Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa
Abstract
To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphologicalmore »
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office
- OSTI Identifier:
- 1658962
- Alternate Identifier(s):
- OSTI ID: 1665996; OSTI ID: 1677474
- Report Number(s):
- NREL/JA-2800-78068
Journal ID: ISSN 1664-462X; 545748
- Grant/Contract Number:
- AC05-00OR22725; AC02-05CH11231; AC36-08GO28308
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Plant Science
- Additional Journal Information:
- Journal Name: Frontiers in Plant Science Journal Volume: 11; Journal ID: ISSN 1664-462X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Populus; wood anatomy; leaf morphology; GWAS; networks; lignin; 29 EE - Bioenergy Technologies Office (EE-3B)
Citation Formats
Chhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A., and DiFazio, Stephen P. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. Switzerland: N. p., 2020.
Web. doi:10.3389/fpls.2020.545748.
Chhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A., & DiFazio, Stephen P. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. Switzerland. https://doi.org/10.3389/fpls.2020.545748
Chhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A., and DiFazio, Stephen P. Wed .
"Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa". Switzerland. https://doi.org/10.3389/fpls.2020.545748.
@article{osti_1658962,
title = {Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa},
author = {Chhetri, Hari B. and Furches, Anna and Macaya-Sanz, David and Walker, Alejandro R. and Kainer, David and Jones, Piet and Harman-Ware, Anne E. and Tschaplinski, Timothy J. and Jacobson, Daniel and Tuskan, Gerald A. and DiFazio, Stephen P.},
abstractNote = {To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.},
doi = {10.3389/fpls.2020.545748},
journal = {Frontiers in Plant Science},
number = ,
volume = 11,
place = {Switzerland},
year = {2020},
month = {9}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fpls.2020.545748
https://doi.org/10.3389/fpls.2020.545748
Other availability
Search WorldCat to find libraries that may hold this journalFigures / Tables:
FIGURE 1: Source locations of 869 P. trichocarpa genotypes sampled in this study (purple dots). The trees were grown in a common garden in Clatskanie, Oregon, USA (black star).
All figures and tables
(12 total)
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus
journal, September 2018
- Du, Qingzhang; Yang, Xiaohui; Xie, Jianbo
- Plant Biotechnology Journal, Vol. 17, Issue 3
RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data: Table 1.
journal, February 2016
- Zhan, Xiaowei; Hu, Youna; Li, Bingshan
- Bioinformatics, Vol. 32, Issue 9
Evolution of Water Transport and Xylem Structure
journal, May 2003
- Sperry, John S.
- International Journal of Plant Sciences, Vol. 164, Issue S3
Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus
journal, June 2018
- Chen, Beibei; Chen, Jinhui; Du, Qingzhang
- New Phytologist, Vol. 219, Issue 4
The prolific ATL family of RING-H2 ubiquitin ligases
journal, August 2012
- Guzmán, Plinio
- Plant Signaling & Behavior, Vol. 7, Issue 8
Association genetics of complex traits in plants: Tansley review
journal, December 2010
- Ingvarsson, Pär K.; Street, Nathaniel R.
- New Phytologist, Vol. 189, Issue 4
Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus
journal, December 2016
- Xi, Wang; Song, Dongliang; Sun, Jiayan
- Plant Molecular Biology, Vol. 93, Issue 4-5
DRB2 Is Required for MicroRNA Biogenesis in Arabidopsis thaliana
journal, April 2012
- Eamens, Andrew L.; Kim, Ki Wook; Curtin, Shaun J.
- PLoS ONE, Vol. 7, Issue 4
Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa
journal, January 2007
- Kalluri, Udaya C.; DiFazio, Stephen P.; Brunner, Amy M.
- BMC Plant Biology, Vol. 7, Issue 1
Aquaporins: Highly Regulated Channels Controlling Plant Water Relations
journal, January 2014
- Chaumont, François; Tyerman, Stephen D.
