Whole-genome sequencing of eight grapevine clones of cv. Tribidrag (Vitis vinifera L.) reveals measurable differentiation not linked directly to phenotypic divergence

Vegetative propagation of grapevine ensures genetically uniform progeny. Tribidrag (syn. Zinfandel, Primitivo, Kratošija) is a red-berried grapevine cultivar that produces high-quality wines. Although clonal variation in Tribidrag has been described at both the phenotypic and molecular levels, the relationship between phenotypic traits and their underlying genomic basis is poorly understood. In this study, productive traits, including yield, yield components, and basic must chemical parameters, were evaluated in eight Tribidrag clones over three consecutive years. There was significant variability in clone productivity and phenotypic plasticity, and significant clone-by-year interaction. Primitivo clones FPS03 and FPS06 had lower productivity, smaller berry size, greater sugar content, and lower total acidity in 2021 and 2022 than the Zinfandel 1–24 clone, which consistently displayed greater productivity in all three years. Genetic variability among clones was assessed using short-read whole-genome resequencing. A high and relatively uniform level of genomic variation was detected, with ~ 3.8 million SNPs and ~ 300,000 InDel variants per sample. Most structural variants were located in intergenic regions. Pairwise SNP differences among eight clones in 100-kb genomic windows revealed candidate signatures of clonal selection. Principal component analysis identified three principal clusters with no clear geographic association among samples. The identified genetic groupings showed no direct association with phenotypic or productive traits of individual clones. These findings contribute to a more comprehensive understanding of the genomic basis of clonal variability in Tribidrag.