OpenSimRoot

OpenSimRoot

Johannes A. Postma; Christian Kuppe

Institute for Bio-and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany

Website

https://gitlab.com/rootmodels/OpenSimRoot

or

http://rootmodels.gitlab.io/OpenSimRoot/

Description

OpenSimRoot is an open‐source, 3D functional–structural plant model. It is an extended version of SimRoot, established to simulate root system architecture, the value of root traits for resource acquisition and plant growth. As research tool it supports experimental designs and mechanistic understanding at system scales by integration of plant phenotypic data with environmental metadata.

OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient and water transport models. For example modules can compute soil water‐dependent water uptake and xylem flow; tiller formation; evapotranspiration; simultaneous simulation of mobile solutes and/or root growth plasticity. 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.

Screen Shot of ParaView Post-processing

Scientific articles

Postma JA, Kuppe C, Owen MR, Mellor N, Griffiths M, Bennett MJ, Lynch JP, Watt M. 2017. OpenSimRoot: widening the scope and application of root architectural models. New Phytologist 215: 1274–1286.

Schneider H, Postma JA, Wojciechowski T, Kuppe C, Lynch J. 2017. Root Cortical Senescence Improves Growth under Suboptimal Availability of N, P, and K. Plant Physiology: pp.00648.2017.

Including SimRoot:

Chen YL, Dunbabin VM, Postma JA, Diggle AJ, Kadambot H. M. Siddique, Rengel Z. 2013. Modelling root plasticity and response of narrow-leafed lupin to heterogeneous phosphorus supply. Plant and Soil 372: 319–337

Chen YL, Dunbabin VM, Postma JA, Diggle AJ, Palta JA, Lynch JP, Siddique KHM, Rengel Z. 2011. Phenotypic variability and modelling of root structure of wild Lupinus angustifolius genotypes. Plant and Soil 348: 345–364.

Dathe A, Postma JA, Lynch JP. 2013. Modeling Resource Interactions Under Multiple Edaphic Stresses. In: Timlin D,, In: Ahuja LR, eds. Advances in Agricultural Systems Modeling. Advances in Agricultural Systems Modeling. Madison, Wis., USA: American Society of Agronomy, Crop Science Society of America, Soil Science Society of America., 273–294.

Dathe A, Postma JA, Postma-Blaauw MB, Lynch JP. 2016. Impact of axial root growth angles on nitrogen acquisition in maize depends on environmental conditions. Annals of Botany: 1–15.

Dunbabin VM, Postma JA, Schnepf A, Loïc Pagès, Mathieu Javaux, Lianhai Wu, Daniel Leitner, Ying L. Chen, Zed Rengel, Art J. Diggle. 2013. Modelling root–soil interactions using three–dimensional models of root growth, architecture and function. Plant and Soil 372: 93–124.

Ge ZY, Rubio G, Lynch JP. 2000. The importance of root gravitropism for inter-root competition and phosphorus acquisition efficiency: results from a geometric simulation model. Plant and Soil 218: 159–171.

Liu KN, Yang QL, Ge ZY, Liu XG. 2012. Simulation of Jatropha curcas L. Root in Response to Salt Stress Based on 3D Visualization. Advanced Materials Research 518– 523: 5330–5334.

Lynch JP, Beebe SE. 1995. Adaptation of beans (Phaseolus vulgaris L.) to low phosphorus availability. HortScience 30: 1165–1171.

Lynch JP, Nielsen KL, Davis RD, Jablokow AG. 1997. SimRoot: Modelling and visualization of root systems. Plant and Soil 188: 139–151.

Ma Z, Walk TC, Marcus A, Lynch JP. 2001. Morphological synergism in root hair length, density, initiation and geometry for phosphorus acquisition in Arabidopsis thaliana: A modeling approach. Plant and Soil 236: 221–235.

Miguel MA, Postma JA, Lynch JP. 2015. Phene Synergism between Root Hair Length and Basal Root Growth Angle for Phosphorus Acquisition. Plant Physiology 167: 1430– 1439.

