Bartley, LauraZhao, Kangmei2016-07-142016-07-142016-08-10http://hdl.handle.net/11244/43952Grass cell walls are environmentally and economically important, including being an abundant and sustainable carbon source to produce lignocellulosic biofuels. However, the crosslinked structure of cell walls limits polysaccharide extraction efficiency, which is a bottleneck for biofuel production. Based on knowledge in Arabidopsis, multiple transcription factors from various protein families can regulate cell wall biosynthesis by forming a series of feed-forward loops. Diverged from dicotyledonous plants approximately 150 million years ago, grasses have evolved different cell wall components and vascular bundle patterning in vegetative organs. In this dissertation, I aimed to characterize transcription factors and corresponding DNA binding sites that control cell wall biosynthesis in grasses. I hypothesized that unstudied grass cell wall transcription factors might fall into the following three categories: (1) orthologs of known dicot cell wall regulators that have conserved functions in regulating the cell wall network; (2) uncharacterized cell wall-associated transcription factors that also likely maintain similar functions with those in dicots; (3) uncharacterized grass cell wall-associated transcription factors that do not exist or have different functions in dicots. In Chapter 2, to analyze conservation and divergence between known dicot cell wall-associated transcription factors and their orthologs in grasses, we examined the phylogeny of R2R3 MYB protein family across selected dicots and grasses. Though we observed dicot-specific, grass-specific, and two panicoid grass-expanded clades, in general, most R2R3 MYBs that regulate SCW in Arabidopsis show evidence of conservation in the grasses. In Chapter 3, we developed a Rice Combined mutual Ranked (RCR) network to identify regulators of grass-specific genes and other uncharacterized cell wall-associated transcription factors in grasses. The RCR network covers approximately 90% of the rice genome and shows high quality in GO-term-based evaluations. Network prediction and further molecular genetic validation suggest that OsMYB61a can directly or indirectly regulate grass cell wall-specific genes, among others. The RCR network includes a cell wall sub-network with 96 novel transcription factors. Eight out of eleven of them altered expression of cell wall-related genes in a transient gene expression assays in rice protoplast. In Chapter 4, I further examined the conservation of cell wall-associated cis-elements in grasses using comparative de novo motif discovery and explored various scenarios for incorporation of grass-specific genes into cell wall biosynthesis pathways. Firstly, we observed that known dicots cell wall-associated cis-elements, such as MYB and NAC DNA binding sites, are significantly enriched within the promoters of CESA, lignin biosynthesis genes, as well as grass cell wall-specific genes. This provides support for the generally held hypothesis that known dicot cell wall-associated cis-elements are conserved in grasses. In addition, cis-elements that are potentially associated with AP2/ERF, C2H2, C2C2, and homeodomain proteins are also significantly enriched within promoters of grass cell wall biosynthesis genes. These results support the prediction and characterization of novel cell wall-associated transcription factors and binding sites. In all, this dissertation provides guidance toward functional characterization of cell wall-associated regulatory elements in grasses, knowledge of which will promote terrestrial biofuel production.Plant Biology