DNA Barcoding and Its Potentials for the Genetic Identification of Grapevine Cultivars.

Vitis vinifera L., with more than 14,000 cultivars in existence on worldwide-scale plantations, is one of society's most important agricultural crops with broad genetic variability. The difficulty in recognizing grapevine varieties based on ampelographical traits and secondary metabolites prompted the development of molecular markers suitable for determining genetic diversity distribution and achieving genetic varietal identification, thus ridding numerous cases of synonymy and homonymy. In the present work, we propose a single-copy nuclear DNA barcoding approach combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes to be exploited as a new diagnostic assay of grapevine accessions. A total of 159 V. vinifera genotypes were analyzed on the basis of five nuclear coding regions, namely the GAI, ATP synthase and UFGT genes along with two ESTs. The sequencing of barcode regions enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 134 distinct haplotypes. Most of the haplotypes were cultivar-specific, and only a few haplotypes were shared by more, although strictly related, cultivars. Overall, the technique was successful for inferring haplotypes suitable for the identification of cultivars and also useful for corroborating some hypotheses regarding the origin of local cultivars, suggesting several issues of misidentification (synonymy/homonymy).