Nielsen KL, Lynch JP, Jablokow AG, Curtis PS. 1994. Carbon cost of root systems: an architectural approach. Plant and Soil 165: 161–169.

Nielsen KL, Lynch JP, Weiss HN. 1997. Fractal geometry of bean root systems: correlations between spatial and fractal dimension. American Journal of Botany 84: 26– 33.

Postma JA, Dathe A, Lynch JP. 2014. The optimal lateral root branching density for maize depends on nitrogen and phosphorus availability. Plant Physiology 166: 590–602.

Postma JA, Jaramillo RE, Lynch JP. 2008. Towards modeling the function of root traits for enhancing water acquisition by crops. In: Ahuja LR,, In: Reddy VR,, In: Saseendran SA,, In: Yu Q, eds. Advances in Agricultural Systems Modeling. Response of Crops to Limited Water: Understanding and Modeling Water Stress Effects on Plant Growth Processes. Madison, Wis., USA: ASA-CSSA-SSSA, 251–276.

Postma JA, Lynch JP. 2011a. Root cortical aerenchyma enhances the growth of maize on soils with suboptimal availability of nitrogen, phosphorus, and potassium. Plant Physiology 156: 1190–1201.

Postma JA, Lynch JP. 2011b. Theoretical evidence for the functional benefit of root cortical aerenchyma in soils with low phosphorus availability. Annals of Botany 107: 829– 841.

Postma JA, Lynch JP. 2012. Complementarity in root architecture for nutrient uptake in ancient maize/bean and maize/bean/squash polycultures. Annals of Botany 110: 521–534.

Postma JA, Schurr U, Fiorani F. 2014. Dynamic root growth and architecture responses to limiting nutrient availability: linking physiological models and experimentation. Biotechnology Advances 32: 53–65.

Rubio G, Walk T, Ge ZY, Yan XL, Liao H, Lynch JP. 2001. Root gravitropism and below-ground competition among neighbouring plants: A modelling approach. Annals of Botany 88: 929–940.

Schulz H, Postma JA, Dusschoten D van, Scharr H, Behnke S. 2013. Plant Root System Analysis from MRI Images. In: Csurka G,, In: Kraus M,, In: Laramee RS,, In: Richard P,, In: Braz J, eds. Communications in Computer and Information Science. Computer Vision, Imaging and Computer Graphics. Theory and Application. Springer Berlin Heidelberg, 411–425.

Walk TC, Jaramillo R, Lynch JP. 2006. Architectural tradeoffs between adventitious and basal roots for phosphorus acquisition. Plant and Soil 279: 347–366.

Walk TC, vanErp E, Lynch JP. 2004. Modelling applicability of fractal analysis to efficiency of soil exploration by roots. Annals of Botany 94: 119–128.

York LM, Galindo-Castañeda T, Schussler JR, Lynch JP. 2015. Evolution of US maize (Zea mays L.) root architectural and anatomical phenes over the past 100 years corresponds to increased tolerance of nitrogen stress. Journal of Experimental Botany 66: 2347–2358.

York LM, Silberbush M, Lynch JP. 2016. Spatiotemporal variation of nitrate uptake kinetics within the maize ( Zea mays L.) root system is associated with greater nitrate uptake and interactions with architectural phenes. Journal of Experimental Botany: erw133.

Technical information

Operating system(s): Linux, Windows, Unix/MacOS

Licence: GPL 3

Output(s): Plant and soil data.

OpenSimRoot includes export modules that can be enabled or disabled to retrieve specified output forms that include tables in text files, 3D models in various VTK formats, 3D raster images and an XML formatted dump of the model in the format of OpenSimRoot’s own input files.

Export format(s): tsv/tab and vtu/pvd/vti/vtp, xml or raw binary

Other information:

OpenSimRoot has a modular program structure. It is now fully C++ and relies only on standard libraries. To run your root simulation you specify a XML input file to give a parameterization.

OpenSimRoot can model three‐dimensional images from magnetic resonance imaging (MRI) and X‐ray computed tomography (CT) of roots in soil.