Quantitative trait locus mapping of Populus bark features and stem diameter
Abstract
Background: Bark plays important roles in photosynthate transport and storage, along with physical and chemical protection. Bark texture varies extensively among species, from smooth to fissured to deeply furrowed, but its genetic control is unknown. This study sought to determine the main genomic regions associated with natural variation in bark features and stem diameter. Quantitative trait loci (QTL) were mapped using an interspecific pseudo-backcross pedigree (Populus trichocarpa x P. deltoides and P. deltoides) for bark texture, bark thickness and diameter collected across three years, two sites and three biological replicates per site. Results: QTL specific to bark texture were highly reproducible in shared intervals across sites, years and replicates. Significant positive correlations and co-localization between trait QTL suggest pleiotropic regulators or closely linked genes. A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. Conclusion: Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. The results presented in this studymore »
- Authors:
-
- Michigan Technological Univ., Houghton, MI (United States). School of Forest Resources and Environmental Science
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Div.
- Eastern Illinois Univ., Charleston, IL (United States). Dept. of Biology
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA; National Science Foundation (NSF)
- OSTI Identifier:
- 1626848
- Grant/Contract Number:
- AC05-00OR22725; 2012–67,013-19,389; 1230803
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Plant Biology
- Additional Journal Information:
- Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2229
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Plant Sciences; Bark texture; Bark thickness; Diameter; Quantitative trait loci (QTL); Stem; Populus trichocarpa
Citation Formats
Bdeir, Roba, Muchero, Wellington, Yordanov, Yordan, Tuskan, Gerald A., Busov, Victor, and Gailing, Oliver. Quantitative trait locus mapping of Populus bark features and stem diameter. United States: N. p., 2017.
Web. doi:10.1186/s12870-017-1166-4.
Bdeir, Roba, Muchero, Wellington, Yordanov, Yordan, Tuskan, Gerald A., Busov, Victor, & Gailing, Oliver. Quantitative trait locus mapping of Populus bark features and stem diameter. United States. https://doi.org/10.1186/s12870-017-1166-4
Bdeir, Roba, Muchero, Wellington, Yordanov, Yordan, Tuskan, Gerald A., Busov, Victor, and Gailing, Oliver. Tue .
"Quantitative trait locus mapping of Populus bark features and stem diameter". United States. https://doi.org/10.1186/s12870-017-1166-4. https://www.osti.gov/servlets/purl/1626848.
@article{osti_1626848,
title = {Quantitative trait locus mapping of Populus bark features and stem diameter},
author = {Bdeir, Roba and Muchero, Wellington and Yordanov, Yordan and Tuskan, Gerald A. and Busov, Victor and Gailing, Oliver},
abstractNote = {Background: Bark plays important roles in photosynthate transport and storage, along with physical and chemical protection. Bark texture varies extensively among species, from smooth to fissured to deeply furrowed, but its genetic control is unknown. This study sought to determine the main genomic regions associated with natural variation in bark features and stem diameter. Quantitative trait loci (QTL) were mapped using an interspecific pseudo-backcross pedigree (Populus trichocarpa x P. deltoides and P. deltoides) for bark texture, bark thickness and diameter collected across three years, two sites and three biological replicates per site. Results: QTL specific to bark texture were highly reproducible in shared intervals across sites, years and replicates. Significant positive correlations and co-localization between trait QTL suggest pleiotropic regulators or closely linked genes. A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. Conclusion: Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. The results presented in this study provide a basis for future genomic characterization of genes found within the QTL for bark texture, bark thickness and diameter in order to better understand stem and bark development in Populus and other woody perennial plants. The QTL mapping approach identified a list of prime candidate genes for further validation using functional genomics or forward genetics approaches.},
doi = {10.1186/s12870-017-1166-4},
journal = {BMC Plant Biology},
number = 1,
volume = 17,
place = {United States},
year = {Tue Nov 28 00:00:00 EST 2017},
month = {Tue Nov 28 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 12 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Fig. 1: Bark texture scale for Populus Family 52–124 offspring. Ranging from smooth (a), medium (b), rough (c) and rough/deeply furrowed bark (d), and level 4 was only found in Oregon
All figures and tables
(3 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:
Studies in Systematic bark Morphology. i. bark Morphology in Dipterocarpaceae
journal, August 1962
- Whitmore, T. C.
