UC Davis – Chevron Research Grant Cover Sheet
Send to: cmonce@ucdavis.edu
Program Information
UC Davis – Chevron 2007 Research Program
Cooperative Research Agreement
Chevron Technology Ventures, LLC (CTV)
December 15, 2006 (required)
February 1, 2007 (by invitation only)
A.
Research Proposal
B.
Technology Transfer
[Four types of proposals will C.
Pilot Demonstration Projects
be considered]
D.
Facilities and Equipment
Program Title
Agreement Name
Sponsor Name
Prelim Proposal Due Date
Full Proposal Due Date
Proposal Type
Principal Investigator(s)
PI Name
Title
Department
Telephone
Fax
e-mail Address
David B. Neale
Professor
Plant Sciences
754-8431
754-9366
dbneale@ucdavis.edu
Project Title
Discovery of Genes for Improved Cellulose and CelluloseExtractability from Poplar Secondary Xylem
A. Start Date: March 1, 2007
B. End Date: February 28, 2010
$446,942
Year 1: $228,000
Year 2: $117,070
Year 3: $101,872
Project Period
Amount Requested
Budget Amount
Co-PI & Senior
Chung-Jui Tsai, Brian J. Stanton, Mark F. Davis
Project Brief Summary
The primary goal of this project is to discover the critically important genes in
cellulose and lignin biosynthetic pathways in poplar and use this knowledge to
breed improved varieties of poplar for cellulosic biofuels production. The
approach to accomplishing this goal is similar that being used to cure complex
diseases such as cancer in humans. An extensive DNA sequencing, SNP
genotyping, bioinformatics and association genetics pipeline has already been
built for pine that we can use with only minor modification in poplar.
Administrative Assistant or other person to notify:
Name
Title
e-mail Address
Telephone
Deidra Madderra
MSO
damadderra@ucdavis.edu
752-2683
Contact this person ONLY if the proposal is selected to move forward.
Additional Contacts, Notification Comments
Project Title: Discovery of Genes for Improved Cellulose and Cellulose-Extractability from
Poplar Secondary Xylem
Total Requested Budget ($):
Project Duration (years): 3 years
Principal Investigator: David B. Neale, Professor, Dept. Plant Sciences, UC Davis
Co-investigators: Chung-Jui Tsai, Professor, School of Forest Resources and Environmental
Science, Michigan Technical University
Brian J. Stanton, Managing Director, Greenwood Resources, Portand, OR
Mark F. Davis, National Renewable Energy Lab, Dept of Energy, Golden, CO
Project Objectives:
1. To develop a high-throughput gene discovery pipeline to identify naturally occurring
variation in genes critically important in cellulose and lignin biosynthesis in poplar using
the DNA sequencing, SNP genotyping and bioinformatic infrastructures previously built
for pine species.
2. To perform single nucleotide polymorphism (SNP) discovery using high throughput
DNA sequencing (Agencourt Biosciences) and SNP genotyping (Illumina and/or
Affymetrix) to associate genetic variation in genes involved in cellulose and lignin
biosynthesis with phenotypic variation in cellulose quantity, quality and extractability in
a large clonal black cottonwood (Populus trichocarpa) genetic test plantation belonging
to GreenWood Resources.
Project Description:
The DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol” report identifies poplar as
one of the key feedstock species for cellulosic ethanol production in many regions of the country,
including California. In contrast to herbaceous biofuels species such as corn, switchgrass and
miscanthus, poplar has several important advantages. The primary advantages are; 1) market
opportunities and 2) storage. Poplar can be grown for multiple products including high-valued
solid wood products and for pulp and paper. This provides growers multiple market
opportunities and additional incentive to produce the crop. Second, poplar is a woody perennial
and can be stored “on the stump” unlike switchgrass that must be dried and stored. Poplar can be
grown on a wide variety of site conditions and in some situations requires few inputs.
There has been modest genetic improvement of poplar in the US. A large number of artificial
hybrids have been developed and many have superior growth and yield qualities. Poplars have
been used extensively in the US and Europe for basic research on wood formation, specifically
on the lignin and cellulose biosynthetic pathways. Some poplars can be genetically transformed
and GMO poplars have been developed by modifying the expression of genes in the lignin and
cellulose biosynthetic pathways. Much less has been done, however, to characterize naturally
occurring variation in genes of these pathways. We have done extensive work in loblolly pine
(Pinus taeda) to characterize naturally occurring genetic variation in the lignin and cellulose
biosynthetic pathways and have used the association genetics approach to show how DNA
sequence variation in these genes underlies phenotypic level variation for wood properties traits
such as wood density, microfibril angle and lignin/cellulose content. These same approaches can
now be applied to poplar. There are two very important resources available in black cottonwood
that will facilitate association genetic studies. First, are the extensive genetic resources, breeding
and genetic test plantations of GreenWood Resources and second is the recently published
complete genome sequence of black cottonwood. These resources, combined with the
resequencing, SNP genotyping and bioinformatics pipeline we have built for pine, ensure rapid
discovery of naturally occurring genetic variation in genes of the lignin and cellulose
biosynthetic pathways.