- Plant Physiology, Vol. 164, Issue 4
Impact of Combined Abiotic and Biotic Stresses on Plant Growth and Avenues for Crop Improvement by Exploiting Physio-morphological Traits
journal, April 2017
- Pandey, Prachi; Irulappan, Vadivelmurugan; Bagavathiannan, Muthukumar V.
- Frontiers in Plant Science, Vol. 8
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression
journal, January 2012
- Vining, Kelly J.; Pomraning, Kyle R.; Wilhelm, Larry J.
- BMC Genomics, Vol. 13, Issue 1
Identification and characterization of core abscisic acid (ABA) signaling components and their gene expression profile in response to abiotic stresses in Setaria viridis
journal, March 2019
- Duarte, Karoline Estefani; de Souza, Wagner Rodrigo; Santiago, Thaís Ribeiro
- Scientific Reports, Vol. 9, Issue 1
Working towards recalcitrance mechanisms: increased xylan and homogalacturonan production by overexpression of GAlactUronosylTransferase12 (GAUT12) causes increased recalcitrance and decreased growth in Populus
journal, January 2018
- Biswal, Ajaya K.; Atmodjo, Melani A.; Pattathil, Sivakumar
- Biotechnology for Biofuels, Vol. 11, Issue 1
Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships
journal, May 2019
- Weighill, Deborah; Jones, Piet; Bleker, Carissa
- Frontiers in Genetics, Vol. 10
Small RNAs, emerging regulators critical for the development of horticultural traits
journal, September 2018
- Chen, Chengjie; Zeng, Zaohai; Liu, Zongrang
- Horticulture Research, Vol. 5, Issue 1
LOB DOMAIN-CONTAINING PROTEIN 15 Positively Regulates Expression of VND7, a Master Regulator of Tracheary Elements
journal, February 2018
- Ohashi-Ito, Kyoko; Iwamoto, Kuninori; Fukuda, Hiroo
- Plant and Cell Physiology, Vol. 59, Issue 5
Fuento: functional enrichment for bioinformatics
journal, March 2017
- Weichselbaum, David; Zagrovic, Bojan; Polyansky, Anton A.
- Bioinformatics, Vol. 33, Issue 16
Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem
journal, September 2010
- Wegrzyn, Jill L.; Eckert, Andrew J.; Choi, Minyoung
- New Phytologist, Vol. 188, Issue 2
Pectin Methylesterases: Cell Wall Remodeling Proteins Are Required for Plant Response to Heat Stress
journal, November 2018
- Wu, Hui-Chen; Bulgakov, Victor P.; Jinn, Tsung-Luo
- Frontiers in Plant Science, Vol. 9
Linkage‐linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus
journal, November 2019
- Lu, Wenjie; Xiao, Liang; Quan, Mingyang
- New Phytologist, Vol. 225, Issue 3
Plant Hormones and Signaling: Common Themes and New Developments
journal, April 2008
- McSteen, Paula; Zhao, Yunde
- Developmental Cell, Vol. 14, Issue 4
Genome-wide association studies of bark texture in Populus trichocarpa
journal, February 2019
- Bdeir, Roba; Muchero, Wellington; Yordanov, Yordan
- Tree Genetics & Genomes, Vol. 15, Issue 1
False discovery control with p-value weighting
journal, September 2006
- Genovese, Christopher R.; Roeder, Kathryn; Wasserman, Larry
- Biometrika, Vol. 93, Issue 3
Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa
journal, April 2014
- McKown, Athena D.; Klápště, Jaroslav; Guy, Robert D.
- New Phytologist, Vol. 203, Issue 2
Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions
journal, July 2013
- Porth, Ilga; Klápště, Jaroslav; Skyba, Oleksandr
- New Phytologist, Vol. 200, Issue 3
The ImageJ ecosystem: An open platform for biomedical image analysis: T
journal, July 2015
- Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.
