GnpSNP, an INRA multi-species database storing plant polymorphism data obtained from various genomic organizations

Goal:

GnpSNP is an INRA URGI platform project whose goal is the development and maintenance of a database dedicated to plant polymorphism: GnpSNP, fully integrated into GnpIS URGI information system.

It stores sequencing/resequencing polymorphisms as well as genotyping array results obtained from several plant species like grapevine, wheat, maize, tomato, and so on.

Description:

 Polymorphisms data stored in GnpSNP are exclusively SNPs (Single Nucleotide Polymorphisms), short DIPs (Deletion Insertion Polymorphisms) and SSRs (Simple Sequence Repeats). GnpSNP stores data from various sequencing or genotyping technologies (Sanger, various NGS platforms data, Axiom genotyping array...etc). It allows to easily filter and export (in csv or VCF format) sub-sets of genotypes and markers information from our favorite organisms and genomic regions.

A bridge between this SNP discovery information system and our genetic association system has been developed to be able to export genotyping data of a relevant association with a trait.  

The system manage the confidentiality of the data using groups that are specified when the user submits the data. 

 The textual web interface allows a wide exploration of the content of the database using simple filters like a genome range restriction and/or a species or organism filter.

Tools have been built in order to ease the data submissions : an excel file to provide the metadata (about the plant material and the SNP calling analysis or the genotyping experiment) in addition to the a VCF file storing the raw data. 

(See Data submission section for more details).

Evolution of the system:

All these developments have been initiated through a Genoplante project (BIEP, M2) in strong collaboration with the INRA EPGV (Etude du Polymorphisme du Génome des Végétaux, located at the Centre National de Génotypage in Evry) and F. Granier (from the Station de Génétique et d'Amélioration des plantes , INRA de Versailles).

Since 2008, user needs and new developments are analysed with the help of a Scientific User Committee (CSU). A steering committee headed by A.F. Adam-Blondon (scientific coordinator of GnpSNP) drives the developpements of GnpSNP by assessing the features of the CSU.

Communication:

• A poster (see the abstract ) and a demo (see the demos ) of the tool were presented in the French bioinformatics conference ( JOBIM 2008 ) and in the European bioinformatics conference ( ECCB 2006 ).
• An overview of the information system possiblilities has been shown in a French Platform workshop in 2008.
• An article has been published (C. Ravel & al. Genome 2006) concerning wheat data available through GnpSnp public URGI Web site.
• A talk describing GnpSNP has been held in the EPGV annual meeting  (9th april 2013)
• A presentation of GnpIS grapevine resource (including GnpSNP features) has been done in Plant Animal Genomes in 2015: Overview of the GnpIS Grape Genomics and Genetic Integrative Resource for Diversity Studies