- New Phytologist, Vol. 61, Issue 2
QTL for yield in bioenergy Populus: identifying G×E interactions from growth at three contrasting sites
journal, June 2007
- Rae, Anne M.; Pinel, Matthieu P. C.; Bastien, Catherine
- Tree Genetics & Genomes, Vol. 4, Issue 1
QTL analysis of growth and wood chemical content traits in an interspecific backcross family of white poplar ( Populus tomentosa × P. bolleana ) × P. tomentosa
journal, August 2006
- Zhang, Deqiang; Zhang, Zhiyi; Yang, Kai
- Canadian Journal of Forest Research, Vol. 36, Issue 8
Photosynthetic physiology of eucalypts along a sub-continental rainfall gradient in northern Australia
journal, November 2011
- Cernusak, Lucas A.; Hutley, Lindsay B.; Beringer, Jason
- Agricultural and Forest Meteorology, Vol. 151, Issue 11
Biophysical properties and functional significance of stem water storage tissues in Neotropical savanna trees
journal, February 2007
- Scholz, Fabian G.; Bucci, Sandra J.; Goldstein, Guillermo
- Plant, Cell & Environment, Vol. 30, Issue 2
Estimates of Agrilus planipennis Infestation Rates and Potential Survival of Ash
journal, January 2013
- Marshall, Jordan M.; Smith, Eric L.; Mech, Roger
- The American Midland Naturalist, Vol. 169, Issue 1
Phenotypic variation in growth and biomass distribution for two advanced-generation pedigrees of hybrid poplar
journal, August 2005
- Wullschleger, Stan D.; Yin, T. M.; DiFazio, S. P.
- Canadian Journal of Forest Research, Vol. 35, Issue 8
Branch architecture QTL for Pinus elliottii var. elliottii � Pinus caribaea var. hondurensis hybrids
journal, July 2002
- Shepherd, Mervyn; Cross, Michael; Dieters, Mark J.
- Annals of Forest Science, Vol. 59, Issue 5-6
Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar
journal, March 2012
- Ko, Jae-Heung; Kim, Hyun-Tae; Hwang, Ildoo
- Plant Biotechnology Journal, Vol. 10, Issue 5, p. 587-596
Phosphorylation-Dependent Differential Regulation of Plant Growth, Cell Death, and Innate Immunity by the Regulatory Receptor-Like Kinase BAK1
journal, April 2011
- Schwessinger, Benjamin; Roux, Milena; Kadota, Yasuhiro
- PLoS Genetics, Vol. 7, Issue 4
Effects of stem anatomical and structural traits on responses to stem damage: an experimental study in the Bolivian Amazon
journal, March 2008
- Romero, Claudia; Bolker, Benjamin M.
- Canadian Journal of Forest Research, Vol. 38, Issue 3
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
Cell wall mutants
journal, January 2000
- Fagard, Mathilde; Höfte, Herman; Vernhettes, Samantha
- Plant Physiology and Biochemistry, Vol. 38, Issue 1-2
Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus
journal, November 2010
- Yin, Tongming; Zhang, Xinye; Gunter, Lee
- PLoS ONE, Vol. 5, Issue 11, Article No. e14021
Gene dosage effects and signatures of purifying selection in lateral organ boundaries domain (LBD) genes LBD1 and LBD18
journal, February 2016
- Bdeir, Roba; Busov, Victor; Yordanov, Yordan
- Plant Systematics and Evolution, Vol. 302, Issue 4
Enzymatic saccharification of Eucalyptus bark using hydrothermal pre-treatment with carbon dioxide
journal, July 2010
- Matsushita, Yasuyuki; Yamauchi, Kazuchika; Takabe, Keiji
- Bioresource Technology, Vol. 101, Issue 13
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
journal, January 2008
- Chu, Vu T.; Gottardo, Raphael; Raftery, Adrian E.
- Genome Biology, Vol. 9, Issue 7
Poplar as a feedstock for biofuels: A review of compositional characteristics
journal, March 2010
- Sannigrahi, Poulomi; Ragauskas, Arthur J.; Tuskan, Gerald A.
- Biofuels, Bioproducts and Biorefining, Vol. 4, Issue 2
Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels
journal, March 2009
- Novaes, Evandro; Osorio, Luis; Drost, Derek R.
- New Phytologist, Vol. 182, Issue 4, p. 878-890
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
journal, January 2003
- Bolstad, B. M.; Irizarry, R. A.; Astrand, M.
- Bioinformatics, Vol. 19, Issue 2
Genetical genomics of Populus leaf shape variation
journal, June 2015
- Drost, Derek R.; Puranik, Swati; Novaes, Evandro
- BMC Plant Biology, Vol. 15, Issue 1
TM4: A Free, Open-Source System for Microarray Data Management and Analysis
journal, February 2003
- Saeed, A. I.; Sharov, V.; White, J.
