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

BackgroundVitis 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.FindingsHere, 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.ConclusionOn 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).

Comparative Transcriptome Analysis of Genes Involved in Anthocyanin Biosynthesis in the Red and Yellow Fruits of Sweet Cherry (Prunus avium L.)

“…The combinations of and interactions between the MYB, bHLH and WD40 transcription factors mediate the regulation of the anthocyanin biosynthetic pathway [ 15 ]. The structural genes and transcription factors that are involved in the anthocyanin biosynthetic pathway have been identified through biochemical and genetic analyses in several fruit trees, including strawberry, apple, and grape [ 16 , 17 , 18 , 19 ].…”

DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy

“…There are many advantages in the use of DNA barcoding as it is reproducible and testable as long as the link between DNA test sequences and reference specimens is supported, and also verifiable at any time and by any researcher [4]. Moreover, the experimental procedure for extracting genomic DNA and amplifying specific DNA markers is technically easy and usually does not require the destruction of the sample, which sometimes is valuable and therefore needs to be safeguarded [6]. It allows all kinds of specimens to be treated, including those non-identifiable by morphology, and represents an universal applicable method that can be linked to any kind of biological or biodiversity information [54].…”

DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy

“…Moreover, the experimental procedure for extracting genomic DNA and amplifying specific DNA markers is technically easy and usually does not require the destruction of the sample, which sometimes is valuable and therefore needs to be safeguarded [6]. It allows all kinds of specimens to be treated, including those non-identifiable by morphology, and represents an universal applicable method that can be linked to any kind of biological or biodiversity information [54].…”

“…This represents a requirement, especially for local and typical products based on specific cultivar and/or production area. With a few exceptions (for instance, see [6,49]), chloroplast DNA barcoding must be replaced by nuclear DNA genotyping for single cultivar identification or authentication.…”

“…Of the protein-coding genes present on the animal mitochondrial genome, the use of cytochrome c oxidase subunit 1 (cox1 or COI) was proposed as a standard barcode marker for animal species for two main reasons: universal primers make a 648 bp fragment at the 5 1 end of this gene easy to amplify in a broad spectrum of phyla, and its nucleotide substitution rate allows not only closely related species to be distinguished but, in some taxa, also different populations, biotypes or races of the same species. Other mitochondrial genes were suggested as barcode markers, including cob, which encodes for apocytochrome b; cox2 and cox3, which encode for the cytochrome oxidase subunits 2 and 3, respectively; nad1, which encodes for NADH dehydrogenase subunit 1; and the mitochondrial 16S-rDNA gene ( [4][5][6] and references therein).…”