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

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

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.01249

DOI=10.3389/fpls.2019.01249

ISSN=1664-462X

ABSTRACT=<p>Understanding the regulatory network controlling cell wall biosynthesis is of great interest in <italic>Populus trichocarpa</italic>, 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 <italic>P. trichocarpa</italic>, 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 (<italic>PtGRF9</italic>). To investigate the role of <italic>PtGRF9</italic> in regulating cell wall biosynthesis, we assessed the genome-wide connections of <italic>PtGRF9</italic> 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 <italic>PtCCoAOMT</italic> and <italic>PtMYB.41</italic>, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that <italic>PtGRF9</italic> 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.</p>