A series of specific tasks will be completed to meet the goals and objectives of this project:
1. Develop a candidate gene list of 200 key genes involved in cellulose and lignin biosynthesis
(Tsai, completed, list available upon request)
2. Resequence 200 candidate genes using a discovery panel of 12 unrelated poplar clones
(Agencourt Biosciences, yr 1)
3. Identify single nucleotide polymorphisms (SNPs) in the 200 genes using an automated
PHRED, PHRAP, POLYPHRED bioinformatics pipeline (Neale, yr 1)
4. SNP genotype 500 poplar clones for ~1536 SNPs (Illumina Golden Gate assay, UC Davis
Genome Center, DNA Technologies Core Facility, yr 1-2)
5. Harvest wood increment cores from 3 ramets of each of 500 poplar clones (1500 trees in total
(Stanton, yr 1)
6. Perform Molecular Beam Mass Spectrometry (MBMS) analysis on all 1500 wood cores to
develop secondary xylem metabolomic profiles (Davis, yr 1)
7. Perform gene expression microarray analysis using the Agilent poplar expression chip with
RNA isolated from 12 unrelated poplar clones to identify genes varying in their expression
among genotypes (Tsai, yr 1-2)
8. Perform association genetics analyses to identify genes controlling cellulose quantity and
quality phenotypic variation in poplar (Neale, Tsai, Stanton, Davis, yr 3))
Justification and Anticipated Impact:
Poplar will undoubtably be a key species in future cellulosic ethanol production. Furthermore,
poplars harbor abundant genetic variation that can be repackaged through traditional plant
breeding approaches, thus avoiding regulatory, biosafety and social concerns over genetically
engineered trees. Traditional breeding methods based on phenotypic selection are, however,
slow and can lack precision for improving certain traits. Genomic-based breeding approaches
offer significant potential for the genetic improvement of poplars for cellulosic ethanol
production. The expected outcome of the project proposed here is the development of a high
throughput gene discovery pipeline that will provide the genomic information to be feed directly
into applied poplar breeding programs.
UC DAVIS - CHEVRON RESEARCH
GRANTS 2007 RESEARCH PROGRAM
Pre-proposal Budget
Personnel
Role
%
Effort
Salary
Requested
PIs
David Neale
Chng-Jui Tsai
Brain Stanton
Mark Davis
5
5
5
5
0
0
0
0
Support Staff
Postdoc (MTU) (2 yr)
Bioinformatician (UCD) (2 yr)
50
50
34,000
68,500
Total Personnel
Supplies and Expenses
Wood Sampling (Greenwood Resources)
Wood Processing (Greenwood Resources)
DNA Isolation (UCD)
Gene Expression (MTU)
DNA Sequencing (Agencourt)
Fringe
Benefits
Totals
0
0
0
0
14,416
17,125
48,416
85,625
$
Description
Totals
5,000
3,000
2,000
10,000
10,000
SNP Genotyping (UCD)
MBMS (DOE)
100,000
30,000
Total Supplies and Expense
Equipment
$
Description
Total Equipment
Travel
Totals
$
Description
Totals
Total Travel
$
Total Direct Costs
Indirect Cost Base
Indirect Costs (52%)
Total Direct and Indirect Costs
5% Non-Exclusive License Advance
$
$
$
$
$
294,041
152,901
446,942
Total Costs
$
446,942
submit to cmonce@ucdavis.edu
CURRICULUM VITAE
David B. Neale
Department of Plant Sciences
University of California, Davis
Davis, California 95616
Tel: (530) 754-8413; Fax: (530) 754-9366
dbneale@ucdavis.edu
http://dendrome.ucdavis.edu/NealeLab
mailto:dneale@dendrome.ucdavis.edu
EXPERIENCE
Professor, Department of Plant Sciences, University of California, Davis, 2005-pressent
Adjunct Faculty, Department of Environmental Horticulture, University of California,
Davis,
1994-2005
Director, Institute of Forest Genetics, USDA Forest Service
1998-2001
Plant Molecular Geneticist, Institute of Forest Genetics, USDA Forest Service
1987-2005
Postdoctoral Fellow, Institute of Forest Genetics, USDA Forest Service, Berkeley
1986-1987
Postdoctoral Fellow, Department of Genetics, University of California, Davis
