title: The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.).
abstract: BACKGROUND
  Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability. The difficulty in recognizing grapevine genotypes based on ampelographic traits and secondary metabolites prompted the development of molecular markers suitable for achieving variety genetic identification.
  
  
  RESULTS
  Here, we propose a comparison between a multi-locus barcoding approach based on six chloroplast markers and a single-copy nuclear gene sequencing method using five coding regions combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes and genotypes to be exploited for the molecular characterization of 157 V. vinifera accessions. The analysis of the chloroplast target regions proved the inadequacy of the DNA barcoding approach at the subspecies level, and hence further DNA genotyping analyses were targeted on the sequences of five nuclear single-copy genes amplified across all of the accessions. The sequencing of the coding region of the UFGT nuclear gene (UDP-glucose: flavonoid 3-0-glucosyltransferase, the key enzyme for the accumulation of anthocyanins in berry skins) enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 130 V. vinifera distinct genotypes. Most of the genotypes proved to be cultivar-specific, and only few genotypes were shared by more, although strictly related, cultivars.
  
  
  CONCLUSIONS
  On the whole, this technique was successful for inferring SNP-based genotypes of grapevine accessions suitable for assessing the genetic identity and ancestry of international cultivars and also useful for corroborating some hypotheses regarding the origin of local varieties, suggesting several issues of misidentification (synonymy/homonymy).
authors.forename: Silvia
authors.initials: S
authors.lastname: Nicolè
authors.affiliation: Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy. gianni.barcaccia@unipd.it.
authors.forename: Gianni
authors.initials: G
authors.lastname: Barcaccia
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.forename: John W
authors.initials: JW
authors.lastname: Kress
authors.forename: Margherita
authors.initials: M
authors.lastname: Lucchin
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D005964:Glucosyltransferases / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D027843:Vitis / Q000235:genetics*
chemical_list: D017931:DNA Primers; D005964:Glucosyltransferases