Gene Regulatory Networks Control Plant Development Cell Identity And Responses To The Environment

As most plants lack the ability to move, they grow and adapt to different environmental conditions. The phenotype of a plant is determined by both its genetic makeup and the environment. Understanding the key molecular players that drive these responses has the potential to guide breeding programs for climate-resilient crops, and advance food security. In this dissertation, I used a systems biology framework to explore how gene regulatory networks underlie plant development and growth in three different contexts: in response to changes in the environment, between root cell types and tissues, and between species. In Chapter I, I link newly identified transcription factors that control nitrogen-associated metabolism with their underlying regulatory network in Arabidopsis thaliana. I further used mutations in key metabolic genes to describe a phenomenon whereby there is extensive transcriptional feedback upon genetic perturbation of metabolism. In Chapter II, I integrate genomic datasets from two different Solanum species. A major finding from analysis of these datasets is the identification of a group of genes with different translational regulation between tomato species upon exposure to elevated CO2. In Chapter III, I describe cases of innovation, conservation, and repurpose of gene function in regulatory circuits controlling cell-type specification in the root of tomato. In Chapter IV I return to gene regulation of nitrogen from a temporal dynamic perspective. I analyze time series expression data to elucidate how the regulation of the nitrogen response changes over time. I propose a subnetwork of genes that are temporally regulated and identify transcription factors that might be important for this mechanism. This work expands our knowledge not only of gene networks at a cell and tissue-specific resolution, but also sheds light on the evolutionary relationships between equivalent cell types in tomato, rice and Arabidopsis