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Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome

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Abstract

Five hundred and six EST-derived markers, 313 SSR markers and 26 BAC end-derived or SCAR markers were anchored by PCR on a subset of a Cabernet Sauvignon BAC library representing six genome equivalents pooled in three dimensions. In parallel, the 12,351 EST clusters of the grapevine UniGene set (build #11) from NCBI were used to design 12,125 primers pairs and perform electronic PCR on 67,543 nonredundant BAC-end sequences. This in silico experiment yielded 1,140 positive results concerning 638 different markers, among which 602 had not been already anchored by PCR. The data obtained will provide an easier access to the regulatory sequences surrounding important genes (represented by ESTs). In total, 1,731 islands of BAC clones (set of overlapping BAC clones containing at least one common marker) were obtained and 226 of them contained at least one genetically mapped anchor. These assigned islands are very useful because they will link the genetic map and the future fingerprint-based physical map and because they allowed us to indirectly place 93 ESTs on the genetic map. The islands containing two or more mapped SSR markers were also used to assess the quality of the integrated genetic map of the grapevine genome.

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Acknowledgements

This research was funded by the GĂ©noplante grant CI2001002-SEP20 and the Institut National de la Recherche Agronomique. The authors warmly thank D. Forest and M. Tabet for technical help, Dr M-L. Martin-Magniette for help with statistics and P. Abbal, N. Terrier and A. Ageorges for providing us with their very first unigene set of EST sequences.

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Author notes

  1. Anne Bernole

    Present address: Gip GEVES Magneraud, Le Magneraud St-Pierre-d’Amilly, BP 52, 17700, Surgères, France

  2. Vincent Thareau

    Present address: Institut de Biotechnologie des Plantes, Université Paris-Sud, Bat. 630, 91 405, Orsay cedex, France

Authors and Affiliations

  1. UMR INRA-CNRS-UEVE de Recherches en Génomique Végétale, 2 rue Gaston Crémieux, BP5708, 91057, Evry Cedex, France

    Didier Lamoureux, Anne Bernole, Isabelle Le Clainche, Sarah Tual, Vincent Thareau, Sophie Paillard, Michel Caboche, Boulos Chalhoub & Anne-Françoise Adam-Blondon

  2. Unité de Recherches en Génomique-Informatique, Infobiogen, 523 place des Terrasses, 91 034, Evry cedex, France

    Fabrice Legeai

  3. Génoscope, 2 rue Gaston Crémieux, BP5708, 91057, Evry Cedex, France

    Carole Dossat & Patrick Wincker

  4. UMR Vigne et Vins d’alsace, 28 rue Herrlisheim, 68021, Colmar cedex, France

    Marilyn Oswald & Didier Merdinoglu

  5. UMR Transport des Assimilats, Bât. Botanique, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022, Poitiers, France

    Céline Vignault & Serge Delrot

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  1. Didier Lamoureux
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  14. Michel Caboche
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  16. Anne-Françoise Adam-Blondon
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Corresponding author

Correspondence to Anne-Françoise Adam-Blondon.

Additional information

Communicated by P. Langridge

Didier Lamoureux and Anne Bernole contributed equally to this work.

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Lamoureux, D., Bernole, A., Le Clainche, I. et al. Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome. Theor Appl Genet 113, 344–356 (2006). https://doi.org/10.1007/s00122-006-0301-7

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  • DOI: https://doi.org/10.1007/s00122-006-0301-7

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