Genomics and Their Applications in Forest HealthAmanda Roe – Natural Resources Canada, Great Lakes Forestry Centre

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

Genomics!

What my husband thinks I do.

What I actually do.

Genomics and their applications in forest health

• Genetics vs Genomics

• Applications in Forest Health

• Diagnostics

• Ecology

• Spread

• Getting involved

Genetics (DNA barcoding)

Genomics(NGS)

Genetics vs Genomics

= hereditySingle gene/few genes

= entirety of an organisms genesInteractions, organization,

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

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

NGS / GBS

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

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

What is it?

Not all questions need genomics!

What is it?

Finding exotic genes in native forests

What is it? Exotic genes in poplars.

Roe et al. 2014a, 2014b Ecol Evol

Base de plein air de Saint-Foy, QC

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.

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.

Roe et al. 2014a, 2014b Ecol Evol

Base de plein air de Saint-Foy, QC

1) Identify exotic genesP. 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

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 √ √

Why does it matter?

Biosecurity and forest certification

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

What is it doing? Ecology & evolution of pests

Population Genomics

• Link genomic variation to key life history traits

AdrianneRice

Janice Cooke

Jack Scott

What is it doing? Mountain Pine Beetle

Talus, Flicker

What is it doing? MPB

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 galleries96 SNPs

CERVUS 3.0 & COLONY 2.0.4.5

What is it doing? MPB

Talus, Flicker

Why does it matter?

Estimating population growth and rate of spread

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

Where is it from? Spread and dispersal

Where is it from? ALB spread and dispersal

Where is it from? ALB spread and dispersal

?

Population Genomics

• Variation across spatial and temporal landscapes

• Link genomic variation to key life history traits

Where is it from? ALB spread and dispersal

Why does it matter?

Refines surveillance & guides trade negotiations

Genomics and their applications in forest health

Genomics = Another source of information to help reduce uncertainty

Genomics and their applications in forest healthPublic Service Announcement

Collecting for genomics project

70%EtOH

>95%EtOH

Genomics and their applications in forest health

70%EtOH

>95%EtOH

Public Service AnnouncementCollecting for genomics project

Questions?

Why does it matter?