1. Learning to date and the way forward for genetics and swine health
Graham Plastow
Breakout Session #6
Swine Health & Genomics

2. Success Factors Leadership – shared vision Collaboration Recipe
Industry – Government – Academic
National and International
Recipe
Genotype + phenotype = information

3. Animals and Samples

4. Breeding for “Disease Resistance”
Or reduced susceptibility
Host Genetic Variation Identified
For every type of pathogen
Probably exists for all diseases
Major opportunity for genomics
As difficult and expensive to measure trait
May be only practical way to breed healthier pigs

5. Can It Be Done? Examples already exist
E.g. Resistance to E. coli F18, a major cause of bowel edema and one of the causes of post-weaning scours
Single gene giving recessive resistance - the gene’s scientific name is FUT1 M307

6. FUT1 M307 – Death loss ** P<0.001
Described in van der Steen, Prall, Plastow (2005) J. Anim. Sci. 83:E1-E8

7. FUT1 M307 – Average Daily Gain
** P<0.001

8. The PRRS Host Genetics Consortium (PHGC)
Understanding the role of host genetics in resistance to PRRSV infection, and the effects of PRRS on pig health and related growth.
Uses a nursery pig model to assess pig resistance/ susceptibility to primary PRRSV infection.
After acclimation, pigs infected with PRRSV and followed for 42 days post infection (dpi).
Blood samples collected at 0, 4, 7, 10, 14, 21, 28, 35 and 42 dpi, and weekly weights recorded.
Joan Lunney. USDA BARC
Bob Rowland, KSU

9. Weight distribution at different
Why PRRS?
$700 million/yr in US
Weight distribution at different
times after infection
Number
Data from PHGC trial 1 (Rowland et al, unpublished data).
Weight

11. “Blood, a window into health…” Leroy Hood PAG 2009

13. Finding the Causative Mutation amongst many candidate genes
Identified DE genes between genotypes (AA vs AG)
3 genes were DE:
Only one was DE across
multiple time points * **
*** NS

14. A SNP introduces a new acceptor splice site, which causes five nucleotides to be added to the transcript
The 5bp transcript causes a frame-shift in the protein that introduced an early stop codon. The susceptible genotype is missing the C-terminus of the protein
Koltes et al. BMC Genomics 16:412.

15. Studying variation in response to Salmonella
Why do some animals develop a carrier state and create a food safety hazard?
Salmonella-free pigs were infected with S. Typhimurium on day 0
9-10 weeks old
Observation: fecal bacteria over 20 days of experiment measured at 0, 2, 7, 14, and 20 days post inoculation
Phenotype: Area under the curve of log-transformed counts from 0-20 days
Tuggle et al see next slides

16. Study “extreme” phenotypes
Uthe, J.J., et al. (2009) Vet. Micro. 135:
Salmonella inoculation
“Persistent Shedders” PS1, PS2
“Low Shedders” LS1, LS2

18. Breeding for “Disease Resistance”
Rather the question is about the target
Specific diseases or Improved “Robustness” or “Resilience”?

19. Can It Be Done?
Examples already exist

20. A new example
Nature Biotechnology 34, 20–22 (2016) doi: /nbt.3434
Published online 07 December 2015

21. NVSL ,

22. Breeding for “Disease Resistance”
Rather the question is about the target
Specific diseases or Improved “Robustness” or “Resilience”?

23. Breeding for “Disease Resistance”
Differentially expressed genes identified in three different environments
Ye, Stothard, Plastow et al. unpublished results

24. Partnership Large scale multidisciplinary projects are doable
Field data while non-ideal provides new insights and can increase confidence for application
Technology advances mean that samples can increase in value over time

25. Thanks!
Agricultural Research
Service
USDA Pig
Genome
Coordinator

27. Multi-dimensional comparison assessment of
Higher throughput vs. in-depth analysis of immune parameters
Proximal vs. distal
Local vs. systemic
Short vs. long term
Basal vs. immune-challenged
Antimicrobial vs. homeostasis
Blood WBCs
Mesenteric lymph nodes
Lung tissue
Alveolar
inflammatory cells
Hematopoietic stem cells
and progenitors
Bone marrow
macrophages
Multi-dimensional comparison assessment of
immune competence and inflammation
Putting it all together – new Large Scale project led by Dyck, Harding……………………………