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 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)

Thank you for your attention!