OpenAlea.HydroRoot: A modelling framework to dissect, predict and phenotype branched root hydraulic architecture

Abstract

Drought is a significant factor in agricultural losses, making it imperative to understand how root system architecture (RSA) adapts to environmental condition like water deficit. HydroRoot is a functional-structural plant model (FSPM) aimed at analyzing and simulating hydraulic and solute transport of RSA. The model integrates a static hydraulic solver, a coupled water-solute transport solver, a statistical generator of RSA based on Markov model, and a dynamic hydraulic model accounting for root growth. This paper presents the model, the mathematical description of the formalism of solvers, and use cases with their associated tutorials. Five use cases illustrate capabilities of HydroRoot, which has been successfully used for phenotyping root hydraulics across various species, including Arabidopsis, maize, and millet. The model-driven phenotyping method "cut and flow" is presented to characterize axial and radial conductivities on a given root genotype. Finally, three step-by-step tutorials provide a structured way to learn how to use HydroRoot 1) to simulate hydraulic on a given architecture, 2) to simulate water and solute transport on a maize root, and 3) to simulate hydraulic on two pearl millet genotypes with varying soil conditions. Hydroroot is an open-source package of the OpenAlea platform, with the code publicly available on Github. A comprehensive documentation is available with a reproducible gallery of examples.