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Title: Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

Abstract

To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphologicalmore » trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.« less

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office
OSTI Identifier:
1658962
Alternate Identifier(s):
OSTI ID: 1665996; OSTI ID: 1677474
Report Number(s):
NREL/JA-2800-78068
Journal ID: ISSN 1664-462X; 545748
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; AC36-08GO28308
Resource Type:
Published Article
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Name: Frontiers in Plant Science Journal Volume: 11; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Country of Publication:
Switzerland
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Populus; wood anatomy; leaf morphology; GWAS; networks; lignin; 29 EE - Bioenergy Technologies Office (EE-3B)

Citation Formats

Chhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A., and DiFazio, Stephen P. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. Switzerland: N. p., 2020. Web. https://doi.org/10.3389/fpls.2020.545748.
Chhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A., & DiFazio, Stephen P. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. Switzerland. https://doi.org/10.3389/fpls.2020.545748
Chhetri, Hari B., Furches, Anna, Macaya-Sanz, David, Walker, Alejandro R., Kainer, David, Jones, Piet, Harman-Ware, Anne E., Tschaplinski, Timothy J., Jacobson, Daniel, Tuskan, Gerald A., and DiFazio, Stephen P. Wed . "Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa". Switzerland. https://doi.org/10.3389/fpls.2020.545748.
@article{osti_1658962,
title = {Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa},
author = {Chhetri, Hari B. and Furches, Anna and Macaya-Sanz, David and Walker, Alejandro R. and Kainer, David and Jones, Piet and Harman-Ware, Anne E. and Tschaplinski, Timothy J. and Jacobson, Daniel and Tuskan, Gerald A. and DiFazio, Stephen P.},
abstractNote = {To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.},
doi = {10.3389/fpls.2020.545748},
journal = {Frontiers in Plant Science},
number = ,
volume = 11,
place = {Switzerland},
year = {2020},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fpls.2020.545748

Figures / Tables:

FIGURE 1 FIGURE 1: Source locations of 869 P. trichocarpa genotypes sampled in this study (purple dots). The trees were grown in a common garden in Clatskanie, Oregon, USA (black star).

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journal, November 2015


A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis
journal, November 2017

  • Escamez, Sacha; Latha Gandla, Madhavi; Derba-Maceluch, Marta
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/s41598-017-16013-0

Farnesylcysteine Lyase is Involved in Negative Regulation of Abscisic Acid Signaling in Arabidopsis
journal, January 2010

  • Huizinga, David H.; Denton, Ryan; Koehler, Kelly G.
  • Molecular Plant, Vol. 3, Issue 1
  • DOI: 10.1093/mp/ssp091

The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates
journal, February 2009

  • Yee, D.; Goring, D. R.
  • Journal of Experimental Botany, Vol. 60, Issue 4
  • DOI: 10.1093/jxb/ern369

Multivariate simulation framework reveals performance of multi-trait GWAS methods
journal, March 2017

  • Porter, Heather F.; O’Reilly, Paul F.
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep38837

Identification of microRNAs Involved in Regeneration of the Secondary Vascular System in Populus tomentosa Carr
journal, May 2016


The Arabidopsis ZINC FINGER PROTEIN3 Interferes with Abscisic Acid and Light Signaling in Seed Germination and Plant Development
journal, May 2014

  • Joseph, Mary Prathiba; Papdi, Csaba; Kozma-Bognár, László
  • Plant Physiology, Vol. 165, Issue 3
  • DOI: 10.1104/pp.113.234294

Sec14-like phosphatidylinositol transfer proteins and the biological landscape of phosphoinositide signaling in plants
journal, September 2016

  • Huang, Jin; Ghosh, Ratna; Bankaitis, Vytas A.
  • Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1861, Issue 9
  • DOI: 10.1016/j.bbalip.2016.03.027