1984-1986
EDUCATION
Ph.D., 1984, Oregon State University, Forest Genetics
M.S., 1978, University of New Hampshire, Forest Genetics
B.S., 1976, University of New Hampshire, Forest Science
LEADERSHIP & SERVICES
Chair, Genetics Graduated Group, UCDavis
Section Chair, Agricultural Plant Biology, Department of Plant Sciences
Principal Investigator, Dendrome Database (dendrome.ucdavis.edu)
Coordinator, Loblolly Pine Genome Project (dendrome.ucdavis.edu/lpgp)
Coordinator, Douglas-fir Genome Project (dendrome.ucdavis.edu/dfgp)
Coordinator, Conifer Comparative Genomics Project (dendrome.ucdavis.edu/ccgp)
Founder, Forest Tree Genome Workshop, Plant and Animal Genome Meeting
Editor in Chief, Tree Genetics and Genomes
Associate Editor, Theoretical and Applied Genetics
Associate Editor, Molecular Breeding
Associate Editor, Silvae Genetica
Textbook Author, Forest Genetics, TL White, WT Adams and DB Neale
Panel Manager, USDA CSREES NRI Plant Genome, 2003
Panel Manager, USDA CSREES NRI Integrated Programs, Plant Functional Genomics, 2003
TEACHING, UC Davis
GGG201D, Population and Quantitative Genetics, team teach with T. Famula and D. Shaw
BIT 195, team teach with J. Dubkovsky
GGG292B Seminar in Quantitative Genetics (no longer offered, to be offered again under Plant
Breeding and Biodiversity Focus Group in GGG)
Guest lectures, ENH 102, PLB 152, PLB 154
Genetics Graduate Group Advisory Committee, 18 advisees
Advisor, Bioinformatics, Biotechnology Major
Graduate thesis committees, 8
Qualifying exam committees, 7
Chair, Dissertation Committee, 1 (Elhan Ersoz)
PUBLICATIONS
Jermstad, K. D., BJeassoni, D. L., Jech, K. S., Wheeler, N. C., and Neale, D. B. (2001).
Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir: I. Timing of
vegetative bud flush. Theor. Appl. Genet. 102:1142-1151.
Jermstad, K. D., Bassoni, D. L., Wheeler, N. C., Anekonda, T. S., Aitken, S. N., Adams, W. T.,
and Neale, D. B. (2001). Mapping of quantitative trait loci controlling adaptive traits in
coastal Douglas-fir: II. Spring and fall cold-hardiness. Theor. Appl. Genet. 102:1152-1158
Temesgen, B., G.R. Brown, D.E. Harry, C.S. Kinlaw, M.M. Sewell, and D.B. Neale. (2001).
Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine
(Pinus taeda L.). Theor. Appl. Genet. 102:664-675.
Brown, G.R., E.E. Kadel III, D.A. Bassoni, K.L. Kiehne, B. Temesgen, J.P. van Buijtenen, M.M.
Sewell, K.A. Marshall and D.B. Neale. (2001) Anchored reference loci in loblolly pine (Pinus
taeda L.) for integrating pine genomics. Genetics 159:799-809.
Sewell, M.M., M.F. Davis, G.A. Tuskin, N.C. Wheeler, C.C. Elam, D.L. Bassoni, and D.B. Neale.
(2002) Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.)
II. Chemical wood properties. Theor. Appl. Genet., 104: 214-222.
Neale, D.B., M.M. Sewell and G.R. Brown. (2002) Molecular dissection of the quantitative
inheritance of wood property traits in loblolly pine. Ann. For. Sci. 59:595-605.
Ahuja, M.R. and D.B. Neale. (2002) Origins of polyploidy in coast redwood (Sequoia
semervirens (D. Don.) Endl.) and relationship of coast redwood to other genera of the
Taxodeaceae. Silvae Genetica, 51:93-100.
Gill, G.P., G.R. Brown, and D.B. Neale. (2003) A sequence mutation in the cinnamyl alcohol
dehydrogenase gene associated with altered lignification in loblolly pine. Plant Biotech. J. 1:
253-258.
Komulainen, P., G.R. Brown, M. Mikkonen, A. Karhu, M.R. Garcia-Gil, D. O'Malley, B. Lee, D.B.
Neale and O. Savolainen. (2003) Comparing EST-based genetic maps between Pinus
sylvestris and P. taeda. Theoret. Appl. Genet. 107:667-678.
Chagne, D., G.R. Brown, C. Lalanne, D. Madur, D. Pot, D.B. Neale and C. Plomion. (2003)
Comparative genome and QTL mapping between maritime and loblolly pines. Molecular
Breeding (in press).
Zhang, Y., G.R. Brown, R. Whetton, C.A. Loopstra, D.B. Neale., M.J. Kieliszewski and R.R.
