OpenSimRoot: widening the scope and application of root architectural models

Postma, Johannes A.; Kuppe, Christian; Owen, Markus R.; Mellor, Nathan L.; Griffiths, Marcus; Bennett, Malcolm J.; Lynch, Jonathan P.; Watt, Michelle

Abstract

© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust 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.

Citation

Postma, J. A., Kuppe, C., Owen, M. R., Mellor, N. L., Griffiths, M., Bennett, M. J., Lynch, J. P., & Watt, M. (2017). OpenSimRoot: widening the scope and application of root architectural models. New Phytologist, 215(3), 1274-1286. https://doi.org/10.1111/nph.14641

• Journal Article Type: Article
• Acceptance Date: Apr 26, 2017
• Online Publication Date: Jun 27, 2017
• Publication Date: Aug 1, 2017
• Deposit Date: Jun 7, 2017
• Publicly Available Date: Jun 27, 2017
• Journal: New Phytologist
• Print ISSN: 0028-646X
• Electronic ISSN: 1469-8137
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 215
• Issue: 3
• Pages: 1274-1286
• DOI: https://doi.org/10.1111/nph.14641
• Keywords: Functional–structural plant model, Model-driven phenotyping, OpenSimRoot, Plant nutrition, Root architectural traits, Root system architecture, Simulation
• Public URL: https://nottingham-repository.worktribe.com/output/868221
• Publisher URL: http://onlinelibrary.wiley.com/doi/10.1111/nph.14641/full
• Additional Information: This is the peer reviewed version of the following article: Postma, J. A., Kuppe, C., Owen, M. R., Mellor, N., Griffiths, M., Bennett, M. J., Lynch, J. P. and Watt, M. (2017), OpenSimRoot: widening the scope and application of root architectural models. New Phytol. doi:10.1111/nph.14641 which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/nph.14641/full This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
• Contract Date: Jun 7, 2017