emerging issues and organizational approachescips.forestry.oregonstate.edu/sites/cips/files/... ·...
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1
Douglas-fir Breeding:
The Technological Cutting Edge
Emerging Issues and Organizational Approaches
Glenn HoweDirector, Pacific Northwest Tree Improvement Research Cooperative
Oregon State University
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Technological advances and applications
Wood stiffness remains a high priority for genetic improvement
Clonal forestry is receiving much attention in the SE, but not in the
PNW
New climate models are available to predict climate and weather for
specific sites (e.g., ClimateWNA)
Genomic markers are being developed and tested in breeding
programs
Genetic considerations will play an important role in assessing the
potential effects of climate change and helping forest managers adapt
Large, collaborative external grant programs increasingly important!
2
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Large collaborative projects are an important foundation for future advances
Pacific Northwest Tree Improvement Research Cooperative
(PNWTIRC)
NSF Center for Advanced Forestry Systems (CAFS)
Conifer Translational Genomics Network (CTGN)
Western Conifer Climate Change Consortium (WCCCC)
These projects need stakeholder involvement to be successful!!
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Trend toward shorter rotations, faster growth
More wood from the juvenile wood core
Juvenile wood:
Genetics of wood stiffness
- Lower wood density
- Higher microfibril angle
- Lower stiffness
- More shrinkage
3
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Rationale
Selection for improved wood stiffness is feasible in 25
year-old Douglas-fir trees
Log-based acoustic tools work very well, but trees must be
harvested (RE = 78-93%)
Standing-tree acoustic tools can be used, but gains are lower
(RE = 57-58%)
Breeders want to select at younger ages (e.g., 6-12)
How well will these or other tools work?
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Wood stiffness of 25 year-old trees
4
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Wood stiffness of young trees?
Genetic selections are often
made at ages 6-12
Current tools are probably
unsuitable
More juvenile wood
Branches a problem
What are age-age
correlations?
Approach
Test alternative methods for measuring stiffness of
young trees in the field (phenotypic analyses)
Can we reliably measure stiffness of young trees?
Test best approaches in progeny tests
Understand the genetics of juvenile wood stiffness
Analyze increment cores collected from mature trees
(phenotypic analyses)
What is the potential for early selection?
Analyze age trends and age-age correlations of wood properties
Juvenile (core) wood Mature (outer) wood
5
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Wood density is measured by x-ray
densitometry
Microfibril angle (MFA) is measured by
x-ray diffractometry
Microfibril angle
Wood density
Wood stiffness (indirect)
Fiber diameter
Fiber wall perimeter
Fiber wall thickness
Fiber Coarseness
Fiber specific surface area
Ring width
SilviScan
www.ffp.csiro.au/photos/SilviScanLayout-small.jpg
10
Other approaches
Method Property Cost Quality
X-ray densitometry Density Moderate High
X-ray diffraction MFA, MOE Moderate-high High
Tensile testing MOE Prohibitive High
Compression testing MOE Prohibitive High
Volumetric density Density Moderate Moderate-high
Contact ultrasonics MOE, MFA Moderate High
Bending 3- and 4-point MOE, MOR Prohibitive High
In-tree acoustics MOE, MFA Low Moderate-high
X-ray μCAT Density Moderate High
Resistograph Density Low Moderate
NIR Density, MFA, MOE Moderate Moderate-high
Modified from Gary Peter et al. 2008
6
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
FAKOPP tools for small trees
TreeSonic with alternative sensors (SD02)
– Standard sensors too large?
