1. Gilt Acclimatization and Sow Health Project & Other Health Genomic Projects
Bob Kemp
PigGen Canada

3. Why?
Need for the swine genetics industry to collaborate on genomics research
Need for the swine genetics industry to speak with one voice
Motivation to assist the competitiveness of the Canadian industry through developments in swine genomics
Clearly we were a stronger group working together

4. Current Members Canadian Centre for Swine Improvement Fast Genetics
Genesus
Génétiporc
Hypor Canada
La Coop fédérée
PIC Canada
Topigs Canada
Canadian Centre for Swine Improvement
Canadian Swine Breeders Association

5. Objectives
Represent the Canadian swine genetics industry with a single voice
Develop strategies and support for Canadian swine genetics research in concert with Canadian pork industry priorities

6. Research Priorities Health and disease resistance
Meat quality and lean meat deposition
Sow lifetime productivity
Production efficiency
Animal welfare

7. Funding Annual membership fees are paid by all active members
Support promotion, programs, small contribution research projects and operations
Large project funding
Project approved by 2/3 of the board
50% of individual members must contribute

8. Genomics of Health Projects
Canadian Projects
Gilt Acclimation
Genome Canada
PRRS/PHGC
Alberta Sire Line trial
Brandon Lillie
International Projects
USDA PRRS/PHGC
Other projects

9. Gilt Acclimation and Sow Health
Development of genetic selection tools to enhance sow health using a novel acclimation challenge model in Canadian commercial herds
Two Projects
Gilt acclimation and sow health phenotyping
Analyses and database development

10. Gilt Acclimation Project Overview
Nucleus / AI Units
SAMPLES+DATA
Multiplier Herds
Gilt Acclimation
Commercial herds
Outbreak Herds

11. Data collection Commercial herds identified by PigGen Canada members
Need to provide a health challenge
Target 30 herds
High health crossbred gilts
PigGen Canada member herds
Target 4,000 gilts
Groups of 20 to 50 gilts per entry, multiple entries per year

12. Data Collection Gilt’s sire, dam, birth date and vaccination status
Blood samples prior to entry, 30 days after entry and at parities 1 and 2
Body weight collected at entry and day 30
Vaccination/treatment records, date of death and reasons during acclimation
Tissue/blood sample of dam of gilts

13. Data Collection DNA extracted from gilt and dam blood samples
Gilts screened for exposure at entry, day 30, parities 1 and 2
PRRS, PCV2, SIV (H1N1 and H3N2), Actinobacillus pleuropneumoniae (APP), Mycoplasma hyopneumoniae (MH)
Standard sow breeding and production data thru parity 4
Sow health treatments, mortality and reasons

14. Outbreak 1 PRRS break Nov. 2011, blood drawn Dec. 2011
All sows in herd confirmed PRRS exposure
Exact date of exposure unknown

15. Outbreak 2 Herd confirmed PRRS exposure
50 PRRS negative gilts exposed to herd PRRS virus on entry to quarantine
Gilts bled at 2 week intervals (0, 2,4,6,8)
Elisa (IgG), SN antibody titres and qPCR in serum over the five time points

16. Gilt Acclimation Project Overview
Nucleus / AI Units
SAMPLES+DATA
Outcomes
General immune capacity of crossbred gilts
Multiplier Herds
GWAS of general immune response of sows
Gilt Acclimation
GBVs using sow health data
Commercial herds
Integrated database resource and collection system
Outbreak Herds

17. Gilt Acclimation Project Status
25 Herds in Alberta, Saskatchewan, Manitoba, Ontario and Quebec
Over 2,000 gilts sampled
Day 0 and 30 samples sent to Delta Genomics laboratory
Data collection using standardized forms
Serum analysis begun
Database development started

18. Gilt Acclimation Project Status
Outbreak 1
60K genotype on 600 affected sows
Litter data on most sows post-PRRS exposure
2 years of historical litter data pre-PRRS infection
Outbreak 2
Examine variation in response
60K genotype strategy being developed
Herd/gilt reproductive and litter data being collated

