Genomic insights into Apulian wine grape varieties through GBS analysis

Abstract

The Apulian grapevine varieties NEGRAMARO, PRIMITIVO, and UVA DI TROIA, all autochthonous to the Apulia region, play a pivotal role in the production of several high-quality wines that rank among the most widely exported Italian wines worldwide. Preserving local viticultural biodiversity is essential to maintaining the distinctive quality traits of these varieties, while strengthening the cultural and territorial identity of the region at the benefit of wineries aiming to expand their domestic and international markets. In this study, we investigated the genomic variability within and among the Apulian grapevine varieties NEGRAMARO, MALVASIA NERA, PRIMITIVO, MINUTOLO BIANCO, and UVA DI TROIA using a genotyping-by-sequencing (GBS) approach. The data obtained were used to assess genetic diversity, population structure, and varietal differentiation. Substantial genetic variation was observed within each variety, and the genetic uniqueness of all examined samples was confirmed. Population structure analysis revealed strong genetic differentiation among varieties (F_ST values ranging from 0.27 to 0.41), in particular between MINUTOLO BIANCO and UVA DI TROIA. The lowest numbers of divergent loci were observed between NEGRAMARO and PRIMITIVO (N = 100) and between NEGRAMARO and MALVASIA NERA (N = 256), indicating closer genetic relationships. A total of 1,785 SNPs were located within genes associated with secondary metabolism, stress responses, and berry quality traits; notably, 13 variants, including seven stop-gained mutations, were predicted to have a high functional impact. The analysis also enabled the development of a six-SNP panel reliable for varietal authentication, providing a useful tool for fraud prevention and labelling compliance. Overall, this study confirms the rich genomic diversity of Apulian grapevine varieties and demonstrates the potential of high-resolution genotyping approaches to support conservation, breeding, and quality control initiatives in viticulture.