Sederoff. (2003) An arabinogalactan protein associated with secondary cell wall formation in
differentiating xylem of loblolly pine. Plant Molecular Biology 52 :91-102
Brown, G.R., D.L. Bassoni, G.P. Gill, J.R. Fontana, N.C. Wheeler, R.A. Megraw, M.F. Davis,
M.M. Sewell, G.A. Tuskan and D.B. Neale. (2003) Identification of quantitative trait loci
influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and
candidate gene mapping. Genetics 164:1537-1546.
Jermstad, K.D., Bassoni, D.L., Jech, K.S., Ritchie, G.A., Wheeler, N.C. and Neale, D.B. 2003:
Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. III. QTL by
environment interactions. Genetics 165:1489-1506.
Ledig, F. T., P. D. Hodgskiss, K. V. Krutovskii, D. B. Neale, and T. Eguiluz-Piedra, (2003)
Relationships among the spruces (Picea, Pinaceae) of Southwestern North America.
Systematic Botany 29:275-295.
Howe, G.T., S.N. Aitken, D.B. Neale, K.D. Jermstad, N.C. Wheeler and T.H.H. Chen. (2003)
From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees.
Can. J. Bot. 81: 1247-1266
Krutovskii K.V., M. Troggio, G.R. Brown, K.D. Jermstad, D.B. Neale. (2004) Comparative
Mapping in the Pinaceae. Genetics 168:447-461.
Neale, D.B. and O. Savolainen (2004) Association genetics of complex traits in conifers. Trends
in Plant Science. 9:325-330.
Peter, G. and D. Neale (2004) Molecular basis for the evolution of xylem lignification. Curr. Op.
Plant Biol. 7:1-6.
Brown, G.R., G.P. Gill, R.J. Kuntz, C.H. Langley and D.B. Neale. (2004) Nucleotide diversity
and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. U.S.A. 101:15255-15260.
Wheeler, N.C, K. Krutovskii, K.D. Jermstad, S.N. Aitken, G.T. Howe, J. Krakowski and D.B.
Neale. (2005) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglasfir. IV. Cold-hardiness QTL verification and candidate gene mapping. Molec. Breeding
15:145-156.
Scotti, Ivan., Burelli, Andrea., Cattonaro, Federica., Chagné, David., Fuller, John., Hedley, Peter
E., Jansson, Gunnar., Lalanne, Celine., Madur, Delphine., Neale, David., Plomion,
Christophe., Powell, Wayne., Troggio Michela., and Morgante, Michele (2005). Analysis of
the distribution of marker classes in a genetic linkage map: a case study in Norway spruce
(Picea abies karst). Tree Genetics & Genomes, 1(3): 93 - 102.
Guevara M.A., Soto A., Collada C., Plomion C., Savolainen O., Neale D.B., González-Martínez
S.C. and Cervera M.T. (2005). Genomics Applied to the Study of Adaption in Pine Species.
Invest Agrar: Sist Rec For, 14(3): 292-306.
Ahuja M.R. and Neale D.B. (2005). Evolution of Genome Size in Conifers. Silvae Genetica,
54(3): 126-137.
Krutovsky,K.V. and D. B. Neale. (2005) Nucleotide diversity and linkage disequilibrium in coldhardiness and wood quality related candidate genes in Douglas-fir. Genetics 171:20292041.
Gonzalez-Martinez, S.C., E.Ersoz, G.R. Brown, N.C. Wheeler and D.B. Neale. (2006)
Candidate genes for drought-stress response in Pinus taeda L. DNA sequence variation and
natural selection. Genetics 172:1915-1926.
Gonzalez-Martinez, S. C., K. V. Krutovsky and D. B. Neale, (2006) Forest tree population
genomics and adaptive evolution. New Phytologist 170:227-238.
KD Jermstad, LA Sheppard, BB Kinloch, A Delfino-Mix, ES Ersoz, KV Krutovsky and DB Neale.
Isolation of a full-length CC-NBS-LRR resistance gene analog candidate from sugar pine
showing low nucleotide diversity. Tree Genetics and Genomes. 2:76-85.
Krutovsky, K. V., and D. B. Neale, 2006 Forest genomics and new molecular genetic
approaches to measuring and conserving adaptive genetic diversity in forest trees. In: Th.
Geburek & J. Turok (eds.) Conservation and Management of Forest Genetic Resources in
Europe, Arbora Publishers, Zvolen (in press).
Gonzalez-Martinez, S.C., Wheeler, N.C., Ersoz, E.S., Nelson, C.D., Neale, D.B. (2007).
