Advancing structural-functional modelling of root growth and root-soilinteractions based on automatic reconstruction of root systems fromMRI

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Root system architecture and root uptake properties are critically important for soil exploration as roots are the major sites of soil-plant interactions. Crop breeding and management have increased interest in below-ground processes and root traits that may lead to more sustainable agricultural practices through reduced input of water and fertilisers. MRI is a non-invasive imaging method used to obtain both structural and functional information about the root-soil system. In combination with mathematical modelling, this will enhance our understanding of root-soil interactions. New techniques for automatic root segmentation and reconstruction of root systems are required to efficiently extract structural information about the root system from the vast amount of information contained in those volumetric measurements. In particular the connectivity of the root segments is important for modelling water flow in the root-soil system. In this project, we will simultaneously monitor root system architecture of soil-grown lupine plants and soil moisture at different times using MRI. With the help of manually annotated root systems, a method for learning fully automated segmentation of roots will be developed. {\textmu}CT images of selected samples will be used for comparison and evaluation of the new segmentation algorithm for root systems from MRI images. From the reconstructed roots, important root architectural features, such as basal and apical zone, internodal distance, curvature, and branching angles will be derived and used to refine the parameters of a root growth model, e.g. by improving proposal tropism angular distributions, branching angle, and axial growth parameters. Feedbacks between root system development and soil moisture conditions under water-sufficient and water-limited conditions will be evaluated. These findings will be used to advance mathematical models of water uptake by plant roots. Explicit 3D simulations of water flow will be performed on reconstructed root architectures using Comsol Multiphysics and evaluated based on measured soil water contents. This will then serve as a benchmark for testing different upscaling methods that result in an effective sink term for root water uptake from soil that can be incorporated into water flow models such as R-SWMS. Main results of this project will be a fully automated root system reconstruction algorithm and, based on this result, an advanced process understanding and mathematical model of root-water dynamics.