A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction

BACKGROUND AND AIMS: Functional-structural plant models (FSPM) constitute a paradigm in plant modelling that combines 3D structural and graphical modelling with the simulation of plant processes. While structural aspects of plant development could so far be represented using rule-based formalisms such as Lindenmayer systems, process models were traditionally written using a procedural code. The faithful representation of structures interacting with functions across scales, however, requires a new modelling formalism. Therefore relational growth grammars (RGG) were developed on the basis of Lindenmayer systems. METHODS: In order to implement and test RGG, a new modelling language, the eXtended L-system language (XL) was created. Models using XL are interpreted by the interactive, Java-based modelling platform GroIMP. Three models, a semi-quantitative gibberellic acid (GA) signal transduction model, and a phytochrome-based shade detection and object avoidance model, both coupled to an existing morphogenetic structural model of barley (Hordeum vulgare L.), serve as examples to demonstrate the versatility and suitability of RGG and XL to represent the interaction of diverse biological processes across hierarchical scales. KEY RESULTS: The dynamics of the concentrations in the signal transduction network could be modelled qualitatively and the phenotypes of GA-response mutants faithfully reproduced. The light model used here was simple to use yet effective enough to carry out local measurement of red:far-red ratios. Suppression of tillering at low red:far-red ratios could be simulated. CONCLUSIONS: The RGG formalism is suitable for implementation of multi-scaled FSPM of plants interacting with their environment via hormonal control. However, their ensuing complexity requires careful design. On the positive side, such an FSPM displays knowledge gaps better thereby guiding future experimental design.