- Molecular Reproduction and Development, Vol. 82, Issue 7-8
Multitrait genome‐wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits
journal, April 2019
- Chhetri, Hari B.; Macaya‐Sanz, David; Kainer, David
- New Phytologist, Vol. 223, Issue 1
Auxin transport through PIN-FORMED 3 (PIN3) controls shade avoidance and fitness during competition
journal, December 2010
- Keuskamp, D. H.; Pollmann, S.; Voesenek, L. A. C. J.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms
journal, July 2013
- Porth, Ilga; Klapšte, Jaroslav; Skyba, Oleksandr
- New Phytologist, Vol. 200, Issue 3, p. 710-726
An Expanded View of Complex Traits: From Polygenic to Omnigenic
journal, June 2017
- Boyle, Evan A.; Li, Yang I.; Pritchard, Jonathan K.
- Cell, Vol. 169, Issue 7
Association genetics, geography and ecophysiology link stomatal patterning in Populus trichocarpa with carbon gain and disease resistance trade-offs
journal, November 2014
- McKown, Athena D.; Guy, Robert D.; Quamme, Linda
- Molecular Ecology, Vol. 23, Issue 23
Association Studies in Populus tomentosa Reveal the Genetic Interactions of Pto-MIR156c and Its Targets in Wood Formation
journal, August 2016
- Quan, Mingyang; Wang, Qingshi; Phangthavong, Souksamone
- Frontiers in Plant Science, Vol. 7
Genetical genomics of Populus leaf shape variation
journal, June 2015
- Drost, Derek R.; Puranik, Swati; Novaes, Evandro
- BMC Plant Biology, Vol. 15, Issue 1
Wood density and vessel traits as distinct correlates of ecological strategy in 51 California coast range angiosperms
journal, June 2006
- Preston, Katherine A.; Cornwell, William K.; DeNoyer, Jeanne L.
- New Phytologist, Vol. 170, Issue 4
Cell adhesion in plants is under the control of putative O-fucosyltransferases
journal, August 2016
- Verger, Stéphane; Chabout, Salem; Gineau, Emilie
- Journal of Cell Science, Vol. 129, Issue 15
Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the Biosynthesis of Pectin and Xylan in Cell Walls and Seed Testa
journal, September 2009
- Caffall, Kerry H.; Pattathil, Sivakumar; Phillips, Sarah E.
- Molecular Plant, Vol. 2, Issue 5
The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein RUB1
journal, December 1999
- del Pozo, J. C.; Estelle, M.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 26
Analytical Enzymatic Saccharification of Lignocellulosic Biomass for Conversion to Biofuels and Bio-Based Chemicals
journal, October 2018
- Gandla, Madhavi; Martín, Carlos; Jönsson, Leif
- Energies, Vol. 11, Issue 11
Mitogen-Activated Protein Kinase Cascades in Plant Hormone Signaling
journal, October 2018
- Jagodzik, Przemysław; Tajdel-Zielinska, Małgorzata; Ciesla, Agata
- Frontiers in Plant Science, Vol. 9
Hydraulic constraints on plant gas exchange
journal, July 2000
- Sperry, John S.
- Agricultural and Forest Meteorology, Vol. 104, Issue 1
Lignin content in natural Populus variants affects sugar release
journal, March 2011
- Studer, M. H.; DeMartini, J. D.; Davis, M. F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 15, p. 6300-6305
Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery
journal, May 2018
- Weighill, Deborah; Jones, Piet; Shah, Manesh
- Frontiers in Energy Research, Vol. 6
SPEECHLESS integrates brassinosteroid and stomata signalling pathways
journal, April 2012
- Gudesblat, Gustavo E.; Schneider-Pizoń, Joanna; Betti, Camilla
- Nature Cell Biology, Vol. 14, Issue 5
A role for SPEECHLESS in the integration of leaf stomatal patterning with the growth vs disease trade‐off in poplar
journal, April 2019
- McKown, Athena D.; Klápště, Jaroslav; Guy, Robert D.
- New Phytologist, Vol. 223, Issue 4
The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes
journal, October 2009
- Eamens, A. L.; Smith, N. A.; Curtin, S. J.
- RNA, Vol. 15, Issue 12
Towards integration of population and comparative genomics in forest trees
journal, August 2016
- Ingvarsson, Pär K.; Hvidsten, Torgeir R.; Street, Nathaniel R.
