Spatial Models of Gene Patterns in Plants

Abstract: The growth and development of plants exhibits a striking symmetry, visible in the regular arrangement of leaves and flowers. Plant development is carefully controlled at the molecular level by gene regulatory networks, and the symmetry of plants can be observed also in the molecular patterns of gene expression.This thesis investigates the molecular basis for spatial patterns of gene expression in plant development with computer models. Understanding the molecular mechanisms for regulating plant development can provide important cues for developing new technologies and methods, improving conditions in agriculture and forest industry.Papers I, II and III investigates spatial gene patterns important in the creation of new plant organs such as leaves and flowers. In Paper I, signalling of the plant hormone auxin is investigated, a key player in the initiation of new plant organs. For Paper I, we developed a model, closely connected to the experimental data, explaining how the depletion of auxin can stabilize the distribution of auxin in a novel plant mutant. For Paper II, we developed a model connecting the radial patterning of the plant shoot to a model for generating peaks of auxin marking new plant organs. With this model, it was shown how the radial patterning of the shoot can restrict the initiation of new organs to a ring of cells around the meristem. Paper III investigates models for creating a mutually exclusive patterning including a gap, observed in the radial patterning of the genes KANADI and REVOLUTA in the shoot. By investigating a collection of different model interactions, we found that diffusion was required to facilitate a mutually exclusive patterning including a gap. We then mapped this result onto a biological network including the genes REVOLUTA, KANADI and diffusing microRNAs, and continued to develop an integrated model describing how the radial patterning affect the dynamics of organ initiation.Papers IV and V investigate models for the initiation of root hairs. Prior to root hair outgrowth, the root hair cells become polarized with a local patch of Rho-of-Plant proteins appearing at one end of the cell. In Paper IV, a molecular model for creating such a patch of Rho-of-Plants proteins is investigated in relation to models of mechanical stresses in root hair cells. Paper V investigates the molecular model of root hair initiation in more detail, demarcating regions of patterning, and extending the single cell model to a root hair cell file, explaining the distant polarization of root hair cells in the root.