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Title: 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 Ca 2+ 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 assaysmore » 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.« less

Authors:
 [1];  [1];  [2];  [1];  [1];  [2];  [1];  [1];  [1];  [3];  [1];  [4];  [5];  [6];  [5];  [5];  [5];  [5];  [7];  [7] more »;  [2];  [1];  [1] « less
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. West Virginia Univ., Morgantown, WV (United States)
  3. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  4. Czech Univ. of Life Sciences, Prague (Czech Republic); Univ. of British Columbia, Vancouver (Canada)
  5. Univ. of British Columbia, Vancouver, BC (Canada)
  6. Univ. of British Columbia, Vancouver, BC (Canada)er
  7. U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA (United States)
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) (SC-23)
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. 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, and Tuskan, Gerald A. Fri . "High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus". United States. doi: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 = {2015},
month = {1}
}

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Works referenced in this record:

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