"Plant architecture is largely determined by branching patterns in the shoot and root systems. Shoots of seed plants, such as the model plant Arabidopsis thaliana, branch via lateral bud outgrowth, where branches are patterned along the stem at the base of a leaf. Roots branch laterally from an internal cell layer surrounded by differentiated tissues, at a distance from the root tip. Despite the differences in ontogeny and the divergent evolutionary origin of root and shoot lateral branches, both processes are controlled by the three redundantly-acting AP2-domain containing transcription factors PLETHORA3, 5 and 7 (PLT3,5,7). These proteins control phyllotaxis, the pattern of lateral organs in the shoot, and rhizotaxis, the spacing of lateral roots. Although the phytohormone auxin is known to be intimately involved in both phyllotaxis and rhizotaxis, the PLT3,5,7 module represents the first genetic element to be implicated in control of both processes. Thus, the goal of this proposal is to illuminate the genetic network surrounding PLT3,5,7 gene activity in both the shoot and root contexts. Early results suggest that auxin lies both upstream and downstream of PLT action, pointing to a positive feedback loop which could be at the heart of a pattern generating system. To investigate this network further, genes surrounding PLT action will be identified using genetic, bioinformatic and biochemical strategies. Physical and genetic interactions will place these genes in a genetic hierarchy. Dynamic expression of these genes in living shoots and roots will be monitored using real-time confocal microscopy, and changes in the network dynamics will be observed in plt mutants and in auxin manipulation experiments. The results from this project will illuminate the similarities and differences between these two PLT-bases patterning pathways and will be of interest to developmental, computational and evolutionary biologists alike."