Association Genetics in Pinus taeda L.I. Wood Property Traits. Genetics (in press)
RESEARCH SUPPORT
Allele Discovery for Economic Traits in Pine, USDA/IFAFS, (2001). $1.8M PI
Discovery of genes controlling adaptive traits in Douglas-fir. USDA Forest Service, Agenda
2020 (2002). $180,000 PI
Association genetics of adaptive traits in Douglas-fir. USDA/NRI Plant Genome (2004)
$490,000 PI
Association genetics of complex traits in Douglas-fir. USDA Forest Service Agenda 2020,
(2004) $180,000 PI
Association genetics of natural variation and complex traits in pine. NSF Plant Genome (2005)
$5.9M CoPI
Plant Genome Comparative Sequencing Program. NSF Plant Genome
(2006) $505,122.00 PI
CURRICULUM VITAE
Chung-Jui Tsai
Professor and Director
Biotechnology Research Center
School of Forest Resources and Environmental Science
Michigan Technological University
Tel: (906) 482-2914; Fax: (906) 487-2915
E-mail: chtsai@mtu.edu
www.biotech.mtu.edu; www.forest.mtu.edu/faculty/tsai
EDUCATION
May 1995 Ph.D. in Forest Science, Outstanding Graduate Student Award (1994)
School of Forestry & Wood Products (name change 02), Michigan Technological
University
June 1991 M.S. in Agriculture (Forestry), University First Rank
Department of Forestry, National Taiwan University, Taiwan
June 1989 B.S. in Agriculture (Forestry/Silviculture core), University First Rank
Department of Forestry, National Taiwan University, Taiwan
EXPERIENCE
05/0603/05 -
Professor, School of Forest Resources and Environmental Science, MTU
Ad Hoc Graduate Faculty, Dept of Forestry & Natural Resources, Purdue
University
08/04 Director, Biotechnology Research Center, Michigan Technological
University
05/02-05/06 Associate Professor, School of Forest Resources and Environmental
Science, MTU
12/02-08/04 Interim Director, Plant Biotechnology Research Center, MTU
03/97-05/02 Assistant Professor, School of Forestry and Wood Products, MTU
05/95-02/97 Post Doctoral Research Fellow, Plant Biotechnology Research Center,
MTU
09/92-05/95 Research Assistant, School of Forestry and Wood Products, MTU
06/91-08/92 Research Associate, Division of Silviculture, Taiwan Forestry Research
Institute
MEMBERSHIP
American Association for the Advancement of Science (AAAS)
American Society of Plant Biologists (ASPB)
International Populus Genome Consortium (IPGC)
International Eucalyptus Genome Consortium (IEuGC)
Japanese Society of Plant Physiologists (JSPP)
Society for In Vitro Biology (SIVB)
RESEARCH SUPPORT (past three years only)
Tsai C-J, Harding SA, Protein engineering for manipulation of phenylpropanoid metabolism
(09/06-08/08). CPBR and ArborGen, $188,000.
Tsai C-J, UVB-induced secondary metabolism (08/06-06/07). Utah State University, $10,000.
Tsai C-J, NSF Plant Genome Research REU Supplement (05/06-06/07). NSF, $24,596.
Harding SA, Tsai C-J, Lindroth RL (UW-Madison), A genomics investigation of partitioning into
and among flavonoid-derived condensed tannins for carbon sequestration in Populus (09/0509/08). DOE, $1,386,389.
Tsai C-J, Harding SA, Protein engineering for manipulation of phenylpropanoid metabolism
(09/05-08/06). CPBR Fellowship, $40,000.
Tsai C-J, Harding SA, Zhang S (Mathematics), Davis MF (DOE-NREL), A functional genomics
approach to investigate regulation of phenolic glycoside metabolism in Populus (11/0412/08). NSF Plant Genome Research Program, $2,114,091.
Tsai C-J, Acquisition of a real-time PCR system for quantitative gene expression analysis in
forest genomics and biotechnology research (11/04-11/05). USDA-NRI Equipment Grant
with MTU Match, $25,000.
Karnosky DF, Taylor G (Univ Southampton, UK), Podila GK (U Alabama-Huntsville),
Tsai C-J, Riemenschneider D (USFS), Rogers A (DOE-BNL), An integrated
functional genomics consortium to increase carbon sequestration in poplars:
Optimizing aboveground carbon gain (03/04-02/07). DOE, $916,231.
Harding SA, Tsai C-J, Designing promoters for precision targeting of gene expression
(01/03-12/05). CPBR, $126,001.
Tsai C-J, Harding SA, Molecular dissection of alpha-tubulins during microfibril
deposition in wood forming tissues of aspen (11/02-11/06). USDA-NRI, $220,000.
Tsai C-J, Cryopreservation of tree germplasm (10/02-9/07). USDA McIntire Stennis,
$35,000.
Tsai C-J, Joshi CP, Harding SA, Acquisition of an ABI Prime 3100-Avant genetic
analyzer for high throughput DNA sequencing and fragment analysis (04/03-06/04).
