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Key words

Fabrice ROUX

Research Director CNRS (co-head of the team)

ECOGEN

RESEARCH SUBJECTS

Fabrice Roux obtained his Ph.D. degree in 2004 on the management of herbicide resistance using Arabidopsis thaliana as an experimental model (under the supervision of Xavier Reboud, laboratory of Biology and Management of Weeds, INRAE Dijon). After his Ph.D., he spent one year as a junior lecturer in the laboratory of Genetics and Evolution of Plant Populations (GEPP, University of Lille 1) and worked on the evolution of early-flowering in plants. He then spent a too short period (only one year) in the laboratory of Joy Bergelson (University of Chicago), where he became interested in identifying the genetic basis of quantitative resistance in the pathosystem A. thaliana-Pseudomonas viridiflava. Recruited as a CNRS researcher in 2006 at the GEPP (University of Lille 1), he developed his own research theme on ecological genomics of adaptation in A. thaliana. In 2012, he then co-led the research theme 'Global change: from ecological genomics to community ecology’. The research of Fabrice mainly focused on (i) the identification of the genetic basis of complex adaptive traits with the desire to replace A. thaliana in an ecologically realistic context, and (ii) the study of adaptation at different spatial and temporal scales. Since July 2013, Fabrice joined the LIPME after obtaining a junior starting grant from the Labex TULIP (Toulouse). His current projects focus on ecological genomics of organism – organism interactions. He is particularly interested in identifying the genetic basis underlying coevolution in plant-microbiota-pathobiota pathogen and plant-plant interacting systems. Since 2021, he co-leds the team with Fabienne Vailleau.

TRAINING

Recent funding

RECENT FUNDING

Recent funding

COLLABORATIONS

Collaborations

EDUCATION

Teachings

COMMITTEE MEMBER

Committee member

EDITORIAL ACTIVITY

Editorial activities

SCIENTIFIC PRODUCTION

Scientific productions

CONNECTIONS

Science & Society

SCIENCE AND SOCIETY

Science & Society

HOBBY

Hobbies

OTHER AFFILIATION

Other affiliations

 
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Fabienne VAILLEAU

Associated Professor INP-ENSAT (co-head of the team)

ECOGEN

RESEARCH SUBJECTS

Fabienne Vailleau obtained her Ph.D. degree in 2003 at the University of Toulouse, Ph.D. realized at the LIPM in Dominique Roby’s group, on the Arabidopsis thaliana/Xanthomonas campestris pv. campestris pathosystem. After her Ph.D. she was Assistant Professor at the INP-ENSAT, where she set up the Medicago truncatula/Ralstonia solanacearum pathosystem.  She was then recruited in Michel Petitprez’s group at the INP-ENSAT with a position of Associate Professor, where she continued her research on plant-bacteria interactions, giving lectures at the same time at INP-ENSAT in Plant Pathology and Weeds Science. From 2008 to 2015, she was the head of the 3rd year of specialization “Plant Agrobiosciences’. In 2008, Fabienne joined LIPM to perform her research in the group of Stéphane Genin and Christian Boucher. She worked on the post translational mechanisms required for the pathogenicity of the bacterium R. solanacearum. She obtained her Habilitation in 2016, and reoriented her projects on searching for plant proteins targeted and manipulated by R. solanacearum effectors, especially with approaches using association genetics. In 2020, she joined the team of Fabrice Roux to continue and integrate her work into a more global research theme in order to characterize and understand the molecular dialogue between the plant and its associated microbial cortege. In this context, she is currently developing a theme in the ECOGEN team on plant-microbiota-pathobiota interactions. Since 2021, she co-leds the team with Fabrice Roux.

TRAINING

Recent funding

RECENT FUNDING

Recent funding

COLLABORATIONS

Collaborations

EDUCATION

Teachings

COMMITTEE MEMBER

Committee member

EDITORIAL ACTIVITY

Editorial activities

SCIENTIFIC PRODUCTION

Scientific productions

CONNECTIONS

Science & Society

SCIENCE AND SOCIETY

Science & Society

HOBBY

Hobbies

OTHER AFFILIATION

Other affiliations

 
 
