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Journal articles
Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome
Didier Lamoureux
1
Anne Bernole
1
Isabelle Le Clainche
1
Sarah Tual
1
Vincent Thareau
1, 2
Sophie Paillard
1
Fabrice Legeai
3
Carole Dossat
4
Patrick Wincker
4
Marylin Oswald
5
Didier Merdinoglu
5
Cécile Vignault
6
Serge Delrot
6
Michel Caboche
1
Boulos Chalhoub
1
Anne-Françoise Adam-Blondon
1
Didier Lamoureux 1
Author
Anne Bernole 1
Author
Isabelle Le Clainche 1
Author IdHAL : isabelle-le-clainche
Sarah Tual 1
Author
Vincent Thareau 1, 2
Author
Sophie Paillard 1
Author IdHAL : sophie-paillard ORCID : https://orcid.org/0000-0001-7516-848X
Fabrice Legeai 3
Author
Carole Dossat 4
Author
Patrick Wincker 4
Author
Marylin Oswald 5
Author
Didier Merdinoglu 5
Author
Cécile Vignault 6
Author
Serge Delrot 6
Author
Michel Caboche 1
Author
Boulos Chalhoub 1
Author
Anne-Françoise Adam-Blondon 1
Author IdHAL : anne-francoise-adam-blondon ORCID : https://orcid.org/0000-0002-3412-9086
1
URGV - Unité de recherche en génomique végétale (2, rue G. Crémieux - BP 5708 91057 EVRY CEDEX - France)
- INRA - Institut National de la Recherche Agronomique : UR1165 (France)
- UEVE - Université d'Évry-Val-d'Essonne (Boulevard François Mitterrand 91025 Evry Cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR8114 (France)
2
IBP - Institut de biotechnologie des plantes (bat. 630 91405 ORSAY CEDEX - France)
- UP11 - Université Paris-Sud - Paris 11 (Bâtiment 300 - 91405 Orsay cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR8618 (France)
3
URGI - Unité de Recherche Génomique Info (INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles - France)
- INRA - Institut National de la Recherche Agronomique : UR1164 (France)
4
UMR 8030 - Génomique métabolique (GENOSCOPE, 2 rue Gaston Crémieux 91057 Evry Cedex - France)
- GENOSCOPE - Genoscope - Centre national de séquençage [Evry] : DRF/JACOB (2, rue Gaston Crémieux CP5706 91057 EVRY Cedex - France)
- Université Paris-Saclay (Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette - France)
- DRF (CEA) - Direction de Recherche Fondamentale (CEA) : DRF/JACOB (Direction de Recherche Fondamentale
Fundamental Research Division
CEA Saclay
91191 Gif-sur-Yvette
- France)
- CEA - Commissariat à l'énergie atomique et aux énergies alternatives (Centre de Saclay Centre de Grenoble Centre de Cadarache etc - France)
- CNRS - Centre National de la Recherche Scientifique : UMR8030 (France)
- UEVE - Université d'Évry-Val-d'Essonne (Boulevard François Mitterrand 91025 Evry Cedex - France)
5
SVQV - Santé de la vigne et qualité du vin (28 rue de Herrlisheim - BP 20507
68021 Colmar Cedex - France)
- INRA - Institut National de la Recherche Agronomique : UMR1131 (France)
- UNISTRA - Université de Strasbourg (4 rue Blaise Pascal - CS 90032 - 67081 Strasbourg cedex - France)
6
UMR EGFV - Ecophysiologie et Génomique Fonctionnelle de la Vigne (I.S.V.V Bordeaux, 210 Chemin de Leysotte 33882 Villenave d’Ornon cedex, France - France)
- Institut des Sciences de la Vigne et du Vin (ISVV) (France)
- Bordeaux Sciences Agro - Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (1 cours du Gal De Gaulle - CS 40201 - 33175 Gradignan Cedex - France)
- INRA - Institut National de la Recherche Agronomique : UMR1287 (France)
- UB - Université de Bordeaux (35, place Pey Berland - 33076 Bordeaux - France)
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.
Document type :
Journal articles
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https://hal.inria.fr/inria-00180148
Contributor : Fabrice Legeai Connect in order to contact the contributor
Submitted on : Wednesday, October 17, 2007 - 6:04:01 PM
Last modification on : Tuesday, April 12, 2022 - 3:27:28 AM
Contributor : Fabrice Legeai Connect in order to contact the contributor
Submitted on : Wednesday, October 17, 2007 - 6:04:01 PM
Last modification on : Tuesday, April 12, 2022 - 3:27:28 AM
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- HAL Id : inria-00180148, version 1
- DOI : 10.1007/s00122-006-0301-7
- PRODINRA : 11462
- WOS : 000238503200016
- PUBMED : 16791700
Collections
CNRS | UNIV-EVRY | INRA | CEA | GENOMIQUE-METABOLIQUE | JACOB | CEA-DRF | SITE-ALSACE | GENOSCOPE | INRAE | IPS2 | UNIV-PARIS-SACLAY
Citation
Didier Lamoureux, Anne Bernole, Isabelle Le Clainche, Sarah Tual, Vincent Thareau, 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. TAG Theoretical and Applied Genetics, Springer Verlag, 2006, 113 (2), pp.344-356. ⟨10.1007/s00122-006-0301-7⟩. ⟨inria-00180148⟩
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