State of Michigan Research Excellence Fund, $50,000.
Tsai C-J, Harding SA, Joshi CP, Chiang VL, Functional genomics of fast-growing
transgenic aspen (03/01-12/04). Michigan Life Sciences Corridor, $2,013,729.
Tsai C-J, Chiang VL, Davis MF (DOE-NREL), Genetic augmentation of syringyl lignin in
low-lignin aspen trees (03/01-08/04). DOE Agenda 2020, $504,903.
Tsai C-J, Vucetich JA, Waite TA (Ohio State U), Richter DL, Assessing ecological
consequences of low-lignin and fast-growth transgenic aspen (09/00-09/04). USDACSREES, $260,000.
PUBLICATIONS (past five years only)
Tsai C-J, El Kayal W, Harding SA (2006) Populus, the new model system for
investigating phenylpropanoid complexity. International Journal of Applied Science
and Engineering (in press).
Brodeur-Campbell SE, Vucetich JA, Richter DL, Waite TA, Rosemier JN, Tsai C-J
(2006) Insect herbivory on low-lignin transgenic aspen. Environmental Entomology
35: (in press).
Tuskan GA, DiFazio S et al. (106 authors including Tsai C-J), Rokhsar D (2006) The
genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:
1596-1604.
Tsai C-J, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y (2006) Genome-wide
analysis of the structural genes regulating defense phenylpropanoid metabolism in
Populus. New Phytologist 172: 47-62.
Harding SA, Jiang H, Jeong ML, Casado FL, Lin H-W, Tsai C-J (2005) Functional
genomics analysis of foliar condensed tannin and phenolic glycoside regulation in
natural cottonwood hybrids. Tree Physiology 25: 1475-1486.
Jeong ML, Jiang H, Chen H-S, Tsai C-J, Harding SA 2004 Metabolic profiling the sink to
source transition in developing leaves of quaking aspen (Populus tremuloides). Plant
Physiology 136: 3364-3375.
Tsai C-J, Hubscher SL 2004 Cryopreservation in Populus functional genomics. New
Phytologist 164: 73-81.
Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J 2004 Suppression
subtractive hybridization-mediated transcriptome analysis from multiple tissues of
aspen (Populus tremuloides) trees altered in phenylpropanoid metabolism. Planta
219: 694-704.
Jiang H, Deng Y, Chen H-S, Tao L, Sha Q, Chen J, Tsai C-J, Zhang S 2004 Joint
analysis of two microarray gene-expression data sets to select lung adenocarcinoma
marker genes. BMC Bioinformatics 5: 81.
Wang Y-S, Harding SA, Tsai C-J 2004 Expression of a glycine decarboxylase complex
H-protein in non-photosynthetic tissues of Populus tremuloides. Biochimica
Biophysica Acta 1676: 267-273.
Aronen T, Tiimonen H, Tsai C-J, Jokipii S, Chen X, Chiang VL, Häggman H 2003
Altered lignin in transgenic silver birch (Betula pendula) expressing PtCOMT gene.
In: Espinel, S., Barredo, Y., Ritter, E. (eds) Sustainable Forestry, Wood Products &
Biotechnology. DFA-AFA Press. Vitoria-Gasteiz, Spain, pp. 149-161.
Cseke LJ, Wu W, Tsai C-J 2003 Isolation and purification of DNA. In: Cseke LJ,
Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular
Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 1-24.
Tsai C-J, Cseke LJ, Harding SA 2003 Isolation and purification of RNA. In: Cseke LJ,
Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular
Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 25-44.
Tsai C-J, Cseke LJ 2003 Southern hybridization. In: Cseke LJ, Kaufman PB, Podila GK,
Tsai C-J (eds) Handbook of Molecular and Cellular Methods in Biology and
Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 85-104.
Touchell DH, Wang Y-S, Harding SA, Tsai C-J 2003 Differential display. In: Cseke LJ,
Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular
Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 305-317
Harding SA, Tsai C-J, Cseke LJ, Chang SC, Chen F 2003 In situ hybridization. In:
Cseke LJ, Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and
Cellular Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp.
487-508.
Touchell DH, Chiang VL, Tsai C-J 2002 Cryopreservation of embryonic cultures of
Picea mariana (black spruce) using a vitrification protocol. Plant Cell Reports 21:
118-124.
Kao Y-Y, Harding SA, Tsai C-J 2002 Differential expression of two distinct
phenylalanine ammonia-lyase genes in condensed tannin-accumulating and
lignifying cells of quaking aspen. Plant Physiology 130: 796-807.
Harding SA, Leshkevich J, Chiang VL, Tsai C-J 2002 Differential substrate inhibition
couples kinetically distinct 4-coumarate:CoA ligases with spatially distinct structural
and metabolic roles in quaking aspen. Plant Physiology 128: 428-438.
