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

2. 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
€ (EC)
CSA
13 partners
10 countries
€ 1 (EC)

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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?