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Key words

Dominique ROBY

Research Director CNRS

ECOGEN

RESEARCH SUBJECTS

Dominique ROBY, Research Director CNRS

Dominique did her PhD in the Laboratory of Plant Physiology in Toulouse; her work concerned the study of defense mechanisms triggered by fungal elicitors in plants and the signalling role of ethylene. She was then recruited in 1982 as a CNRS researcher to work on the regulation of chitinase genes in plants upon fungal infection. After 4 years, she moved to Rutgers University (USA) and then to the Department of Agricultural Products of E. DuPont de Nemours (USA) where she investigated the role and transcriptional regulation of chitinase genes during plant immune responses. Then she joined the LIPM in 1990 and started a group in collaboration with Yves Marco, working on plant-bacteria interactions, and more particularly on plant genes involved in the control of the Hypersensitive Response, a form of programmed cell death for which there was still very limited information. The main goals of her research are now to identify  key components of quantitative disease resistance (QDR) in Arabidopsis to an agronomically important pathogen: Xanthomonas campestris, and to understand the role of some QDR components on the plant microbiota. In parallel, she is exploring the genetic and molecular bases of competitive plant-plant interactions. These projects, first developed in tight collaboration with Fabrice Roux, are now run in the ECOGEN team. 

Dominique has been director of the LIPM from 2011 to 2015, coordinator of the LabEx TULIP from 2011 until 2019 (https://www.labex-tulip.fr/Le-LabEx) and is currently Deputy Head of INRA Division - Plant Health & Environment  (http://www.spe.inra.fr/) since 2013.

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Mathieu HANEMIAN

Researcher INRAE

ECOGEN

RESEARCH SUBJECTS

During my 1st postdoc in Olivier Loudet's team at INRA Versailles, I used quantitative genetics combined with high throughput phenotyping to identify the genetic and molecular bases of vegetative growth in A. thaliana. The use of natural variation in these experiments led me to work on the ecological reasons of plant adaptation and in evolutionary biology. I did a 2nd postdoc in Cris Kuhlemeier's team at the University of Bern, where I studied the influence of pollinators on speciation in the Petunia genus, combining quantitative genetics, functional genomics and molecular biology.

I joined the ECOGEN team as a researcher since October 2019, to work on the molecular mechanisms involved in natural variation of the response to other plant species in A. thaliana. This is a fascinating subject because despite the importance of the interactions between plants in shaping plant communities, we know very little about the mechanisms of adaptation and co-evolution between them. In addition, a better understanding of these interactions may be useful for the agroecological transition.

TRAINING

2006 - BSc Sciences, Technologies, Health major in Biology - University of Burgundy, France

2007 - MSc (1st year) Sciences & Plant Technologies - University of Burgundy, France

2008 - MSc (2nd year) Microbiology-Agrobiosciences - University Toulouse III, France

2012 - PhD in Plant-Microbe Interactions - University Toulouse III, France

RECENT FUNDING

2020-2023 – PhD project – Plant-Plant interactions : Functional analysis of a gene involved in the response to competition in A. thaliana. Co-funded INRAE Plant Health Department (47 k€) - Occitanie Région (55 k€). Co-Pis with Dominique Roby

2021-2022 – PIPPIN project. Pathways involved in Plant-Plant interactions. Département INRAE – SPE. 27k€. PI

2019 - Unibe initiator grant 2019 (#38990), 20kCHF, PI (declined)

EDUCATION

2021 – Practical « From QTL mappingto gene identification and more » over 2 days

2021/2022 – Tutelage in the Junior Lab (master international Functional Biology & Ecology)

COMMITTEE MEMBER

  • Member of the LIPME sustainable development committe (2020-)

  • Member of the LIPME lab council (2021-)

  • Member of the pedagogic council of the labex (2020-), with a particular focus on the Guided Tour and Junior Lab modules from the international TULIP master « Functional Biology and Ecology »

SCIENTIFIC PRODUCTION

Hanemian, M., Vasseur, F., Marchadier, E., Gilbault, E., Bresson, J., Gy, I., Violle, C., and Loudet, O. (2020). Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana. Nature Communications 11: 4140.

Yarahmadov, T., Robinson, S., Hanemian, M., Pulver, V., and Kuhlemeier, C. (2020). Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes. The Plant Journal 104(2):289-301.

Marchadier, E., Hanemian, M., Tisné, S., Bach, L., Bazakos, C., Gilbault, E., Haddadi, P., Virlouvet, L., and Loudet, O. (2019). The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana. PLOS Genetics 15: e1007954.

Bazakos, C., Hanemian, M., Trontin, C., Jiménez-Gómez, J.M., and Loudet, O. (2017). New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype. Annual Review of Plant Biology 68: 435–455.

Hanemian, M. et al. (2016). Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway. New Phytologist 211: 502–515.

