When Genetics Meets Ecology: Genomics and Taxonomy of Vitis Species and Cultivars

Knowledge of the biology of the genus Vitis has undergone a profound transformation, evolving from the morphological descriptions of classical ampelography to the high-resolution analyses enabled by modern phylogenomics. This review explores the “Paradox of the Vine”—the remarkable phenotypic plasticity that historically complicated botanical nomenclature—and examines how genomic tools have helped resolve many of these long-standing taxonomic challenges. We trace the development of grapevine genomics from the first near-homozygous reference genome (PN40024) to the current era of telomere-to-telomere (T2T) assemblies and phased diploid genomes. Attention is given to the genomic “dark matter” represented by transposable elements and structural variation, which contribute substantially to varietal identity and species-specific adaptation to changing environmental conditions. Advances in bioinformatic methodologies, including pangenome graph construction and machine learning-based variant detection, now enable clonal discrimination and complex parentage analysis with unprecedented precision. The definition of genuine wild grapevines (Vitis vinifera subsp. sylvestris) remains a critical issue in studies of grapevine evolution, domestication, and genome structure. The traditional concept of wild populations free from introgression by cultivated grapevines has been increasingly challenged by ecological observations and molecular evidence. Distinguishing truly wild populations from feral lineages is therefore essential for reconstructing the history of grapevine domestication and understanding patterns of gene flow between cultivated and wild compartments. Future progress in Vitis systematics will depend on the integration of genomic, ecological, and morphometric approaches. We propose that the next generation of grapevine taxonomy will combine the historical insights of ampelography with high-throughput phenotyping and comprehensive pangenomic resources, leading to a predictive and evolutionarily informed framework for the classification of Vitis species and cultivars.