Genomics and Swine Health: Introduction: Canada to Date Graham Plastow Breakout Session #6 Swine Health & Genomics

What is a Genome? ge•nome [jee-nohm] noun The complete set of genetic material of an organism; responsible for all inheritable traits.

What is Genomics? Genomics is the study of the structure, function, evolution, and mapping of genomes. Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome—more than 3 billion DNA base pairs—is contained in all cells that have a nucleus.

Genomics It’s as easy as ABC… Or, “As easy as ACGT” SNP This single difference is known as a Single Nucleotide Polymorphism (SNP)

Genotype vs. Phenotype Genotype Phenotype

Today is the Age of Genome Sequence 15 November 2012

Genomics Catch 22 Genomics requires lots of data Adds real value for difficult or expensive to measure traits Where do we have lots of data? For easy to measure traits (& dairy bulls) So, we develop markers for easy to measure traits These markers have a relatively small impact (except for dairy) 7

Health is the Biggest Opportunity for Genomics A classic example of a difficult and expensive trait to measure It represents an opportunity for the Canadian swine industry to build on its reputation for healthy genetics

Breeding for “Disease Resistance” Or reduced susceptibility Host Genetic Variation Identified For every type of pathogen Probably exists for all diseases Major opportunity for genomics As difficult and expensive to measure trait May be only practical way to breed healthier pigs Specific diseases or Improved “Robustness”?

Can It Be Done? Examples already exist E.g. resistance to E.coli F18 and K88

Resistance may not always exist Multiple routes of entry (receptors) Receptor function may be essential Variation in response to disease is a complex/polygenic trait Selection for faster recovery or reduced impact of disease (“robustness”)

Application of genomics to improve swine health and welfare An international industry/research partnership Project Leaders: Graham Plastow (UofA), John Harding (UofS), Bob Kemp (PigGen Canada)

The Need (Canadian Swine Health Forum Oct 2010) PRRS in Canada Very costly - in excess of $130 million/year in Canada PCVAD in Canada Total Direct Impact $500M plus on-going cost to cure of $600M

A Coordinated effort PigGen Canada Livestock Gentec US PRRS Host Genetics Consortium Genome Alberta/ALMA Applied Livestock Genomics Program Genome Canada Large-Scale Applied Research Project Competition (PRRSv/PVC2) Canadian Swine Health Board ……………………..

>$1M other co-funding A Coordinated effort PigGen Canada Livestock Gentec US PRRS Host Genetics Consortium Genome Alberta/ALMA Applied Livestock Genomics Program Genome Canada Large-Scale Applied Research Project Competition (PRRSv/PVC2) Canadian Swine Health Board …………………….. $9.3M new funding >$5M PHGC >$1M other co-funding

The Partnership Agricultural Research Service University of Lincoln-Nebraska

Key Activities Year 1 Year 2 Year 3 GE3LS Animal “models” sample and data collection Database & Bio- informatics Next-gen Genomics 60k SNPs/ GWAS RNAseq FMIA Kinomics Application: GEBVs Year 1 Year 2 McGill University and Génome Québec Year 3

Coordinated effort Phalanx of phenomic/genomic tests Blood for r/t “window on health” Serum components In vitro tests (proliferation assays, MDMs, transcriptomics….) Post-hoc analyses (transcriptomics, proteomics, kinomics) Genotype Dedicated pool of experts/analysts (across models) Linked animal resources providing discovery, validation, calibration, and demonstration Banked samples providing options for new tests/hypothesis testing