skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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

Abstract

3-O-caffeoylquinic acid, also known as chlorogenic acid (CGA), functions as an intermediate in lignin biosynthesis in the phenylpropanoid pathway. It is widely distributed among numerous plant species and acts as an antioxidant in both plants and animals. Using GC-MS, we discovered consistent and extreme variation in CGA content across a population of 739 4-yr-old Populus trichocarpa accessions. We performed genome-wide association studies (GWAS) from 917 P. trichocarpa accessions and expression-based quantitative trait loci (eQTL) analyses to identify key regulators. The GWAS and eQTL analyses resolved an overlapped interval encompassing a hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2 (PtHCT2) that was significantly associated with CGA and partially characterized metabolite abundances. PtHCT2 leaf expression was significantly correlated with CGA abundance and it was regulated by cis-eQTLs containing W-box for WRKY binding. Among all nine PtHCT homologs, PtHCT2 is the only one that responds to infection by the fungal pathogen Sphaerulina musiva (a Populus pathogen). Validation using protoplast-based transient expression system suggests that PtHCT2 is regulated by the defense-responsive WRKY. These results are consistent with reports of CGA functioning as an antioxidant in response to biotic stress. This study provides insights into data-driven and omics-based inference of gene function in woody species.

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [2];  [2];  [3];  [4];  [1];  [5];  [1];  [1];  [1]
  1. Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge TN 37831 USA
  2. US Department of Energy Joint Genome Institute, Walnut Creek CA 94598 USA
  3. US Department of Energy Joint Genome Institute, Walnut Creek CA 94598 USA; HudsonAlpha Institute for Biotechnology, Huntsville AL 35806 USA
  4. Institute of Agriculture, University of Tennessee, Knoxville TN 37996 USA
  5. Department of Botany and Plant Pathology, Oregon State University, Corvallis OR 97331 USA
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory-National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1529114
DOE Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 220; Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Country of Publication:
United States
Language:
English

Citation Formats

Zhang, Jin, Yang, Yongil, Zheng, Kaijie, Xie, Meng, Feng, Kai, Jawdy, Sara S., Gunter, Lee E., Ranjan, Priya, Singan, Vasanth R., Engle, Nancy, Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Zhao, Nan, Tschaplinski, Timothy J., LeBoldus, Jared, Tuskan, Gerald A., Chen, Jin-Gui, and Muchero, Wellington. 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. United States: N. p., 2018. Web. doi:10.1111/nph.15297.
Zhang, Jin, Yang, Yongil, Zheng, Kaijie, Xie, Meng, Feng, Kai, Jawdy, Sara S., Gunter, Lee E., Ranjan, Priya, Singan, Vasanth R., Engle, Nancy, Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Zhao, Nan, Tschaplinski, Timothy J., LeBoldus, Jared, Tuskan, Gerald A., Chen, Jin-Gui, & Muchero, Wellington. 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. United States. doi:10.1111/nph.15297.
Zhang, Jin, Yang, Yongil, Zheng, Kaijie, Xie, Meng, Feng, Kai, Jawdy, Sara S., Gunter, Lee E., Ranjan, Priya, Singan, Vasanth R., Engle, Nancy, Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Zhao, Nan, Tschaplinski, Timothy J., LeBoldus, Jared, Tuskan, Gerald A., Chen, Jin-Gui, and Muchero, Wellington. Wed . "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". United States. doi:10.1111/nph.15297.
@article{osti_1529114,
title = {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},
author = {Zhang, Jin and Yang, Yongil and Zheng, Kaijie and Xie, Meng and Feng, Kai and Jawdy, Sara S. and Gunter, Lee E. and Ranjan, Priya and Singan, Vasanth R. and Engle, Nancy and Lindquist, Erika and Barry, Kerrie and Schmutz, Jeremy and Zhao, Nan and Tschaplinski, Timothy J. and LeBoldus, Jared and Tuskan, Gerald A. and Chen, Jin-Gui and Muchero, Wellington},
abstractNote = {3-O-caffeoylquinic acid, also known as chlorogenic acid (CGA), functions as an intermediate in lignin biosynthesis in the phenylpropanoid pathway. It is widely distributed among numerous plant species and acts as an antioxidant in both plants and animals. Using GC-MS, we discovered consistent and extreme variation in CGA content across a population of 739 4-yr-old Populus trichocarpa accessions. We performed genome-wide association studies (GWAS) from 917 P. trichocarpa accessions and expression-based quantitative trait loci (eQTL) analyses to identify key regulators. The GWAS and eQTL analyses resolved an overlapped interval encompassing a hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2 (PtHCT2) that was significantly associated with CGA and partially characterized metabolite abundances. PtHCT2 leaf expression was significantly correlated with CGA abundance and it was regulated by cis-eQTLs containing W-box for WRKY binding. Among all nine PtHCT homologs, PtHCT2 is the only one that responds to infection by the fungal pathogen Sphaerulina musiva (a Populus pathogen). Validation using protoplast-based transient expression system suggests that PtHCT2 is regulated by the defense-responsive WRKY. These results are consistent with reports of CGA functioning as an antioxidant in response to biotic stress. This study provides insights into data-driven and omics-based inference of gene function in woody species.},
doi = {10.1111/nph.15297},
journal = {New Phytologist},
issn = {0028-646X},
number = 2,
volume = 220,
place = {United States},
year = {2018},
month = {7}
}

