GrapeReSeq
Large scale re-sequencing in the Vitis genus for identification of resistance genes, SNP discovery and high throughput genotyping
Research project of Transnational Plant Alliance for Novel Technologies toward implementing the Knowledge Based Bio-Economy (PLANT - KBBE2008) in Europe (France, Germany and Spain)
The aim of this project is to take advantage of the existence of the grapevine genome sequence to develop strategies and comprehensive tools for allele mining in the Vitaceae gene pool and genetic improvement of grapevine for resistance to disease.
Two main approaches will be developed.
The first one will allow targeting regions known to undergo fast structural rearrangements. It will combine the development of a draft sequence (pyrosequencing, 454/Roche) of a V. cinerea x V. riparia F1 hybrid and BAC end sequences (BES) in order to quickly identify regions involved into important traits, such as disease resistance.
The second approach, will aim at the development of a large EU SNP resource, which will be the basis to the development of high throughput genotyping tools for breeding and of association genetics studies. A microarray-based method will be employed to trap all the predicted exons and UTR of the grapevine genome in 15-20 individuals in order to re-sequence them using the Solexa/Illumina platform.
Finally, high throughput genotyping chips will be developed.
Duration: 01/01/2009 to 31/12/2011
Coordinator: Anne-Françoise Adam-Blondon
| Laboratories | Address | Person | Links |
|
UMR INRA CNRS Université d’Evry Génomique Végétale 2 rue Gaston Crémieux, BP 5008, F-91057 Evry cedex, FRANCE | Coordinator Dr. Anne-Françoise Adam-Blondon | Grapevine and Forest Trees Genomics |
|
UMR DiaPC 2 place P. Viala F-34060 Montpellier Cedex 1, FRANCE | Dr. Jean-Michel Boursiquot | Equipe Diversité Génétique et Génomique de la vigne |
|
URGI INRA de Versailles Route de Saint-Cyr F-78000 Versailles, FRANCE | Dr. Hadi Quesneville | Unité de Recherche en Génomique Info |
| EPGV |
EPGV INRA; CEA/ IG-CNG 2 rue Gaston Crémieux, CP 57021 F-91057 Evry Cedex, FRANCE | Dr. Dominique Brunel | Etude du Polymorphisme des Génomes Végétaux |
| S&G |
Statistique & Génome Tour Evry 2, 523, Place des Terrasses de l’Agora F-91034 Evry cedex, FRANCE | Prof. Bernard Prum | Statistique et Génome |
|
CNB-CSIC C/ Darwin 3, Cantoblanco E-28049 Madrid, SPAIN | Dr. José M. Martinez-Zapater | Genetic and molecular control of plant reproductive development |
|
Institute for Genome Research and Systems Biology / CeBiTec, Universität Bielefeld, Universitätsstraße 25 D-33615 Bielefeld, GERMANY | Prof. Dr. Bernd Weisshaar | Genome Research |
|
Julius Kühn-Institut Bundesforschungsinstitut für Kulturpflanzen Institut für Rebenzüchtung, Geilweilerhof D-76833 Siebeldingen, GERMANY | Dir. and Prof. Dr. Reinhard Töpfer | Institute for Grapevine Breeding Geilweilerhof |
|
Universita degli Studi di Verona Strada le Grazie 15 I-37134 Verona, ITALY The Italian partner is providing fund for its own needs | Prof. Massimo Delledonne | Dipartimento di Biotecnologie |
Data
- Access to GrapeReSeq_Illumina_20K_SNP_chip data
- Download the data (raw reads, cleaned and trimmed reads and SNP): restricted access
- Description of the data in GnpSeqNGS
- Quality control & Cleaning process for Illumina runs :
README_EPGV_DataTransfer_Illumina_Sequencing.pdf (626.79 kB)
- A dataset obtained from the genotyping of a Vitis vinifera cultivated pool (using the SNPs of the 20k chip): see
Tools
| URGI shared area | GrapeReSeq directory with Alfresco
|
To share documents with other GrapeReSeq project members, use Alfresco, our web software of electronic documents management .
To access to the Alfresco tool :
- the first form is the secured web server authentification with the URGI login/password.
- the 2nd form is Alfresco authentification with the Alfresco login/password.
The GrapeReSeq directory path is Compagny Home > Projects > GrapeReSeq.
To ask for an account on the URGI secure server, please complete the
form
To ask for an account on the Alfresco tool, please
contact us
Funding
Creation date: 02 Dec 2009
eZ PublishPublication supervisor: A-F. Adam-Blondon
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