National Report on Forest Genetics Activities in the United States

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National Report on Forest Genetics Activities in the United States


Report to the Forest Genetic Resources Working Group

of the FAO North American Forestry Commission

XXX
I
I
I

Meeting

April 11
-
14, 2011

O
tto, North Carolina, U.S.A.


prepared by Brad St.Clair

USDA Forest Service, Pacific Northwest Research Station

3200 SW Jefferson Way, Corvallis, OR 97331, USA

email:
bstclair@fs.fed.us
; phone: 541
-
750
-
7294


Note

: This report provides general information on forest genetics activities in the United States and
updates by
topic or
organization from information gathered by Brad St.Clair as of

April 2011
. The
information does not represent any official policy positions by the U
.
S
.

Forest Service or any other
organization. Please send any new information or in
quiries to Brad St.Clair (contact information above).


Climate change

Forest genetics research is highly relevant to addressing issues associated with climate change, both with
respect to improving productivity of forests for purposes of mitigation through

carbon sequestration and
with respect to adaption by ensuring adapted, healthy, and productive plant populations for reforestation
and restoration in changing
climates.

The USDA
National Institute of Food and Agriculture (NIFA)
recognized the importance
of forests to climate change by
recently
awarding a 5
-
year $20 million grant

to
study climate change mitigation and adaptation in southern pines, with an emphasis on loblolly pine. Tim
Martin at the University of Florida is the lead on the

project. Colla
borators include

nine

universities,
eight

forestry research cooperatives, the US Forest Service, state climate offices, and the multi
-
state Southeast
Climate Consortium. There are genetics components to the project, including genomics work that buil
ds
upo
n earlier work

in loblolly pine
.


Last year, the
same program of the
USDA awarded a planning grant to Glenn Howe at Oregon State
University to prepare a proposal for a similar
large
-
scale, multi
-
million dollar
project focusing on climate
change mitigatio
n and adaptation in western conifers. Unfortunately, despite considerable progress on
organizing collaborators and preparing a proposal, the USDA will not put forth a request for proposal
s this
year due to
federal
budget concerns.


The USFS Pacific Northw
est Research Station

and Oregon State University

have produced
two
web
-
bas
ed
tool
s that will be useful for addressing the choice of appropriate seed sources given climate change. The
first tool, called the Seedlot Selection Tool, matches seed
lots

and planting sites given current climates or
future climates assuming different climate change scenarios (
http://sst.forestry.oregonstate.edu/pnw/
).
It
uses GIS and either current seed zones or seed movement guidelines to map current and future climates
as
determined by
those zones or guidelines. To date,
the tool is
available for

three regions in

the United
States: the Pacific Northwest, the Central U.S., and the Eastern U.S.

The second tool, called the Center for
Forest Provenance Data, is a website f
or researchers to use to archive valuable provenance test data that
might otherwise be lost as people ret
ire or move on to new positions
(
http://cenforgen.forestry.oregonstate.edu/index.php
). The hope is that the data archive and web site will
encourage re
searchers to collaborate to use this data

in new ways

for exploring population responses to
climate change
.

It is envisioned that results from research made possible by the Center for Forest
Provenance Data will feed into the seed movement guidelines that

will help determine appropriate seed
sources using the Seedlot Selection Tool.


2


Efforts are underway by the US Forest Service
in the Southeast and in the Pacific Northwest
to
prioritize
the vulnerability of
forest tree

species to
climate change. In the S
outheast, Kevin Potter of the USFS and
North Carolina State University working with Barbara Crane, USFS Region 8 geneticist, have developed a
system to rank the relative risk of genetic degradation from climate change and other threats for 131 forest
trees

species in the southern Appalachian Mountains

(
http://www.forestthreats.org/current
-
projects/project
-
summaries/assessing
-
forest
-
tree
-
risk
)
. The Forest Tree Genetic Risk Assessment System gives each
species a rating for risk factors such as population str
ucture, regeneration capacity, dispersal ability, and
threats from pests or climate change. The score is used to prioritize species that deserve attention for
genetic co
nservation or management. The project in the Pacific Northwest, led by USFS geneticis
t Carol
Aubry, adopted a similar methodology as that developed by Kevin Potter, to prioritize 34 native tree
species in western Washington, and recommend
ed

management options for those species most at risk.


Genomics

and
Biotechnology

The
USDA NIFA

recently award
$14.6 million
over 5 years

to a team led by David Neale at UC Davis to
sequence the genomes of loblolly pine, sugar pine, and Douglas
-
fir

(
http://pinegenome.org/pinerefseq/
)
.
Other goals of the project include transcriptome sequencing from

a wide representation of loblolly pine
tissue, growth stages an
d stress conditions, and
augment
ing

the Dendrome and TreeGenes databases f
or
annotation, data integration

and data delivery. The genome sequences of these important species will
accelerate br
eeding efforts and ar
e expected to enhance their use

as feedstocks for bioenergy. This should
in turn contribute to carbon sequestration and help mitigate climate change. Collaborating institutions
include Washington State University, Texas A&M Universit
y, Indiana University, University of Maryland,
and the Childr
en’s Hospital of Oakland Rese
arch Institute.


