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Simulating Crop Root Systems Using OpenSimRoot

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Plant Systems Biology

Abstract

Functional–structural plant models are valuable modeling tools in analyzing plant development. A functional–structural plant model combines a three-dimensional representation of plant structure with models for physiological functions in order to better understand plant development. We present a guide to simulating crop root systems with OpenSimRoot, a feature-rich, highly cited, and open-source functional–structural root architecture model. We describe in detail how to create your own input files in conjunction with some examples. The aim of this guide is to highlight the potential of computational modeling in biology and to make modeling more accessible to the plant science community.

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References

  1. Dunbabin VM, Postma JA, Andrea S et al (2013) Modelling root-soil interactions using three-dimensional models of root growth, architecture and function. Plant Soil 372(1–2):93–124

    Article  CAS  Google Scholar 

  2. Dunbabin VM, Diggle AJ, Zdenko R et al (2002) Modelling the interactions between water and nutrient uptake and root growth. Plant Soil 239(1):19–38

    Article  CAS  Google Scholar 

  3. Frédéric G, Céline B-F, Philippe H et al (2017) Modelling the interactions between root system architecture, root functions and reactive transport processes in soil. Plant Soil 413(1–2):161–180

    Google Scholar 

  4. Mathieu J, Tom S, Jan V et al (2008) Use of a threedimensional detailed modeling approach for predicting root water uptake. Vadose Zone J 7(3):1079

    Article  Google Scholar 

  5. Daniel L, Sabine K, Gernot B et al (2010) A dynamic root system growth model based on l-systems. Plant Soil 332(1–2):177–192

    Google Scholar 

  6. Guillaume L, Loïc P, Xavier D (2014) A modeling approach to determine the importance of dynamic regulation of plant hydraulic conductivities on the water uptake dynamics in the soil-plant-atmosphere system. Ecol Model 290:65–75

    Article  Google Scholar 

  7. Loïc P, Gilles V, Jean-Louis D et al (2004) Root typ: a generic model to depict and analyse the root system architecture. Plant Soil 258(1):103–119

    Article  Google Scholar 

  8. Alain P, Claude D, Yvan C et al (2007) Root functional architecture: a framework for modeling the interplay between roots and soil. Vadose Zone J 6(2):269

    Article  Google Scholar 

  9. Wu L, McGechan MB, Neil MR et al (2007) Spacsys: integration of a 3d root architecture component to carbon, nitrogen and water cycling—model description. Ecol Model 200(3–4):343–359

    Article  Google Scholar 

  10. Bingham IJ, Wu L (2011) Simulation of wheat growth using the 3D root architecture model SPACSYS: validation and sensitivity analysis. Eur J Agron 34(3):181–189

    Article  Google Scholar 

  11. Berntson GM (1994) Modelling root architecture: are there tradeoffs between efficiency and potential of resource acquisition? New Phytol 127(3):483–493

    Article  Google Scholar 

  12. Postma JA, Lynch JP (2012) Complementarity in root architecture for nutrient uptake in ancient maize/bean and maize/bean/squash polycultures. Ann Bot 110(2):521–534

    Article  CAS  Google Scholar 

  13. Postma JA, Annette D, Lynch JP (2014) The optimal lateral root branching density for maize depends on nitrogen and phosphorus availability. Plant Physiol 166(2):590–602

    Article  Google Scholar 

  14. Postma JA, Christian K, Owen MR et al (2017) Opensimroot: widening the scope and application of root architectural models. New Phytol 215(3):1274–1286

    Article  Google Scholar 

  15. Andrea S, Black CK, Valentin C et al (2020) Call for participation: collaborative benchmarking of functional-structural root architecture models. The case of root water uptake. Front Plant Sci 11:316

    Article  Google Scholar 

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Schäfer, E.D., Owen, M.R., Postma, J.A., Kuppe, C., Black, C.K., Lynch, J.P. (2022). Simulating Crop Root Systems Using OpenSimRoot. In: Lucas, M. (eds) Plant Systems Biology. Methods in Molecular Biology, vol 2395. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1816-5_15

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  • DOI: https://doi.org/10.1007/978-1-0716-1816-5_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1814-1

  • Online ISBN: 978-1-0716-1816-5

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