Section: Partnerships and Cooperations

National Initiatives


Participants : Mikaël Lucas [IRD] , Christophe Pradal, Christophe Godin, Yann Boursiac [BPMP] , Christophe Maurel [BPMP] .

Funding: ANR (Contractor for Virtual Plants: Cirad, From 2012 to 2016)

The HydroRoot project proposes a unique combination of approaches in the model plant Arabidopsis thaliana to enhance our fundamental knowledge of root water transport. Accurate biophysical measurements and mathematical modeling are used, in support of reverse and quantitative genetics approaches, to produce an integrated view of root hydraulics. The HydroRoot project will address as yet unknown facets of root water transport. It will lead to an integrated view of root hydraulics that considers both tissue hydraulics and root architecture and explains how these components are controlled at the molecular level by physiological and/or environmental cues. Because of its strong physiological and genetic background, this research may also directly impact on breeding programs, for production of crops with optimised water usage and stress responses.


Participants : Christian Fournier, Christophe Pradal, Yann Guédon, Sarah Cohen-Boulakia, Simon Artzet, Jerome Chopard, Patrick Valduriez.

Funding: ANR-Investissement d'avenir (Contractor for Virtual Plants: INRA, From 2015 to 2018)

The goal of Phenome is to provide France with an up-to-date, versatile, high- throughput infrastructure and suite of methods allowing characterisation of panels of genotypes of different species under climate change scenarios. We are involved in the methodological part of the project, that aims at developping a software framework dedicated to the analysis of high throughput phenotyping data and models. It will based on the OpenAlea platform that provides methods and softwares for the modelling of plants, together with a user-friendly interface for the design and execution of scientific workflows. We also develop the InfraPhenoGrid infrastructure that allows high throughput computation and recording of provenance during the execution of Workflows.


Participants : Christophe Godin, Grégoire Malandain, Patrick Lemaire.

Funding: ANR (Contractor for Virtual Plants: Inria, From 2015 to 2019)

In this project, we will use advanced ligh-sheet imaging of live embryos to quantitatively describe embryonic morphogenesis in ascidians, a class of animals that undergo very rapid genomic divergence, yet show an extraordinary stasis of embryonic morphologies, based on invariant early cell lineages shared by all studied species. The global aims of the proposal, which will bridge micro- and macroevolutionary scales of analysis, are: i) to provide a global systems-level description at cellular resolution of an animal embryonic program; ii) to use this description to characterize intra-specific and inter-specific patterns of morphogenetic variations; iii) to analyze possible molecular mechanisms explaining the unusual robustness of this program to environmental and genetic perturbations. To achieve these aims, we will combine advanced live light-sheet microscopy, computational biology, functional gene assays and evolutionary approaches.

Leaf Serration

Participants : Christophe Godin, Eugenio Azpeitia.

Funding: ANR (Contractor for Virtual Plants: Inria, From 2014 to 2019)

Leaf growth and development result from the coordination in time and space of cellular divisions and cellular expansion, and expansion of certain plant cells reaches up to one thousand times their size when living the meristem. Transcription factors belonging to the CUP-SHAPED COTYLEDON (CUC) genes and homeodomain genes of the KNOTTED-LIKE (KNOXI) family were shown to be essential for the control of leaf size and shape. In addition, the phytohormone auxin is a critical regulator of growth and development, involved in the regulation and coordination of cell division and cell expansion. The mechanisms of auxin signalling are based on a complex set of co-receptors exhibiting high to low affinity for auxin and an even more complex modular network of transcriptional repressors and activators tightly controlling the expression of a large set of genes.

The SERRATIONS project is based on recent data relative to key transcription factors regulating leaf morphogenesis and advanced knowledge on the generic signalling mechanisms of the phytohormone auxin that plays a critical role in the control and coordination of cellular responses sustaining leaf size and shape. The goal of the project is to identify auxin signalling modules involved in leaf morphogenesis and to integrate these data in mathematical modelling to provide new insights into complex regulatory networks acting on leaf morphogenesis and to further test model-derived hypotheses.

Other national grants


Participants : Pierre Fernique, Yann Guédon, Christophe Pradal, Christophe Godin, Frédéric Boudon, Jean-Baptiste Durand.

Funding: Inria ADT (Contractors for Virtual Plants: Inria from 2014 to 2016)

The goal of this project is to improve the software quality and the dissemination of Vplants components for plant phenotyping. Virtual Plants team has played a pioneering role in the development of methods for analyzing plant development that take account of the complexity of plant architecture. Numerous software components has been developed for more than 20 years and a profound re- engineering is now necessary to facilitate the collaborations with biologist and agronomists of CIRAD, INRA and IRD and to help the dissemination of ours methods in the scientific community.


Participants : Christophe Godin, Frédéric Boudon, Olivier Ali, Jean Phillipe Bernard, Hadrien Oliveri, Christophe Pradal, Guillaume Cerutti, Grégoire Malandain, François Faure, Jan Traas, François Parcy, Arezki Boudaoud, Teva Vernoux.

Funding: Inria Project Lab (From 2013 to 2017)

Morphogenetics is an Inria transversal project gathering 3 Inria teams and two Inra teams. It aimed at understanding how flower shape and architecture are controlled by genes during development. Using quantitative live-imaging analysis at cellular resolution we will determine how specific gene functions affect both growth patterns and the expression of other key regulators. The results generated from these experiments will be integrated in a specially designed database (3D Atlas) and used as direct input to new predictive computational models for morphogenesis and gene regulation. Model predictions will then be further tested through subsequent rounds of experimental perturbation and analysis. A particular emphasis will be put on the modeling of mechanics in tissues for which different approaches will be developed.

Partners: RDP ENS-Lyon; Imagine Inria Team (Grenoble); Morpheme Inria Team (Sophia-Antipolis), UMR PCV (Grenoble).


Participants : Christophe Godin, Frédéric Boudon.

Funding: INRA - PhD project (From 2016 to 2019)

In this project we want to quantify and understand how sugars interfere with hormonal signals (auxin, cytokinins) to regulate lateral bud outgrowth of aerial stems of roses. Experiments will be made on Rose stems to test different levels of sugar conditions and hormonal concentrations on bud outgrowth. An extension of the recently published hormonal model of apical dominance will be made to take into account the role of carbon as a signaling molecule.

Partners: UMR SAGAH, Angers


Participants : Christophe Pradal, Sarah Cohen-Boulakia, Jerome Chopard.

In the life science domain, scientists are facing the deluge and the size of available data, the composition of a myriad of existing tools, and the complexity of computational experiment. In this context, reproducing an experiment is particularly difficult, as evidenced by numerous recent studies. The aim of this GDR CNRS project is to make a complete review of existing approaches in this field, considering in priority as elements of solution: (i) scientific worklfows, (ii) data provenance, and (iii) virtual machines. This project brings together experts in data bases, algorithms and virtual environments, working in the domain of life science.

Funding: GDR - CNRS