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

Hari B. Chhetri, Anna Furches, David Macaya-Sanz, Alejandro R. Walker, David Kainer, Piet Jones, Anne E. Harman-Ware, Timothy J. Tschaplinski, Daniel Jacobson, Gerald A. Tuskan, Stephen P. DiFazio

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23 Scopus citations

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 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.

Original languageEnglish
Article number545748
JournalFrontiers in Plant Science
Volume11
DOIs
StatePublished - Sep 9 2020

Funding

This research was supported by the Center for Bioenergy Innovation (CBI) and the Bioenergy Science Center. CBI is supported by the Office of Biological and Environmental Research in the DOE Office of Science. This manuscript has been coauthored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research described herein was supported by an award of computer time provided by the INCITE program and used resources of the Oak Ridge Leadership Computing Facility (OLCF) at the Oak Ridge National Laboratory. This work was We thank the multitude of researchers from the Bioenergy Science Center and the DOE Joint Genome Institute who provided invaluable logistical support for this work. In particular, we would like to thank Kat Haiby, Brian Stanton, Rich Shuren, Carlos Gantz, and Austin Himes of Greenwood Resources for their work in establishing and maintaining the plantation, for facilitating our work at the site, and for the many insights that they have provided about Populus biology and silviculture. We would also like to thank Crissa Doeppke and Robert Sykes for their help with py-MBMS analysis.

Keywords

  • GWAS
  • Populus
  • leaf morphology
  • lignin
  • networks
  • wood anatomy

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