Genomic selection and management of bovine populations

Moderators: Pascal Croiseau, Chris Hozé

The team has historically been responsible for national bovine genetic evaluations, from their design, evolution to production within an ISO9001 certified framework. Since the application of the European Zootechnical Regulations in November 2018, this activity is under the responsibility of Selection Organizations. The team has, therefore, refocused activities on research and development. Their main activities concern genetic evaluation methods, in particular the development of single step evaluation methods and the inclusion of variant functional annotation. The prediction of genetic x environment interactions and the integration of crossbreeding into evaluations are also priorities. We are also developing work on the definition of selection objectives for sustainable production and their adaptation to production systems, on population management minimizing the loss of variability, and on the optimal use of within-herd information. International collaborations are focused on Eurogenomics' main partners but also on the South (India, South Africa) within the framework of the Associated International Laboratory GIMIC.

Analysis of the genetic determinism of different traits

Moderators: Hélène Leclerc, Pauline Martin

The diverse needs for sustainable breeding and the opportunities of high throughput phenotyping have led us to analyze unconventional traits such as feed efficiency, health, resilience and adaptation, quality of products, heat tolerance, as well as genetic defects within the framework of the National Observatory of Bovine Anomalies. Phenotypic data originate from Le Pin experimental facility or from commercial farms in collaboration with our industrial partners. The objective is to identify the causal variants with a high throughput sequencing and imputation approach, and to infer the gene networks involved.

Structure and Dynamics of the Genome

Moderators: Mekki Boussaha, Marie-Pierre Sanchez

The team is one of the founding members of the "1000 bovine genomes" project and invests in the knowledge of the genome, in particular the characterization and annotation of all types of genetic variants with bioinformatics or wet lab approaches. After a strong activity in short reads sequencing in the last 10 years, the team now invests in long read technology and pangenome characterization. A strong experience has been obtained in whole genome sequence imputation, a prerequisite to large scale GWAS at sequence level. This data feeds the other two axes of the team. Regulatory genomics work is aimed at improving the annotation of variants. A reverse genetic approach makes it possible to predict and test on a large scale the a priori harmful variants chosen on the basis of their annotation. Finally, the team has started to study the relationships between genetic variants and methylation marks.

The phenotypes at the basis of our activity come from the national animal breeding database and the Le Pin experimental farm. The CTIG computer centre is a close partner, providing both data access and IT resources. Genotyping data originate from research projects or from French genomic selection activity. The sequences are produced on the GetPlage platform in Toulouse and bioinformatics work is carried out in collaboration with Sigenae.

• Collaborations with France Génétique Elevage and numerous French genetic and animal breeding organizations, as well as with Apisgene as a funding body

• Within Inrae, collaborations with various laboratories in the Animal Genetics division (in particular GenPhySe Toulouse), and with Phase, Animal Health, and Social Sciences.

• Collaboration with veterinary schools within the framework of the ONAB

• International collaboration in genomic selection (Eurogenomics, Eurogenetics, Intergenomics, Interbull, Interbeef) and with India (GIMIC international lab) and South Africa

• Founding member and important contributor to the "1000 bull genomes" consortium leaded by Melbourne University.

SELGEN, Genomic Selection

• Integration of complete genome sequence data into genomic selection.
• Management of diversity in selection.
• Prediction of genotype x environment interactions.
• Cross-cutting approaches between species.
• interactions with the social sciences on the organizational consequences of genomic selection.

GISA, Integrated management of animal health

• Study of genetic determinism of mastitis and paratuberculosis.