- New Phytologist, Vol. 212, Issue 2
Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus
journal, July 2018
- Quan, Mingyang; Du, Qingzhang; Xiao, Liang
- Plant Biotechnology Journal, Vol. 17, Issue 1
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
journal, October 2019
- Furches, Anna; Kainer, David; Weighill, Deborah
- Frontiers in Plant Science, Vol. 10
Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)
journal, September 2016
- Allwright, Mike Robert; Payne, Adrienne; Emiliani, Giovanni
- Biotechnology for Biofuels, Vol. 9, Issue 1
Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families
journal, January 2012
- Hansen, Sara Fasmer; Harholt, Jesper; Oikawa, Ai
- Frontiers in Plant Science, Vol. 3
Population genomics of the eastern cottonwood ( Populus deltoides )
journal, October 2017
- Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Márcio F. R.
- Ecology and Evolution, Vol. 7, Issue 22
Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time
journal, June 2009
- Franks, P. J.; Beerling, D. J.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 25
Cinnamoyl-CoA reductase, a key enzyme in lignin biosynthesis, is an effector of small GTPase Rac in defense signaling in rice
journal, December 2005
- Kawasaki, T.; Koita, H.; Nakatsubo, T.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 1, p. 230-235
High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus
journal, January 2015
- Muchero, Wellington; Guo, Jianjun; DiFazio, Stephen P.
- BMC Genomics, Vol. 16, Issue 1
The Arabidopsis GRAS Protein SCL14 Interacts with Class II TGA Transcription Factors and Is Essential for the Activation of Stress-Inducible Promoters
journal, November 2008
- Fode, Benjamin; Siemsen, Tanja; Thurow, Corinna
- The Plant Cell, Vol. 20, Issue 11
Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus ( QTL ) analysis and association studies
journal, October 2015
- Du, Qingzhang; Gong, Chenrui; Wang, Qingshi
- New Phytologist, Vol. 209, Issue 3
Statistical significance for genomewide studies
journal, July 2003
- Storey, J. D.; Tibshirani, R.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 16, p. 9440-9445
Forest tree genomics: growing resources and applications
journal, January 2011
- Neale, David B.; Kremer, Antoine
- Nature Reviews Genetics, Vol. 12, Issue 2
Genome-wide analysis of lectin receptor-like kinases in Populus
journal, September 2016
- Yang, Yongil; Labbé, Jessy; Muchero, Wellington
- BMC Genomics, Vol. 17, Issue 1
Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships
journal, March 1997
- Lacombe, Eric; Hawkins, Simon; Van Doorsselaere, Jan
- The Plant Journal, Vol. 11, Issue 3
Global Analysis of DELLA Direct Targets in Early Gibberellin Signaling in Arabidopsis
journal, October 2007
- Zentella, Rodolfo; Zhang, Zhong-Lin; Park, Mehea
- The Plant Cell, Vol. 19, Issue 10
Contrasting transcriptional responses of PYR1/PYL/RCAR ABA receptors to ABA or dehydration stress between maize seedling leaves and roots
journal, April 2016
- Fan, Wenqiang; Zhao, Mengyao; Li, Suxin
- BMC Plant Biology, Vol. 16, Issue 1
A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus
journal, December 2018
- Badmi, Raghuram; Payyavula, Raja S.; Bali, Garima
- Frontiers in Plant Science, Vol. 9
The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides
journal, January 2019
- Tschaplinski, Timothy James; Abraham, Paul E.; Jawdy, Sara S.
- Annals of Botany, Vol. 124, Issue 4
Regulation of Lignin Biosynthesis and Its Role in Growth-Defense Tradeoffs
journal, September 2018
- Xie, Meng; Zhang, Jin; Tschaplinski, Timothy J.
- Frontiers in Plant Science, Vol. 9
Variance component model to account for sample structure in genome-wide association studies
journal, March 2010
- Kang, Hyun Min; Sul, Jae Hoon; Service, Susan K.
