Broad overview of the application of genomic techniques to issues around forest health. Examples based on insect and tree research. Presented at 40th annual Ontario Forest Pest Review at Orillia, ON.

1. Genomics and Their Applications in Forest Health
Amanda Roe – Natural Resources Canada, Great Lakes Forestry Centre

2. Key Questions in Forest Health
• What is it?
• Where is it from?
• How did it get here?
• What is it doing?
• How far will it spread?
= Uncertainty

3. Genomics!

4. What my husband
thinks I do.
What I actually do.

6. Genomics and their applications in forest health
• Genetics vs Genomics
• Applications in Forest Health
• Diagnostics
• Ecology
• Spread
• Getting involved

7. Genetics
(DNA barcoding)
Genomics
(NGS)
Genetics vs Genomics
= heredity
Single gene/few genes
= entirety of an organisms genes
Interactions, organization,

8. Kress & Erickson PNAS 2008;105:2761-2762©2008 by National Academy of Sciences

9. Kress & Erickson PNAS 2008;105:2761-2762©2008 by National Academy of Sciences
NGS / GBS

10. Applications to Forest Health
1. What is it? (= diagnostics)
2. What is it doing? (= Ecology)
3. Where is it from & going? (= spread & dispersal)
D Huber

11. Applications to Forest Health
1. What is it? (= diagnostics)
2. What is it doing? (= Ecology)
3. Where is it from & going? (= spread & dispersal)
D Huber

12. What is it?
Not all
questions
need
genomics!

13. What is it?
Finding exotic genes in native forests

14. What is it? Exotic genes in poplars.
Roe et al. 2014a, 2014b Ecol Evol
Base de plein air de Saint-Foy, QC

15. Roe et al. 2014a, 2014b Ecol Evol
Base de plein air de Saint-Foy, QC
1) Identify exotic genes
What is it? Exotic genes in poplars.

16. What is it? Exotic genes in poplars.
Roe et al. 2014a, 2014b Ecol Evol
P. balsamifera
P. deltoides
P. nigra (exotic)
P. maximowiczii (exotic)
STRUCTURE (K=4) of 35 SNP panel
Trees bearing exotic genes.

17. Roe et al. 2014a, 2014b Ecol Evol
Base de plein air de Saint-Foy, QC
1) Identify exotic genes
P. balsamifera (B) - 10%
P. deltoides (D) - 70%
DxB hybrids (DB) - 10%
Exotic hybrids (X) - 10%
What is it? Exotic genes in poplars.
Adult trees
P. balsamifera (B) - 76%
P. deltoides (D) - 14%
DxB hybrids (DB) - 0%
Exotic hybrids (X) - 10%
Seedlings

18. Roe et al. 2014a, 2014b Ecol Evol
2) Track movement via gene flow.
What is it? Exotic genes in poplars
Seed types
Female
Trees
P. balsamifera (B) - 3.50%
P. deltoides (D) - 0%
DxB hybrids (DB) - 2.11%
Spontaneous exotic
hybridization rate
B D DB X
B √ √ √
D √ √
DB √ √

19. Why does it matter?
Biosecurity and forest certification

20. Applications to Forest Health
1. What is it? (= diagnostics)
2. What is it doing? (= Ecology)
3. Where is it from & going? (= spread & dispersal)
D Huber

21. What is it doing? Ecology & evolution of pests
Population Genomics
• Link genomic variation to
key life history traits

22. Adrianne
Rice
Janice
Cooke
Jack
Scott
What is it doing? Mountain Pine Beetle

23. Talus, Flicker
What is it doing? MPB

24. Janes et al. 2015 Heredity
• Polygamous mating systems
• in contrast to Reid 1958, 1962
• Supports observations pre-emergence mating
 Bleiker et al. 2013; Safranyik & Wilson 2006
404 beetles from 174 galleries
96 SNPs
CERVUS 3.0 & COLONY 2.0.4.5
What is it doing? MPB

25. Talus, Flicker
Why does it matter?
Estimating population growth and rate of spread

26. Applications to Forest Health
1. What is it? (= diagnostics)
2. What is it doing? (= Ecology)
3. Where is it from & going? (= spread & dispersal)
D Huber

27. Where is it from? Spread and dispersal

28. Where is it from? ALB spread and dispersal

29. Where is it from? ALB spread and dispersal
?

30. Population Genomics
• Variation across spatial
and temporal landscapes
• Link genomic variation to
key life history traits
Where is it from? ALB spread and dispersal

31. Why does it matter?
Refines surveillance & guides trade negotiations

32. Genomics and their applications in forest health
Genomics =
Another source of information to help reduce uncertainty

33. Genomics and their applications in forest health
Public Service Announcement
Collecting for genomics project
70%
EtOH
>95%
EtOH

34. Genomics and their applications in forest health
70%
EtOH
>95%
EtOH
Public Service Announcement
Collecting for genomics project

35. Questions?

36. Why does it matter?