10.3389/fpls.2019.01249.s001 Anna Furches Anna Furches David Kainer David Kainer Deborah Weighill Deborah Weighill Annabel Large Annabel Large Piet Jones Piet Jones Angelica M. Walker Angelica M. Walker Jonathon Romero Jonathon Romero Joao Gabriel Felipe Machado Gazolla Joao Gabriel Felipe Machado Gazolla Wayne Joubert Wayne Joubert Manesh Shah Manesh Shah Jared Streich Jared Streich Priya Ranjan Priya Ranjan Jeremy Schmutz Jeremy Schmutz Avinash Sreedasyam Avinash Sreedasyam David Macaya-Sanz David Macaya-Sanz Nan Zhao Nan Zhao Madhavi Z. Martin Madhavi Z. Martin Xiaolan Rao Xiaolan Rao Richard A. Dixon Richard A. Dixon Stephen DiFazio Stephen DiFazio Timothy J. Tschaplinski Timothy J. Tschaplinski Jin-Gui Chen Jin-Gui Chen Gerald A. Tuskan Gerald A. Tuskan Daniel Jacobson Daniel Jacobson Table_1_Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence.docx Frontiers 2019 lines of evidence cell wall regulation Genome Wide Association Study candidate gene identification network analysis multi-omic Populus trichocarpa 2019-10-08 04:05:50 Dataset https://frontiersin.figshare.com/articles/dataset/Table_1_Finding_New_Cell_Wall_Regulatory_Genes_in_Populus_trichocarpa_Using_Multiple_Lines_of_Evidence_docx/9947636 <p>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.</p>