Yadeta, K.A., Valkenburg, D.-J., Hanemian, M., Marco, Y., and Thomma, B.P.H.J. (2014). The Brassicaceae-Specific EWR1 Gene Provides Resistance to Vascular Wilt Pathogens. PLOS ONE 9: e88230.

Hanemian, M., Zhou, B., Deslandes, L., Marco, Y., and Trémousaygue, D. (2013). Hrp mutant bacteria as biocontrol agents. Plant Signal Behav 8: e25678.

Feng, D.X., Tasset, C., Hanemian, M., Barlet, X., Hu, J., Trémousaygue, D., Deslandes, L., and Marco, Y. (2012). Biological control of bacterial wilt in Arabidopsis thaliana involves abscissic acid signalling. New Phytologist 194: 1035–1045.

Yadeta, K.A., Hanemian, M., Smit, P., Hiemstra, J.A., Pereira, A., Marco, Y., and Thomma, B.P.H.J. (2011). The Arabidopsis thaliana DNA-Binding Protein AHL19 Mediates Verticillium Wilt Resistance. MPMI 24: 1582–1591.

CONNECTIONS

HOBBY

Gardening (where I most probably learn more about plants than during research work!)

Hiking

 
 
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Carine HUARD-CHAUVEAU

Engineer INRAE

ECOGEN

RESEARCH SUBJECTS

During her PhD in the Protein Biochemistry and Structure laboratory, INRAE Jouy-en Josas, Carine worked on the characterization of peptidoglycan hydrolases of Lactococcus lactis. She was then recruited in the Small Ruminant Pathology unit of Sophia-Antipolis laboratory of ANSES (French Agency for food, environmental, and occupational health and safety). She joined the LIPM in 2005. She developed projects to characterize genes controlling quantitative resistance of Arabidopsis to Xanthomonas campestris pv campestris. She used approaches including molecular biology, transcriptomic, system biology and functional genomic.

TRAINING

1997 - Maîtrise de Biologie Cellulaire et Physiologie - Université de Versailles St Quentin-en-Yvelines (78)

1998 - DEA Activités Biologiques des Substances Naturelles - Muséum National d’Histoire Naturelle, Paris (75)

2002 - Thèse spécialité « Sciences Alimentaires » - Université Paris-Saclay (91)

RECENT FUNDING

2020-2023 – PhD project – Plant-Plant interactions : Functional analysis of a gene involved in the response to competition in A. thaliana. Co-funded INRAE Plant Health Department (47 k€) - Occitanie Région (55 k€). Co-Pis with Dominique Roby

2021-2022 – PIPPIN project. Pathways involved in Plant-Plant interactions. Département INRAE – SPE. 27k€. PI

2019 - Unibe initiator grant 2019 (#38990), 20kCHF, PI (declined)

COMMITTEE MEMBER

  • Référente Développement Durable pour le LIPME et animateur comité DD du LIPME (2020-   )

  • Membre de la « Commission avancement ITA » (2011-  ).

  • Membre élu du Conseil Scientifique du laboratoire LIPME (2016 - 2020)

  • Membre élu au Conseil De Laboratoire (2007 et 2015)

  • Membre nommé au CLHS (2005 - 2017)

  • Assistant Prévention INRA (2005 – 2017)

SCIENTIFIC PRODUCTION

  • F. Delplace*,. Huard-Chauveau; R Berthomé, D. Roby. Network organization of the plant immune system: from pathogen perception to robust defense induction. Review The Plant Journal. On line August 2021 ; https://doi.org/10.1111/tpj.15462.

  • F. Delplace*, C. Huard-Chauveau*, U. Dubiella, E. Alvarez, G. Langin, M. Khafif, F. Roux, R. Peyraud, D. Roby. 2020. Robustness of plant quantitative disease resistance is provided by a decentralized immune network. PNAS 117(30):18099-18109. (*co-premier auteur). ; https://doi.org/10.1073/pnas.2000078117.

  • M. Debieu*, C. Huard-Chauveau*, A. Genissel, F. Roux, D. Roby. 2016 Quantitative Disease Resistance to the bacterial pathogen Xanthomonas campestris involves an Arabidopsis immune receptor pair and a gene of unknown function. Molecular Plant Pathology. (*co-premier auteur).  doi: 10.1111/mpp.12298.

  • C. Huard-Chauveau, L. Perchepied, M. Debieu, S. Rivas,T, Kroj, I. Kars, J. Bergelson, F. Roux and D. Roby. 2013. An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis. PLoS Genetics 9(9): e1003766. https://doi.org/10.1371/journal.pgen.1003766.

