Model selection and parameter estimation for root architecture models using likelihood-free inference.

Abstract

Plant root systems play vital roles in the biosphere, environment and agriculture, but the quantitative principles governing their growth and architecture remain poorly understood. The 'forward problem' of what root forms can arise from given models and parameters has been well studied through modelling and simulation, but comparatively little attention has been given to the 'inverse problem': what models and parameters are responsible for producing an experimentally observed root system? Here, we propose the use of approximate Bayesian computation (ABC) to infer mechanistic parameters governing root growth and architecture, allowing us to learn and quantify uncertainty in parameters and model structures using observed root architectures. We demonstrate the use of this platform on synthetic and experimental root data and show how it may be used to identify growth mechanisms and characterize growth parameters in different mutants. Our highly adaptable framework can be used to gain mechanistic insight into the generation of observed root system architectures.

Plant phenotyping relevance

観測された根系構造から成長モデルとパラメータを推定するABCベースの計算フレームワークを提案・実証しており、根系形態という植物表現型の解析手法が中心である。

Code and data availability

The authors explicitly state that the data and code used for the root-architecture ABC SMC inference (including experimental Arabidopsis root measurements and analysis scripts) are freely available in a public GitHub repository, and the electronic supplementary material (containing additional posterior figures) is公开ly