Aubrac cow. © INRA, SLAGMULDER Christian

High throughput genomics: a rapidly changing field

Agenae: pioneering research in animal genomics

The Scientific Interest Group Agenae, created ten years ago during the race for gene sequencing, pools the resources, equipment and expertise of INRA, CIRAD and various French livestock breeders, and has developed genomic selection tools for competitive and sustainable livestock rearing.

Investments in technology and methodology necessary for the collection of genomic data has led INRA to create specialised platforms. © MAITRE Christophe
Investments in technology and methodology necessary for the collection of genomic data has led INRA to create specialised platforms. © MAITRE Christophe
The Scientific Interest Group Agenae (Analyse du Génome des Animaux d'Élevage) was created in 2002 to pool the resources, equipment and skill sets of research teams from INRA, CIRAD and the different French players in fish, cattle, pig and poultry farming. Its budget amounts to €120 million, of which €50 million is provided by founding members, the French Ministry of Research, the French national research agency and Europe. INRA’s contribution amounts to €70 million. 

Specialised platforms 

The past ten years, Agenae has provided gene sequencing and mapping for the genomes of the four reference species, representing a major French contribution to consortiums dedicated to sequencing the entire range of animal genomes. Investments in technology and methodology necessary for the collection of genomic data has led INRA to create specialised platforms organised into networks, such as the Biological Resource Centre Gadie (DNA banks, transcriptome), Labogena or GenoToul (sequencing and genotyping) and the bioinformatic platform Sigenae. These platforms are all in line with the organisation of genomics structure in France and part of the European Research Area. National technological platforms emerged in France in response to the scientific need for high throughput technologies.

The Information System of Agenae

A group of bioinformatics technicians from Sigenae, the Information System of Agenae, (www.sigenae.org), was created to contribute in several ways to the European Animal Disease Genomics Network of Excellence for Animal Health and Food Safety (Eadgene). Together with English and Dutch researchers, the team has developed a process for re-annotating DNA microarray probes. This process provides biologists with annotation files for their analyses. Our knowledge of genomes and the genes they contain is constantly growing. That is why it is important that information gained from the probes be updated in real time, as soon as new knowledge is made public. In 2010, Sigenae released no less than 26 publications. 

The National Genetic Resource Centre for domestic animals

INRA also hosts the National Genetic Resource Centre for domestic animal breeds (CRB-Gadie). Collecting genomic data from domestic animals, this platform gathers, stores and distributes large DNA fragments (BACs and YACs) and cDNA. Two years ago, the secured management of the platform broadened its scope to include other types of biological samples (eg. blood, milk, tissue, etc.). The advent of new generations of sequencing techniques is opening new doors in terms of re-sequencing and analysis of genome expression. CRB-Gadie has developed a capture technique of targeted genomic regions for re-sequencing, and is a partner in a sequence network with the goal of creating libraries. Agenae prides itself on the creation of platforms which, backed by research laboratories, are in synch with new trends in technologies and an expanding knowledge base.