The
Conifer Translational Genomics Network (CTGN)
is in its f
inal year of a 4
-
yr $6

million Coordinated
Agriculture Project (CAP) funded by USDA NIFA

(
http://dendrome.ucdavis.edu/ctgn/
)
.
The goal of
CTGN is

to bring marker
-
informed breeding into greater application in operational breeding programs.
The cumulative resources from CTGN CAP include validated SNP markers for loblolly

pine
, slash

pine

and
D
ouglas
-
fir
, breeding and genetic research populations genotypes for these SNP markers, protocols and
pipelines for high
-
throughput SNP genotyping, databases for marker, genotype and population data, a stock
center (field genebanks for parents and mapping
populations and repository of genomic resources), and
personnel trained in the use of the tools and analyses of genomic data. This work built upon work done
earlier by the ADEPT2 project (
A
llele Discovery of Economic
Traits in Pine 2) funded by NSF, and w
ill
contribute to recently funded projects for responding to climate change in southern pines and sequencing
the genome of loblolly pine. CTGN is
organizing
an International Symposium on Genomics
-
Based
Breeding in Forest Trees

to be held in Davis, Californ
ia,

in
June of this year.


The
Western Forest Transcriptome Surve
y is
a collaboration

among Forest Service research stations in the
W
est to identify genes and “gene networks” that are temperature
-
responsive and may contribute to climatic
adaptation

(
http://www.fs.fed.us/pnw/olympia/silv/wfts/index.html
)
.
Initial work with Douglas
-
fir is
funded by the USDA with a grant to Rich Cronn at the Pacific Northwest Research Station for $450,000 for
three years. In the first year, they have found an astoundin
g 38,000 genes expressed in needles, buds, stem
and roots, with 34,000 genes expressed in needles alone. Further work will explore differences in
expression associated with temperature, time of year, time of day, and seed source. W
ork
with other
species i
s being funded by USFS funds, and includes sugar pine, aspen, and sagebrush.


The National Science Foundation (
NSF
) recently
funded
a $3.
7

million
four
-
year project to study the
comparative genomics of environmental stress responses in North American
hardw
ood
s. The project is l
ed
by John Carlson
at
Penn
sylvania

State

University, and includes collaborators at six other universities
.

The
project includes
creati
on of
EST databases, BAC libraries, framework genetic maps, and high
-
density QTL
maps for
up to ei
ght
economically important and phylogen
e
tically representativ
e hardwood species.


3


Genetic resources conservation


The greatest effort in genetic resources conservation is focused on those species threatened by disease or
insects
, as well as climate change
.

Significant efforts at breeding for disease resistance continue in several
species including
American chestnut,
white pines, butternut
, and Port Orford cedar
.
The American Chestnut
Association and the Forest Service Region 8 have established planting of
blight
-
resistant trees on three
National Forests in the Southeast
during

the last two years.
The

Forest Health Protection division of USFS
State and Private branch

has a large effort underway for a range
-
wide collection for
ex situ

conservation of
high
-
elevation
five
-
needle pines, which are threatened by both blister rust and climate change.
CAMCORE
has been primarily responsible for collections of eastern and Carolina hemlock and have established
conservation orchards and sent seed

for long
-
term storage to the USFS National Seed Laboratory. The
effort to collect seed of ash for
ex situ

storage has been led by the USDA Natural Resources Conservation
Service with significant contributions from the USFS.


The Agricultural Research S
ervice provides long
-
term storage for native plant seeds at their National
Center for Genetic Resources Preservation facility in Fort Collins, Colorado. An agreement between the
USFS and ARS was just renewed for this service. In general, the USFS maintai
ns
working collections of
native plants for conservation and restoration at local facilities throughout the United States, but sends
collections of high priority species to Fort Collins for long
-
term storage.


Tree improvement

Tree improvement in major con
ifer species continues through cooperatives established at universities.
These include the North Carolina State University Tree Improvement Cooperative, the Western Gulf Tree
Improvement Cooperative at Texas A&M University, the Cooperative Forest Genetics

Research Program at
the University of Florida, the Northwest Tree Improvement Cooperative at Oregon State University, the
Inland Empire Tree Improvement Cooperative at University of Idaho, and the Minnesota Tree
Improvement Cooperative at the University o
f Minnesota.
In addition, several organizations and agencies
continue selection and breeding work for disease resistance, in particular, breeding for resistance to white
pine blister rust in the West and Northeast, and chestnut blight and butternut canker

in the East.