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Open Access Research article

A SNP transferability survey within the genus Vitis

Silvia Vezzulli1*, Diego Micheletti1, Summaira Riaz2, Massimo Pindo1, Roberto Viola1, Patrice This3, M Andrew Walker2, Michela Troggio1 and Riccardo Velasco1

Author Affiliations

1 IASMA Research Centre, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy

2 Department of Viticulture and Enology, University of California, One Shields Avenue, CA-95616 Davis, USA

3 UMR 1097, DIA-PC Equipe Génétique Vigne, INRA-Supagro, 2 place Viala, F-34060 Montpellier, France

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BMC Plant Biology 2008, 8:128  doi:10.1186/1471-2229-8-128

Published: 16 December 2008

Abstract

Background

Efforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115) genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus.

Results

This study was performed by genotyping 137 SNPs through the SNPlex™ Genotyping System (Applied Biosystems Inc.) and by comparing the SNPlex sequencing results across 35 (of the 137) regions from 69 grape accessions. A heterozygous state transferability of 31.5% across the unrelated cultivars of V. vinifera, of 18.8% across the wild forms of V. vinifera, of 2.3% among non-vinifera Vitis species, and of 0% with Muscadinia rotundifolia was found. In addition, mean allele frequencies were used to evaluate SNP informativeness and develop useful subsets of markers.

Conclusion

Using SNPlex application and corroboration from the sequencing analysis, the informativeness of SNP markers from the heterozygous grape cultivar Pinot Noir was validated in V. vinifera (including cultivars and wild forms), but had a limited application for non-vinifera Vitis species where a resequencing strategy may be preferred, knowing that homology at priming sites is sufficient. This work will allow future applications such as mapping and diversity studies, accession identification and genomic-research assisted breeding within V. vinifera.