Novel candidate genes for lignin structure identified through genome-wide association study of naturally varying Populus trichocarpa

Nathan Bryant; Jin Zhang; Kai Feng; Mengjun Shu; Raphael Ployet; Jin-Gui Chen; Wellington Muchero; Chang Geun Yoo; Timothy J Tschaplinski; Yunqiao Pu; Arthur J Ragauskas

doi:10.3389/fpls.2023.1153113

Novel candidate genes for lignin structure identified through genome-wide association study of naturally varying Populus trichocarpa

Front Plant Sci. 2023 May 5:14:1153113. doi: 10.3389/fpls.2023.1153113. eCollection 2023.

Authors

Affiliations

¹ Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, United States.
² Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
³ Department of Chemical Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States.
⁴ Center for Renewable Carbon, Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN, United States.

Abstract

Populus is a promising lignocellulosic feedstock for biofuels and bioproducts. However, the cell wall biopolymer lignin is a major barrier in conversion of biomass to biofuels. To investigate the variability and underlying genetic basis of the complex structure of lignin, a population of 409 three-year-old, naturally varying Populus trichocarpa genotypes were characterized by heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR). A subsequent genome-wide association study (GWAS) was conducted using approximately 8.3 million single nucleotide polymorphisms (SNPs), which identified 756 genes that were significantly associated (-log₁₀(p-value)>6) with at least one lignin phenotype. Several promising candidate genes were identified, many of which have not previously been reported to be associated with lignin or cell wall biosynthesis. These results provide a resource for gaining insights into the molecular mechanisms of lignin biosynthesis and new targets for future genetic improvement in poplar.

Keywords: Populus; genome-wide association studies (GWAS); lignin; nuclear magnetic resonance (NMR) analysis; p-hydroxybenzoate.

Grants and funding

Funding provided by The Center for Bioenergy Innovation, a U.S. Department of Energy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. This manuscript has been authored 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, world-wide 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 views and opinions of the authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.