Works referenced in this record:

Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula
journal, January 2008

  • Naoumkina, Marina A.; He, XianZhi; Dixon, Richard A.
  • BMC Plant Biology, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2229-8-132

Lignin Biosynthesis
journal, June 2003


Wheat cells accumulate a syringyl-rich lignin during the hypersensitive resistance response
journal, February 2007


COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
journal, May 2017

  • Zhang, Chengxin; Freddolino, Peter L.; Zhang, Yang
  • Nucleic Acids Research, Vol. 45, Issue W1
  • DOI: 10.1093/nar/gkx366

I-TASSER server: new development for protein structure and function predictions
journal, April 2015

  • Yang, Jianyi; Zhang, Yang
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv342

Circumventing multiple testing: A multilocus Monte Carlo approach to testing for association
journal, January 2000


Lignin modification improves fermentable sugar yields for biofuel production
journal, June 2007

  • Chen, Fang; Dixon, Richard A.
  • Nature Biotechnology, Vol. 25, Issue 7, p. 759-761
  • DOI: 10.1038/nbt1316

Genome-wide efficient mixed-model analysis for association studies
journal, June 2012

  • Zhou, Xiang; Stephens, Matthew
  • Nature Genetics, Vol. 44, Issue 7
  • DOI: 10.1038/ng.2310

Impact of Phenolic Compounds and Related Enzymes in Sorghum Varieties for Resistance and Susceptibility to Biotic and Abiotic Stresses
journal, October 2005

  • Dicko, Mamoudou H.; Gruppen, Harry; Barro, Clarisse
  • Journal of Chemical Ecology, Vol. 31, Issue 11
  • DOI: 10.1007/s10886-005-7619-5

The phenylpropanoid pathway and plant defence-a genomics perspective
journal, September 2002


Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize
journal, June 2007

  • Salvi, S.; Sponza, G.; Morgante, M.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 27
  • DOI: 10.1073/pnas.0704145104

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013


Two Classes of Plant Antibiotics: Phytoalexins versus "Phytoanticipins"
journal, September 1994


Transcriptional regulation of secondary metabolite biosynthesis in plants
journal, November 2013

  • Patra, Barunava; Schluttenhofer, Craig; Wu, Yongmei
  • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1829, Issue 11
  • DOI: 10.1016/j.bbagrm.2013.09.006

A Structural Basis for the Biosynthesis of the Major Chlorogenic Acids Found in Coffee
journal, July 2012

  • Lallemand, Laura A.; Zubieta, Chloe; Lee, Soon Goo
  • Plant Physiology, Vol. 160, Issue 1
  • DOI: 10.1104/pp.112.202051

Salicylic acid mediates the reduced growth of lignin down-regulated plants
journal, November 2011

