High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

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.

doi:10.1186/s12864-015-1215-z

Title: High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

Journal Article · Fri Jan 23 04:00:00 UTC 2015 · BMC Genomics

DOI: https://doi.org/10.1186/s12864-015-1215-z · OSTI ID:1214456

Muchero, Wellington ^[1]; Guo, Jianjun ^[1]; Difazio, Stephen P. ^[2]; Chen, Jay ^[1]; Ranjan, Priya ^[1]; Slavov, Gancho ^[2]; Gunter, Lee E. ^[1]; Jawdy, Sara ^[1]; Bryan, Anthony C. ^[1]; Sykes, Robert ^[3]; Ziebell, Angela L. ^[1]; Klapste, Jaroslav ^[4]; Porth, Ilga ^[5]; Skyba, Oleksandr ^[6]; Unda, Faride ^[5]; El-Kassaby, Yousry ^[5]; Douglas, Carl ^[5]; Mansfield, Shawn ^[5]; Martin, Joel ^[7]; Schackwitz, Wendy ^[7] 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)

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.

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1214456

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 24 Vol. 16; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Association genetics of chemical wood properties in black poplar ( Populus nigra ) Guerra, Fernando P.; Wegrzyn, Jill L.; Sykes, Robert New Phytologist, Vol. 197, Issue 1 https://doi.org/10.1111/nph.12003	journal	November 2012
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Fuel Ethanol from Cellulosic Biomass Lynd, L. R.; Cushman, J. H.; Nichols, R. J. Science, Vol. 251, Issue 4999 https://doi.org/10.1126/science.251.4999.1318	journal	March 1991
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The UDP-Glucuronate Decarboxylase Gene Family in Populus: Structure, Expression, and Association Genetics Du, Qingzhang; Pan, Wei; Tian, Jiaxing PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0060880	journal	April 2013
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Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus McKown, Athena D.; Klápště, Jaroslav; Guy, Robert D. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-01893-z	journal	May 2017
A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis Escamez, Sacha; Latha Gandla, Madhavi; Derba-Maceluch, Marta Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-16013-0	journal	November 2017
Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.) Carlson, Craig H.; Gouker, Fred E.; Crowell, Chase R. Annals of Botany, Vol. 124, Issue 4 https://doi.org/10.1093/aob/mcz047	journal	April 2019
Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra† Wildhagen, Henning; Paul, Shanty; Allwright, Mike Tree Physiology, Vol. 38, Issue 3 https://doi.org/10.1093/treephys/tpx054	journal	May 2017
Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar Clifton-Brown, John; Harfouche, Antoine; Casler, Michael D. GCB Bioenergy, Vol. 11, Issue 1 https://doi.org/10.1111/gcbb.12566	journal	October 2018
Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Márcio F. R. New Phytologist, Vol. 213, Issue 2 https://doi.org/10.1111/nph.14154	journal	September 2016
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 Zhang, Jin; Yang, Yongil; Zheng, Kaijie New Phytologist, Vol. 220, Issue 2 https://doi.org/10.1111/nph.15297	journal	July 2018
Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction Conway, Jonathan M.; McKinley, Bennett S.; Seals, Nathaniel L. Applied and Environmental Microbiology, Vol. 83, Issue 24 https://doi.org/10.1128/aem.01828-17	journal	October 2017
De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies Mousavi, Mohaddeseh; Tong, Chunfa; Liu, Fenxiang BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3003-9	journal	August 2016
Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa Guerra, Fernando P.; Suren, Haktan; Holliday, Jason BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6160-9	journal	November 2019
Quantitative trait locus mapping of Populus bark features and stem diameter Bdeir, Roba; Muchero, Wellington; Yordanov, Yordan BMC Plant Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12870-017-1166-4	journal	November 2017
Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode Lu, Nan; Zhang, Miaomiao; Xiao, Yao BMC Plant Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s12870-019-2207-y	journal	December 2019
Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure Dumitrache, Alexandru; Akinosho, Hannah; Rodriguez, Miguel Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0445-x	journal	February 2016
Natural genetic variability reduces recalcitrance in poplar Bhagia, Samarthya; Muchero, Wellington; Kumar, Rajeev Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0521-2	journal	May 2016
Multiple levers for overcoming the recalcitrance of lignocellulosic biomass Holwerda, Evert K.; Worthen, Robert S.; Kothari, Ninad Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1353-7	journal	January 2019
Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population Ohlsson, Jonas A.; Hallingbäck, Henrik R.; Jebrane, Mohamed Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1479-7	journal	June 2019
Defining the genetic components of callus formation: A GWAS approach Tuskan, Gerald A.; Mewalal, Ritesh; Gunter, Lee E. PLOS ONE, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pone.0202519	journal	August 2018
A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein Bryan, Anthony C.; Zhang, Jin; Guo, Jianjun G3: Genes\|Genomes\|Genetics, Vol. 8, Issue 8 https://doi.org/10.1534/g3.118.200188	journal	June 2018
Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery Weighill, Deborah; Jones, Piet; Shah, Manesh Frontiers in Energy Research, Vol. 6 https://doi.org/10.3389/fenrg.2018.00030	journal	May 2018
High Throughput Screening Technologies in Biomass Characterization Decker, Stephen R.; Harman-Ware, Anne E.; Happs, Renee M. Frontiers in Energy Research, Vol. 6 https://doi.org/10.3389/fenrg.2018.00120	journal	November 2018
A Protoplast Transient Expression System to Enable Molecular, Cellular, and Functional Studies in Phalaenopsis orchids Lin, Hsiang-Yin; Chen, Jhun-Chen; Fang, Su-Chiung Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00843	journal	June 2018
Hardwood Tree Genomics: Unlocking Woody Plant Biology Tuskan, Gerald A.; Groover, Andrew T.; Schmutz, Jeremy Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01799	journal	December 2018
Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects Du, Qingzhang; Lu, Wenjie; Quan, Mingyang Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01912	journal	December 2018
Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [Salix viminalis (L.)] Hallingbäck, Henrik R.; Berlin, Sofia; Nordh, Nils-Erik Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00753	journal	June 2019

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