User menu

CRootBox: a structural–functional modelling framework for root systems

  • Open access
  • PDF
  • 3.62 M
  1. Barraclough P. B., Kuhlmann H., Weir A. H., The Effects of Prolonged Drought and Nitrogen Fertilizer on Root and Shoot Growth and Water Uptake by Winter Wheat, 10.1111/j.1439-037x.1989.tb00778.x
  2. Bingham Ian J., Wu Lianhai, Simulation of wheat growth using the 3D root architecture model SPACSYS: Validation and sensitivity analysis, 10.1016/j.eja.2011.01.003
  3. Bittelli, Soil physics with Python: transport in the soil-plant-atmosphere system (2015)
  4. Bourion Virginie, Martin Chantal, de Larambergue Henri, Jacquin Françoise, Aubert Grégoire, Martin-Magniette Marie-Laure, Balzergue Sandrine, Lescure Geoffroy, Citerne Sylvie, Lepetit Marc, Munier-Jolain Nathalie, Salon Christophe, Duc Gérard, Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant, 10.1093/jxb/eru124
  5. Chen Ying Long, Dunbabin Vanessa M., Postma Johannes A., Diggle Art J., Palta Jairo A., Lynch Jonathan P., Siddique Kadambot H. M., Rengel Zed, Phenotypic variability and modelling of root structure of wild Lupinus angustifolius genotypes, 10.1007/s11104-011-0939-z
  6. Chimungu, Plant biotechnology, 181 (2014)
  7. Chochois V., Vogel J. P., Watt M., Application of Brachypodium to the genetic improvement of wheat roots, 10.1093/jxb/ers044
  8. Clausnitzer V., Hopmans J. W., Simultaneous modeling of transient three-dimensional root growth and soil water flow, 10.1007/bf00010082
  9. Diggle A. J., ROOTMAP—a model in three-dimensional coordinates of the growth and structure of fibrous root systems, 10.1007/bf02376780
  10. DOUSSAN C, Modelling of the Hydraulic Architecture of Root Systems: An Integrated Approach to Water Absorption—Distribution of Axial and Radial Conductances in Maize, 10.1006/anbo.1997.0541
  11. Doussan Claude, Pierret Alain, Garrigues Emmanuelle, Pagès Loïc, Water Uptake by Plant Roots: II – Modelling of Water Transfer in the Soil Root-system with Explicit Account of Flow within the Root System – Comparison with Experiments, 10.1007/s11104-004-7904-z
  12. Drouet J.-L., Pagès L., GRAAL: a model of GRowth, Architecture and carbon ALlocation during the vegetative phase of the whole maize plant, 10.1016/s0304-3800(03)00072-3
  13. Dunbabin Vanessa M., Diggle Art J., Rengel Zdenko, van Hugten Robert, 10.1023/a:1014939512104
  14. Dupuy Lionel, Gregory Peter J., Bengough A. Glyn, Root growth models: towards a new generation of continuous approaches, 10.1093/jxb/erp389
  15. Feddes, Simulation of field water use and crop yield (1978)
  16. Flemisch, New Computational Methods and Software Tools, 34, 1102 (2011)
  17. Gregory, Plant roots: growth, activity and interactions with the soil (2006)
  18. Hochholdinger Frank, Park Woong June, Sauer Michaela, Woll Katrin, From weeds to crops: genetic analysis of root development in cereals, 10.1016/j.tplants.2003.11.003
  19. Huber Katrin, Vanderborght Jan, Javaux Mathieu, Schröder Natalie, Dodd Ian C., Vereecken Harry, Modelling the impact of heterogeneous rootzone water distribution on the regulation of transpiration by hormone transport and/or hydraulic pressures, 10.1007/s11104-014-2188-4
  20. Jacques D., Šimůnek J., Mallants D., van Genuchten M.Th., Operator-splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles, 10.1016/j.jconhyd.2006.06.008
