Update on the host genetics of resistance to porcine diseases - Dr. Jack Dekkers, Animal Breeding and Genetics, Department of Animal Science, Iowa State University, from the 2016 North American PRRS Symposium, December 3‐4, 2016, Chicago, Illinois, USA. More presentations at http://www.swinecast.com/2016-north-american-prrs-symposium

1. Update on the host genetics of
resistance to porcine diseases
Wean-Finish
Jack Dekkers
Department of Animal Science
Iowa State University

2. Evolution of PRRS
Host Genetics Research
1. Experimental infection of nursery pigs with NVSL
2. Experimental infection of nursery pigs with KS06
1. Experimental co-infection of nursery pigs: PRRS + PCV2 (incl. PRRS vaccination)
1. Field trials
2. Natural Challenge Model
NIFA
NIFA
NIFA
Trial Number n Breed PRRSv Isolate
1-3 530 LW x LR
NVSL
4 195 Duroc x LW/LR
5 184 Duroc x LR/LW
6 123 LR x LR
7 194 Pietran x LW/LR
8 188 Duroc x LW/LR
15 184 LR x LW
10 176 LR x LW
KS06
11 176 LW x LR
12 174 LR x LW
14 180 Duroc x LR/LW
Lunney, Rowland
Dekkers, Reecy

3. 0
1
2
3
4
5
6
7
0 5 10 15 20 25 30 35 40
Viremia(Log10Templates/ml,qPCR)
Days Post Infection
AA
AB
P=3*10-7
1*10-9
1*10-16
9*10-12
2*10-6
7*10-4
0.07
Boddicker et al. 2012, 2014a,b
Effects of a Major Gene
on SSC4 NVSL
Boddicker et al. 2012, 2014a,b
Nursery pig model for PRRS
0 4 7 11 14 21 28 35 42
0
2
4
6
8
Days Post Infection
Viremia(Log)

4. 5
10
15
20
25
0
1
2
3
4
5
6
7
0 5 10 15 20 25 30 35 40
Weight(kg)
Viremia(Log10Templates/ml,qPCR)
Days Post Infection
AA
AB
P=3*10-7
1*10-9
1*10-16
9*10-12
2*10-6
7*10-4
0.07
0.01
3*10-7
2*10-8
6*10-9
Boddicker et al. 2012, 2014a,b
Effects of a Major Gene
on SSC4 NVSL
Boddicker et al. 2012, 2014a,b
Nursery pig model for PRRS

5. VIRAL LOAD WEIGHT GAIN
Effects of a Major Gene
on SSC4 NVSL / KS06
Boddicker et al. 2012, 2014a,b
Trial Number n Breed PRRSv Isolate
1-3 530 LW x LR
NVSL
4 195 Duroc x LW/LR
5 184 Duroc x LR/LW
6 123 LR x LR
7 194 Pietran x LW/LR
8 188 Duroc x LW/LR
15 184 LR x LW
10 176 LR x LW
KS06
11 176 LW x LR
12 174 LR x LW
14 180 Duroc x LR/LW
Laura Constance et al.
Abstract # 37

6. 2016. Cell Host & Microbe 19, 504–514

7. Arrive
Vacci-
nate
Days post
vaccination -1 0 4 7 11 14 21 28 32 35 39 42 49 56 63 70
Days post
infection 0 4 7 11 14 21 28 35 42
Infect
Vaccination response Vaccination + infection response
Early response Later response
Body weight and Blood samples
Vaccination & Co-infection Trials
4 groups of 200 commercial crossbred piglets (18-21 d)
50 AA Vaccinated (PRRS MLV) 50 AB
50 AA Non-vaccinated 50 AB
GBP5 GBP5
Co-infection with PRRSv and PCV2  PCVAD
Translational Genomics
USDA-NIFA grant # 2013-68004-20362NIFA

8. Effect of GBP5 on PCV2b viremia
following PRRS vaccination
Jenelle Dunkelberger et al.
0
1
2
3
4
5
6
0 4 7 11 14 21 28 35 42
PCV2bViremia
(log10templates/reaction)
Day Post Infection
Non-Vx AA
Non-Vx AB

9. 0
1
2
3
4
5
6
0 4 7 11 14 21 28 35 42
PCV2bViremia
(log10templates/reaction)
Day Post Infection
Non-Vx AA
Non-Vx AB
Vx AA
Vx AB
Effect of GBP5 on PCV2b viremia
following PRRS vaccination
Jenelle Dunkelberger et al.

