Structural Variation and Resistance Gene Clusters Drive Disease Defense in Wild Grapes

Grapes are a cornerstone of global agriculture and the foundation of the wine and table grape industries. Yet cultivated Vitis vinifera varieties remain highly vulnerable to fungal pathogens, leading to significant yield and quality losses. Traditional breeding has struggled to keep pace with the evolutionary "arms race" between plants and pathogens. Wild grape species, however, harbor untapped resistance traits, making them vital genetic resources for modern breeding. Advances in high-fidelity sequencing and telomere-to-telomere genome assembly now enable researchers to explore these traits at unprecedented resolution. Based on these challenges, there is a need to conduct in-depth research on wild grape genomes to identify novel resistance loci.

On February 1, 2025, a team from the Chinese Academy of Agricultural Sciences and collaborators reported (DOI: 10.1093/hr/uhae306) in Horticulture Research the first phased telomere-to-telomere genome assemblies of Vitis davidii and the susceptible cultivar Vitis vinifera 'Manicure Finger'. By mapping structural variations and resistance gene clusters, the study highlights genetic factors underlying white rot resistance in wild grapes. The work reveals candidate genes and quantitative trait loci that could serve as powerful tools for breeding grape cultivars with improved disease resistance.

The researchers generated two high-quality phased genome assemblies for V. davidii and V. vinifera using PacBio HiFi and Hi-C sequencing. Comparative analysis revealed that transposable elements contributed to genome expansion in V. davidii and were closely associated with resistance genes. The team catalogued 424–478 R genes across haplotypes, finding that NBS-type genes showed stronger expression in wild grapes than in cultivated ones. Strikingly, five NBS-type R gene clusters were unique to V. davidii, absent in the cultivated genome. Transcriptomic profiling during infection with Coniella diplodiella (the white rot pathogen) uncovered hundreds of differentially expressed genes, including six NBS-type candidates with strong resistance-related expression shifts. Genetic mapping across three years of field data identified seven quantitative trait loci (QTLs), three of them novel, linked to white rot resistance. Together, these results chart the dynamic landscape of resistance genes and emphasize the evolutionary power of structural variation in shaping grape defenses.

Our study demonstrates the critical role of wild grape genomes in safeguarding viticulture. By assembling the first phased telomere-to-telomere genome of Vitis davidii, we gained unprecedented insights into how resistance genes are organized, expanded, and activated under pathogen attack. These findings not only deepen our understanding of grape evolution but also provide breeders with concrete genetic targets to develop cultivars that can withstand devastating fungal diseases".

Ying Zhang, corresponding author of the study

The discovery of unique resistance clusters and candidate genes in Vitis davidii paves the way for marker-assisted breeding and genome editing strategies in grape improvement. By integrating these resistance loci into cultivated V. vinifera backgrounds, breeders can reduce reliance on chemical fungicides, enhance sustainability, and protect global grape production. Beyond grapes, the phased genome assemblies serve as a model for exploring resistance gene evolution in other crops. This research highlights the value of conserving and sequencing wild relatives, ensuring that biodiversity continues to provide solutions to agricultural challenges under climate change.