title: A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species.
abstract: BACKGROUND
  Recently, there has been interest in establishing a monocot C4 model species with a small genome, short lifecycle, and capacity for genetic transformation. Setaria viridis has been adopted to fill this role, since reports of Agrobacterium-mediated transformation in 2010, and sequencing of its genome in 2012. To date, S. viridis has primarily been used to further our understanding of C4 photosynthesis, but is also an ideal system for the study of biomass crops, which are almost exclusively C4 panicoid grasses. Biogenesis of stem tissue, its cell wall composition, and soluble sugar content are important determinants of bioenergy crop yields. Here we show that a developing S. viridis internode is a valuable experimental system for gene discovery in relation to these important bioenergy feedstock traits.
  
  
  RESULTS
  The rate of maximal stem biomass accumulation in S. viridis A10 under long day growth was at the half-head emergence developmental stage. At this stage of development, internode 5 (of 7) was found to be rapidly expanding with an active meristem, a zone of cell expansion (primary cell walls), a transitional zone where cell expansion ceased and secondary cell wall deposition was initiated, and a mature zone that was actively accumulating soluble sugars. A simple method for identifying these zones was established allowing rapid dissection and snap-freezing for RNAseq analysis. A transcriptome profile was generated for each zone showing a transition from cell division and nucleic acid synthesis/processing in the meristem, to metabolism, energy synthesis, and primary cell wall synthesis in the cell expansion zone, to secondary cell wall synthesis in the transitional zone, to sugar transport, and photosynthesis in the mature zone.
  
  
  CONCLUSIONS
  The identification of these zones has provided a valuable experimental system for investigating key bioenergy traits, including meristematic activity, cell wall biosynthesis, and soluble sugar accumulation, in a C4 panicoid grass that has genetic resources, a short life cycle, and small stature allowing controlled experimental conditions in growth cabinets. Here we have presented a comprehensive map of gene expression and metabolites in this experimental system to facilitate gene discovery and controlled hypothesis testing for bioenergy research in S. viridis.
authors.affiliation: School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia.
authors.forename: Antony P
authors.initials: AP
authors.lastname: Martin
authors.affiliation: School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia.
authors.forename: William M
authors.initials: WM
authors.lastname: Palmer
authors.affiliation: School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia.
authors.forename: Christopher
authors.initials: C
authors.lastname: Brown
authors.affiliation: Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
authors.forename: Christin
authors.initials: C
authors.lastname: Abel
authors.affiliation: Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
authors.forename: John E
authors.initials: JE
authors.lastname: Lunn
authors.affiliation: ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT 2601 Australia ; CSIRO Agriculture Flagship High Resolution Plant Phenomics Centre, GPO Box 1600, Canberra, ACT 2601 Australia.
authors.forename: Robert T
authors.initials: RT
authors.lastname: Furbank
authors.affiliation: School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308 Australia.
authors.forename: Christopher P L
authors.initials: CP
authors.lastname: Grof
keywords: Bioenergy; C4 grass; Cell wall; RNAseq; Setaria viridis; Stem; Sugar