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1.  Towards aspect-oriented functional–structural plant modelling 
Annals of Botany  2011;108(6):1025-1041.
Background and Aims
Functional–structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty.
Methods
The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module.
Key Results
The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes.
Conclusions
This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further extended into an aspect-oriented programming language for FSPMs.
doi:10.1093/aob/mcr121
PMCID: PMC3189837  PMID: 21724653
L-system; aspect-oriented programming; Actinidia deliciosa (kiwifruit); functional–structural plant model; plant architecture; carbon dynamics; biomechanics; hormone transport
2.  A functional–structural kiwifruit vine model integrating architecture, carbon dynamics and effects of the environment 
Annals of Botany  2010;107(5):747-764.
Background and Aims
Functional–structural modelling can be used to increase our understanding of how different aspects of plant structure and function interact, identify knowledge gaps and guide priorities for future experimentation. By integrating existing knowledge of the different aspects of the kiwifruit (Actinidia deliciosa) vine's architecture and physiology, our aim is to develop conceptual and mathematical hypotheses on several of the vine's features: (a) plasticity of the vine's architecture; (b) effects of organ position within the canopy on its size; (c) effects of environment and horticultural management on shoot growth, light distribution and organ size; and (d) role of carbon reserves in early shoot growth.
Methods
Using the L-system modelling platform, a functional–structural plant model of a kiwifruit vine was created that integrates architectural development, mechanistic modelling of carbon transport and allocation, and environmental and management effects on vine and fruit growth. The branching pattern was captured at the individual shoot level by modelling axillary shoot development using a discrete-time Markov chain. An existing carbon transport resistance model was extended to account for several source/sink components of individual plant elements. A quasi-Monte Carlo path-tracing algorithm was used to estimate the absorbed irradiance of each leaf.
Key Results
Several simulations were performed to illustrate the model's potential to reproduce the major features of the vine's behaviour. The model simulated vine growth responses that were qualitatively similar to those observed in experiments, including the plastic response of shoot growth to local carbon supply, the branching patterns of two Actinidia species, the effect of carbon limitation and topological distance on fruit size and the complex behaviour of sink competition for carbon.
Conclusions
The model is able to reproduce differences in vine and fruit growth arising from various experimental treatments. This implies it will be a valuable tool for refining our understanding of kiwifruit growth and for identifying strategies to improve production.
doi:10.1093/aob/mcq180
PMCID: PMC3077975  PMID: 20855486
Actinidia deliciosa; kiwifruit; L-systems; plant architecture; carbon allocation; functional–structural plant model
3.  A functional–structural modelling approach to autoregulation of nodulation 
Annals of Botany  2010;107(5):855-863.
Background and Aims
Autoregulation of nodulation is a long-distance shoot–root signalling regulatory system that regulates nodule meristem proliferation in legume plants. However, due to the intricacy and subtleness of the signalling nature in plants, molecular and biochemical details underlying mechanisms of autoregulation of nodulation remain largely unknown. The purpose of this study is to use functional–structural plant modelling to investigate the complexity of this signalling system. There are two major challenges to be met: modelling the 3D architecture of legume roots with nodulation and co-ordinating signalling-developmental processes with various rates.
Methods
Soybean (Glycine max) was chosen as the target legume. Its root system was observed to capture lateral root branching and nodule distribution patterns. L-studio, a software tool supporting context-sensitive L-system modelling, was used for the construction of the architectural model and integration with the internal signalling.
Key Results
A branching pattern with regular radial angles was found between soybean lateral roots, from which a root mapping method was developed to characterize the laterals. Nodules were mapped based on ‘nodulation section’ to reveal nodule distribution. A root elongation algorithm was then developed for simulation of root development. Based on the use of standard sub-modules, a synchronization algorithm was developed to co-ordinate multi-rate signalling and developmental processes.
Conclusions
The modelling methods developed here not only allow recreation of legume root architecture with lateral branching and nodulation details, but also enable parameterization of internal signalling to produce different regulation results. This provides the basis for using virtual experiments to help in investigating the signalling mechanisms at work.
doi:10.1093/aob/mcq182
PMCID: PMC3077977  PMID: 20826439
Legume; soybean; soya bean; virtual plant; L-system; root reconstruction; synchronization; nodulation
4.  A Canopy Architectural Model to Study the Competitive Ability of Chickpea with Sowthistle 
Annals of Botany  2008;101(9):1311-1318.
Background and Aims
Improving the competitive ability of crops is a sustainable method of weed management. This paper shows how a virtual plant model of competition between chickpea (Cicer arietinum) and sowthistle (Sonchus oleraceus) can be used as a framework for discovering and/or developing more competitive chickpea cultivars.
Methods
The virtual plant models were developed using the L-systems formalism, parameterized according to measurements taken on plants at intervals during their development. A quasi-Monte Carlo light-environment model was used to model the effect of chickpea canopy on the development of sowthistle. The chickpea–light environment–sowthistle model (CLES model) captured the hypothesis that the architecture of chickpea plants modifies the light environment inside the canopy and determines sowthistle growth and development pattern. The resulting CLES model was parameterized for different chickpea cultivars (viz. ‘Macarena’, ‘Bumper’, ‘Jimbour’ and ‘99071-1001’) to compare their competitive ability with sowthistle. To validate the CLES model, an experiment was conducted using the same four chickpea cultivars as different treatments with a sowthistle growing under their canopy.
Results and Conclusions
The growth of sowthistle, both in silico and in glasshouse experiments, was reduced most by ‘99071-1001’, a cultivar with a short phyllochron. The second rank of competitive ability belonged to ‘Macarena’ and ‘Bumper’, while ‘Jimbour’ was the least competitive cultivar. The architecture of virtual chickpea plants modified the light inside the canopy, which influenced the growth and development of the sowthistle plants in response to different cultivars. This is the first time that a virtual plant model of a crop–weed interaction has been developed. This virtual plant model can serve as a platform for a broad range of applications in the study of chickpea–weed interactions and their environment.
doi:10.1093/aob/mcn040
PMCID: PMC2710251  PMID: 18375962
Plant architecture; virtual plant modelling; L-systems formalism; crop/weed competition; integrated weed management; chickpea; Cicer arietinum; sowthistle; Sonchus oleraceus

Results 1-4 (4)