PATENTS
Chiang VL, Tsai C-J, Podila GK 1999 Genetic engineering of wood color in plants. US
Patent Number 5886243, March 1999.
Chiang VL, Tsai C-J, Podila GK 1999 Genetic transformation and regeneration of
plants. US Patent Number 5,922,928, July 1999.
Chiang VL, Tsai C-J, Hu W-J 2002 Methods of modifying lignin in plants by
transformation with a 4-coumarate:coenzyme A ligase nucleic acid. US Patent
Number 6455762, September 2002.
Chiang VL, Tsai C-J, Hu W-J 2004 4-coumarate:coenzyme A ligase promoter. US
Patent Number 6831208, December 2004.
Chiang VL, Tsai C-J, Hu W-J 2005 genetic engineering of plants through manipulation
of lignin biosynthesis. US Patent Number 6969784, November 2005.
CURRICULUM VITAE
Brian J. Stanton, Ph. D.
GreenWood Resources
Managing Director, Resource Management and Tree Improvement
One World Trade Center
121 SW Salmon Street, Suite 1020
Portland, OR 97204
www.greenwoodresources.com
Tel: 503.274.0438
Fax: 503.478.0751
Email: bstanton@greenwoodresources.com
www.greenwoodresources.com
EDUCATION
1984 Ph. D. Forest Resources, The Pennsylvania State University
1979 M.S. Forestry, University of Maine
1975 B. A. Natural Resources, West Chester State College
EXPERIENCE
2000 – present GreenWood Resources, Managing Director, Tree Improvement
Managing director of poplar breeding and varietal selection programs in support
of commercial poplar plantations in the Pacific Northwest and the lower
Mississippi River Valley. Collaborator with the Chinese Academy of Forestry,
Beijing and the University of Talca, Chile in the establishment of a poplar genetic
improvement program for China and South American operations.
1984 - 1999
Crown Zellerbach/James River/Fort James Corp., Research Associate
Perfected artificial controlled crossing procedures for Populus trichocarpa, P.
deltoides, and P. maximowiczii. Refined embryo rescue procedure to recover
hybrid genotypes from recalcitrant crosses. Designed and implemented multiple
stage clonal field evaluation process tailored to the selection of specific traits at
successive stages. Developed disease screening protocols for Melampsora leaf
rust, Venturia shoot blight, and Septoria leaf spot. Constructed selection index
routine and economic weights for multiple-trait clone ranking. Conducted clonesite matching trials to track mono-clonal stand development patterns and
validate plantation yield improvements.
1983 - 1984
New York Botanical Garden, Cary Arboretum, Research Assistant
Project leader of an urban tree management program. Evaluated street-tree
cultivars for adaptability to urban settings. Investigated environmental factors
responsible for tree decline. Produced tree selection guide for urban plantings
compatible with overhead distribution lines.
PROFESSIONAL AFFILIATIONS
2001 - present Adjunct professor, Department of Natural Resource Sciences,
Washington State University
2000 - present Chair, IUFRO Poplar and Willow Genetics Working Party
2001 - 2003
Chair, SAF Forest Genetics and Tree Improvement Working Group
RESEARCH SUPPORT
2003
Modification of the Composition and Quality of Hybrid Poplar Biomass in the
Pacific Northwest - Department of Energy
2006
Improved Carbon Sequestration with Bio-Fuels Production in Managed Hybrid
Poplar Plantations - Department of Energy
KEY PUBLICATIONS
Stanton, B. J., 2005. The effect of reciprocal hybridization on reproduction of the intersectional
cross, Populus x generosa. Forest Genetics, 12: 131-140.
Stanton, B.J., 2001. Clonal variation in basal area growth patterns during stand development
in hybrid poplar. Can. J. For. Res. 31: 2059-2066.
Stanton, B. J., 2004. Poplars. The Encyclopedia of Forest Sciences. Elsevier, Ltd. 1441-1449.
Stanton, B. J., J. A. Eaton, J. D. Johnson, D. E. Rice, W. R. Schuette, B. W. Moser, 2002.
Hybrid Poplar in the Pacific Northwest: The Effects of Market-Driven Management. Journal of
Forestry. 100: 28-33.
Meilan, R., K. Han, C. Ma, S. P. DiFazio, J. A. Eaton, E. A. Hoien, B. J. Stanton, R. P. Crockett,
M. L. Taylor, R. R. James, J. S. Skinner, L. Jouanin, G. Pilate, and S. H. Strauss, 2002. The
CP4 trangene provides high levels of tolerance to Roundup herbicide in field-grown hybrid
poplars. Can. J. For. Res. 32: 967-976.
Riemenschneider, D. E., B. J. Stanton, G. Vallee, and P. Perinet, 2000.
