Genome-wide genetic diversity in grapevine rootstocks and wild Vitis reveals adaptive potential in rootstocks breeding

Abstract

Grapevine rootstocks are a key determinant of vineyard performance, yet the genetic diversity supporting rootstock relevant phenotypes and environmental adaptation in commercial rootstocks remains poorly characterized. In this study, we compared the genetic diversity between 59 commercial rootstocks and a germplasm collection of 280 wild Vitis accessions using whole-genome sequencing data. We identified 3M highly reliable single nucleotide polymorphisms across all genotypes and used this information to assess genetic diversity. Measures of nucleotide diversity, heterozygosity, and linkage disequilibrium permitted to quantify and compare genomic diversity between commercial and wild groups, while population structure and phylogenomic analyses were conducted to assess genetic relationships. We compared commercial rootstocks genetic diversity relative to wild Vitis accessions, to estimate the impact of targeted selection during breeding. We hypothesize that wild accessions carry high allelic diversity with adaptive potential, especially in genomic regions where QTLs related to stress tolerance were previously identified. This study investigate how wild Vitis germplasm can be a potential reservoir of adaptive genetic variation that remains underutilized in rootstock breeding. Our findings provide a genomic framework for identifying candidate alleles and introgression targets to improve resilience and adaptive capacity in future grapevine rootstock breeding programs, supporting viticulture under increasingly variable environmental conditions.