  21. Janott Michael, Gayler Sebastian, Gessler Arthur, Javaux Mathieu, Klier Christine, Priesack Eckart, A one-dimensional model of water flow in soil-plant systems based on plant architecture, 10.1007/s11104-010-0639-0
  22. Javaux Mathieu, Schröder Tom, Vanderborght Jan, Vereecken Harry, Use of a Three-Dimensional Detailed Modeling Approach for Predicting Root Water Uptake, 10.2136/vzj2007.0115
  23. Klepper, Root-shoot relationships. Plant roots: the hidden half (1991)
  24. Kutschera, Wurzelatlas mitteleuropäischer Ackerunkräuter und Kulturpflanzen (1960)
  25. Kutschera, Wurzelatlas mitteleuropäischer Grünlandpflanzen (1982)
  26. Leitner Daniel, Klepsch Sabine, Bodner Gernot, Schnepf Andrea, A dynamic root system growth model based on L-Systems : Tropisms and coupling to nutrient uptake from soil, 10.1007/s11104-010-0284-7
  27. Leitner Daniel, Klepsch Sabine, Knieß Astrid, Schnepf Andrea, The algorithmic beauty of plant roots – an L-System model for dynamic root growth simulation, 10.1080/13873954.2010.491360
  28. Leitner D., Felderer B., Vontobel P., Schnepf A., Recovering Root System Traits Using Image Analysis Exemplified by Two-Dimensional Neutron Radiography Images of Lupine, 10.1104/pp.113.227892
  29. Leitner Daniel, Meunier Félicien, Bodner Gernot, Javaux Mathieu, Schnepf Andrea, Impact of contrasted maize root traits at flowering on water stress tolerance – A simulation study, 10.1016/j.fcr.2014.05.009
  30. Lobet G., Couvreur V., Meunier F., Javaux M., Draye X., Plant Water Uptake in Drying Soils, 10.1104/pp.113.233486
  31. Lobet Guillaume, Pound Michael P., Diener Julien, Pradal Christophe, Draye Xavier, Godin Christophe, Javaux Mathieu, Leitner Daniel, Meunier Félicien, Nacry Philippe, Pridmore Tony P., Schnepf Andrea, Root System Markup Language: Toward a Unified Root Architecture Description Language, 10.1104/pp.114.253625
  32. Lynch Jonathan P., Nielsen Kai L., Davis Robert D., Jablokow Andrei G., 10.1023/a:1004276724310
  33. Osher Stanley, Fedkiw Ronald, Signed Distance Functions, Applied Mathematical Sciences (2003) ISBN:9781468492514 p.17-22, 10.1007/0-387-22746-6_2
  34. PAGÈS LOÏC, Links between root developmental traits and foraging performance : Root developmental traits and foraging performance, 10.1111/j.1365-3040.2011.02371.x
  35. Pagès Loíc, Glyn Bengough Anthony, 10.1023/a:1004288430467
  36. Pagès L., Jordan M. O., Picard D., A simulation model of the three-dimensional architecture of the maize root system, 10.1007/bf02370279
  37. Pagès Loïc, Vercambre Gilles, Drouet Jean-Louis, Lecompte François, Collet Catherine, Le Bot Jacques, Root Typ: a generic model to depict and analyse the root system architecture, 10.1023/b:plso.0000016540.47134.03
  38. Pagès Loïc, Xie Jun, Serra Valérie, Potential and actual root growth variations in root systems: modeling them with a two-step stochastic approach, 10.1007/s11104-013-1820-z
  39. Pagès Loïc, Bécel Carole, Boukcim Hassan, Moreau Delphine, Nguyen Christophe, Voisin Anne-Sophie, Calibration and evaluation of ArchiSimple, a simple model of root system architecture, 10.1016/j.ecolmodel.2013.11.014
  40. Perez Fernando, Granger Brian E., Hunter John D., Python: An Ecosystem for Scientific Computing, 10.1109/mcse.2010.119
  41. Pierret A., Doussan C., Pagès L., Spatio-temporal Variations in Axial Conductance of Primary and First-order Lateral Roots of a Maize Crop as Predicted by a Model of the Hydraulic Architecture of Root Systems, 10.1007/s11104-005-5373-7
