VIRTUAL PLANTS Research team
Modeling plant morphogenesis at different scales, from genes to phenotype
- Leader : Christophe Godin
- Research center(s) : CRI Sophia Antipolis - Méditerranée
- Field : Digital Health, Biology and Earth
- Theme : Computational Biology
- Partner(s) : CIRAD,INRA
- Collaborator(s) : Amélioration génétique et adaptation des plantes (AGAP)
Plants are branching living organisms that develop throughout their lifetimes. Organs are created by small embryogenetic regions at the tip of each axis, called apical meristems. In the project Virtual Plants, we are interested in studying plant apical meristem functioning and development. We believe that a detailed analysis at different temporal and spatial scales of apical meristem processes, based on advanced mathematical and computational methods and tools, will lead us to get a deeper and better understanding of plant development. In particular, we intend to exploit the new data that come from developmental biology and genetics to build up new models of plant development that integrate genetic and hormonal mechanisms.
This study is performed from two complementary perspectives:
- Axis 1: Analysis of structures produced by meristems. At a macroscopic level, we develop an extensive methodology to analyze the structures produced by meristems. This can be seen as a methodology that aims to solve an inverse problem in which one tries to infer meristem functioning from the complex structures they produce. This analysis is carried out at different spatial and temporal scales. Here, we develop methods in domains such as stochastic modeling (Markovian models, renewal processes), fractal analysis, graph theory (multiscale graphs, tree comparison).
- Axis 2: Meristem functioning aand development. At a more microscopic level, we intend to exploit the recent spectacular scientific and technological progresses in developmental biology in order to understand how physiological and genetic processes control meristem growth at cell and tissue scale. For this we build detailed 3D models of meristem using 3D geometrical modeling, partial differential equations, dynamic systems with dynamic structures, mechanical models of tissues, transport models at cellular scale, gene networks
All these tools are integrated in a common software platform V-Plants that is available to all the partners of Virtual Plants. At a national and international level, we coordinate the development of an open software platform OpenAlea for plant modelling (based on V-Plants).
International and industrial relations
- LABRI (U. Bordeaux), IBISC(U. Evry), UMR PIAF (INRA), UMR DAP (INRA, ENSAM), UMR LEPSE (INRA), UMR DIAPC (IRD), PHIV (CIRAD), LIRMM (Montpellier), ENS-Lyon, INRIA (project-teams Asclepios, Evasion).
- ACI Project Arborescences (LABRI Bordeaux, U. Claude-Bernard Lyon, UMR DAP, U. Joseph-Fourier Grenoble)
- ANR project NatSim (IRIT Toulouse, INRIA-Futur, INRIA Rhône-Alpes)
- ANR project CarpVirtuel (ENS-Lyon)
- ATP project Meristème (CIRAD, INRA, INRIA-Sophia Antipolis-Méditerranée)
- U. Calgary (Canada), U. Queensland (Bresban, Australy), Norwich Center (UK) HortResearch (New Zealand), U. Kasetsart (Bangkok, Thailand), U. Bel Abes (Algeria).
- Marie-Curie Research Training Network SY-STEM: modelling of the apical meristem development in Arabidopsis.
- ANR-BCSRC Flower Models: modelling flower development and its control by genes.