Rather than targeting a particular cell wall synthesis enzyme, another promising direction for improving biomass quality is to modulate the expression of suites of enzymes by altering regulators of cell wall synthesis, especially transcription factors. Indeed, population genetic analyses have found that markers in known cell wall synthesis genes associate with only a few percentage points of cell wall quality variation (Wegrzyn et al.

2010) . As discussed in recent reviews, a growing network of transcription factors regulates secondary cell wall synthesis (Zhao et al. 2011; Gray et al. 2012; Handakumbura et al. 2012) (Fig. 4). As with all other aspects of cell wall biology, knowledge of cell wall transcriptional regulation networks specifically in grasses lags behind that in dicots. Still, where factors have been studied in both grass and dicot systems, it seems likely that many aspects of regulation are conserved (Handakumbura et al. 2012). Here, we will give an overview of the emerging cell wall regulatory hierarchy in Arabidopsis and grasses.

Many transcription factors implicated in secondary cell wall regulation belong to the NAC and the MYB R2R3 protein families. The relevant NAC-domain transcription factors known are known simply as NACs, or Secondary Wall NACs (SWNs), and include SND1 (SECONDARY WALL- ASSOCIATED NAC-DOMAIN PROTEIN 1, also known as NST3), NST1 (NAC SECONDARY WALL THICKENING FACTOR1), NST2, VND6 (VASCULATURE-RELATED NAC-DOMAIN 6) and VND7 (Handakumbura et al. 2012). Different secondary cell wall regulatory pathways appear to function in different cell types in different organs.

Figure 4. Schematic model of the regulatory network of secondary cell wall biosynthesis based primarily on studies in Arabidopsis. Peach circles represent transcription factors known to function in Arabidopsis. The red circles demarcate the transcription factors whose function has been studied in grasses. The yellow octagons represent enzymes. The grey squares represent secondary cell wall polymers. The green triangle represents a property of the cell wall, saccharification. Arrows signify positive regulation; whereas, dashed edges with T ends indicate negative regulation. Cis-elements are labeled on the edges as follows: Secondary wall NAC Binding Element (SNBE), Tracheary Element Responsive Element (TERE), Secondary wall MYB Responsive Element (SMRE), and the AC-rich elements found in lignin biosynthesis gene promoters (AC). See text for references and further discussion. For simplicity, not all known or suspected interactions are shown. Abbreviations are as follows: Lig Bios Enz, lignin biosynthesis enzymes; SCW Enz, secondary cell wall biosynthesis enzymes the specific identity of which has not been specified; PAL1, Phenylalanine Ammonium Lyase 1; 4CL1, 4-Coumaroyl Ligase 1; COMT, Caffeic acid O-MethylTransferase; C4H, Cinnamate 4-Hydroxylase; CESA, Cellulose Synthase A; SHN, shine/wax inducer 1; VND, Vasculature-related NAC-Domain; SND, Secondary wall-associated NAC-Domain protein; NST, NAC Secondary wall Thickening factor; VNI2, VND-interacting 2 NAC protein 2.