- BioTechniques, Vol. 34, Issue 2
A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation: Physical mapping of the Populus genome
journal, May 2007
- Kelleher, Colin T.; Chiu, Readman; Shin, Heesun
- The Plant Journal, Vol. 50, Issue 6
Wood Formation in Trees
journal, December 2001
- Plomion, Christophe; Leprovost, Grégoire; Stokes, Alexia
- Plant Physiology, Vol. 127, Issue 4
Detection and stability of quantitative trait loci (QTL) in Eucalyptus globulus
journal, May 2007
- Bundock, Peter C.; Potts, Brad M.; Vaillancourt, René E.
- Tree Genetics & Genomes, Vol. 4, Issue 1
Universality of phloem transport in seed plants: Universality of phloem transport in seed plants
journal, January 2012
- Jensen, KÅRe Hartvig; Liesche, Johannes; Bohr, Tomas
- Plant, Cell & Environment, Vol. 35, Issue 6
The role of bark type in relative tolerance to fire of three central Victorian Eucalypts
journal, January 1968
- Gill, Am; Ashton, Dh
- Australian Journal of Botany, Vol. 16, Issue 3
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
journal, September 2006
- Tuskan, G. A.; DiFazio, S.; Jansson, S.
- Science, Vol. 313, Issue 5793, p. 1596-1604
The mechanical role of bark
journal, April 1999
- Niklas, Karl J.
- American Journal of Botany, Vol. 86, Issue 4
Poplar genes encoding fasciclin-like arabinogalactan proteins are highly expressed in tension wood
journal, September 2004
- Lafarguette, Florian; Leplé, Jean-Charles; Déjardin, Annabelle
- New Phytologist, Vol. 164, Issue 1, p. 107-121
QTLs and candidate genes for wood properties in maritime pine (Pinus pinaster Ait.)
journal, February 2006
- Pot, David; Rodrigues, Jose-Carlos; Rozenberg, Philippe
- Tree Genetics & Genomes, Vol. 2, Issue 1
Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus: FLAs specialized for stem biomechanics and cell walls
journal, February 2010
- MacMillan, Colleen P.; Mansfield, Shawn D.; Stachurski, Zbigniew H.
- The Plant Journal, Vol. 62, Issue 4
Ecology and ecophysiology of tree stems: corticular and wood photosynthesis
journal, April 2002
- H., Pfanz; G., Aschan; R., Langenfeld-Heyser
- Naturwissenschaften, Vol. 89, Issue 4
Adaptation of tree growth to elevated CO 2 : quantitative trait loci for biomass in Populus
journal, July 2007
- Rae, Anne M.; Tricker, Penny J.; Bunn, Stephen M.
- New Phytologist, Vol. 175, Issue 1
Bark properties and fire resistance of selected tree species from the central hardwood region of North America
journal, April 1994
- Hengst, Gretel E.; Dawson, Jeffrey O.
- Canadian Journal of Forest Research, Vol. 24, Issue 4
Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens
journal, November 2009
- Thumma, Bala R.; Southerton, Simon G.; Bell, John C.
- Tree Genetics & Genomes, Vol. 6, Issue 2
QTL mapping for fiber yield-related traits by constructing the first genetic linkage map in ramie (Boehmeria nivea L. Gaud)
journal, April 2014
- Liu, Touming; Tang, Shouwei; Zhu, Siyuan
- Molecular Breeding, Vol. 34, Issue 3
Genetical genomics: combining genetics with gene expression analysis
journal, October 2005
- Li, Jun; Burmeister, Margit
- Human Molecular Genetics, Vol. 14, Issue suppl_2
Effects of pretreatment on morphology, chemical composition and enzymatic digestibility of eucalyptus bark: a potentially valuable source of fermentable sugars for biofuel production – part 1
journal, January 2013
- Lima, Marisa A.; Lavorente, Gabriela B.; da Silva, Hana KP
- Biotechnology for Biofuels, Vol. 6, Issue 1
The ELONGATED gene of Arabidopsis acts independently of light and gibberellins in the control of elongation growth
journal, March 1996
- Halliday, Karen; Devlin, Paul F.; Whitelam, Garry C.
- The Plant Journal, Vol. 9, Issue 3
Does frequent burning affect longleaf pine ( Pinus palustris ) bark thickness?
journal, July 2011
- Wang, G. Geoff; Wangen, Steve R.
- Canadian Journal of Forest Research, Vol. 41, Issue 7
Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression
journal, March 2011
- Beaulieu, Jean; Doerksen, Trevor; Boyle, Brian
- Genetics, Vol. 188, Issue 1
Genetics of gene expression surveyed in maize, mouse and man
journal, March 2003
- Schadt, Eric E.; Monks, Stephanie A.; Drake, Thomas A.
