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 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

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 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 SAMPLES+DATA Multiplier Herds Gilt Acclimation Commercial herds Outbreak Herds

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 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

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 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

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

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

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!