Abstract
In the last decade, functional-structural plant modelling (FSPM) has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse (by modularisation), combination and comparison, and the enhancement of existing models. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization.
Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim (e.g., photosynthesis, organ formation and growth). Simulation runs with several general parameter sets adopted from the literature show that the present prototypewas able to reproduce a plausible output range for different crops (rapeseed, barley, etc.) in terms of both the dynamics and final values (at harvest time) of model state variables such as assimilate production, organ biomass, leaf area and architecture.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Goudriaan J, Van Laar H H. Modelling Potential Crop Growth Processes: Textbook with Exercises. Dordrecht: Kluwer Academic Publishers, 1994
Lopez G, Favreau R P, Smith C, Costes E, Prusinkiewicz P, DeJong T M. Integrating simulation of architectural development and source-sink behaviour of peach trees by incorporating Markov chains and physiological organ function submodels into L-PEACH. Functional Plant Biology, 2008, 35(10): 761–771
Allen M T, Prusinkiewicz P, DeJong T M. Using L-systems for modeling source-sink interactions, architecture and physiology of growing trees: the L-PEACH model. New Phytologist, 2005, 166(3): 869–880
Xu L F, Henke M, Zhu J, Kurth W, Buck-Sorlin G H. A rule-based functional-structural model of rice considering source and sink functions. In: Proceedings of the 3rd International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications. 2009, 245–252
Buck-Sorlin G H, de Visser P H B, Sarlikioti V, Burema B S, Heuvelink E, Marcelis L F M, van der Heijden G W A M, Vos J. SIMPLER: an FSPM coupling shoot production, human interaction with the structure, morphogenesis, photosynthesis and light environment in cut-Rose. In: Proceedings of the 6th International Workshop on Functional-Structural Plant Models. 2010, 222–224
Groer C, Kniemeyer O, Hemmerling R, Kurth W, Becker H, Buck-Sorlin G H. A dynamic 3D model of rape (Brassica napus L.) computing yield components under variable nitrogen fertilization regimes. In: Proceedings of the 5th International Workshop on Functional-Structural Plant Models. 2007
Buck-Sorlin G H, Kniemeyer O, Kurth W. Barley morphology, genetics and hormonal regulation of internode elongation modelled by a relational growth grammar. New Phytologist, 2005, 166(3): 859–867
Buck-Sorlin G H, Kniemeyer O, Kurth W. A grammar-based model of barley including genetic control and metabolic networks. In: Vos J et al., eds. Functional-Structural Plant Modelling in Crop Production. Dordrecht: Springer, 2007, 243–252
Buck-Sorlin G H, Hemmerling R, Kniemeyer O, Burema B, Kurth W. A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction. Annals of Botany, 2008, 101(8): 1109–1123
Barczi J F, Rey H, Caraglio Y, Reffye d P, Barthélémy D, Dong Q X, Fourcaud T. AmapSim: a structural whole-plant simulator based on botanical knowledge and designed to host external functional models. Annals of Botany, 2008, 101(8): 1125–1138
Hu B G, Reffye P D, Zhao X, Yan H P, Kang M Z. GreenLab: a new methodology towards plant functional-structural model — structural aspect. In: Hu B, Jaeger M, eds. Plant Growth Modeling and Applications. Beijing: TsingHuo University Press and Springer, 2003, 21–35
Letort V. Analyse multi-échelle des relations source-puits dans les modèles de développement et croissance des plantes pour l’identification paramétrique. Cas du modèle GreenLab. Dissertation for the Doctoral Degree. Châtenay-Malabry: École Centrale Paris, 2008
Breckling B. An individual based model for the study of pattern and process in plant ecology: an application of object oriented programming. EcoSys, 1996, 4: 241–254
Perttunen J, Sievänen R, Nikinmaa E, Salminen H, Saarenmaa H, Väkevä J. LIGNUM: A tree model based on simple structural units. Annals of Botany, 1996, 77(1): 87–98
Kniemeyer O. Design and implementation of a graph grammar based language for functional-structural plant modelling. Dissertation for the Doctoral Degree. Cottbus: Brandenburg University of Technology, 2008
Kurth W. Morphological models of plant growth. Possibilities and ecological relevance. Ecological Modelling, 1994, 75: 299–308
Prusinkiewicz P, Lindenmayer A. The Algorithmic Beauty of Plants. New York: Springer Science & Business Media, 2012
