Precise Identification of Vitis vinifera L. Varieties Using Cost-Effective NGS-Based SNP Genotyping

Abstract

In this study, we developed, validated and applied an NGS-based SNP genotyping protocol for the molecular identification of Vitis vinifera varieties, demonstrating a reliable and efficient approach for distinguishing grapevine cultivars. By utilizing a small but highly informative set of SNP loci, this method provides effective molecular genotyping while capturing the genetic diversity needed for accurate identification. This straightforward and accessible approach allows for the rapid generation of genetic profiles, which can be compared with the profiles in existing databases to precisely identify grapevine varieties, even in cases where traditional morphological methods fall short due to environmental variability or developmental differences. The process is designed to be both time-efficient and cost-effective, making it a practical tool for routine use in vineyard management, breeding programs, and conservation efforts. Furthermore, the workflow minimizes the need for whole-genome sequencing or other resource-intensive techniques, making molecular profiling accessible to a wider range of researchers, growers, and industry professionals. Analysis of the molecular profiles of known varieties validated the accuracy of the protocol. Moreover, 14 autochthonous Greek grapevine varieties that have not been previously identified were also genotyped and the data were compared with those of all Greek varieties in the Vitis International Variety Catalogue, revealing no matching multilocus genotypes across Greece.