10. GBP5 QTL does NOT affect
overall performance in clean environments
Jenelle Dunkelberger et al. (Abstract #44)
Line
Selection Index
P-value
Dam
A 0.74
B 0.15
Sire
C 0.48
D 0.69

11. • Marker assisted selection based on GBP5 genotype is a
promising strategy to select for improved response…
– Not just to PRRSV infection, also co-infection with PCV2b
– And perhaps other pathogens?
– No negative effect on performance without major disease
• For PCV2b VL, the effect of GBP5 was significant
for Vx pigs, but not for Non-Vx pigs
• Numerically, the effect of GBP5 was greater upon
primary vs. secondary PRRSV exposure
• Consistent with role of GBP5 in innate response
Conclusions

12. Transcriptome
Analyses
NIFA

13. Ongoing Transcriptome analyses
Objectives
Identify differentially expressed genes and
pathways related to host response to co-
infection with/out prior vaccination for PRRS
Determine the effect of tonsil PRRS viral level
and PRRS isolate on tonsil gene expression
Qian (Jessie) Dong, Joan Lunney,
Elyn Fritz-Waters, Yet Nguyen, Bob Rowland
Andrew Hess, James Reecy, Jack Dekkers

14. Gene expression analyses
7 x 4 litter mates from PHGC16
Vx
AA AB
Non-Vx
AA
n=7
AB
n=7 n=7n=7
GBP5Arrive
Vacci-
nate
Days post
vaccination -1 0 4 7 11 14 21 28 32 35 39 42 49 56 63 70
Days post
infection 0 4 7 11 14 21 28 35 42
Infect
Vaccination response Vaccination + infection response
Early response Later response
Serum 3’ RNAseq  192 samples

15. 4 lanes on Hiseq 2500 Rapid mode,50 cycl, single end
Total Reads
No Feature
Ambiguous
Too low Quality
Not aligned
Hemoglobin A
Hemoglobin B
All Other Genes
4 lanes on Hiseq 2500 Rapid mode,50 cycl, single end
4,731,750 %
1,030,178 21.8
12,596 0.3
1,041,451 22.0
421,149 8.9
1,287,966 27.2
455,002 9.6
483,408 10.2
3’ RNA seq

16. The effect of PRRS viral level and
isolate on tonsil gene expression
42 days after infection
Abstract # 43
Qian (Jessie) Dong1, Joan Lunney2,
Elyn Fritz-Waters1, Yet Nguyen1, Bob Rowland3
Andrew Hess1, James Reecy1, Jack Dekkers1
1Iowa State University
2USDA, ARS, BARC, APDL
4Kansas State University

17. Relationship between the serum
viremia and tonsil viremia at 42 dpi
SerumViralLoad0-21dpi
SerumViremia42dpi
Tonsil viremia 42 dpi Tonsil viremia 42 dpi
Tonsil virus class # pigs for RNA-seq
NVSL
High 15
Low 15
KS06
High 12
Low 10
0 4 7 11 14 21 28 35 42
0
2
4
6
8
Days Post Infection
Viremia(Log)

18. # DEG between Isolate
and Tonsil Viremia
Dong et al.
Abstract # 43

19. 0
0.25
0.5
0.75
1
1.25
1.5
1.75
2
0 0.25 0.5 0.75 1
PathogenLoad
Level of Exposure
0.4
0.6
0.8
1
1.2
1.4
0 0.25 0.5 0.75 1 1.25 1.5
Growthrate(lbs/d)
Pathogen Load
0.4
0.6
0.8
1
1.2
1.4
0 0.25 0.5 0.75 1
GrowthRate(lbs/d)
Level of Exposure
B
A
PLA
PLB
B
A
GA
GB
B
A
PLA PLB
GA
GB
Resistance
Ability to prevent
infection or limit
replication
Resistance, Tolerance, or Resilience?
Tolerance
Ability to maintain
performance as
pathogen load increases
Resilience
Robustness
Ability to maintain
performance upon
exposure to a pathogen

20. 13
14
15
16
17
18
19
20
21
22
23
80 85 90 95 100 105 110 115 120 125
42-dGrowth(kg)
Viral Load
NVSL
AA
AB
WUR*slope p-value = 0.29
13
14
15
16
17
18
19
20
21
22
23
80 85 90 95 100 105 110 115 120 125
42-dGrowth(kg)
Viral Load
KS06
WUR*slope p-value = 0.21
GBP5 QTL for PRRS
Resistance, Tolerance,
or Resilience?
Trial Number n Breed PRRSv Isolate
1-3 530 LW x LR
NVSL
4 195 Duroc x LW/LR
5 184 Duroc x LR/LW
6 123 LR x LR
7 194 Pietran x LW/LR
8 188 Duroc x LW/LR
15 184 LR x LW
10 176 LR x LW
KS06
11 176 LW x LR
12 174 LR x LW
14 180 Duroc x LR/LW
Hess et al. (unpublished)
AAAB AA
AB

