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Handakumbura, Pubudu, "Understanding the transcriptional regulation of secondary cell wall biosynthesis in the model grass Brachypodium distachyon" (2014). Doctoral Dissertations 2014-current. Paper 208. Understanding the transcriptional regulation of secondary cell wall biosynthesis in the model grass Brachypodium distachyon DEDICATION To my loving husband Rasitha. v ACKNOWLEDGMENTS I would like to thank my advisor, Samuel Hazen, for his mentoring, Hazen lab members and my colleagues from the Plant Biology graduate program. I would also like to thank my family and friends for their support and encouragement throughout my graduate studies. Secondary cell wall synthesis occurs in specialized cell types following completion of cell enlargement. By virtue of mechanical strength provided by a wall thickened with cellulose, hemicelluloses, and lignin, these cells can function as water-conducting vessels and provide structural support. Several transcription factor families regulate genes encoding wall synthesis enzymes. Certain NAC and MYB proteins directly bind upstream of structural genes and other transcription factors. The most detailed model of this regulatory network is established predominantly for a eudicot, Arabidopsis thaliana. In grasses, both the patterning and the composition of secondary cell walls are distinct from that of eudicots. These differences suggest transcriptional regulation is similarly distinct. Putative rice and maize orthologs of several eudicot cell wall regulators genetically complement mutants of A. thaliana or result in wall defects when constitutively over-expressed; nevertheless, aside from maize ZmMYB31, switchgrass PvMYB4, and Brachypodium BdSWN5, function has not been tested in a grass. Similar to the seminal work conducted in A. thaliana, gene expression profiling in vii maize, rice, and other grasses implicates additional genes as regulators. Characterization of these genes in a grass species will continue to elucidate the relationship between the transcription regulatory networks of eudicots and grasses. In the context of this dissertation two cell wall genes responsible for synthesizing cellulose in the secondary cell walls were characterized. Several MYBs, a NAC and a bZIP protein was found to interact with the cellulose gene promoters. A reverse genetics approach was used to functionally characterize two of those regulators, MYB48 and GNRF. MYB48 is the first grass specific cell wall regulator found to positively regulate cell wall biosynthesis by binding to the cellulose and lignin gene promoters. It regulates above ground biomass in B. distachyon. GNRF, on the hand, unlike the characterized NAC proteins, was shown to repress cell wall biosynthesis. GNRF is also repressing flowering in B. distachyon, a novel regulatory …