Genetics of PRRS in growing pigs Jack Dekkers Nick Boddicker Emily Waide Andrew Hess Iowa State University Bob Rowland Kansas State University Joan Lunney USDA-ARS Graham Plastow University of Alberta  

Strong Industry Participation PHGC Breeding Companies 60K SNP chip Illumina 2007 Objective Use genomics to identify genes / genomic regions associated with resistance / susceptibility to PRRS virus infection Led by Joan Lunney – USDA – ARS Beltsville Bob Rowland – Kansas State University Jim Reecy – Iowa State University Jack Dekkers – Iowa State University Strong Industry Participation PHGC Breeding Companies Fast Genetics, Genesus, Choice Genetics PIC/Genus, TOPIGS, PigGen Canada

Nursery Pig Challenge Model R.R.R. Rowland et al., Kansas State University Groups of ~200 commercial crossbred pigs infected with PRRS virus isolate NVSL97-7985 between 18 and 28 d of age Weight Serum Slaughter Ear for DNA -7 7 11 14 21 35 42 4 28 Antibiotics Acclimation Birth Inoculation Day post infection

Host Response Phenotypes Body weight Log(viremia) h2 = 0.29 h2 = 0.41 Rebound rp = -0.25 rg = -0.47 Viral Load Area Under Curve

First Generation PHGC trials Boddicker et al. J. Anim. Sci First Generation PHGC trials Boddicker et al. J. Anim. Sci. 2012, Animal Genetics 2014, Genetics Selection Evolution 2014 Trial Parents Parental Breeds # piglets Sex PHGC 1-3 Sires LW 562 All Barrows Dams LR PHGC 4 Duroc 195 Barrows + gilts LW/LR comp PHGC 5 199 LR/LW comp PHGC 6 198 All Barrows PHGC 7 Pietran 197 + gilts PHGC 8 200 Y/LR

Results of Genomic Analyses Viral Load Weight Gain Chr 4 Chr 4 11% of genetic variance 1 Mb region explains 15% of genetic variance Includes important candidate genes GBP1 GBP2 GBP5 GTF2B PKN2

Effects of WUR10000125 on Viral Load Trials 1-8 WUR genotype a b ab a a n=1023 n=347 n=44 n=376 n=139 n=15 n=163 n=28 n=4 n=124 n=57 n=3 n=112 n=11 n=87 n=85 n=22 n=158 n=29 MAF = 0.17 Boddicker et al. 2012, 2014a,b

Effects of WUR10000125 on Weight Gain Trials 1-8 WUR genotype ab b b b ab a b b a b ab a a a a a a b a n=11 n=983 n=58 n=3 n=95 n=345 n=43 n=362 n=137 n=14 n=161 n=28 n=4 n=122 n=87 n=85 n=22 n=156 n=26 Boddicker et al. 2012, 2014a,b

SSC 4 region effects over time PHGC1-8 1*10-9 1*10-16 P=3*10-7 9*10-12 2*10-6 7*10-4 0.07 Boddicker et al. 2012, 2014a,b

SSC 4 region effects over time PHGC1-8 1*10-9 1*10-16 P=3*10-7 9*10-12 6*10-9 2*10-8 2*10-6 7*10-4 3*10-7 0.07 0.01 Boddicker et al. 2012, 2014a,b

Generation 1 & 2 PRRS trials Trial Number n Breed PRRSv Isolate 1-3 530 LW x LR NVSL 4 195 Duroc LW/LR 5 184 LR/LW 6 123 7 194 Pietran 8 188 15 10 176 KS06 11 12 174 14 180 Total 2304 challenged pigs with deep phenotypes

A major QTL for host response to PRRS on SSC 4 Boddicker et al. 2012, 2014a,b; Hess et al. 2015 VIRAL LOAD WEIGHT GAIN Results Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype. Conclusions GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.

A major QTL for host response to PRRS on SSC 4 Hess et al. 2015 rg(VL) = 0.86 (+0.19)

A major QTL for host response to PRRS on SSC 4 Hess et al. 2015 rg(VL) = 0.86 (+0.19) rg(WG) = 0.86 (+0.27)

Identification of other host response QTL Waide et al. KS06 NVSL WUR = 21 Viral Load WUR = 7 WUR = 7 rg(NVSL, KS06) = 0.86 (+0.19) WUR = 21 KS06 WG P 0.295 NVSL WG –log10(P) = 16 Genomic regions do not overlap between PRRSV isolates But pathways do

Identification of other host response QTL KS06 NVSL WUR = 16 Weight Gain rg(NVSL, KS06) = 0.86 (+0.27) WUR = 16 KS06 WG P 0.295 NVSL WG –log10(P) = 16

Genomic Prediction Prediction using high-density SNPs Meuwissen et al. 2001 Training population Estimate SNP effects Phenotypes SNP Genotypes Selection candidates SNP Genotypes Genomic Prediction

Can we use Genomic Prediction across isolates? NVSL Trials KS06 Trials r/h KS06 NVSL

Conclusions Piglet response to experimental PRRSv challenge has a sizeable genetic component. Chromosome 4 contains a major gene for host response to PRRSv in growing piglets. Genetic selection for improved host response to PRRS is possible and can be an important component in the fight against PRRS

Evolution of PRRS Host Genetics Research Experimental infection of nursery pigs with a specific PRRSV strain Experimental infection of nursery pigs with another PRRSV strain Experimental co-infection of nursery pigs: PRRS + PCV2 (incl. PRRS vaccination) Field trials

Kansas State University Thanks to all Partners Scientific Collaborators Iowa State University Nick Boddicker Andrew Hess Emily Waide Chris Eisley Jenelle Dunkelberger James Koltes Eric Fritz-Waters Martine Schroyen Nick Serao Jim Reecy Chris Tuggle Susan Carpenter Kansas State University Bob Rowland PRRS group Ben Trible Megan Niederwerder Maureen Kerrigan Becky Eaves et al USDA-ARS Joan Lunney group Igseo Choi Sam Abrams University of Alberta Graham Plastow group Univ. Saskatchewan John Harding group Roslin Institute Steve Bishop Andrea Doeschl-Wilson Zeenath Islam Graham Lough Univ. Minnesota Monserat Torremorrell Funding Industry Partners NIFA