M-H Pinard-van der Laan INRA – Animal Genetics Division (France) EADGENE/EADGENE_S Coordinator

EADGENE : European Animal Disease Genomics NoE for animal health and food safety EADGENE_S : Strengthening the implementation of durable integration of EADGENE Partners INRA, FR Liege University, BE Aarhus University, DK PTP, IT FBN, DE EFFAB, NL DLO-LR, NL Wageningen University, NL NVS, Norway Ljubljana University, Slovenia Cordoba University, Spain Institute for Animal Health UK Edinburgh University, UK NoE 13 partners 10 countries 2004-2010 € 11.52 (EC) CSA 13 partners 10 countries 2011-2013 € 1 (EC)

GENOMICS: New possibilities for infection biology RESEARCH APPROACH & OBJECTIVES Targets (genes) Genome mapping annotation Profiling DNA (SNP) mRNA’s proteins Functional studies Association GENOMICS: New possibilities for infection biology Host genetic variation GENOMICS APPROACH Pathogen genetic variation Molecular mechanisms HOST PATHOGEN Overcome fragmentation Orientate research priorities Spread excellence BUT…FRAGMENTED RESEARCH COMMUNITIES

GOALS, MEANS & IMPACTS SHARING, PRODUCING, UPDATING DATA + GENOMICS & BIOINFORMATICS TOOLS + METHODOLOGIES FOR JOINT COLLABORATIVE RESEARCH Breeding industries ` Pharma + Vet. industries Targets (genes) Breeding for resistance Genomic markers for selection Host genetic variation Modul. immune awareness Improved diagnostics Pathogen genetic variation Targets for diagnostics Improved therapeutics Molecular mechanisms

ACHIEVEMENTS (1) Virtual Laboratory Provision + annotation of chicken, pig, bovine microarrays Provision of SNP panels for large scale genotyping Development and distribution of bioinformatics tools Promotion and organisation of workshops, courses and conferences Exchange of scientists Common Genomics Tools Collaborative research on many major pathogens Comparative transcriptomics & meta-analyses in hosts and pathogens Sequencing and annotation of animal and microbial genomes Mathematical models of disease Joint Research Club of Interest: over 70 industry members Collaborations between research and industry Guidelines for addressing Intellectual Property issues Ethical Guidelines TTransfer

Technological triangle SHARING & PRODUCING GENOMIC TOOLS ACHIEVEMENTS (2) Analytical Tools Technological triangle Technological Facilities Bioinformatics Tools Biological Resources Exchange of procedures, methods … => Quality Control Virtual Laboratory Produced Microarrays Hosts & Pathogens 60K SNP chips Chicken, pig, cattle SHARING & PRODUCING GENOMIC TOOLS Improved

Common sets ACHIEVEMENTS (2) Analytical Tools Re-annotation Pathway analyses Regulatory networks Integration of gene expression studies with QTL detection studies Prediction of phenotypic outcomes Bioinformatics Tools Common sets Virtual Laboratory RESULTS ANALYSED Annotation and post-analyses of microarray data Workshop SHARING & PRODUCING & USING GENOMIC TOOLS

WHAT WAS NOT ACHIEVED Interactions with environment Breaking scales of genomics benefits from gene -> population -> (territories) Refine + adopted ontology (gene, phenotype) Health data collection to feed in genomics Integration of means of prevention (genomics+nutrition+vaccines+..) at large scale & in practice HOST PATHOGEN Collaborative research on “in kind participation” base Uptake of genomic tools/methodologies by industry

CHALLENGES Integrating interactions with environment, a.o. microbiome Improving impact of advanced genomic tools on higher scales (gene -> population -> territories), developing a.o. epidemiogenetics Revisiting genetic architecture of health traits, exploring a.o. Epigenetics and immune traits, improved predictive understanding of phenotypic expression Renewing breeding strategies with true “Integrated management of health” approach Knowledge Gaps HOST PATHOGEN Better balance (in projects) between “blue sky” FAANG type research vs “applied research” Uptake of genomic tools/methodologies by industry through better knowledge exchange of science & constraints (e.g. trade –offs) towards innovation

WHAT WE LEARNT / “GENOMICS” (& should keep!) Critical mass + flexibility = Essential elements ! “Genomics” = Learning process ! Genomics as part of Multi(inter)disciplinary Research Make best use of differences ! Sharing knowledge & data in a structured way Common data/interest + Elements of trust ! We have as much more to learn from “Industry + field” than them. Best model partnership? Effective KT? Innovation?