Structural genomics provides genetic and physical maps to facilitate assembly of the nucleotide sequences in production as well as advanced molecular tools for the study of genetic variability in grape.
In addition, the placement on physical and genetic maps of genes confering resistance to microbial pathogens is envisaged. This last objective will contribute to the eventual isolation of such genes.

Sequencing
The production 1.2 billion basepairs (equivalent to around a 2.5 fold coverage of the genome) is envisaged. This sequence data will derive from around 1.9 million capillary sequence reads. These data will be integrated with sequence data produced by Genoscope corresponding to a mean 3 fold genome coverage.

Mapping
A physical map of the highly homozygous genotype used for sequencing will be produced. Mapping data relative to segregating populations will be produced. In addition, mapping technology not dependent on segregation (Happy Mapping) will be adapted to grape, allowing development of new molecular markers and of new mapping tools.

Aims to use the information provided by structural genomics to develop technolgies and advanced analytical tools to characterize the entire genome and the various steps which allow and control the flow of genetic information to regulate functional processes at the  cellular, tissue, organ and organismal levels.

This work forsees the implementation of technological platforms for the study of primary genetic products (transcriptomics), protein products (Proteomics), and metabolites (Metabolomics). Given that genomic analysis is charactrized by high throughput analyses, it is necessary to develop a bioinformatics platform that allows the integration of various types of data into a coherent whole (Bioinformatics).

Transcriptomics
A platform for the analysis of transcripts based on DNA arrays and laser microdissection. Two series of DNA oligoarrays will be produced, specifically designed to study responses to biotic stress and the maturation of the berry. Databases of complete cDNA sequences will be provided as well as 3’ and 5’ reads of 30000 cDNA clones.

Proteomics
The 2-DE (DIGE)/MS system will be implemented for the study of proteins involved in the maturation of the berry and in abiotic and biotic stress responses. Data produced will subsequently be used to make protein chips. A total of around 150 DIGE analyses will be performed on grape berry tissues at various developmental stages.

Metabolomics
Metabolites present in the berry at various stages of maturation, and in tissues infected with pathogens will be analysed using at least 100 samples.

Bioinformatics
The bioinformatics groups will assemble the genome sequence and provide first draft annotations. A genome browser allowing various types of in-silico analyses will be implemented.

Aim to transfer technology from the Structural and Function Genomics projects to address problems at the applied level. Although the true value of a program such as VIGNA can only be appreciated inthe long term, some findings can be expected to have direct and immediate impact at the applied level. For this reason VIGNA envisages a series of applied pilot studies exemplifying the problems that can be addressed immediately with the new tools made available by the grape genome project.

• Rationalized reorganization of the large collections of germplasm, and development of tools for the evaluation and preservation of local varieties
• Advanced tools for disease control with low environmental impact
• Definition of genetic, biochemical and molecular indices to monitor berry maturation
• Development of biological approaches for monitoring flowering and bud development