Sharma Sadikshya, Cochetel Noe, Munoz Jose R, Banayad Hollywood, Lupo Yaniv, Nunez Veronica, Gaspar Ana, Chen Christopher, Bhattarai Krishna, Gaut Brandon S, Cantu Dario, Diaz-Garcia Luis
Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, United States.
Cooperative Extension, Division of Agriculture and Natural Resources, Hopland Research and Extension Center, University of California, Hopland, CA 95449, United States.
G3 (Bethesda). 2025 Sep 3;15(9). doi: 10.1093/g3journal/jkaf149.
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 analyzed natural variation in chloride exclusion using a diverse panel of 335 accessions representing 18 wild and cultivated Vitis species. This panel, comprising accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress and provides a valuable genetic resource for breeding efforts aimed at introducing novel traits. Using genome-wide association and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8, now designated qClEx8.1, containing candidate genes encoding cation/H⁺ exchangers (CHXs), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from Vitis acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed nonsynonymous substitutions within CHX genes that may influence protein function and 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 phenotypic and genomic data across a diverse Vitis collection, this study advances our understanding of the genetic architecture underlying chloride exclusion and highlights candidate genes for breeding salt-tolerant rootstocks.
地中海地区是全球葡萄生产的重要区域之一，其气候干燥，土壤盐碱化问题频发。在这些环境中，氯离子毒性是限制葡萄藤生长和果实品质的主要因素。尽管氯离子排斥在耐盐性中起着关键作用，但该性状背后的遗传机制仍知之甚少。在本研究中，我们使用了一个由335份种质组成的多样化群体来分析氯离子排斥的自然变异，这些种质代表了18个野生和栽培葡萄品种。该群体包括来自美国西南部和墨西哥的种质，涵盖了对非生物胁迫的广泛进化适应性，为旨在引入新性状的育种工作提供了宝贵的遗传资源。通过全基因组关联分析和数量性状位点（QTL）定位，我们在8号染色体上鉴定出一个主要的QTL，现命名为qClEx8.1，其中包含编码阳离子/H⁺ 交换体（CHXs）的候选基因，这些基因参与离子运输和体内平衡。为了验证这些发现，我们分析了一个由长叶 Acerifolia 葡萄9018和商业砧木GRN3衍生而来的作图群体，证实8号染色体位点是氯离子排斥的主要决定因素。结构变异分析揭示了CHX基因内的非同义替换，这些替换可能影响蛋白质功能和耐盐性。此外，我们在19号染色体上发现了一个新丰富了G型凝集素S受体样丝氨酸/苏氨酸蛋白激酶的QTL，这些激酶是已知的胁迫信号调节因子。通过整合不同葡萄品种的表型和基因组数据，本研究推进了我们对氯离子排斥遗传结构的理解，并突出了用于培育耐盐砧木的候选基因。