Hemmerling R. Extending the programming language XL to combine graph structures with ordinary differential equations. Dissertation for the Doctoral Degree. Göttingen: University of Göttingen, 2012
Hemmerling R, Kniemeyer O, Lanwert D, Kurth W, Buck-Sorlin G H. The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition. Functional Plant Biology, 2008, 35(9/10): 739–750
Van Antwerpen D G. Unbiased physically based rendering on the GPU. Dissertation for the Master Degree. Delft: Delft University of Technology, 2011
Veach E. Robust Monte Carlo Methods for Light Transport Simulation. Dissertation for the Doctoral Degree. Palo Alto: Stanford University, 1998
Buck-Sorlin G H, Hemmerling R, Vos J, de Visser P H. Modelling of spatial light distribution in the greenhouse: Description of the model. In: Proceedings of the 3rd International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications. 2009, 79–86
Evers J B, Vos J, Yin X, Romero P, Van Der Putten P E L, Struik P C. Simulation of wheat growth and development based on organlevel photosynthesis and assimilate allocation. Journal of Experimental Botany, 2010, 61(8): 2203–2216
Preetham A J, Shirley P, Smits B. A practical analytic model for daylight. In: Proceedings of the 26th Annual Conference on Computer Graphics and Interactive Techniques. 1999, 91–100
Gijzen H. Development of a simulation model for transpiration and water uptake and an integral growth model. AB-DLO Report 18. 1994
Nikolov N T, Massman WJ, Schoettle AW. Coupling biochemical and biophysical processes at the leaf level: an equilibrium photosynthesis model for leaves of C3 plants. Ecological Modelling, 1995, 80: 205–235
Müller J, Wernecke P, Diepenbrock W. LEAFC3-N: a nitrogensensitive extension of the CO2 and H2O gas exchange model LEAFC3 parameterised and tested for winter wheat (Triticum aestivum L.). Ecological Modelling, 2005, 183: 183–210
Müller J, Braune H, Diepenbrock W. Photosynthesis-stomatal conductance model LEAFC3-N: specification for barley, generalised nitrogen relations, and aspects of model application. Functional Plant Biology, 2008, 35: 797–810
Baldocchi D. An analytical solution for coupled leaf photosynthesis and stomatal conductance models. Tree Physiology, 1994, 14: 1069–1079
Kim S H, Lieth J H. A coupled model of photosynthesis, stomatal conductance and transpiration for a rose leaf (Rosa hybrida L.). Annals of Botany, 2003, 91(7): 771–781
Lieth J H, Pasian C C. A simulation model for the growth and development of flowering rose shoots. Scientia Horticulturae, 1991, 46: 109–128
Thornley J H M. A model to describe the partitioning of photosynthate during vegetative plant growth. Annals of Botany, 1969, 33: 419–430
Thornley J H M. Dynamic model of leaf photosynthesis with acclimation to light and nitrogen. Annals of Botany, 1998, 81(3): 421–430
Johnson I R, Thornley J H M. Dynamic model of the response of a vegetative grass crop to light, temperature and nitrogen. Plant, Cell and Environment, 1985, 8(7): 485–499
Marshall B, Biscoe P V. A model for C3 leaves describing the dependence of net photosynthesis on irradiance I. Derivation. Journal of Experimental Botany, 1980, 31(1): 29–39
Marshall B, Biscoe P V. A model for C3 leaves describing the dependence of net photosynthesis on irradiance II. Application to the analysis of flag leaf photosynthesis. Journal of Experimental Botany, 1980, 31(1): 41–48
Rauscher H M, Isebrands J G, Host G E, Dickson R E, Dickmann D I, Crow T R, Michael D A. ECOPHYS: an ecophysiological growth process model for juvenile poplar. Tree Physiology, 1990, 7: 255–281
Yin X Y, Goudriaan J, Lantinga E A, Vos J, Spiertz H J. A flexible sigmoid function of determinate growth. Annals of Botany, 2003, 91(3): 361–371
Richards F J. A flexible growth function for empirical use. Journal of Experimental Botany, 1959, 29(10): 290–300
Thornley J H M. Growth, maintenance and respiration: a reinterpretation. Annals of Botany, 1977, 41(6): 1191–1203
Bertin N, Gary C. Évaluation d’un modèle dynamique de croissance et de développement de la tomate (Lycopersicon esculentum Mill), TOMGRO, pour différents niveaux d’offre et de demande en assimilats. Agronomie, 1993, 13: 395–405
Marcelis L F M. A simulation model for dry matter partitioning in cucumber. Annals of Botany, 1994, 74(1): 43–52
Marcelis L F M. Sink strength as a determinant of dry matter partitioning in the whole plant. Journal of Experimental Botany, 1996, 47: 1281–1291
Qi R, Ma Y T, Hu B G, de Reffye P, Cournède P H. Optimization of source-sink dynamics in plant growth for ideotype breeding: a case study on maize. Computers and Electronics in Agriculture, 2010, 71(1): 96–105