  42. Postma J. A., Lynch J. P., Root Cortical Aerenchyma Enhances the Growth of Maize on Soils with Suboptimal Availability of Nitrogen, Phosphorus, and Potassium, 10.1104/pp.111.175489
  43. Postma Johannes A., Kuppe Christian, Owen Markus R., Mellor Nathan, Griffiths Marcus, Bennett Malcolm J., Lynch Jonathan P., Watt Michelle, Open Sim Root : widening the scope and application of root architectural models, 10.1111/nph.14641
  44. Pradal Christophe, Dufour-Kowalski Samuel, Boudon Frédéric, Fournier Christian, Godin Christophe, OpenAlea: a visual programming and component-based software platform for plant modelling, 10.1071/fp08084
  45. Raats P. A. C., Steady Flows of Water and Salt in Uniform Soil Profiles with Plant Roots1, 10.2136/sssaj1974.03615995003800050012x
  46. Roose T., Fowler A.C., A mathematical model for water and nutrient uptake by plant root systems, 10.1016/j.jtbi.2003.12.013
  47. Roose T., Fowler A.C., Darrah P.R., A mathematical model of plant nutrient uptake, 10.1007/s002850000075
  48. Schnepf A., Leitner D., Klepsch S., Modeling Phosphorus Uptake by a Growing and Exuding Root System, 10.2136/vzj2012.0001
  49. Schnepf A., Leitner D., Schweiger P. F., Scholl P., Jansa J., L-System model for the growth of arbuscular mycorrhizal fungi, both within and outside of their host roots, 10.1098/rsif.2016.0129
  50. Schröder Tom, Javaux Mathieu, Vanderborght Jan, Körfgen Bernd, Vereecken Harry, Implementation of a Microscopic Soil–Root Hydraulic Conductivity Drop Function in a Three-Dimensional Soil–Root Architecture Water Transfer Model, 10.2136/vzj2008.0116
  51. Schröder Natalie, Lazarovitch Naftali, Vanderborght Jan, Vereecken Harry, Javaux Mathieu, Linking transpiration reduction to rhizosphere salinity using a 3D coupled soil-plant model, 10.1007/s11104-013-1990-8
  52. Somma F., Hopmans J.W., Clausnitzer V., 10.1023/a:1004378602378
  53. Spek Louise Y., 10.1023/a:1004236626479
  54. Tsegaye Tezera, Mullins C. E., Diggle A. J., An experimental procedure for obtaining input parameters for the ?ROOTMAP? root simulation program for peas (Pisum sativum L.), 10.1007/bf00020855
  55. Vansteenkiste Joachim, Van Loon Jelle, Garré Sarah, Pagès Loïc, Schrevens Eddie, Diels Jan, Estimating the parameters of a 3-D root distribution function from root observations with the trench profile method: case study with simulated and field-observed root data, 10.1007/s11104-013-1942-3
  56. Wasson (2017)
  57. Weaver, Root development of vegetable crops (1927)
  58. Wu L., McGechan M.B., McRoberts N., Baddeley J.A., Watson C.A., SPACSYS: Integration of a 3D root architecture component to carbon, nitrogen and water cycling—Model description, 10.1016/j.ecolmodel.2006.08.010
  59. Zobel R. W., Waisel Y., A plant root system architectural taxonomy: A framework for root nomenclature, 10.1080/11263501003764483
  60. Dunbabin Vanessa M., Postma Johannes A., Schnepf Andrea, Pagès Loïc, Javaux Mathieu, Wu Lianhai, Leitner Daniel, Chen Ying L., Rengel Zed, Diggle Art J., Modelling root–soil interactions using three–dimensional models of root growth, architecture and function, 10.1007/s11104-013-1769-y
Bibliographic reference Schnepf, Andrea ; Leitner, Daniel ; Landl, Magdalena ; Lobet, Guillaume ; Mai, Trung Hieu ; et. al. CRootBox: a structural–functional modelling framework for root systems. In: Annals of Botany, Vol. mcx221, no.1, p. 1-12 (2018)
Permanent URL