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>