21. Application of Genomics to Improve
Disease Resilience and Sustainability
in Pork Production
Michael Dyck, John Harding, Bob Kemp
NIFA

22. 3500 YXLR WEANER PIGS
FROM HIGH-HEALTH HERDS
BATCHES OF 60-75 PIGS/3 WEEKS
NATURAL CHALLENGE FACILITYQUARANTINE NURSERY
SEEDER PIGS
Continuous flow
Genetics of Resilience under Natural Challenge

23. Pathogens in Natural Challenge Farm (October
2016) (Harding)

24. 3500 YXLR WEANER PIGS
FROM HIGH-HEALTH HERDS
BATCHES OF 60-75 PIGS/3 WEEKS
PREDICTIVE
PHENOTYPES collected on
young healthy pigs
Immune Response
• High Immune Response
• In vitro immune tests
• Phagocytosis tests
Blood Transcriptome
Blood Metabolome
Blood Proteome
RESILIENCE PHENOTYPES
collected on all pigs
Mortality/Morbidity
Growth performance
Feed intake
Water intake
Disease diagnostics
Gut Microbiome
Blood transcriptome
Gut Microbiome
NATURAL CHALLENGE FACILITYQUARANTINE NURSERY
SEEDER PIGS
Continuous flow
Genetics of Resilience under Natural Challenge

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Batch 1 Batch 2 Batch 3
Batch 4 Batch 5 Batch 6
Batch 7
0
50
100
150
0
50
100
150
0
50
100
150
50 100 150 200
Age (days)
Weight(kg)
Weights for each pig by Age and Batch
Austin Putz

26. Austin Putz

27. 3500 YXLR WEANER PIGS
FROM HIGH-HEALTH HERDS
BATCHES OF 60-75 PIGS/3 WEEKS
PREDICTIVE
PHENOTYPES collected on
young healthy pigs
80 K SNP
genotypes
Immune Response
• High Immune Response
• In vitro immune tests
• Phagocytosis tests
Blood Transcriptome
Blood Metabolome
Blood Proteome
TARGET RESILIENCE
PHENOTYPES
RESILIENCE
collected on all 3500 pigs
Mortality/Morbidity
Growth performance
Feed intake
Water intake
Disease diagnostics
Trait Genetics
• Parameters
• Architecture
• Mechanisms
Genetic
Prediction
of Resilience
Phenotypic
Prediction
of Resilience
PROJECT
DELIVE-
RABLES
Gut Microbiome
Integrated
statistical
and
bioinformatic
analyses
Blood transcriptome
Gut Microbiome
NATURAL CHALLENGE FACILITYQUARANTINE NURSERY
SEEDER PIGS
Continuous flow

28. Evolution of PRRS Host
Genetics Research
1. Experimental infection of nursery pigs with NVSL
2. Experimental infection of nursery pigs with KS06
1. Experimental co-infection of nursery pigs: PRRS + PCV2 (incl. PRRS vaccination)
1. Field trials
2. Natural Challenge Model
NIFA
NIFA
NIFA
Trial Number n Breed PRRSv Isolate
1-3 530 LW x LR
NVSL
4 195 Duroc x LW/LR
5 184 Duroc x LR/LW
6 123 LR x LR
7 194 Pietran x LW/LR
8 188 Duroc x LW/LR
15 184 LR x LW
10 176 LR x LW
KS06
11 176 LW x LR
12 174 LR x LW
14 180 Duroc x LR/LW

29. 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
Scientific
Collaborators
NIFA
Thanks to all Partners

30. Coming Spring 2017: Online course

31. Goal: Train veterinarians and geneticists on
concepts of genetic selection & genomics
and their application to improve animal health
What: On-line, asynchronous, videos made
by experts, essential readings, self-paced
Unit 1:
Introduction
to disease
biology
Unit 2:
Genetics
and genetic
selection
Unit 3:
Genetic
selection for
disease
resistance
Unit 4:
Genetic
selection for
PRRS virus
Principles and Applications of Genetics and
Genomics to Improve Animal Health

32. More information
Poster on display at
this conference.

33. Coming Spring 2017: Online course