GnpIS Plant Information System : New Updates for NGS and meta-QTL Analysis data

The URGI (Unité de Recherche en Génomique-Info) is an INRA research unit which aimed to develop tools, integrate data and acquire a better understanding of plant's genome structure, evolution and functioning. It hosts a bioinformatics facility, labelized at INRA level and also at national level by GIS IBISA and member of the national bioinformatics facilities network RENABI-IFB. This facility develops and maintains a modular and interoperable information system for plant and pest genomics called GnpIS (http://urgi.versailles.inra.fr/gnpis). GnpIS can store mapping data (genetic maps, markers, QTLs and MetaQTL), polymorphism and genotyping data (SNP markers), transcriptomic data, sequence and genomic annotations, genetic resources descriptors, phenotypic and environmental experiments.

Due to technological advances in high-throughput sequencing (Next Generation Sequencing), it is now possible to quickly obtain large volumes of sequence data at low cost. This is why the number of sequencing, genotyping and phenotyping projects using these technologies, and subsequently the volume of data to analyze, increased.

1) To answer NGS needs, the facility had to improve its information system in order to manage NGS experiments and also to links the experiments and their runs to the analysis to do on these NGS reads. Thereby, GnpIS databases schema (UML), its insertion tools (ETL Talend) and interface (Java J2E) was improved. We will present here a demo of this new tool and we will ilustrate it on Wheat and Grapevine projects data.

2) To answer scientists and breeders needs, the facility has to improve its information system GnpIS, to manage the meta-analysis of QTLs and the storage of the results of these meta-analysis experiments in the database, in relationship with the other mapping data of the system in particular the mapping data (genetic maps, QTLs and the metaQTLs themselves). We will present the new query interface developped in GnpIS and we will illustrate the tool with wheat data.

the talk will be associated to 2 posters that will describe these new tools.