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

Journal Article · · Frontiers in Plant Science
 [1];  [2];  [1];  [3];  [1]; ORCiD logo [4];  [1]; ORCiD logo [2]; ORCiD logo [5];  [2];  [2];  [6];  [7];  [8];  [9];  [10];  [2];  [11];  [11];  [9] more »; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [1] « less
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Oak Ridge Associated Univ. (ORAU), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Oak Ridge Associated Univ. (ORAU), Oak Ridge, TN (United States); Johns Hopkins Univ., Baltimore, MD (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States). Univ. of Tennessee Inst. of Agriculture
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  8. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  9. West Virginia Univ., Morgantown, WV (United States)
  10. Univ. of Tennessee, Knoxville, TN (United States). Univ. of Tennessee Inst. of Agriculture
  11. Univ. of North Texas, Denton, TX (United States). BioDiscovery Inst.
+ Show Author Affiliations

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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
OSTI ID:
1633173
Alternate ID(s):
OSTI ID: 1616073
Journal Information:
Frontiers in Plant Science, Vol. 10, Issue n/a; ISSN 1664-462X
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

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A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks journal December 2019

Figures / Tables (7)

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59 BASIC BIOLOGICAL SCIENCES
lines of evidence
cell wall
regulation
Genome Wide Association Study
candidate gene identification
network analysis
multi-omic
Populus trichocarpa