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DigR

DigR is a generic root architectural and structural model.


Many models already exist through literature dealing with root system representation, among which pure structure models such as Root Typ (Pagès et al. 2004)SimRoot (Lynch et al. 1997), AmapSim (Jourdan and Rey 1997); diffusion PDE models (Bastian et al. 2008; Bonneu et al. 2009); and structure/function that are rather scarce and recent [6 Dupuy] may be aroused.

Nevertheless in these studies, root architecture modelling was not carried out at organ level including environmental influence and not designed for integration into a whole plant characterization. We propose here a multidisciplinary study on root system from field observations, architectural analysis, formal and mathematical modeling and finally software simulation. Each speciality is individually investigated through an integrative and coherent approach that leads to a generic model (DigR) and its software simulator. This representation is designed for further integration into a global structure/function plant model.

DigR model is based on three main key points: (i) independent root type identification (ii) architectural analysis and modeling of root system at plant level; (iii) management of root architecture setup indexed on root length. Architecture analysis applied to root system (Atger and Edelin 1994) leads to root type organisation for each species. Roots belonging to a particular type share dynamical and morphological characteristics. Root architectural setup consists in topological features as apical growth, lateral branching, senescence and death, and geometrical features as secondary growth and axes spatial positioning. These features are modeled in DigR through 23 parameters whose values can evolve as a function of length position along the root axes for each root type. Topology rules apical growth speed, delayed growth, death and self pruning probabilities. Branching is characterized by spacing and mixture of lateral root types. Geometry rules root diameter increase, branching angles and growth directions (including local deviations and global reorientation).

DigR simulator provides a user interface to input parameter values specific to each species. It is integrated into the Xplo environment, which means that its multi-scale memory representation is ready for dynamical 3D visualization, statistical analysis and saving to standard format. DigR is simulated in a quasi-parallel computing algorithm and may be used either as a standalone application or integrated in other simulation platforms. This will allow further implementation of functional – structural interactions during growth simulation. The software is distributed under free LGPL license and is dedicated both to biologists and modelers.
Rey, H., Barczi, J.-F., Jourdan, C., 2011. DigR : how to model root system in its environment? 1 - the model . IBC 2011 - XVIII International Botanical congress. Melbourne : IBC 2011 - XVIII International Botanical congress, 23-30/07/2011, Melbourne, Australia.

JF. Barczi, H. Rey (Cirad AMAP) - from September 2010

soft/digr/abstract.txt · Last modified: 2014/11/21 15:44 by herve.rey