metabolomics‐driven understanding and genetic improvement of maize SIOS tolerance. • With LC‐MS‐based untargeted metabolomics approach, we profiled the metabolomes of 266 maize inbred lines under control and salt conditions, and then identified 37 metabolite biomarkers of SIOS tolerance (METO1‐37). Follow‐up metabolic GWAS (mGWAS) and genotype‐to‐phenotype modeling identified 10 candidate genes significantly associating with the SIOS tolerance and METO abundances. Furthermore, we validated that a citrate synthase, a glucosyltransferase and a cytochrome P450 underlie the genotype‐METO‐SIOS tolerance associations, and showed that their favorable alleles additively improve the SIOS tolerance of elite maize inbred lines. • Our study provides a novel insight into the natural variation of maize SIOS tolerant, which boosts the genetic improvement of maize salt tolerance, and demonstrates a metabolomics‐based approach for mining crop genes associated with complex agronomic trait.