Benny Mote, Ph.D. University of Nebraska-Lincoln Impacts of moving “clean” gilts into “health challenged” commercial sow farms: Gilt Acclimation Benny Mote, Ph.D. University of Nebraska-Lincoln

Background PRRS and PCVAD alone cost the Canadian swine industry over $100 million dollars every year Researchers have identified genetic regions in the pig genome associated with these diseases The trials are often criticized as they are often single disease challenge models and controlled environments Most trials focus on the growing piglet or are reactive to disease outbreaks in sow farms and haven’t tied in genomics

Background Trial needed to: Focus on commercial F1 females in real commercial settings Capture and understand the challenges gilts face transitioning from clean multipliers to challenged commercial barns Developed two separate proposals with support of Canadian Swine Health Board (submitted November 2010) Split overall goal into essentially a phenotyping proposal and a database and analysis proposal Each proposal totaled $1 million with funding from CSHB and PigGen Members

Project 1: Phenotyping Project Title: Gilt acclimation and sow health phenotyping towards the development of genetic selection tools to enhance sow health using a novel acclimation challenge model in Canadian commercial herds. Objective 1. Phenotyping of crossbred gilts under acclimation conditions on commercial farms. Objective 2. Phenotyping of gilts following acclimation for subsequent health, reproduction, productivity, longevity, and mortality (sow, piglet).

Project 2: Database and Analyses Project Title: Development of genetic selection tools to enhance sow health using a novel acclimation challenge model in Canadian commercial herds: analyses and database development Objective 1. Study relationships and evaluate general immune capacity of crossbred gilts during acclimation, among acclimation (health, growth) and subsequent sow health and performance (reproduction, productivity, longevity, and mortality) and early life indicators of sow health and performance. Objective 2. Identify and evaluate genetic markers associated with general immune response of sows to a variety of disease challenges, including those for health of the growing pig (as identified in other research), and identify and evaluate opportunities for the use of commercial sow health data for genetic evaluation of nucleus boars.

Outbreak Farms After award of grants, two high health sow farms broke with PRRS Teams captured blood, serum, and reproduction records on these “outbreak” farms N=774 females Allowed for training and analysis during initiation of main project Offered insight on variation of antibody response following PRRS break

General Project Layout – Gilt Acclimation Identify existing customers utilizing genetics from PigGen Canada members that Had farms with health challenges Had good record keeping Willing to cooperate on project!!! Producers paid for each gilt in the project and for each reproduction record reported Producers or their veterinarians had to bleed the females 4 times if females remain in production Not incentivized to the point of producers retaining females beyond their normal farm practices

Data Collected Birthdates of females Sire and dam information (when available) Entry date to isolation/commercial sow farms Thriftiness scores

Phenotypic Data Collected Producers/vets drew blood on females up to 4 times Day 0 (D0) – for initial health levels when gilts were leaving or just arrived at commercial farms. Day 30 (D30) – target of 30 days post introduction to farm Parity 1 (P1) – as close to farrowing first litter as commercially reasonable Parity 2 (P2) – as close to farrowing second litter as commercially reasonable

Phenotypic Data Collected Production records Treatment/vaccination records Mortality records Culling records Reproduction records Breedings, farrowings, abortions, recycles Total born, born alive, stillborn, mummies, foster on/off, lactation length, number weaned

Blood Disease Analysis Samples processed, aliquoted and stored at Delta Genomics Samples quantified individually at GREMIP PRRS, PCV2, SIV (H1N1 & H3N2), Actinobacillus pleuropneumoniae (APP; multi-ELISA types 1, 2, 3, 5, 7, 10, 12 and 13) and Mycoplasma hyopneumoniae (MH) All samples received for D0, D30, P1 and P2 were quantified N=8748 Drs. Stephen Bishop and Andrea Wilson at The Roslin Institute, University of Edinburgh lead the immunity analysis

Genotyping Genotyping performed at Delta Genomics All gilts (n=3033) were genotyped using either the Illumina 60K or 80K bead chip Genotypes on select sires and dams of commercial females (n=667) Genome Wide Association Studies (GWAS) led by Dr. Jack Dekkers at Iowa State University

Secure Database Database developed and housed at Livestock Gentec Centre of the University of Alberta under direction of Dr. Graham Plastow Secure access Coded to protect identity of farm, multiplier source, and genetic company Includes all individual phenotypic and genotypic information

Sow Farms Sourced from 7 genetic suppliers Sourced from 17 multiplier barns 23 Commercial Farms Single source genetics predominately all YxL or LxY F1s females. Sized 100-6,000 head sow farms Median 680 head Farms varied introductions to herds from isolation barns to direct entry Farms targeted entry age averaged 188 days

Vaccination Intentions PRRS – 16/23 farms PCV2 – 20/23 farms SIV – 15/23 farms Parvo, Lepto, and Erysipelas – 23/23 HPS – 16/23 Myco – 19/23 Ileitis – 8/23

Gilt Entry Gilts entered farms in batches 10-65 gilts per batch First batch entered January 31, 2012 Last batch entered August 13, 2013 Multiple batches per farm (3-9) Batches help account for seasonality Gilts averaged 123.5 kg at entry Predominately mature gilts but some feeder pig size as well Total of 3033 gilts started trial

Current Situation Massive amounts of data All bloodwork done and in database Cleaning Quality control Early phases of analysis Lots to come www.courtneyhopp.com

PRRS Antibodies At Farms Large majority of females PRRS + Large % still PRRS + at farrowing Have yet to track individuals PRRS levels through timepoints Culling/removal records Treatment records

Reproductive Averages Parity Total Born Born Alive Stillborn Mummies Number Weaned Parity 1 13.02 12.15 0.53 0.36 10.70 Parity 2 13.42 12.59 0.44 0.34 11.38 Parity 3 14.37 13.44 0.51 0.40 11.39 Parity 4 15.09 13.90 0.46 11.32

Cull and Death Reasons Thus Far

Early Major Scientific Findings, Serao et al. Antibody response to PRRS outbreak is highly heritable PRRS response is highly correlated to reproductive performance during PRRS outbreak Two major quantitative trait loci (QTL) on chromosome 7 are responsible for 40% of the genetic variation to PRRS antibody response

Industry Impact Possible to measure PRRS antibody response in commercial animals to help select nucleus replacement stock Marker/Genomic assisted selection for PRRS antibody response Enhanced understanding of PRRS on an individual basis in commercial farms Tip of iceberg

Acknowledgements Commercial producers/vets Funding Agencies CSHB Genome Canada Genome Alberta Swine Innovation Porc PigGen Members Philip Wilson – project coordinator