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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

Authors

Johannes A. Postma j.postma@fz-juelich.de

Christian Kuppe

Markus R. Owen Markus.Owen@nottingham.ac.uk

Nathan L. Mellor nathan.mellor@nottingham.ac.uk

Marcus Griffiths

Jonathan P. Lynch

Michelle Watt



Abstract

Research Conducted and Rationale: OpenSimRoot is an open sourced, 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.

Description: 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.

Key results and unique features: The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate 1) resource costs of developmental and anatomical traits, 2) trait synergisms, 3) (inter species) root competition. OpenSimRoot can model 3D images from MRI and X-ray CT of roots in soil. New modules include: 1) soil water dependent water uptake and xylem flow, 2) tiller formation, 3) evapotranspiration, 4) simultaneous simulation of mobile solutes, 5) mesh refinement, and 6) root growth plasticity.

Conclusion: OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and gain mechanistic understanding at system scales.

Journal Article Type Article
Journal New Phytologist
Print ISSN 0028-646X
Electronic ISSN 1469-8137
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 215
Issue 3
APA6 Citation Postma, J. A., Kuppe, C., Owen, M. R., Mellor, N. L., Griffiths, M., Bennett, M. J., …Watt, M. (in press). OpenSimRoot: widening the scope and application of root architectural models. New Phytologist, 215(3), doi:10.1111/nph.14641
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
Publisher URL http://onlinelibrary.wiley.com/doi/10.1111/nph.14641/full
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingh.../end_user_agreement.pdf
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.wi.../10.1111/nph.14641/full This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf





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