– Physical signal
Microsecond timer
Ultrasonic timer
– Electrical signal
SD02
IML tools for small trees
Acoustic velocity
IML Micro Hammer
Wood density
Resistograph
7
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Center for Advanced Forestry Systems (CAFS)
http://cnr.ncsu.edu/fer/cafs/researchareas.html
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Center for Advanced Forestry Systems (CAFS)
National Science Foundation
Industrial Innovation Partnership (IIP) Division
Industry / University Cooperative Research Centers
Center for Advanced Forestry SystemsNorth Carolina State University – Jose Stape
Oregon State University – Glenn Howe
Purdue University – Charles Michler
University of Florida – Eric Jokela
University of Georgia – Michael Kane
University of Idaho – Mark Coleman
University of Maine – Robert Wagner
University of Washington – David Briggs
Virginia Tech – Thomas Fox
8
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Clone-specific modeling and silviculture
Developing Varietal Precision Silvicultural Regimes in Pine and
Hardwood Plantations Based on Crown Ideotype (Fox; VT)
Developing Growth and Yield Predictions for Diverse Genotypes
and Silvicultural Practices (Burkhart; VT)
Developing Growth and Yield Predictions for Enhanced Genotypes
(Borders; UGA)
Integrating Wood Quality Predictions into Growth and Yield Models
for Evaluating Advanced Genotypes and Silvicultural Responses
(Daniels; UGA)
Scaling Competitive Dynamics from the Individual to the Stand
Using Clonal and Full-Sib Family Block Trials (Jokela; UF)
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Other CAFS genetics projects
Genetic Architecture of Growth, Disease Resistance and Wood
Quality Traits in Loblolly Pine (Peter; UF)
Early genetic selection for wood stiffness in Douglas-fir (Howe;
OSU)
Effects of Site and Genetics on Douglas-fir Growth, Stem Quality,
and Adaptability (Howe; OSU)
9
Economic Environment ($)
Industry
organization
Products
Rotations
Crop value
Seedlings
produced ~1000 M
100 M
20-35 yrs
45-70 yrs
Pulp/paper/OSB
more important
Pulp/paper/OSB less important
TIMOs/REITs increasing
Implications: Douglas-fir Loblolly pine
Interest in growth and wood quality High High
Investment in breeding/research Lower Higher
Interest in clonal forestry Lower Higher
Interest in GMOs ~Non-existent Some
Higher
Lower
= Douglas-fir
= Loblo lly p ine
= Douglas-fir
= Loblo lly p ine
Physical Environment & Lands
Implications: Douglas-fir Loblolly pine
Seed zones/Breeding zones 123 / 10-13 <<123 / 7
First-gen breeding pops Larger Smaller
Breeding program More costly Less costly
Breeding objectives More on adaptability, diversity Less on adaptability, diversity
Clonal forestry/GMOs More difficult, expensive Easier, less expensive
Public land
Frosts
Drought
Environmental
variability Low
Important
High
Important
Important
Rarely a problem?
Lots
Little
= Douglas-fir
= Loblo lly p ine
= Douglas-fir
= Loblo lly p ine
10
Social Environment
Implications: Douglas-fir Loblolly pine
Interest in clonal forestry Lower Higher
Interest in GMOs ~Non-existent Some
= Douglas-fir
= Loblo lly p ine
= Douglas-fir
= Loblo lly p ine
Environmental
activism
Concerns about
genetics/GMOs
Skepticism about
forest mgmt.
