OpenSimRoot: widening the scope and application of root architectural models

OpenSimRoot is an open-source, functional–structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. OpenSimRoot is an extended version of SimRoot, established...

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Bibliographic Details
Published in:	The New phytologist 2017-08, Vol.215 (3), p.1274-1286
Main Authors:	Postma, Johannes A., Kuppe, Christian, Owen, Markus R., Mellor, Nathan, Griffiths, Marcus, Bennett, Malcolm J., Lynch, Jonathan P., Watt, Michelle
Format:	Article
Language:	eng
Subjects:	Anatomy Biological competition Competition Computed tomography Computer Simulation Costs Crops Data processing Evapotranspiration Finite element method functional–structural plant model Imaging techniques Magnetic resonance imaging Mathematical models Methods Mineral nutrients Modelling Models, Biological model‐driven phenotyping Modules Moisture content NMR Nuclear magnetic resonance Nutrient transport Nutrients OpenSimRoot Phenotype Phenotypic plasticity Plant communities Plant growth plant nutrition Plant Roots - anatomy & histology Plant Roots - growth & development Quantitative Trait, Heritable Resonance root architectural traits root system architecture Roots Simulation Software Soil Soil water Soils Solutes Structure-function relationships Three dimensional models Tomography Transportation models Uptake Water transport Water uptake Widening Xylem
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Summary:	OpenSimRoot is an open-source, functional–structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate the following: resource costs of developmental and anatomical traits; trait synergisms; and (interspecies) root competition. OpenSimRoot can model three-dimensional images from magnetic resonance imaging (MRI) and X-ray computed tomography (CT) of roots in soil. New modules include: soil water-dependent water uptake and xylem flow; tiller formation; evapotranspiration; simultaneous simulation of mobile solutes; mesh refinement; and root growth plasticity. OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and to gain a mechanistic understanding at system scales.
ISSN:	0028-646X 1469-8137