- Nature Genetics, Vol. 42, Issue 4
Stress-Related Gene Expression Reflects Morphophysiological Responses to Water Deficit
journal, May 2017
- Rymaszewski, Wojciech; Vile, Denis; Bediee, Alexis
- Plant Physiology, Vol. 174, Issue 3
Genome-wide efficient mixed-model analysis for association studies
journal, June 2012
- Zhou, Xiang; Stephens, Matthew
- Nature Genetics, Vol. 44, Issue 7
Genome-wide analysis of the phospholipase D family in Oryza sativa and functional characterization of PLDβ1 in seed germination
journal, September 2007
- Li, Gang; Lin, Fang; Xue, Hong-Wei
- Cell Research, Vol. 17, Issue 10
Involvement of calmodulin and calmodulin-like proteins in plant responses to abiotic stresses
journal, August 2015
- Zeng, Houqing; Xu, Luqin; Singh, Amarjeet
- Frontiers in Plant Science, Vol. 6
Functional Analysis of the Kunitz Trypsin Inhibitor Family in Poplar Reveals Biochemical Diversity and Multiplicity in Defense against Herbivores
journal, November 2007
- Major, Ian T.; Constabel, C. Peter
- Plant Physiology, Vol. 146, Issue 3
The Mechanical Diversity of Stomata and Its Significance in Gas-Exchange Control
journal, November 2006
- Franks, Peter J.; Farquhar, Graham D.
- Plant Physiology, Vol. 143, Issue 1
Germin and Germin-like Proteins: Evolution, Structure, and Function
journal, September 2008
- Dunwell, Jim M.; Gibbings, J. George; Mahmood, Tariq
- Critical Reviews in Plant Sciences, Vol. 27, Issue 5
Genomic insights into salt adaptation in a desert poplar
journal, November 2013
- Ma, Tao; Wang, Junyi; Zhou, Gongke
- Nature Communications, Vol. 4, Issue 1
Polymorphic simple sequence repeat (SSR) loci within cellulose synthase ( PtoCesA ) genes are associated with growth and wood properties in Populus tomentosa
journal, December 2012
- Du, Qingzhang; Pan, Wei; Xu, Baohua
- New Phytologist, Vol. 197, Issue 3
A Chloroplast-Localized Rubredoxin Family Protein Gene from Puccinellia tenuiflora (PutRUB) Increases NaCl and NaHCO3 Tolerance by Decreasing H2O2 Accumulation
journal, May 2016
- Li, Ying; Liu, Panpan; Takano, Tetsuo
- International Journal of Molecular Sciences, Vol. 17, Issue 6
Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects
journal, December 2018
- Du, Qingzhang; Lu, Wenjie; Quan, Mingyang
- Frontiers in Plant Science, Vol. 9
Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica
journal, April 2020
- Jia, Huixia; Liu, Guangjian; Li, Jianbo
- Journal of Experimental Botany, Vol. 71, Issue 14
Structural Insights into the Mechanism of Protein O-Fucosylation
journal, September 2011
- Lira-Navarrete, Erandi; Valero-González, Jessika; Villanueva, Raquel
- PLoS ONE, Vol. 6, Issue 9
10 Years of GWAS Discovery: Biology, Function, and Translation
journal, July 2017
- Visscher, Peter M.; Wray, Naomi R.; Zhang, Qian
- The American Journal of Human Genetics, Vol. 101, Issue 1
DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L.
journal, December 2005
- González-Martínez, Santiago C.; Ersoz, Elhan; Brown, Garth R.
