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Plant Biotechnol J. 2019 Mar;17(3):580-593. doi: 10.1111/pbi.13000. Epub 2018 Sep 17.

Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum).

Rao X1,2, Chen X3, Shen H1,2, Ma Q4, Li G5, Tang Y2,5, Pena M2,6, York W2,6, Frazier TP7, Lenaghan S8, Xiao X1, Chen F1,2,9, Dixon RA1,2,9.

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BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA.
BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Center for Applied Mathematics, Tianjin University, Tianjin, China.
Department of Agronomy, Horticulture, and Plant Science and Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA.
Noble Research Institute, Ardmore, OK, USA.
Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
Department of Food Science, University of Tennessee, Knoxville, TN, USA.
Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, USA.


Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (Panicum virgatum), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (TFs) involved in lignin biosynthesis, we developed a modified method to perform co-expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co-expression network was further extended by adding 14 TFs identified in this study, and seven TFs identified in previous studies, as bait genes. Six TFs (PvMYB58/63, PvMYB42/85, PvMYB4, PvWRKY12, PvSND2 and PvSWN2) were targeted to generate overexpressing and/or down-regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the TFs in controlling secondary wall formation. RNA-seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall-related TFs and crosstalk with other biological pathways. In vitro transactivation assays further confirmed the regulation of specific lignin pathway genes by four of the TFs. Our meta-analysis provides a hierarchical network of TFs and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.


Bi-clustering algorithm; bioenergy crop; co-expression analysis; secondary cell wall biosynthesis; transcription factors; transgenic switchgrass

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