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. 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.
- Authors:
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[1];
[1];
[1];
[1];
[1];
[1];
[1];
[1]
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- Univ. of Tennessee, Knoxville, TN (United States)
- Oregon State Univ., Corvallis, OR (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1468259
- Alternate Identifier(s):
- OSTI ID: 1459725; OSTI ID: 1633225
- Grant/Contract Number:
- AC05-00OR22725; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- 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
- 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
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. https://doi.org/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. https://doi.org/10.1111/nph.15297. https://www.osti.gov/servlets/purl/1468259.
@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 = {Wed Jul 11 00:00:00 EDT 2018},
month = {Wed Jul 11 00:00:00 EDT 2018}
}
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