A Metabolome Atlas of Grape Biodiversity

Grapevine (Vitis spp.) is one of the world’s most economically, culturally, and biologically important fruit crops, with remarkable diversity spanning thousands of V. vinifera cultivars together with rootstocks and wild relatives. Yet grapevine biodiversity has never been systematically explored at the metabolome scale, despite its importance for chemotaxonomy, breeding, and sustainable viticulture. Here, we present the Grape Metabolome (GM) Project, the first systematic liquid chromatography–mass spectrometry (LC–MS) survey of grapevine biodiversity, comprising 462 samples from 126 accessions collected across four vintages. Advanced and well-established chemometric tools resolved the major grape chemotypes together with finer cultivar-related substructure, while annotation-guided interpretation linked this organization to distinctive patterns in anthocyanins, flavonols, aroma-related compounds, and tannin-associated phenolics. This data set provides a reference framework for chemotaxonomy, breeding, authenticity, precision viticulture and enology.