High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus
Abstract
We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggestedmore »
- Authors:
-
more »
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- West Virginia Univ., Morgantown, WV (United States)
- National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Czech Univ. of Life Sciences, Prague (Czech Republic); Univ. of British Columbia, Vancouver (Canada)
- Univ. of British Columbia, Vancouver, BC (Canada)
- Univ. of British Columbia, Vancouver, BC (Canada)er
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1214456
- Alternate Identifier(s):
- OSTI ID: 1220715
- Report Number(s):
- NREL/JA-5100-64000
Journal ID: ISSN 1471-2164; KP1601050; ERKP695
- Grant/Contract Number:
- AC05-00OR22725; AC05-00OR2272; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 16; Journal Issue: 24; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; QTL cloning; association genetics; cell wall recalcitrance; lignin; cellulose; hemicellulose; 09 BIOMASS FUELS
Citation Formats
Muchero, Wellington, Guo, Jianjun, Difazio, Stephen P., Chen, Jay, Ranjan, Priya, Slavov, Gancho, Gunter, Lee E., Jawdy, Sara, Bryan, Anthony C., Sykes, Robert, Ziebell, Angela L., Klapste, Jaroslav, Porth, Ilga, Skyba, Oleksandr, Unda, Faride, El-Kassaby, Yousry, Douglas, Carl, Mansfield, Shawn, Martin, Joel, Schackwitz, Wendy, Evans, Luke M., Czarnecki, Olaf, and Tuskan, Gerald A. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. United States: N. p., 2015.
Web. doi:10.1186/s12864-015-1215-z.
Muchero, Wellington, Guo, Jianjun, Difazio, Stephen P., Chen, Jay, Ranjan, Priya, Slavov, Gancho, Gunter, Lee E., Jawdy, Sara, Bryan, Anthony C., Sykes, Robert, Ziebell, Angela L., Klapste, Jaroslav, Porth, Ilga, Skyba, Oleksandr, Unda, Faride, El-Kassaby, Yousry, Douglas, Carl, Mansfield, Shawn, Martin, Joel, Schackwitz, Wendy, Evans, Luke M., Czarnecki, Olaf, & Tuskan, Gerald A. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. United States. https://doi.org/10.1186/s12864-015-1215-z
Muchero, Wellington, Guo, Jianjun, Difazio, Stephen P., Chen, Jay, Ranjan, Priya, Slavov, Gancho, Gunter, Lee E., Jawdy, Sara, Bryan, Anthony C., Sykes, Robert, Ziebell, Angela L., Klapste, Jaroslav, Porth, Ilga, Skyba, Oleksandr, Unda, Faride, El-Kassaby, Yousry, Douglas, Carl, Mansfield, Shawn, Martin, Joel, Schackwitz, Wendy, Evans, Luke M., Czarnecki, Olaf, and Tuskan, Gerald A. Fri .
"High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus". United States. https://doi.org/10.1186/s12864-015-1215-z. https://www.osti.gov/servlets/purl/1214456.
@article{osti_1214456,
title = {High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus},
author = {Muchero, Wellington and Guo, Jianjun and Difazio, Stephen P. and Chen, Jay and Ranjan, Priya and Slavov, Gancho and Gunter, Lee E. and Jawdy, Sara and Bryan, Anthony C. and Sykes, Robert and Ziebell, Angela L. and Klapste, Jaroslav and Porth, Ilga and Skyba, Oleksandr and Unda, Faride and El-Kassaby, Yousry and Douglas, Carl and Mansfield, Shawn and Martin, Joel and Schackwitz, Wendy and Evans, Luke M. and Czarnecki, Olaf and Tuskan, Gerald A.},
abstractNote = {We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.},
doi = {10.1186/s12864-015-1215-z},
journal = {BMC Genomics},
number = 24,
volume = 16,
place = {United States},
year = {Fri Jan 23 00:00:00 EST 2015},
month = {Fri Jan 23 00:00:00 EST 2015}
}
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Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus
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Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.)
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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
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A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis
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Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects
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High Throughput Screening Technologies in Biomass Characterization
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Multiple levers for overcoming the recalcitrance of lignocellulosic biomass
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Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa
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