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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.).

Nicolè S, Barcaccia G, Erickson DL, Kress JW, Lucchin M - BMC Res Notes (2013)

Bottom Line: Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability.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.

View Article: PubMed Central - HTML - PubMed

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.

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.

Findings: 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.

Conclusion: 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).

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Part of the Neighbour-Joining tree based on Kimura 2-parameter for 164 grapevine entries belonging to Vitis spp. and rooted using as outgroup the accessions from V. labrusca, V. cinerea, V. berlandieri, V. rupestris and V. riparia species. In detail, only the branches showing the relationships among Vitis spp. and the interspecific hybrids are indicated (see Additional file 3 for the complete Neighbour-Joining tree). The branch labelled with V. vinifera accessions indicates the whole accessions of V. vinifera and includes also the putative hybrid 516_Tintoria that resulted to be indistinguishable from other cultivated grapevines. The numbers above the nodes represent the bootstrap support after 1,000 replicates.
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Figure 4: Part of the Neighbour-Joining tree based on Kimura 2-parameter for 164 grapevine entries belonging to Vitis spp. and rooted using as outgroup the accessions from V. labrusca, V. cinerea, V. berlandieri, V. rupestris and V. riparia species. In detail, only the branches showing the relationships among Vitis spp. and the interspecific hybrids are indicated (see Additional file 3 for the complete Neighbour-Joining tree). The branch labelled with V. vinifera accessions indicates the whole accessions of V. vinifera and includes also the putative hybrid 516_Tintoria that resulted to be indistinguishable from other cultivated grapevines. The numbers above the nodes represent the bootstrap support after 1,000 replicates.

Mentions: The NJ tree constructed on the basis of the sequence polymorphisms of all five target barcodes allowed splitting of the accessions of the species V. labrusca, V. cinerea, V. berlandieri, V. rupestris and V. riparia into distinct main branches with bootstrap values higher than 75% (Figure 4), whereas the branching nodes of V. vinifera cultivars were weakly supported (see Additional file 3). Because of the lack of resolution of the NJ tree for V. vinifera accessions, a new approach based on genotype reconstruction was tested using the characteristic attributes by exploring the information content of single SNPs.


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.).

Nicolè S, Barcaccia G, Erickson DL, Kress JW, Lucchin M - BMC Res Notes (2013)

Part of the Neighbour-Joining tree based on Kimura 2-parameter for 164 grapevine entries belonging to Vitis spp. and rooted using as outgroup the accessions from V. labrusca, V. cinerea, V. berlandieri, V. rupestris and V. riparia species. In detail, only the branches showing the relationships among Vitis spp. and the interspecific hybrids are indicated (see Additional file 3 for the complete Neighbour-Joining tree). The branch labelled with V. vinifera accessions indicates the whole accessions of V. vinifera and includes also the putative hybrid 516_Tintoria that resulted to be indistinguishable from other cultivated grapevines. The numbers above the nodes represent the bootstrap support after 1,000 replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222114&req=5

Figure 4: Part of the Neighbour-Joining tree based on Kimura 2-parameter for 164 grapevine entries belonging to Vitis spp. and rooted using as outgroup the accessions from V. labrusca, V. cinerea, V. berlandieri, V. rupestris and V. riparia species. In detail, only the branches showing the relationships among Vitis spp. and the interspecific hybrids are indicated (see Additional file 3 for the complete Neighbour-Joining tree). The branch labelled with V. vinifera accessions indicates the whole accessions of V. vinifera and includes also the putative hybrid 516_Tintoria that resulted to be indistinguishable from other cultivated grapevines. The numbers above the nodes represent the bootstrap support after 1,000 replicates.
Mentions: The NJ tree constructed on the basis of the sequence polymorphisms of all five target barcodes allowed splitting of the accessions of the species V. labrusca, V. cinerea, V. berlandieri, V. rupestris and V. riparia into distinct main branches with bootstrap values higher than 75% (Figure 4), whereas the branching nodes of V. vinifera cultivars were weakly supported (see Additional file 3). Because of the lack of resolution of the NJ tree for V. vinifera accessions, a new approach based on genotype reconstruction was tested using the characteristic attributes by exploring the information content of single SNPs.

Bottom Line: Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability.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.

View Article: PubMed Central - HTML - PubMed

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.

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.

Findings: 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.

Conclusion: 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).

Show MeSH