Unveiling clonal and intra-varietal diversity in Apulia’s representative grape varieties

The Apulian wine industry, a cornerstone of Italian viticulture, benefits from the great genetic diversity of local grape varieties that are closely linked to the traditional and cultural heritage of Apulian landscape. The aim of this study is to investigate the genomic diversity of five representative Apulian grapevine varieties, ‘Negramaro’, ‘Malvasia Nera’, ‘Primitivo’, ‘Minutolo Bianco’ and ‘Uva di Troia’ using genotyping-by-sequencing. By analysing 59 183 high-quality single nucleotide polymorphism (SNP) markers across 75 clones, we were able to detect significant genetic variation within and between varieties. The fixation index was calculated for each individual SNP, identifying 5 363 non-redundant divergent SNPs. Of these, 1 785 were located within genes, including 887 in untranslated regions, 518 in introns, and 380 in coding sequences. The results highlighted divergent loci associated with genes crucial for secondary metabolism, stress resilience, and berry quality traits. Key genes identified in this study include WRKY transcription factors, MYB regulators, and enzymes such as glycosyltransferases and O-methyltransferases, all of which play an important role in the biosynthesis of secondary metabolites that influence wine flavour, aroma, and pigmentation. Additionally, six SNP loci were validated for varietal discrimination by PCR amplification and Sanger sequencing, confirming their potential for traceability. These results provide a solid genomic foundation for the preservation and valorisation of Apulia's rich wine heritage and for the development of targeted breeding programs to enhance the quality and resilience of Apulian wines in the face of changing consumer’s preferences, market and climatic conditions.