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A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers

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Abstract

We have developed an integrated map from five elite cultivars of Vitis vinifera L.; Syrah, Pinot Noir, Grenache, Cabernet Sauvignon and Riesling which are parents of three segregating populations. A new source of markers, SNPs, identified in ESTs and unique BAC-end sequences was added to the available IGGP reference set of SSRs. The complete integrated map comprises 1,134 markers (350 AFLP®, 332 BESs, 169 ESTs, 283 SSRs) spanning 1,443 cM over 19 linkage groups and shows a mean distance between neighbouring loci of 1.27 cM. Marker order was mainly conserved between the integrated map and the highly dense Syrah × Pinot Noir consensus map except for few inversions. Moreover, the marker order has been validated through the assembled genome sequence of Pinot Noir. We have also assessed the transferability of SNP-based markers among five V. vinifera varieties, enabling marker validation across different genotypes. This integrated map can serve as a fundamental tool for molecular breeding in V. vinifera and related species and provide a basis for studies of genome organization and evolution in grapevines.

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Acknowledgments

The authors are grateful to Marco Facci, Jessica Zambanini, Diego Micheletti and Alexandre Fournier-Level for their technical support, and to Alessandro Cestaro, Paolo Fontana and Lorenzo Dematté for their bioinformatics assistance. They also wish to thank Agnès Doligez for helpful discussions. This work was supported in part by the Fondazione Cassa di Risparmio di Trento e Rovereto, the Autonomous Province of Trento, CSIRO Plant Industry and the Commonwealth Cooperative Research Centre Program, and specifically the Cooperative Research Centre for Viticulture (CRCV) and the Grape and Wine Research and Development Cooperation (GWRDC).

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Authors and Affiliations

  1. IASMA Research Centre, San Michele a/Adige, Italy

    Silvia Vezzulli, Michela Troggio, Giuseppina Coppola, Marco Stefanini, M. Stella Grando, Roberto Viola & Riccardo Velasco

  2. CSIRO Plant Industry, Glen Osmond, Australia

    Angelica Jermakow & Mark Thomas

  3. Myriad Genetics Inc., Salt Lake City, UT, USA

    Dustin Cartwright & Andrey Zharkikh

  4. UMR 1165, INRA-CNRS-Université d Evry Génomique Végétale, Paris Cedex, France

    Anne-Françoise Adam-Blondon

  5. UMR 1097, DIA-PC Equipe génétique Vigne, INRA Supagro, Montepellier, France

    Patrice This

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  1. Silvia Vezzulli
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  2. Michela Troggio
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  3. Giuseppina Coppola
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  4. Angelica Jermakow
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  6. Andrey Zharkikh
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  7. Marco Stefanini
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  8. M. Stella Grando
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  9. Roberto Viola
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  10. Anne-Françoise Adam-Blondon
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  11. Mark Thomas
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  12. Patrice This
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  13. Riccardo Velasco
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Correspondence to Silvia Vezzulli.

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Communicated by H. Nybom.

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Supplementary Figure S1 (PPT 265 kb)

Supplementary Figure S2 (PPT 1366 kb)

Table S1 (supplementary information). The 501 SNP-based markers mapped in the integrated map. (XLS 196 kb)

122_2008_794_MOESM4_ESM.xls

Table S2 (supplementary information). Distribution of marker type in the linkage groups and physical genome contigs. (XLS 28 kb)

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Vezzulli, S., Troggio, M., Coppola, G. et al. A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers. Theor Appl Genet 117, 499–511 (2008). https://doi.org/10.1007/s00122-008-0794-3

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