Overview of the GnpIS Grape Genomics and Genetic Integrative Resource for Diversity Studies

The GnpIS information system dedicated to genetics and genomics data for plants and their pathogens maintains an integrative repository for grape research (https://urgi.versailles.inra.fr/Species/Vitis). In this frame, we maintain data linked to grape accessions like crops descriptors, genetic markers (SNPs and SSR), genetic maps, genotyping, re-sequencing SNPs data and phenotypes. We also offer an interesting bridge towards genomics annotations (genes, repeats).

The connection between the different modules of the system permits to easily browse through heterogeneous genetics and genomics data. To achieve this purpose, we use our in-house pipelines or existing tools to map the SNPs on the genome and to determine the impact of the SNPs on the available functional annotations.

This interoperability is provided both by the system and the pre-computing of the data. The GnpIS Genome module, relying on the international open source GMOD components, is displaying all these features on the official grape PN40024 genome assembly using GBrowse graphical interface.

An interesting use case is to browse from a genomic scope to a genetic scope by querying all SNPs that are located in a region of the genome using different tools like Intermine (Grapemine), Biomart or GBrowse. Our system then allows to retrieve all the information about the SNP discovery analysis and, if the marker has been genotyped, the results for this marker on the Grapereseq 18K array.  

To ease the data-mining by the user, GnpIS proposes to export the results in tabulated formats.