Abstract
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.
Highlights
The biosynthesis and regulation of the plant cell wall has been the subject of a large body of research due to the industrial importance of lignocellulosic biomass, as well as the role of the cell wall in the function of other plant biological systems such as stress response, inter-cellular transport, and disease resistance
This study makes use of various data accumulated for P. trichocarpa that have been used in previous investigations, including Single nucleotide polymorphisms (SNPs) data from a Genome Wide Association Study (GWAS) population, foliar metabolites measured in this GWAS population, and DNA methylation data across 10 different P. trichocarpa tissues (Vining et al, 2012), as well as the P. trichocarpa Department of Energy (DOE) Joint Genome Institute Plant
We examined each phenotype for the presence of outliers using Median Absolute Deviation (MAD)
Summary
The biosynthesis and regulation of the plant cell wall has been the subject of a large body of research due to the industrial importance of lignocellulosic biomass, as well as the role of the cell wall in the function of other plant biological systems such as stress response, inter-cellular transport, and disease resistance. Exploring the regulatory network controlling the cell wall in order to find new functional mechanisms is a challenging task due to the number of genes involved, extensive functional redundancy, and the multitude of transcriptional feedback loops Such complex genetic architecture has contributed to the view that many quantitative traits are “omnigenic” (Boyle et al, 2017), such that virtually any expressed gene has a non-zero effect on the core biosynthetic genes at one or more transcriptional, post-transcriptional, post-translational, signaling or proteinprotein interaction levels. Alejandro et al (2012) identified the ABCG29 genes as transporting monolignol to the cell wall in A. thaliana by first analyzing co-expression networks followed by expression and functional analyses These methods often produce an extensive list of candidate genes but with little more to support their involvement in cell wall regulation than the clustering or enrichment evidence. The result is a set of 330 high-ranking candidate genes, which we filter to a subset of regulatory genes not previously discussed in the context of the cell wall biosynthesis
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