Pradal C, Dufour-Kowalski S, Boudon F, Fournier C, Godin C. Open-Alea: a visual programming and component-based software platform for plant modelling. Functional Plant Biology, 2008, 35(10): 751–760
Vos J, Evers J B, Buck-Sorlin G H, Andrieu B, Chelle M, de Visser P H B. Functional-structural plant modelling: a new versatile tool in crop science. Journal of Experimental Botany, 2010, 61(8): 2101–2115
Wilson G V. Where’s the real bottleneck in scientific computing? American Scientist, 2006, 94(1): 5–6
McMaster G S, Hargreaves J N G. CANON in D(esign): composing scales of plant canopies from phytomers to whole-plants using the composite design pattern. NJAS-Wageningen Journal of Life Sciences, 2009, 57(1): 39–51
Bouman B A M, Keulen v H, Laar v H H, Rabbinge R. The ‘school of de Wit’ crop growth simulation models: A pedigree and historical overview. Agricultural Systems, 1996, 52(2): 171–198
Spitters C J T. Crop growth models: their usefulness and limitations. ISHS Acta Horticulturae 267: VI Symposium on the Timing of Field Production of Vegetables. 1990, 349–368
Van Keulen H, Penning de Vries FWT, Drees EM. A summary model for crop growth. In: Penning de Vries F W T, van Laar H H, eds. Simulation of plant growth and crop production, Wageningen: Centre for Aqricultural Publishing and Documentation, 1982
Lithourgidis A S, Dordas C A, Damalas C A, Vlachostergios D N. Annual intercrops: an alternative pathway for sustainable agriculture. Australian Journal of Crop Science, 2011, 5(4): 396–410
Ouma G P J. Sustainable horticultural crop production through intercropping: the case of fruits and vegetable crops: a review. Agriculture and Biology Journal of North America, 2010, 1(5): 1098–1105
Henke M, Sarlikioti V, Kurth W, Buck-Sorlin G H, Pagès L. Exploring root developmental plasticity to nitrogen with a three-dimensional architectural model. Plant and Soil, 2014, 385(1): 49–62
Author information
Authors and Affiliations
Corresponding author
Additional information
Michael Henke received his Diploma degree in computer science from the Cottbus University of Technology, Germany. Currently, he is working on his PhD in applied computer science at the Department of Ecoinformatics, Biometrics and Forest Growth, University of Gottingen, Germany. From 2009 to 2010, he was a visiting scholar at Zhejiang University, China. He worked as an assistant lecturer at Cottbus University of Technology and University of Gottingen, Germany, and as a researcher at French National Institute for Agricultural Research, Angers, France in 2013 and 2014, and also worked inWageningen UR, the Netherlands from 2014 to 2016. His research interests are functional-structural plant modelling and light calculation.
Winfried Kurth received his Diploma degree in mathematics, and PhD in theoretical computer science from Clausthal University of Technology, Germany. Subsequently, he was a junior researcher at the Universities of Göttingen and Bayreuth. From 2001 to 2008, he was a professor in practical computer science and graphics systems at Cottbus University of Technology, Germany. Since 2008, he is a professor in computer graphics and ecological informatics at University of Göttingen, Germany. His research fields include rulebased languages, representation of 3D data, functional-structural plant models, and simulation.
Gerhard H. Buck-Sorlin received his Diploma degree in biology at the University of Göttingen, Germany, and his PhD in biology at the University of Wales in Bangor, UK in 1997. Subsequently, he worked as a postdoctoral scientist at the Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany, and at Cottbus University of Technology, Germany from 1997 to 2007, and as a guest professor at the Zhejiang University, China from 2005 to 2009. Between 2007 and 2011, he worked as a senior scientist at Wageningen UR, the Netherlands. Since 2011, he is a professor in Fruit Tree Culture andModelling at Agrocampus Ouest, Centre d’Angers, France. His research fields include ecophysiology of crop plants, and functional-structural plant modelling.
Rights and permissions
About this article
Cite this article
Henke, M., Kurth, W. & Buck-Sorlin, G.H. FSPM-P: towards a general functional-structural plant model for robust and comprehensive model development. Front. Comput. Sci. 10, 1103–1117 (2016). https://doi.org/10.1007/s11704-015-4472-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11704-015-4472-8