Research Interests

Regulatory Genomics of Plant Growth

The cell wall is a distinguishing feature of plants. It is a complex composite of polysaccharides, proteins, and lignin, with lignin and cellulose representing two of the most abundant bio-organic compounds on the planet. It is essential to plants that structurally important polysaccharides are resistant to facile deconstruction by herbivores and microbes. Cell wall properties leading to increased crop health and productivity may in fact have a negative consequence on their quality as livestock feed or as a biofuel feedstock. My research focuses on understanding the regulatory mechanism underlying plant cell wall biosynthesis and the nature of natural genetic variation leading to differences in cell wall phenotypes.

There has been an explosion of interest and optimism in the prospect of exploiting plant cell wall sugars to produce biofuel. Amenability to such a process is dependent upon overall cell wall composition and the manner in which those components interact. One mechanism regulating cell wall biosynthesis is the activity of transcription factors that control higher order events of growth and differentiation and the likely direct regulation of processive and non-processive glycosyltransferases as well as the phenylpropanoid metabolic grid. We seek systems level insight into regulatory networks affecting monocot and dicot growth and development and cell wall biosynthesis that will ultimately lead to a better understanding of bioenergy-related properties.

Our approach relies on the well developed resources of the model plant species Arabidopsis thaliana which include a fully sequenced genome, a whole genome tiling array, large collections of full-length cDNAs, loss-of-function and gain-of-function mutants, and extensive recombinant and association mapping populations. We also study Brachypodium distachyon, a new model system for herbaceous plants that are candidates for biofuel crops such as switchgrass and Miscanthus. In the case of Arabidopsis and soon Brachypodium, we are aware of the upstream regulatory sequences and have captured full length genes as an experimental reagent. We now seek to find direct interactions between proteins and promoter sequences in order to assemble a model that describes the system. Accordingly, we perturb the system model to determine function and provide insight into exactly how crop plants can be deterministically improved. The exploration of natural genetic variation can provide insight into how this might be done. Understanding the type of variation that is exploited by plant breeders, DNA sequence variation leading to changes in gene expression or amino acid sequence, for example, will provide more educated decisions on future crop improvement approaches.