1. 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  

2. 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

3. Nursery Pig Challenge Model
R.R.R. Rowland et al., Kansas State University Groups of ~200 commercial crossbred pigs infected with PRRS virus isolate NVSL 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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 rs genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs 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, rs , 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 rs SNP was also 100 % concordant with rs 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 rs is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.

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

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

15. 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

16. 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

17. 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

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

19. 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

20. 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

21. 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