The Genetic Basis of Chloride Exclusion in Grapevines

Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we leveraged one of the largest Vitis germplasm collections, comprising 335 accessions from 18 wild and cultivated Vitis species, to characterize natural variation in chloride exclusion. This diverse panel, which includes accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress, providing an unprecedented opportunity to investigate the genetic basis of salinity tolerance. Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H⁺ exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from V. acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse Vitis collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.