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

Journal Article · · BMC Genomics
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  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)
+ Show Author Affiliations

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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725; AC05-00OR2272; AC02-05CH11231
OSTI ID:
1214456
Alternate ID(s):
OSTI ID: 1220715
Report Number(s):
NREL/JA-5100-64000; KP1601050; ERKP695
Journal Information:
BMC Genomics, Vol. 16, Issue 24; ISSN 1471-2164
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 80 works
Citation information provided by
Web of Science

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Cited By (35)

Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure journal February 2016
A Protoplast Transient Expression System to Enable Molecular, Cellular, and Functional Studies in Phalaenopsis orchids journal June 2018
Progress in understanding and overcoming biomass recalcitrance: a BioEnergy Science Center (BESC) perspective journal November 2017
Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus journal May 2017
Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [Salix viminalis (L.)] journal June 2019
Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies journal January 2020
Quantitative trait locus mapping of Populus bark features and stem diameter journal November 2017
Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides journal September 2016
Hardwood Tree Genomics: Unlocking Woody Plant Biology journal December 2018
Lignin Engineering in Forest Trees journal July 2019
Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing journal March 2016
Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery journal May 2018
De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies journal August 2016
Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar journal October 2018
Adaptive combination of Bayes factors as a powerful method for the joint analysis of rare and common variants journal October 2017
Differences in S/G ratio in natural poplar variants do not predict catalytic depolymerization monomer yields journal May 2019
Genome-wide association studies of bark texture in Populus trichocarpa journal February 2019
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 journal December 2019
Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra† journal May 2017
A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein journal June 2018
Natural genetic variability reduces recalcitrance in poplar journal May 2016
Defining the genetic components of callus formation: A GWAS approach journal August 2018
An In-Depth Understanding of Biomass Recalcitrance Using Natural Poplar Variants as the Feedstock journal December 2016
QTL Mapping of Wood FT-IR Chemotypes Shows Promise for Improving Biofuel Potential in Short Rotation Coppice Willow (Salix spp.) journal March 2018
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Mediation of plant–mycorrhizal interaction by a lectin receptor-like kinase journal July 2019
A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis journal November 2017
Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population journal June 2019
Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects journal December 2018
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence journal October 2019
Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.) journal April 2019
Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa journal November 2019
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High Throughput Screening Technologies in Biomass Characterization journal November 2018
Multiple levers for overcoming the recalcitrance of lignocellulosic biomass journal January 2019

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59 BASIC BIOLOGICAL SCIENCES
QTL cloning
association genetics
cell wall recalcitrance
lignin
cellulose
hemicellulose
09 BIOMASS FUELS