  • Gallego-Giraldo, L.; Escamilla-Trevino, L.; Jackson, L. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 51
  • DOI: 10.1073/pnas.1117873108

Wounding-Induced WRKY8 Is Involved in Basal Defense in Arabidopsis
journal, May 2010

  • Chen, Ligang; Zhang, Liping; Yu, Diqiu
  • Molecular Plant-Microbe Interactions, Vol. 23, Issue 5
  • DOI: 10.1094/MPMI-23-5-0558

Purification, Cloning, and Properties of an Acyltransferase Controlling Shikimate and Quinate Ester Intermediates in Phenylpropanoid Metabolism
journal, October 2002

  • Hoffmann, Laurent; Maury, Stéphane; Martz, Françoise
  • Journal of Biological Chemistry, Vol. 278, Issue 1
  • DOI: 10.1074/jbc.M209362200

Regulation of Specialized Metabolism by WRKY Transcription Factors
journal, December 2014


The nature of lignin-like compounds in cucumber hypocotyls induced by alpha-1,4-linked oligogalacturonides
journal, July 1990


Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants
journal, December 2010

  • Wang, H.; Avci, U.; Nakashima, J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 51, p. 22338-22343
  • DOI: 10.1073/pnas.1016436107

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations
journal, August 2014

  • Evans, Luke M.; Slavov, Gancho T.; Rodgers-Melnick, Eli
  • Nature Genetics, Vol. 46, Issue 10
  • DOI: 10.1038/ng.3075

Selective lignin downregulation leads to constitutive defense response expression in alfalfa (Medicago sativa L.)
journal, January 2011


Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
journal, March 2012


featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013


The potential effects of chlorogenic acid, the main phenolic components in coffee, on health: a comprehensive review of the literature
journal, April 2017

  • Tajik, Narges; Tajik, Mahboubeh; Mack, Isabelle
  • European Journal of Nutrition, Vol. 56, Issue 7
  • DOI: 10.1007/s00394-017-1379-1

Production of novel antioxidative phenolic amides through heterologous expression of the plant’s chlorogenic acid biosynthesis genes in yeast
journal, May 2010


Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis
journal, January 2012

  • Grunewald, W.; De Smet, I.; Lewis, D. R.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 5
  • DOI: 10.1073/pnas.1121134109

The I-TASSER Suite: protein structure and function prediction
journal, December 2014

  • Yang, Jianyi; Yan, Renxiang; Roy, Ambrish
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3213

Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus
journal, October 2006


Silencing of Hydroxycinnamoyl-Coenzyme A Shikimate/Quinate Hydroxycinnamoyltransferase Affects Phenylpropanoid Biosynthesis
journal, May 2004

  • Hoffmann, Laurent; Besseau, Sébastien; Geoffroy, Pierrette
  • The Plant Cell, Vol. 16, Issue 6
  • DOI: 10.1105/tpc.020297

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes
journal, December 2009

  • Shi, Rui; Sun, Ying-Hsuan; Li, Quanzi
  • Plant and Cell Physiology, Vol. 51, Issue 1
  • DOI: 10.1093/pcp/pcp175

Chlorogenic acids and related depsides
journal, October 1964


Role of HXXXD-motif/BAHD acyltransferases in the biosynthesis of extracellular lipids
journal, December 2014


Linking Metabolic QTLs with Network and cis-eQTLs Controlling Biosynthetic Pathways
journal, January 2007


Highly Efficient Isolation of Populus Mesophyll Protoplasts and Its Application in Transient Expression Assays
journal, September 2012


The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
journal, September 2006


Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.)
journal, November 2013

  • Escamilla-Treviño, Luis L.; Shen, Hui; Hernandez, Timothy
  • Plant Molecular Biology, Vol. 84, Issue 4-5
  • DOI: 10.1007/s11103-013-0152-y

The Growth Reduction Associated with Repressed Lignin Biosynthesis in Arabidopsis thaliana Is Independent of Flavonoids
journal, May 2010


Physical and Functional Interactions between Pathogen-Induced Arabidopsis WRKY18, WRKY40, and WRKY60 Transcription Factors
journal, April 2006


