Growth and Development of higher plants

We will pursue running efforts in P1C, P4C and EU1 labs towards the development of high throughput imaging-based root growth quantification (time-lapse kinematic analysis, P1C) and root architecture (segmentation, morphological image analysis, vectorization of root trees, P4C) integrated with the strong mathematical engineering expertise of EU1. These methods are aimed to replace current generation, low-throughput for the quantitative analysis of root growth and form. They will be made available to the network (mainly WP2) and to the wider scientific community.

We will create a multi-scale modelling framework, to allow for simultaneous, seamless inter-operation of multiple, pre-existing models developed for problems at different levels of organization (P4C). This is important because a model of cell needs to be placed in the context of the entire organ and those of a growing organ in the context of the entire plant and its environment. We will make use of standardized software interfaces, to couple existing, legacy computer codes without major modification. This requires extensive of modelling standards, including the popular Systems Biology Modelling Language (SBML). Although the plant will be central, the framework will also allow integration of soil (e.g. 3D hydrodynamics and solute transport) and canopy models (e.g. light interception).

The framework will include a three-dimensional, dynamic and structural model of whole plant growth and architecture; it will model the (long and short-range) transport, consumption and transformation of proteins, fytohormones and other chemicals (P4C and Loïc Pagès, INRA-Avignon). It will benefit from the multi-disciplinary expertise of the network. The structural model will be designed in a multi-scale context, allowing empirical growth, branching, and decay functions to be replaced by systems biology sub-models, paving the way to the progressive assembly of whole plant systems biology models to probe genetic-environment interactions associated with root growth and function. It will also rely on the experience gained with the RootTyp model allowing the simulation of a very broad range of root architectures (including, but not restricted to Arabidopsis).

One of the main questions we aim to tackle with our modelling framework is to understand how (genetically regulated) cell-level phenomena, including the cell-cycle, translate to the growth and morphology of the whole plant. We will analyze growth of the primary root tip using kinematic analyses, analogous to earlier work on the leaf (P1C) and lateral root initiation (P1A and P1C), and we will study the regulatory effect of auxin on the cell cycle in both primary root tip and lateral root initiation (P1A, P1C and EU1).

We will then use these data to develop a spatial model of early cell division patterns of lateral root initiation, and its molecular regulation (P1A, P1C and EU1). This work stems from the recent finding (P1A) that lateral root initiation in Arabidopsis thaliana responds to pulses of auxin presumably transported through the lateral root cap and epidermal cells and possibly mediated through the bending of the root induced by gravitropic stimuli. This model will be instrumental to unravel the mechanisms of lateral root initiation, and will be the cornerstone of a larger modelling initiative (P1C, EU1) aiming at the creation of a virtual root.