The European Vitis Database (www.eu-vitis.de) – a technical innovation through an online uploading and interactive modification system

The objective of the European Vitis Database is to safeguard and enhance germplasm by monitoring its preservation. Two issues are strongly related to that purpose: (1) participation of collections covering almost all grape biodiversity and (2) assessment of accessions trueness to type. In the scope of the European project GrapeGen06 efforts have been made towards both objectives. The 35 participating grape germplasm repositories are found between the Iberian Peninsula and Transcaucasia, thus covering a broad range of grape diversity. Altogether they maintain 32,410 accessions. However with respect to biodiversity, gaps are still evident and further collections need to be included and trueness to type assessment absolutely needs to be pursued to organize duplication of endangered genotypes. Within the GrapeGen06 project focus was laid on the establishment of a database conferring the collection holders a high degree of responsibility and independence. Hence for the first time in a European Central Crop Database an on-line uploading application and an interactive modification system for data administration was implemented. These innovations disburden the database manager and offer the curators of collections more flexibility. Prerequisites for data import, descriptors applied, access levels, database contents, uploading, export and search functions are described

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France

Les clones de vigne agréés en 2007

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Looking for genetic polymorphism through clonal variation of Pinot noir

International audienceClonal variation among cultivars of Vitis vinifera L. has been known formany years and its use achieved very significant gains for the wine industry. Nowadays, the basis of clonal phenotypic variation is barely known: hypothesis of genetic mutations or epigenetic modifications have nevertheless been considered. The objective of this study is to get a better insight of the genetic basis of clonal variation to develop a tool for clonal identification and selection. The current scientific context, access at the whole genome sequences of the individual PN40024 derived from Pinot noir and of a heterozygous clone of Pinot noir ENTAV-INRA® 115 and the development of the NGS (new generation sequencing) technologies, allows now exhaustive studies of the grapevine genome. Towards this aim, we used the 454 GX FLX Titanium technology on three official clones of Pinot noir ENTAV-INRA® 386, 583 and 777, selected for their different phenotypic traits. We firstly developed a nuclear DNA extraction method to limit the contamination from cytoplasmic DNA. We then realized one 454 run by clone and we obtained in mean 1 million reads of 350 bases by run. Our data sets from the 454 and the contigs from the whole sequence of Pinot noir ENTAV-INRA® 115 have been aligned on the reference genome, PN40024 with a compilation of different software: Mosaik-assembler, and RepeatMasker. Sixty-six percent of the reads obtained from each of the 454 runs have been aligned at a unique locus. Thanks to NGS technologies, we could compare a large portion of the genome with 3X coverage: i) in mean 8Mb between Pinot noir ENTAV-INRA® 115 and with each of the three others clones and ii) 0.5 Mb between the three clones themselves. The different sequence data obtained from these clones will be compared to identify the major molecular events which separate the clones analyzed. Preliminary results showed that SNPs are less important than insertions/deletions to be polymorphic between clones. We will validate this polymorphism and will develop method to perform identification of the clones

Die Europäische Vitis datenbank, eine technische innovation für die langfristige Erhaltung der genetischen ressourcen der rebe

Equipe DAVEM = Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesThe European Vitis Database (www.eu-vitis.de) - a technical innovation through an online uploading and interactive modification syste

The European Vitis Database (www.eu-vitis.de) - a technical innovation through an online uploading and interactive modification system

UMR 1334 AGAP : Equipe DAVEM = Diversité et Adaptation de la Vigne et des Espèces Méditerranéennesabsen