Poplar breeding strategies. Chapter 2. In Poplar Culture in North America. Edited by D. I.
Dickman, J. G. Isebrands, J. E. Eckenwalder, and J. Richardson. NRC Research Press,
National Research Council of Canada, Ottawa, ON, Canada. pp. 43-76.
Joint Conference of the Western Mensuration Association and the Western Forest Genetics
Association, Vancouver, Washington.
“Short Rotation Hardwood Forestry – Advantages and Disadvantages of Poplar Farming with
Clones” Invited presentation to the Western Gulf Forest Tree Improvement Program’s Contact
Representative’s
Meeting, Hattiesburg, Mississippi, May, 2000.
CURRICULUM VITAE
MARK F. DAVIS
National Bioenergy Center
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
Tel: (303) 384-6140; Fax: (303) 384-6363
E-mail:mark_davis@nrel.gov
EDUCATION
Ph.D.
Wood Chemistry, Colorado State University, 1990.
M.S.
Physical Chemistry, Colorado State University, 1987.
B.S.
Chemistry, University of Cincinnati, 1981.
EXPERIENCE
2004-present
Senior Chemist II - National Renewable Energy Laboratory
1997–2004
Senior Chemist I - National Renewable Energy Laboratory
1995-1997
Staff Chemist - National Renewable Energy Laboratory
1993-1994
Postdoctoral Research Associate - National Renewable Energy
Laboratory
Staff Spectroscopist - National Center for NMR Applications,
Colorado State University
1983-1985
1988-1992
PUBLICATIONS MOST RELATED TO PROPOSED PROJECT (past five years only)
Davis, M. F., Dinus, R., Tuskan, G.A., A Rapid Method for Measuring Syringyl-to-Guaiacyl
Ratios in Populus using Pyrolysis Molecular Beam Mass Spectrometry Holforschung
(accepted for publication).
Brown, G. R., Bassoni, D. L, Gill, G. P., Fontana, J. R., Wheeler, N. C., Megraw, R. A., Davis,
M. F., Sewell, M. M., Tuskan, G. A., Neale, D. B. Identification of quantitative trait loci
influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and
candidate gene mapping. Genetics 164, 1537-1546 (2003).
Sewell, M. M. Davis, M. F., Tuskan, G. A., Wheeler, N. C., Elam, C. C., Bassoni, D. L., Neale,
D. B. Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda
L.). II. Chemical wood properties. Theoretical and Applied Genetics 104, 214-222 (2002).
Magrini, K. A., Evans, R. J., Hoover, C. M., Elam, C. C. & Davis, M. F. Use of pyrolysis
molecular beam mass spectrometry (py-MBMS) to characterize forest soil carbon: method
and preliminary results. Environmental Pollution (Oxford, United Kingdom) 116, S255S268 (2001).
OTHER SIGNIFICANT PUBLICATIONS
Davis, M.F., Tuskan, G.A., Payne. P.M., Tschaplinski. T.J., and Meilan, R. Assessment of
Populus wood chemistry following the introduction of a Bt toxin gene. Tree Phys. 26, 557–
564 (2006).
Engtrakul C, Davis M.F., Gennett T., Dillon A.C., Jones K.M., and Heben M.J. Protonation of
Carbon Single-Walled Nanotubes Studied Using 13C and 1H-13C Cross Polarization Nuclear
Magnetic Resonance and Raman Spectroscopies. J. Am. Chem. Soc. 127: 17548-17555
(2005).
SYNERGISTIC ACTIVITIES
1. Ad hoc reviewer for international journals
2. Reviewer for competitive grant programs (USDA-NRICGP (panel))
3. Judge and Moderator for Colorado High School and National Middle School Science
Bowls
COLLABORATORS AND OTHER AFFILIATIONS
Advisors: Gary Maciel (CSU), Herb Schroeder (CSU)
Collaborators: D.L. Bassoni (UC Davis), Vincent Chiang (NCSU), Janet Cooke (Lavel
University), John Davis (UF), Ron Dinus, (Ind.), Scott Harding (MTU), Joe Iwamiya (Lockheed
Martin), Jon Johnson (OSU), Kurt Johnson (NCSU), Robert Megraw (Weyerhaeuser, ret.), Rick
Meilan (OSU), David Neale (UCDavis), Peggy Payne (Boise), Mitch Sewell (Ind.), Steve
Strauss (OSU), Chung-Jui Tsai (MTU), Jerry Tuskan (ORNL), Nick Wheeler (Weyerhaeuser),
Stan Wullschleger (ORNL)
Postdoctoral Associates Sponsored: Wil Lin (IPST), Mohammed Meetani (Colorado School of
Mines), Janette Berglez (Royal Melbourne Institute of Technology)