Low
High
Low
High
Low
High
Low
High
Agrarian culture
Desktop version
Web version
ClimateWNA provides easy access
to over 20,000 climate surfaces
ClimateWNA - Climate interpolation
11
Mean Annual Temperature (MAT) by PRISM (4 x 4 km)
21A mountain area near North Vancouver
Downscaled MAT by ClimateWNA (90m)
22A mountain area near North Vancouver
12
Many derived climate variables in ClimateWNA
Degree-days <0°C
Degree-days>5°C
Frost-freeperiod
Number of frost-free days
Extreme minimumtemperature
Snow fall
23Wang et al. 2006. Intl. J. Climatology 23
ClimateWNA generates climate data for the past (1901 – 2009)
2424
13
It predicts climate data for the future periods
2525
Spatial pattern of temperature for baseline period
ClimateBC output (90m) overlaid on a satellite image (1970s)26
14
GCM changes added onto the baseline data
ClimateBC output (90m) overlaid on a satellite image (CGCM2 A2_2050s)27
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Site characterization: parent trees
3458 parent trees estimated to be within 80
meters of the real world location
Elevation: 6 to 954 meters
Parents are from 21 NWTIC testing programs
Analyses include 158 progeny test sites
Methods of verification and digitization
– Spatial database of parent trees within a GIS
– Cooperator maps were used with NAIP and Google
Earth (NAIP = National Agricultural Imagery
Program)
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#####################################################
15
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Site characterization: progeny tests
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205 progeny test sites in Oregon and
Washington
Sites belong to 32 NWTIC testing programs
Elevation 15 to 1090 meters
Average of 3500 trees per site (400 to 9400)
Measured variables− Height at ages ~5, 10, 15
− DBH at ages ~5, 10 15
− Sinuosity
− Forking
− Ramicorn branching
ClimateWNA variables related to height growth
Annual height growth from sowing
to ~15 years-old
Importance of climatic and other variables
evaluated using Random Forest
Program code
Sowing year
Precip as snow
Aspect
Ave spring temp
Degree-days < 0°
Winter precip
Annual heat-moisture index
Winter ave temp
Mean annual precip
Degree-days > 5°
Elev
Fall precip
Mean coldest month temp
Min spring temp
16
Seedlot Selection Tool (SST)
Given a specific planting site …
Which seedlot is well adapted today?…
And in the future given a climate change scenario?
http://sst.forestry.oregonstate.edu/PNW/
Transfer limits for Douglas-fir
Statistic MAT MAP MCMT MWMT FFP MSP AHM
Mean 1.6 667 1.9 1.6 43 96 4.7
Min 0.4 80 0.5 0.3 12 15 0.8
Max 2.5 1915 3.5 4.0 72 221 17.5
Std 0.5 454 0.6 0.5 14 53 3.2
MAT = mean annual temperature
MAP = mean annual precipitation
MCMT = mean coldest month temperature
MWMT = mean warmest month temperature
FFP = length of frost-free period
MSP = mean summer precipitation
AHM = annual heat:moisture index
ClimateWNA variables
Mean transfer distances for Douglas-fir Oregon modified seed zones (Randall 1996)
17
Find seedlots for my planting site
2010-2039
2070-20992040-2069
1961-1990
Conifer Translational Genomics Network
Coordinated Agricultural Project
www.pinegenome.org/ctgn
18
www.pinegenome.org/ctgn
Single nucleotide polymorphism (SNP)
Tree 1 is heterozygous Trees 2 and 3 are homozygous
A C G T G T C G G T C T T A Maternal chrom.
A C G T G T C A G T C T T A Paternal chrom.
A C G T G T C G G T C T T A Maternal chrom.
A C G T G T C G G T C T T A Paternal chrom.
A C G T G T C A G T C T T A Maternal chrom.
A C G T G T C A G T C T T A Paternal chrom.
Tree 1
Tree 2
Tree 3
SNP
www.pinegenome.org/ctgn
A genome from many short sequences
Next-generation
sequencing
19
www.pinegenome.org/ctgn
Find SNP markers
www.pinegenome.org/ctgn
Potential SNP markers in Douglas-fir
Douglas-fir variety No. of SNPsNo. of genes
with SNPs
Coastal 238,760 17,556
Interior 151,918 16,580
Both (in common) 71,376 13,759
20
www.pinegenome.org/ctgn
The promise of genomic selection
Paradigm shift in perspective
Forget about finding individual markers associated with desirable
traits
Explain desirable traits by using many, many markers at the same
time
Now possible because we can genotype many SNP markers at
modest cost
– SNP, single nucleotide polymorphism, = changes between A, G, C, T
Why might it be useful?
