gilt acclimatization and sow health project & other health genomic projects bob kemp piggen...
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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 GeneticsGenesusGénétiporcHypor CanadaLa Coop fédéréePIC CanadaTopigs 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 and disease resistance
Meat quality and lean meat deposition
Sow lifetime productivity
Production efficiency
Animal 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 HealthDevelopment of genetic selection tools to
enhance sow health using a novel acclimation challenge model in Canadian commercial herds
Two ProjectsGilt acclimation and sow health phenotypingAnalyses and database development
Nucleus / AI Units
Multiplier Herds
Gilt Acclimation
Commercial herds
SAMPLES+DATAOutbreak Herds
Gilt Acclimation Project Overview
Data collection
Commercial herds identified by PigGen Canada membersNeed to provide a health challengeTarget 30 herds
High health crossbred giltsPigGen Canada member herds Target 4,000 giltsGroups of 20 to 50 gilts per entry, multiple
entries per year
Data CollectionGilt’s sire, dam, birth date and vaccination
statusBlood samples prior to entry, 30 days after entry
and at parities 1 and 2Body weight collected at entry and day 30Vaccination/treatment records, date of death
and reasons during acclimationTissue/blood sample of dam of gilts
Data Collection
DNA extracted from gilt and dam blood samplesGilts screened for exposure at entry, day 30,
parities 1 and 2PRRS, 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 1PRRS break Nov. 2011, blood drawn Dec.
2011All sows in herd confirmed PRRS exposureExact date of exposure unknown
Outbreak 2Herd confirmed PRRS exposure50 PRRS negative gilts exposed to herd
PRRS virus on entry to quarantineGilts bled at 2 week intervals (0, 2,4,6,8)Elisa (IgG), SN antibody titres and qPCR in
serum over the five time points
Nucleus / AI Units
Multiplier Herds
Gilt Acclimation
Commercial herds
SAMPLES+DATA
Outcomes
General immune capacity of crossbred gilts
GWAS of general immune response of sows
GBVs using sow health data
Integrated database resource and collection systemOutbreak Herds
Gilt Acclimation Project Overview
Gilt Acclimation Project Status25 Herds in Alberta, Saskatchewan,
Manitoba, Ontario and QuebecOver 2,000 gilts sampledDay 0 and 30 samples sent to Delta
Genomics laboratoryData collection using standardized formsSerum analysis begunDatabase development started
Gilt Acclimation Project StatusOutbreak 1
60K genotype on 600 affected sowsLitter data on most sows post-PRRS exposure2 years of historical litter data pre-PRRS
infectionOutbreak 2
Examine variation in response60K genotype strategy being developedHerd/gilt reproductive and litter data being
collated
Nucleus / AI Units
Multiplier Herds
Gilt Acclimation
Commercial herds
SAMPLES+DATA
Outcomes
Genetic selection toolsEarly life indicators of health and performance
Reduced cost of productionImproved sow health, longevity and welfare
Health data genetic collection system and data resourceLeverage industry funding
Reinforce Canada’s high health pork and genetic reputation
Benefits
General immune capacity of crossbred gilts
GWAS of general immune response of sows
GBVs using sow health data
Integrated database resource and collection systemOutbreak Herds
Gilt Acclimation Project Overview
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
ActivitiesGenomics and it’s ethical, economic,
environmental, legal and social aspectsFocus 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 healthCombine challenge experiments, industry datasets
and in vitro analyses
Application of genomics to improve swine health and welfare
ActivitiesNext-generation genomic analysis of swine
health (genome function focus)Include genome wide association studies,
trancriptomics, proteomics and kinomicsApplication 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 ChallengeSaskatchewan
SAMPLES+DATA
Project database
60k SNP chip
Transcriptomics:Gene expression
Proteomics: proteins and pathways
Genome Wide AssociationsGenomic Breeding Values (GBVs) Models of PRRS infection dynamics
Application
Kinomics: protein kinases
In Vitro Assays
Canadian Component of the PRRS Host Genetics Consortium
Groups involvedAlberta Livestock Genomics ProgramLivestock Gentec / U of AlbertaPigGen CanadaUSDA – ARS
GoalsComplete 60K genotyping on final 3 groupsGWAS completed on all 1600 pigsEnhance 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 tocollect detailed performance and health data on
approximately 8,000 pigsidentify genetic variation for performance and
susceptibility to specific diseaseslarge scale validation of the utility of DNA panels
for better immune response
Establishing a commercial dataset to support genomics of swine health
DeliverablesCollect 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 healthImmune 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 participantsPigs sourced from breeding companies Weaned pig challenge model for PRRSWeights, viral load and many other samples and
blood data8 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)
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