Section: New Results

Applications

Study of the rapeseed genome structure

Participants : Sebastien Letort, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre, Fabrice Legeai.

In collaboration with IGEPP (Institut de Génétique, Environnement et Protection des Plantes), INRA, and through two national projects, PIA Rapsodyn and France-Génomique Polysuccess, we are involved in the genome analysis of several rapeseed varieties. The Rapsodyn project has the ambition to insure long-term competitiveness of the rapeseed production through improvement of the oil yield and reduction of nitrogen inputs during the crop cycle. Rapeseed varieties must thus be selected from genotypes that favor low nitrogen input. DiscoSnp++ is here used to locate new variants among the large panel of rapeseed varieties which have been sequenced during the project.

The PolySuccess project aims to answer the following question: how a polyploid, such as the oilseed rape plant, becomes a new species? Oilseed rape (Brassica napus) being a natural hybrid between B.rapa and B.oleracea, different genomes of these three species have been sequenced to study their structures. The Minia assembly pipeline provides a fast way to generate contigs that are used for studying gene specificities.

GATB Production Pipeline

Participants : Patrick Durand, Charles Deltel.

The entire set of libraries and tools related to the GATB Software have been introduced within a professional environment to support high-quality C++ developments. It relies on the use of technology platforms available at Inria: OpenStack and Jenkins. Considering the latter, we have setup more than 50 Jenkins tasks to automate the entire software development based on GATB: C++ code compiling and testing, documentation creation, packaging and preparation of official releases, mirroring on public Github repositories. Code compilation and tests are done on Linux and MacOSX VMs. https://ci.inria.fr/gatb-core/

Variant predictions in the pea genome

Participant : Pierre Peterlongo.

Progress in genetics and breeding in pea suffered from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes without the need for prior genome reduction or a reference genome allow the discovery of thousands of molecular markers.

We have been involved with IGEPP (Institut de Génétique, Environnement et Protection des Plantes, INRA) in the application of the discoSnp++ tool, discovering SNPs on HiSeq whole genome sequencing of four pea lines. Validation of a subset of predicted SNPs showed that almost all generated SNPs are highly designable and that most (95 %) deliver highly qualitative genotyping result [13].

Analysis of insect pest genomes

Participant : Fabrice Legeai.

Within a large international network of biologists, GenScale has contributed to various projects for identifying important components involved in the adaptation of major agricultural pests to their environment. We provided the assemblies, the annotations and the comparisons of various insects genomes [29]. Following specific agreement or policy, these results are available for browsing and consulting to a restricted consortium or a large community through the BioInformatics platform for Agro-ecosystems Arthropods (http://bipaa.genouest.org/is). In particular, this year our work helped to identify aphid genes involved in the adaptation to their favorite plant [15], or genes that are differentially expressed between leaf- and root-feeding phylloxera [21]. Furthermore, in order to help scientists to consult and cross genomics and postgenomics data, we are developping AskOmics, an integration and interrogation software for (linked) biological data, within a strong partnership, with Dyliss and GenOuest [36], [27].