- Nature, Vol. 422, Issue 6929
The Lateral Organ Boundaries Gene Defines a Novel, Plant-Specific Gene Family
journal, May 2002
- Shuai, Bin; Reynaga-Peña, Cristina G.; Springer, Patricia S.
- Plant Physiology, Vol. 129, Issue 2
Coordinated Genetic Regulation of Growth and Lignin Revealed by Quantitative Trait Locus Analysis of cDNA Microarray Data in an Interspecific Backcross of Eucalyptus
journal, August 2004
- Kirst, Matias; Myburg, Alexander A.; De León, José P. G.
- Plant Physiology, Vol. 135, Issue 4
Members of the LATERAL ORGAN BOUNDARIES DOMAIN Transcription Factor Family Are Involved in the Regulation of Secondary Growth in Populus
journal, November 2010
- Yordanov, Yordan S.; Regan, Sharon; Busov, Victor
- The Plant Cell, Vol. 22, Issue 11
Antisense expression of the fasciclin-like arabinogalactan protein FLA6 gene in Populus inhibits expression of its homologous genes and alters stem biomechanics and cell wall composition in transgenic trees
journal, November 2014
- Wang, Haihai; Jiang, Chunmei; Wang, Cuiting
- Journal of Experimental Botany, Vol. 66, Issue 5
The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis
journal, March 2012
- Tuskan, Gerald A.; DiFazio, Steve; Faivre-Rampant, Patricia
- Tree Genetics & Genomes, Vol. 8, Issue 3
Stem responses to damage: the evolutionary ecology of Quercus species in contrasting fire regimes
journal, January 2009
- Romero, Claudia; Bolker, Benjamin M.; Edwards, Christine E.
- New Phytologist, Vol. 182, Issue 1
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
Genetical genomics: the added value from segregation
journal, July 2001
- Jansen, R.
- Trends in Genetics, Vol. 17, Issue 7
Characterization of NAC domain transcription factors implicated in control of vascular cell differentiation in Arabidopsis and Populus
journal, May 2010
- Grant, Emily H.; Fujino, Takeshi; Beers, Eric P.
- Planta, Vol. 232, Issue 2
Genetic Improvement of Poplar Feedstock Quality for Ethanol Production
journal, January 2001
- Dinus, Ronald J.
- Applied Biochemistry and Biotechnology, Vol. 91-93, Issue 1-9
AtFLA11, a Fasciclin-Like Arabinogalactan-Protein, Specifically Localized in Screlenchyma Cells
journal, January 2005
- Ito, Shinsaku; Suzuki, Yoshihito; Miyamoto, Kensuke
- Bioscience, Biotechnology, and Biochemistry, Vol. 69, Issue 10
Genome Anchored QTLs for Biomass Productivity in Hybrid Populus Grown under Contrasting Environments
journal, January 2013
- Muchero, Wellington; Sewell, Mitchell M.; Ranjan, Priya
- PLoS ONE, Vol. 8, Issue 1
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
How do small savanna trees avoid stem mortality by fire? The roles of stem diameter, height and bark thickness
journal, April 2011
- Lawes, Michael J.; Adie, Hylton; Russell-Smith, Jeremy
- Ecosphere, Vol. 2, Issue 4
The Arabidopsis Somatic Embryogenesis Receptor Kinase 1 Gene Is Expressed in Developing Ovules and Embryos and Enhances Embryogenic Competence in Culture
journal, November 2001
- Hecht, Valérie; Vielle-Calzada, Jean-Philippe; Hartog, Marijke V.
- Plant Physiology, Vol. 127, Issue 3
Wood, Bark, and Stem Anatomy of Gnetales: A Summary
journal, November 1996
- Carlquist, Sherwin
- International Journal of Plant Sciences, Vol. 157, Issue S6
Genetic Improvement of Poplar Feedstock Quality for Ethanol Production
book, January 2001
- Dinus, Ronald J.
- Twenty-Second Symposium on Biotechnology for Fuels and Chemicals
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
text, January 2008
- Chu, Vu T.; Gottardo, Raphael; Raftery, Adrian E.
- BioMed Central
Works referencing / citing this record:
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
Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
journal, October 2018
- Clifton-Brown, John; Harfouche, Antoine; Casler, Michael D.
- GCB Bioenergy, Vol. 11, Issue 1
Bark Features for Identifying Resonance Spruce Standing Timber
journal, September 2019
- Dinulică, Florin; Albu, Cristian-Teofil; Vasilescu, Maria Magdalena
- Forests, Vol. 10, Issue 9
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.