Dissecting the genetic basis of grapevine phenology: from multi parental QTL mapping to the improvement of local varieties

This doctoral thesis investigates the genetic basis of grapevine phenology in Vitis vinifera L., integrating genetic mapping, multi-population quantitative trait loci (QTL) analysis, marker-assisted breeding and the characterization of local grapevine diversity. The overall aim is to support sustainable viticulture by improving local varieties and identifying genetic resources for adaptation to climate change. Grapevine phenology, including budbreak, flowering, veraison and ripening, strongly influences berry composition and wine quality. Climate change and increasing biotic and abiotic stresses highlight the need to identify the genetic determinants underlying these complex developmental processes. A segregating F1 population derived from the cross between Corvina Veronese, a traditional late-ripening cultivar used for high-quality wines such as Amarone and Valpolicella, and Solaris, a resistant interspecific hybrid, was developed and characterized. Genotyping with SSR markers and the GrapeReSeq 18K Vitis genotyping chip enabled the construction of a consensus genetic map using JoinMap v5.0. The final map comprised 6,545 markers spanning approximately 1,300 cM across all 19 grapevine chromosomes, showing strong collinearity with the PN40024 12X.v2 reference genome and Spearman correlation coefficients above 0.99 for all linkage groups. Parental maps were also developed to investigate parent-specific genetic effects. Phenological traits were evaluated across multiple growing seasons, and QTL analyses were conducted in the Corvina x Solaris population and two additional mapping populations. The integration of these populations enabled the identification of genomic regions associated with different phenological stages, including loci shared across populations and traits. Candidate gene analysis highlighted putative regulators involved in hormonal signalling, dormancy release, flowering and stress responses. These findings provide a framework for identifying genomic regions potentially useful for marker-assisted breeding. A further objective was to identify genotypes combining disease resistance with desirable agronomic and enological characteristics. Progeny from the Corvina x Solaris cross were screened using molecular markers for the resistance loci Rpv3.3, Rpv10 and Ren3. Selected genotypes were subsequently evaluated through field monitoring, leaf-disc infection assays, agronomic assessments, grape-drying trials, microvinification and wine analyses. This integrated approach supports the selection of promising genotypes combining resistance to fungal diseases with traits relevant to the production of high-quality wines in the Verona wine-growing region. The thesis also investigated the genetic diversity and relationships of traditional grapevine varieties from the Northern Adriatic region using molecular and genomic approaches. SNP-based relatedness analysis, identity-by-state parameters and Mendelian inconsistency testing were used to infer parent–offspring relationships and reconstruct pedigrees. Trio validation identified reliable relationships with Mendelian error rates below 0.2%, confirming documented genealogies and providing evidence for previously unreported relationships among regional cultivars. The results contribute to understanding varietal relatedness, historical dissemination and the evolution of regional viticulture, while supporting the identification of potential synonymies and other genetic relationships. Overall, this research demonstrates the value of integrating genetic mapping, breeding and germplasm characterization. The identification of candidate genes and potentially stable QTLs, together with the evaluation of disease-resistant genotypes and the characterization of local genetic diversity, provides a foundation for breeding strategies aimed at preserving grape and wine quality under changing environmental conditions.