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

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

3. 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.

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

5. Genotype vs. Phenotype
Genotype
Phenotype

6. Today is the Age of Genome Sequence
15 November 2012

7. 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

8. 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

9. 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”?

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

11. 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”)

12. 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)

13. 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

14. 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 ……………………..

15. >$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

16. The Partnership Agricultural Research Service
University of Lincoln-Nebraska

17. 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

19. 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