Cytoscape 2.8: new features for data integration and network visualization
journal, December 2010


Haploview: analysis and visualization of LD and haplotype maps
journal, August 2004


Elicitor-Induced Spruce Stress Lignin (Structural Similarity to Early Developmental Lignins)
journal, July 1995

  • Lange, B. M.; Lapierre, C.; Sandermann Jr, H.
  • Plant Physiology, Vol. 108, Issue 3
  • DOI: 10.1104/pp.108.3.1277

NMR Characterization of C3H and HCT Down-Regulated Alfalfa Lignin
journal, October 2009


Production of the Isoflavones Genistein and Daidzein in Non-Legume Dicot and Monocot Tissues
journal, October 2000


The grapevine transcription factor WRKY2 influences the lignin pathway and xylem development in tobacco
journal, November 2009

  • Guillaumie, Sabine; Mzid, Rim; Méchin, Valérie
  • Plant Molecular Biology, Vol. 72, Issue 1-2
  • DOI: 10.1007/s11103-009-9563-1

Modifying lignin to improve bioenergy feedstocks: strengthening the barrier against pathogens?†
journal, January 2013


Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study
journal, February 2013

  • Vanholme, Bartel; Cesarino, Igor; Goeminne, Geert
  • New Phytologist, Vol. 198, Issue 3
  • DOI: 10.1111/nph.12179

Systemic acquired resistance: the elusive signal(s)
journal, August 2008

  • Vlot, A. Corina; Klessig, Daniel F.; Park, Sang-Wook
  • Current Opinion in Plant Biology, Vol. 11, Issue 4
  • DOI: 10.1016/j.pbi.2008.05.003

The Transcription Factors WRKY11 and WRKY17 Act as Negative Regulators of Basal Resistance in Arabidopsis thaliana
journal, November 2006

  • Journot-Catalino, Noëllie; Somssich, Imre E.; Roby, Dominique
  • The Plant Cell, Vol. 18, Issue 11
  • DOI: 10.1105/tpc.106.044149

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus
journal, January 2015


Dissecting the WRKY Web of Plant Defense Regulators
journal, January 2006


Modification of phenolic metabolism in soybean hairy roots through down regulation of chalcone synthase or isoflavone synthase
journal, August 2006


Identifying the molecular basis of QTLs: eQTLs add a new dimension
journal, February 2008


Patterns of differential gene expression in Brassica napus cultivars infected with Sclerotinia sclerotiorum
journal, September 2009


The Diurnal Project: Diurnal and Circadian Expression Profiling, Model-based Pattern Matching, and Promoter Analysis
journal, January 2007

  • Mockler, T. C.; Michael, T. P.; Priest, H. D.
  • Cold Spring Harbor Symposia on Quantitative Biology, Vol. 72, Issue 1
  • DOI: 10.1101/sqb.2007.72.006

The effect of chlorogenic acid on blood pressure: a systematic review and meta-analysis of randomized clinical trials
journal, June 2014

  • Onakpoya, I. J.; Spencer, E. A.; Thompson, M. J.
  • Journal of Human Hypertension, Vol. 29, Issue 2
  • DOI: 10.1038/jhh.2014.46

Engineering plants with increased levels of the antioxidant chlorogenic acid
journal, April 2004

  • Niggeweg, Ricarda; Michael, Anthony J.; Martin, Cathie
  • Nature Biotechnology, Vol. 22, Issue 6
  • DOI: 10.1038/nbt966

WRKY8 transcription factor functions in the TMV-cg defense response by mediating both abscisic acid and ethylene signaling in Arabidopsis
journal, May 2013

  • Chen, L.; Zhang, L.; Li, D.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 21
  • DOI: 10.1073/pnas.1221347110

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog
journal, January 2012

  • Tschaplinski, Timothy J.; Standaert, Robert F.; Engle, Nancy L.
  • Biotechnology for Biofuels, Vol. 5, Issue 1
  • DOI: 10.1186/1754-6834-5-71

    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
    • DOI: 10.1007/s11295-019-1320-2

    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
    • DOI: 10.1007/s11295-019-1320-2