Genetic characterizations in grapevine: phenology regulation and ancient varieties

Grapevine (Vitis vinifera spp. vinifera) is an important crop grown worldwide, playing a key role in the economic and historical context of the Verona region. Like many other crops, grapevine is vulnerable to the effects of climate change, particularly rising temperatures, which can accelerate phenological stages and negatively impact the quality of the final product. Consequently, understanding the genetic factors influencing key phenological stages, such as flowering, veraison, and the interval between these events, is critical for developing grapevine cultivars that are better suited to a changing climate. The first aim of this thesis was to identify promising genomic regions involved in the phenology regulations in order to point out interesting candidate genes for more deeper analysis. We conducted a Genome-Wide Association (GWA) analysis to identify Single Nucleotide Polymorphisms (SNPs) significantly associated with flowering time, veraison time, and the interval between these two stages. We characterized a wide germplasm collection of grapevine accessions, from the CREA-VE in Susegana, Treviso (Italy) and constructed a genotypic dataset from new and published data including 6.679 SNPs for 365 unique genotypes. Over a period of 11 years, all cultivars were phenotyped for flowering and veraison times. The distribution of these traits was examined and corrected if necessary. The flowering-veraison interval was derived and analyzed similarly. We conducted GWA analysis using two software, TASSEL 5.0 and GAPIT 3, applying different statistical model, that allowed to identify a total of 228 SNPs associated to the three phenological traits. Twelve SNPs resulted consistently associated to the phenological traits in the analysis conducted with both software. As conclusion, we highlighted genomic regions including putative candidate genes and functional annotation and Geno Ontology (GO)were considered to point out those more interesting for further analysis. The second aim of this thesis was to explore the historical context of viticulture in Verona area by establishing the genetic characterization of archeological grapevine’s seeds excavated from four archeological sites and four different period (from 20th century BC to 13th century CE). To this aim we have set up a pipeline on the archeological remains starting with the optimization of an ancient DNA extraction protocol from grapevine seeds and libraries preparation for NGS sequencing. Once optimized the pipeline was applied on different remains from the four different archeological sites obtaining 37 libraries suitable for sequencing. We conducted bioinformatic analysis of sequencing data in order to validate the authenticity of aDNA and the presence of endogenous DNA. In this way we were able to point out samples more suitable for target enrichment sequencing, in order to retrieve SNPs profiles from ancient varieties to be compared to modern ones.