19. Gilt Acclimation Project Overview
Nucleus / AI Units
SAMPLES+DATA
Outcomes
General immune capacity of crossbred gilts
Multiplier Herds
GWAS of general immune response of sows
Gilt Acclimation
GBVs using sow health data
Commercial herds
Integrated database resource and collection system
Outbreak Herds
Benefits
Genetic selection tools
Early life indicators of health and performance
Reduced cost of production
Improved sow health, longevity and welfare
Health data genetic collection system and data resource
Leverage industry funding
Reinforce Canada’s high health pork and genetic reputation

20. Application of genomics to improve swine health and welfare
Genome Canada and many Canadian and international groups
Overall goal
Provide new genomic-based, diagnostic tools to select pigs that are genetically less susceptible to PRRS and PCVAD
Builds on existing projects both within Canada and internationally
Very large leverage of existing funding

21. Application of genomics to improve swine health and welfare
Activities
Genomics and it’s ethical, economic, environmental, legal and social aspects
Focus on developing risk-perception models to characterize Canadian attitudes and perceptions about the use of genomic technologies in pork production
Phenomic resources for genomics of swine health
Combine challenge experiments, industry datasets and in vitro analyses

22. Application of genomics to improve swine health and welfare
Activities
Next-generation genomic analysis of swine health (genome function focus)
Include genome wide association studies, trancriptomics, proteomics and kinomics
Application strategies to deliver healthier pigs
Reduced SNP panels for selection, genomic estimated breeding values, integration into existing improvement programs

23. Genome Wide Associations
SAMPLES+DATA
Project database
PRRS Consortium (PHGC) - Kansas
60k SNP chip
PCV2 Consortium Nebraska
Transcriptomics:
Gene expression
Gilt Acclimation PigGen Canada
Proteomics: proteins and pathways
Kinomics: protein kinases
Pregnant Gilt Challenge
Saskatchewan
In Vitro Assays
Application
Genome Wide Associations
Genomic Breeding Values (GBVs)
Models of PRRS infection dynamics

24. Canadian Component of the PRRS Host Genetics Consortium
Groups involved
Alberta Livestock Genomics Program
Livestock Gentec / U of Alberta
PigGen Canada
USDA – ARS
Goals
Complete 60K genotyping on final 3 groups
GWAS completed on all 1600 pigs
Enhance identification of genes and pathways (transcriptomics)
Enhance identification of biomarkers (proteomics)
Transfer technology to Canadian lab

25. Establishing a commercial dataset to support genomics of swine health
Builds on an existing sire line project with Sunhaven Farms (AB) and Gowans Feed Consulting
Opportunity to
collect detailed performance and health data on approximately 8,000 pigs
identify genetic variation for performance and susceptibility to specific diseases
large scale validation of the utility of DNA panels for better immune response

26. Establishing a commercial dataset to support genomics of swine health
Deliverables
Collect health/mortality data and tissue sample on 8,000 pigs, supplemented by detailed performance data on 2,100 of the pigs
Determine variation in terminal sire lines with respect to performance and susceptibility of disease within this system
Recommendations on procedures required for future health data collection from commercial systems
Effect of DNA marker panels developed for improved immune response or for susceptibility to PRRS and PCVAD

27. Dr. Brandon Lillie, University of Guelph
Research program in genomics of health
Immune response panel development
Found several markers (SNP) associated with pigs diagnosed at necropsy with various diseases or pathogens
Results suggest that these SNPs are associated with disease susceptibility
Might be genetic markers of impaired innate immune function
Immune response panel will be evaluated in other projects and data sets

28. International Projects
PRRS Host Genetics Consortium (PHGC)
USDA lead project with many participants
Pigs sourced from breeding companies
Weaned pig challenge model for PRRS
Weights, viral load and many other samples and blood data
8 tests, 1600 pigs
Salmonella resistance (USA, UK, Netherlands)
Immune response (Germany, UK, France)

29. International Projects
Mycoplasmal pneumonia (Japan)
Psuedorabies virus (Germany)
Protein biomarkers for infectious disease (Netherlands)

30. Thoughts on the use of genomics for health
Use of genomic information will become integrated into selection programs
Data collection systems will be key for research, improvement and monitoring of health outcomes
Large, integrated databases will be required for development and validation
Prediction of individual pig susceptibility to disease within a given environment (Biomarkers)

31. Thank you for your attention!