- Genetics, Vol. 172, Issue 3
Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network
journal, January 2013
- Pendergrass, Sarah A.; Brown-Gentry, Kristin; Dudek, Scott
- PLoS Genetics, Vol. 9, Issue 1
Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations
journal, August 2014
- Evans, Luke M.; Slavov, Gancho T.; Rodgers-Melnick, Eli
- Nature Genetics, Vol. 46, Issue 10
How wood evolves: a new synthesis
journal, October 2012
- Carlquist, Sherwin
- Botany, Vol. 90, Issue 10
Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus
journal, July 2018
- Zhang, Jin; Yang, Yongil; Zheng, Kaijie
- New Phytologist, Vol. 220, Issue 2
Phytozome: a comparative platform for green plant genomics
journal, November 2011
- Goodstein, David M.; Shu, Shengqiang; Howson, Russell
- Nucleic Acids Research, Vol. 40, Issue D1
Knights in Action: Lectin Receptor-Like Kinases in Plant Development and Stress Responses
journal, September 2013
- Vaid, Neha; Macovei, Anca; Tuteja, Narendra
- Molecular Plant, Vol. 6, Issue 5
A CBL-Interacting Protein Kinase TaCIPK2 Confers Drought Tolerance in Transgenic Tobacco Plants through Regulating the Stomatal Movement
journal, December 2016
- Wang, Yan; Sun, Tao; Li, Tingting
- PLOS ONE, Vol. 11, Issue 12
Wood traits related to size and life history of trees in a Panamanian rainforest
journal, August 2016
- Hietz, Peter; Rosner, Sabine; Hietz-Seifert, Ursula
- New Phytologist, Vol. 213, Issue 1
The Role of Serine-Threonine Protein Phosphatase PP2A in Plant Oxidative Stress Signaling—Facts and Hypotheses
journal, June 2019
- Máthé, Csaba; Garda, Tamás; Freytag, Csongor
- International Journal of Molecular Sciences, Vol. 20, Issue 12
Efficient multivariate linear mixed model algorithms for genome-wide association studies
journal, February 2014
- Zhou, Xiang; Stephens, Matthew
- Nature Methods, Vol. 11, Issue 4
Genetic Design and Statistical Power of Nested Association Mapping in Maize
journal, January 2008
- Yu, Jianming; Holland, James B.; McMullen, Michael D.
- Genetics, Vol. 178, Issue 1
A Multivariate Genome-Wide Association Analysis of 10 LDL Subfractions, and Their Response to Statin Treatment, in 1868 Caucasians
journal, April 2015
- Shim, Heejung; Chasman, Daniel I.; Smith, Joshua D.
- PLOS ONE, Vol. 10, Issue 4
Mediation of plant–mycorrhizal interaction by a lectin receptor-like kinase
journal, July 2019
- Labbé, Jessy; Muchero, Wellington; Czarnecki, Olaf
- Nature Plants, Vol. 5, Issue 7
QUASIMODO1 is expressed in vascular tissue of Arabidopsis thaliana inflorescence stems, and affects homogalacturonan and xylan biosynthesis
journal, July 2005
- Orfila, Caroline; Sørensen, Susanne Oxenbøll; Harholt, Jesper
- Planta, Vol. 222, Issue 4
Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
journal, August 2012
- Slavov, Gancho T.; DiFazio, Stephen P.; Martin, Joel
- New Phytologist, Vol. 196, Issue 3, p. 713-725
Calcium Signaling Network in Plants: An Overview
journal, March 2007
- Tuteja, Narendra; Mahajan, Shilpi
- Plant Signaling & Behavior, Vol. 2, Issue 2
The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA
journal, February 2017
- Zentella, Rodolfo; Sui, Ning; Barnhill, Benjamin
- Nature Chemical Biology, Vol. 13, Issue 5
Effects of abiotic stress on plants: a systems biology perspective
journal, January 2011
- Cramer, Grant R.; Urano, Kaoru; Delrot, Serge
- BMC Plant Biology, Vol. 11, Issue 1
PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger
journal, April 2018
- Verma, Anurag; Lucas, Anastasia; Verma, Shefali S.
- The American Journal of Human Genetics, Vol. 102, Issue 4
Natural acetylation impacts carbohydrate recovery during deconstruction of Populus trichocarpa wood
journal, February 2017
- Johnson, Amanda M.; Kim, Hoon; Ralph, John
- Biotechnology for Biofuels, Vol. 10, Issue 1
A Mutant Arabidopsis Heterotrimeric G-Protein beta Subunit Affects Leaf, Flower, and Fruit Development
journal, December 2001
- Lease, K. A.
