Anna Furches, Oak Ridge National Laboratory, University of Tennessee
David Kainer, Oak Ridge National Laboratory
Deborah Weighill, Oak Ridge National Laboratory, University of Tennessee
Annabel Large, Oak Ridge National Laboratory, University of Tennessee, Oak Ridge Associated Universities
Piet Jones, Oak Ridge National Laboratory, University of Tennessee
Angelica M. Walker, ak Ridge National Laboratory, Oak Ridge Associated Universities, Johns Hopkins University
Jonathon Romero, Oak Ridge National Laboratory, University of Tennessee
Joao Gabriel Felipe Machado Gazolla, Oak Ridge National Laboratory
Wayne Joubert, Oak Ridge Leadership Computing Facility
Manesh Shah, Oak Ridge National Laboratory
Jared Streich, Oak Ridge National Laboratory
Priya Ranjan, Oak Ridge National Laboratory,The University of Tennessee Institute of Agriculture
Jeremy Schmutz, Joint Genome Institute, HudsonAlpha Institute for Biotechnology
Avinash Sreedasayam, HudsonAlpha Institute for Biotechnology
David Macaya-Sanz, West Virginia University
Nan Zhao, The University of Tennessee Institute of Agriculture
Madhavi Z. Martin, Oak Ridge National Laboratory
Xiaolan Rao, University of North Texas
Richard A. Dixon, University of North Texas
Stephen DiFazio, West Virginia University
Timothy J. Tschaplinski, Oak Ridge National Laboratory
Jin-Giu Chen, Oak Ridge National Laboratory
Gerald A. Tuskan, Oak Ridge National Laboratory
Daniel Jacobson, Oak Ridge National Laboratory, University of Tennessee, Knoxville

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Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation.

Source Citation

Furches A, Kainer D, Weighill D, Large A, Jones P, Walker AM, Romero J, Gazolla JGFM, Joubert W, Shah M, Streich J, Ranjan P, Schmutz J, Sreedasyam A, MacayaSanz D, Zhao N, Martin MZ, Rao X, Dixon RA, DiFazio S, Tschaplinski TJ, Chen J-G, Tuskan GA and Jacobson D (2019) Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. Front. Plant Sci. 10:1249. doi: 10.3389/fpls.2019.01249


Copyright © 2019 Furches, Kainer, Weighill, Large, Jones, Walker, Romero, Gazolla, Joubert, Shah, Streich, Ranjan, Schmutz, Sreedasyam, Macaya-Sanz, Zhao, Martin, Rao, Dixon, DiFazio, Tschaplinski, Chen, Tuskan and Jacobson. This is an openaccess article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these term.

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