Pangenomic framework for globe artichoke supports SNP-based varietal fingerprinting

Globe artichoke (Cynara cardunculus var. scolymus L.) comprises a broad range of local ecotypes and varietal groups whose genetic diversity has been investigated through different molecular markers. However, recent advances in next-generation sequencing and pangenomic approaches provide new opportunities to capture genome-wide variation at higher resolution and to develop practical tools for varietal discrimination, traceability, and germplasm conservation. In this study, we developed the first pangenomic framework for cultivated artichoke and evaluated pangenome-informed single-nucleotide polymorphism (SNP) markers for varietal fingerprinting. Whole-genome resequencing data from the Italian local ecotype Asti Sorì were integrated with publicly available genomic data from representative globe artichoke and cultivated cardoon accessions to construct and annotate a pangenome. Genome-wide SNP and presence/absence variation (PAV) analyses were combined with pangenome-anchored genotyping-by-sequencing (GBS) data from 45 accessions representing the main cultivated varietal groups. The pangenome revealed a largely conserved core gene repertoire alongside a smaller accessory component, with gene accumulation curves suggesting a tendency toward saturation within the sampled cultivated germplasm. SNP- and PAV-based analyses provided complementary views of accession relationships and consistently resolved the principal cultivated groups. Across the broader germplasm panel, pangenome-anchored GBS-derived SNPs identified well-supported phylogenetic clusters corresponding to recognized varietal types. The best-performing 50-SNP panel showed a high correlation with the pairwise genetic-distance matrix obtained from the complete dataset (Pearson's r = 0.96) and largely reproduced its main varietal structure. This compact marker set provides a practical foundation for varietal fingerprinting, DUS (distinctness, uniformity, and stability)-oriented applications, traceability, and conservation of traditional globe artichoke germplasm.