- THE PLANT CELL ONLINE, Vol. 13, Issue 12
Brassinosteroids: Multidimensional Regulators of Plant Growth, Development, and Stress Responses
journal, November 2019
- Nolan, Trevor M.; Vukašinović, Nemanja; Liu, Derui
- The Plant Cell, Vol. 32, Issue 2
Brassinosteroid-regulated GSK3/Shaggy-like Kinases Phosphorylate Mitogen-activated Protein (MAP) Kinase Kinases, Which Control Stomata Development in Arabidopsis thaliana
journal, January 2013
- Khan, Mamoona; Rozhon, Wilfried; Bigeard, Jean
- Journal of Biological Chemistry, Vol. 288, Issue 11
THE ROLE OF KNOX GENES IN PLANT DEVELOPMENT
journal, November 2004
- Hake, Sarah; Smith, Harley M. S.; Holtan, Hans
- Annual Review of Cell and Developmental Biology, Vol. 20, Issue 1
Improving plant stress tolerance and yield production: is the tonoplast aquaporin SlTIP2;2 a key to isohydric to anisohydric conversion?
journal, November 2008
- Sade, Nir; Vinocur, Basia J.; Diber, Alex
- New Phytologist, Vol. 181, Issue 3
Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa
journal, November 2013
- McKown, Athena D.; Guy, Robert D.; Klápště, Jaroslav
- New Phytologist, Vol. 201, Issue 4
Specific targeting of proteins to outer envelope membranes of endosymbiotic organelles, chloroplasts, and mitochondria
journal, April 2014
- Lee, Junho; Kim, Dae Heon; Hwang, Inhwan
- Frontiers in Plant Science, Vol. 5
The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: genome-wide characterization and expression analyses during developmental processes and stress responses
journal, November 2017
- Grimplet, Jérôme; Pimentel, Diana; Agudelo-Romero, Patricia
- Scientific Reports, Vol. 7, Issue 1
Characterization of a Small Auxin-Up RNA (SAUR)-Like Gene Involved in Arabidopsis thaliana Development
journal, November 2013
- Markakis, Marios Nektarios; Boron, Agnieszka Karolina; Van Loock, Bram
- PLoS ONE, Vol. 8, Issue 11
Evolutionary Quantitative Genomics of Populus trichocarpa
journal, November 2015
- Porth, Ilga; Klápště, Jaroslav; McKown, Athena D.
- PLOS ONE, Vol. 10, Issue 11
A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis
journal, November 2017
- Escamez, Sacha; Latha Gandla, Madhavi; Derba-Maceluch, Marta
- Scientific Reports, Vol. 7, Issue 1
Farnesylcysteine Lyase is Involved in Negative Regulation of Abscisic Acid Signaling in Arabidopsis
journal, January 2010
- Huizinga, David H.; Denton, Ryan; Koehler, Kelly G.
- Molecular Plant, Vol. 3, Issue 1
The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates
journal, February 2009
- Yee, D.; Goring, D. R.
- Journal of Experimental Botany, Vol. 60, Issue 4
Multivariate simulation framework reveals performance of multi-trait GWAS methods
journal, March 2017
- Porter, Heather F.; O’Reilly, Paul F.
- Scientific Reports, Vol. 7, Issue 1
Identification of microRNAs Involved in Regeneration of the Secondary Vascular System in Populus tomentosa Carr
journal, May 2016
- Tang, Fang; Wei, Hairong; Zhao, Shutang
- Frontiers in Plant Science, Vol. 7
The Arabidopsis ZINC FINGER PROTEIN3 Interferes with Abscisic Acid and Light Signaling in Seed Germination and Plant Development
journal, May 2014
- Joseph, Mary Prathiba; Papdi, Csaba; Kozma-Bognár, László
- Plant Physiology, Vol. 165, Issue 3
Sec14-like phosphatidylinositol transfer proteins and the biological landscape of phosphoinositide signaling in plants
journal, September 2016
- Huang, Jin; Ghosh, Ratna; Bankaitis, Vytas A.
- Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1861, Issue 9
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.