skip to main content

DOE PAGESDOE PAGES

This content will become publicly available on July 11, 2019

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

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. Finally, these results are consistent with reports of CGA functioning as an antioxidant in response to biotic stress. In conclusion, this study provides insights into data–driven and omics–based inference of gene function in woodymore » species.« less
Authors:
ORCiD logo [1] ; ORCiD logo [1] ;  [1] ; ORCiD logo [1] ;  [1] ;  [1] ; ORCiD logo [1] ;  [1] ;  [2] ;  [1] ;  [2] ;  [2] ;  [3] ;  [4] ; ORCiD logo [1] ;  [5] ; ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  4. Univ. of Tennessee, Knoxville, TN (United States)
  5. Oregon State Univ., Corvallis, OR (United States)
Publication Date:
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 220; Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; expression quantitative trait loci (eQTLs); genome‐wide association studies (GWAS); hydroxycinnamoyl‐CoA; metabolome; Populus trichocarpa; shikimate hydroxycinnamoyl transferase (HCT); WRKY
OSTI Identifier:
1468259
Alternate Identifier(s):
OSTI ID: 1459725

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., 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. 2018. "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_1468259,
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. Finally, these results are consistent with reports of CGA functioning as an antioxidant in response to biotic stress. In conclusion, 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},
number = 2,
volume = 220,
place = {United States},
year = {2018},
month = {7}
}

Works referenced in this record:

Lignin Biosynthesis
journal, June 2003

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

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

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