Gilt Acclimatization and Sow
Health Project & Other Health
Genomic Projects
Bob Kemp
PigGen Canada
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
Current Members
Fast Genetics
Genesus
Génétiporc
Hypor Canada
La Coop fédérée
PIC Canada
Topigs Canada
Canadian Centre
for Swine
Improvement
Canadian Swine
Breeders
Association
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
Research Priorities
 Health
 Meat
 Sow
and disease resistance
quality and lean meat deposition
lifetime productivity
 Production
 Animal
efficiency
welfare
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
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
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
Gilt Acclimation Project Overview
Nucleus / AI Units
Multiplier Herds
Gilt Acclimation
Commercial herds
Outbreak Herds
S
A
M
P
L
E
S
+
D
A
T
A
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
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
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
Outbreak 1
PRRS break Nov. 2011, blood drawn Dec.
2011
All sows in herd confirmed PRRS exposure
Exact date of exposure unknown
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
Gilt Acclimation Project Overview
Nucleus / AI Units
Multiplier Herds
Gilt Acclimation
Commercial herds
Outbreak Herds
S
A
M
P
L
E
S
+
D
A
T
A
Outcomes
General immune capacity
of crossbred gilts
GWAS of general immune
response of sows
GBVs using sow health data
Integrated database resource
and collection system
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
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
Gilt Acclimation Project Overview
Nucleus / AI Units
Multiplier Herds
Gilt Acclimation
Commercial herds
Outbreak Herds
S
A
M
P
L
E
S
+
D
A
T
A
Outcomes
General immune capacity
of crossbred gilts
GWAS of general immune
response of sows
GBVs using sow health data
Integrated database resource
and collection system
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
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
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
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
PRRS Consortium
(PHGC) - Kansas
PCV2 Consortium
Nebraska
Gilt Acclimation
PigGen Canada
Pregnant Gilt
Challenge
Saskatchewan
S
A
M
P
L
E
S
+
D
A
T
A
Project database
60k SNP chip
Transcriptomics:
Gene expression
Proteomics: proteins and
pathways
Kinomics: protein kinases
In Vitro Assays
Application
Genome Wide Associations
Genomic Breeding Values (GBVs)
Models of PRRS infection dynamics
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
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
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
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
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)
International Projects
Mycoplasmal pneumonia (Japan)
Psuedorabies virus (Germany)
Protein biomarkers for infectious disease
(Netherlands)
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)
Thank you for your attention!