Now we're cooking with auxin: Using synthetic and genomic tools to probe the root recipe

Thesis (Ph.D.)--University of Washington, 2021Multicellular organisms rely on the specification and development of complex organ systems for survival. These organ systems regulate distinct physiological functions, allowing for complexity and resilience in the growth and development of the organism as a whole. Nowhere is this more true than in plants, whose sessile nature require them to use variation in growth and modifications of their own form to respond to adverse environmental conditions. The plant root system is essential for plant fitness, regulating the uptake of water and nutrients and anchoring plants in the soil. Root architecture is principally governed by the formation of lateral roots, which extend from the axis of the primary root. Lateral root development is consequently fundamental to plant growth, but much remains unknown about the molecular and cellular mechanics of this process. This dissertation examines lateral root development through the lens of auxin-mediated transcription. Auxin, a plant hormone, regulates lateral root development at every stage. Using synthetic and evolutionary approaches, I define the design rules of auxin- responsive promoters and their interactions with transcription factors. Subsequent genomic and genetic approaches allow for the identification of novel parallel and downstream genetic players regulating lateral root development. Using a diversity of methods leads to a clearer picture of how plants use a core hormone pathway to regulate this essential developmental process