www.pinegenome.org/ctgn
BC Forest Service
21
www.pinegenome.org/ctgn
The promise of genomic selection
GEBV = genomic estimated breeding value
Phenotypic selection
(select on BLUP BV)
Phenotype
progeny
(field tests)
Genotype
progeny
(SNP markers)
Genomic selection
(select on GEBV)
Make
crosses
Genomic
Selection
Cycle
Phenotypic
Selection
Cycle
Genotype, then use existing phenotypes
to train GEBV model
Model training step
Phenotypic selection
(select on BLUP BV)
Phenotype
progeny
(field tests)
Genotype
progeny
(SNP markers)
Genomic selection
(select on GEBV)
Make
crosses
Genomic
Selection
Cycle
Phenotypic
Selection
Cycle
Genotype, then use existing phenotypes
to train GEBV model
Model training step
Western Conifer Forest Systems:
Strategies for Climate Change
Adaptation and Mitigation
Western Conifer
Climate Change Consortium (WCCCC)
USDA Coordinated Agricultural Project
22
Large climatic transfer distances can result in maladapted
plantations
Transfer limits can be determined directly from provenance tests
Sufficiently large provenance tests are rare
Sufficiently large transfer distances are rarely tested
Lodgepole pine provenances from maritime areas
are not adapted to the winters of eastern Finland
Superior adaptability of a Douglas-fir seed
source from California growing in Spain
(Hernandez et al 1993)
Finnish Forest Research Institute Lodgepole pine provenance test in
New Zealand (Wright 1976)
Seed source adaptability is criticalSeed source adaptability is critical
Lodgepole pine provenance test in B.C.
Local = productivity increases by 7% up to 1.5ºC (2030), but then decreases.
Optimal = productivity increased by 14-36%.
-70
-50
-30
-10
10
30
50
70
0
2012
|
1
2038
|
2
2063
|
3
2088
|
4
2114
|
5
2139
6
M AT increase (°C )
Ch
an
ge
in
pro
du
cti
vit
y (
m3/h
a)
— O ptim ized sources
— Local sources
-70
-50
-30
-10
10
30
50
70
0
2012
|
1
2038
|
2
2063
|
3
2088
|
4
2114
|
5
2139
6
M AT increase (°C )
Ch
an
ge
in
pro
du
cti
vit
y (
m3/h
a)
— O ptim ized sources
— Local sources
Wang et al. (2006) Global Change Biol. 12:2404.
140 populations 60 test sites
20 years old
Effects of climate change on lodgepole pineEffects of climate change on lodgepole pine
23
Regional CAP for 2011
Regional approaches to Climate Change: CAP
Application deadline – July 16, 2011?
$4,000,000 per year ($20 million total) for up to 5 years
Anticipates making 5 to 8 awards in FY 2011?
Regional integrated CAP focusing on mitigation and
adaptation, involving research, education, and outreach in:
– Cropping systems: legume or forage production systems
– Animal systems: ruminant livestock and dairy
– Forest systems: western conifers
– Grassland, pastureland, and rangeland systems
Stakeholders are critical
“Demonstrate the adoption of approaches and practices
across the region…”
Stakeholders are seed orchard managers, nursery
managers, silviculturists, managers of forest operations,
wood products manufacturers, managers of carbon offsets
programs, policy makers, teachers, and students
Organizations are forest industry, governmental agencies,
tribes, small private landowners, NGOs, and universities
Included in project advisory groups
24
Long-term goal
Synthesize existing knowledge and develop new
knowledge on the impacts of climate change on western
forest production systems, and then design, convey,
and implement management strategies that maximize
forest health, forest productivity, and greenhouse gas
mitigation under changing climates
WCCCC planning meeting tomorrow
25
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
PACIFIC NORTHWEST TREE IMPROVEMENT
RESEARCH COOPERATIVE
Technological advances and applications
Wood stiffness remains a high priority for genetic improvement
Clonal forestry is receiving much attention in the SE, but not in the
PNW
New climate models are available to predict climate and weather for
specific sites (e.g., ClimateWNA)
Genomic markers are being developed and tested in breeding
programs
Genetic considerations will play an important role in assessing the
potential effects of climate change and helping forest managers adapt
Large, collaborative external grant programs increasingly important!
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