Frontiers in Plant Science (Oct 2019)

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence

  • Anna Furches,
  • Anna Furches,
  • David Kainer,
  • Deborah Weighill,
  • Deborah Weighill,
  • Annabel Large,
  • Annabel Large,
  • Annabel Large,
  • Piet Jones,
  • Piet Jones,
  • Angelica M. Walker,
  • Angelica M. Walker,
  • Angelica M. Walker,
  • Angelica M. Walker,
  • Jonathon Romero,
  • Jonathon Romero,
  • Joao Gabriel Felipe Machado Gazolla,
  • Wayne Joubert,
  • Manesh Shah,
  • Jared Streich,
  • Priya Ranjan,
  • Priya Ranjan,
  • Jeremy Schmutz,
  • Jeremy Schmutz,
  • Avinash Sreedasyam,
  • David Macaya-Sanz,
  • Nan Zhao,
  • Madhavi Z. Martin,
  • Xiaolan Rao,
  • Richard A. Dixon,
  • Stephen DiFazio,
  • Timothy J. Tschaplinski,
  • Jin-Gui Chen,
  • Gerald A. Tuskan,
  • Daniel Jacobson,
  • Daniel Jacobson

DOI
https://doi.org/10.3389/fpls.2019.01249
Journal volume & issue
Vol. 10

Abstract

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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.

Keywords