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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}
}