  • Brevet européen : DI CNRS 05912/01 - INRA DI-RV-11-0051 – Resistance to black rot disease in plants from , and families ; dépôt le 27/01/2012.

 

Others publications since 2017 :

  • C. Bartoli, L. Frachon, M. Barret, M. Rigal, C. Huard-Chauveau, B. Mayjonade, C. Zanchetta, O. Bouchez, D. Roby, S. Carrère and F. Roux. 2018. In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana. The ISME Journal. doi: 10.1038/s41396-018-0152-7.

  • Wang, F. Roux, C. Bartoli, C. Huard-Chauveau, H. Lee, C. Meyer, D. Roby, M. S. McPeeky, J. Bergelson. 2018. Two-Way Mixed-Effects Methods for Joint Association Analysis Using Both Host and Pathogen Genomes. PNAS. https://doi.org/10.1073/pnas.

  • L. Frachon*, C. Libourel*, R. Villoutreix, S. Carrère, C. Glorieux, , M. Navascués, L. Gay, R. Vitalis, E. Baron, L. Amsellem, O. Bouchez, M. Vidal, V. Le Corre, D. Roby, J. Bergelson and F. Roux. 2017. Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nature Ecology & Evolution. Erratum in Nat Ecol Evol. 2018 (* co-contributeurs). doi: 10.1038/s41559-017-0297-1.

  • M. Khafif*, C. Balague*, , D. Roby. 2017. An essential role for the VASt domain of the Arabidopsis VAD1 protein in the regulation of defense and cell death in response to pathogens. PloS One. (* co-contributeurs).  https://doi.org/10.1371/journal.pone.0179782.

  • F. Roux, D. Voisin, T. Badet, C. Balagué, X. Barlet, , D. Roby, S. Raffaele. Resistance to phytopathogens e tutti quanti: placing plant Quantitative Disease Resistance on the map. Molecular Plant Pathology 2014 : 15(5) :427-432. doi: 10.1111/mpp.12138.

 
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Baptiste MAYJONADE

Engineer INRAE

ECOGEN

RESEARCH SUBJECTS

Baptiste obtained a Master degree at the University of Limoges in 2010. He spent two years in the laboratory of molecular biology of Limagrain Europe (Chappes). In the context of molecular breeding and marker-assisted selection, he developed molecular markers on crops. In 2012, he joined the LIPME to work on the genetics and genomics of response to biotic and abiotic stresses in sunflower. He was in charge of projects related to transcriptomics and genomics. He was also involved in the development of technologies in molecular biology. Since September 2015, he has a permanent position in the ECOGEN team. He is responsible for the genomic, ecological and phenotypic characterization of 168 populations of Arabidopsis thaliana located southwest of France, and their associated plant and microbial communities. To do this, it implements innovative methodologies, in particular based on the most recent high-throughput sequencing technologies.

Key words

 
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Chrystel GIBELIN-VIALA

Engineer Assistant INRAE

ECOGEN

RESEARCH SUBJECTS

Chrystel Gibelin-Viala was recruited at INRA Poitou-Charentes in 2000. She worked in the molecular biology laboratory of URP3F, unit which study the functioning of the forage crop on grassland. She joined the LIPME in 2009 in the group of Clare Gough and Julie Culimore, where she studied the arbuscular mycorrhizal symbiosis using potential mutants of mycorrhization. She also developed genetic approaches to dissect the host range control in the rhizobium-legume symbiosis. Since January 2020, she joined the team of Fabrice Roux, ECOGEN (Ecological genomics of adaptation in plant communities). Her main missions are focused on the plant-microbiota-pathobiota interactions, one of the ECOGEN team themes of research. One of her main objectives is to contribute to characterize and understand the molecular dialog between Arabidopsis thaliana and its microbial cortege. Chrystel has skills in molecular biology (DNA extraction, PCR, genotyping), microscopy, plant biology (plant supply, plant experimentation, phenotyping), microbiology.

Key words

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Béatrice GABINAUD

Technician INRAE

ECOGEN

RESEARCH SUBJECTS

Béatrice joined INRAE ​​in 1993 at Nantes veterinary school, after a master's degree in organism and population biology and a master in parasitology. Her assignments focused on model animal surgery (Duchene muscular dystrophy), primary satellite cell cultures, histology and microscopy (image analysis). Following a mobility in 1999 at GenPhySE (genetics, physiology and breeding systems), she worked for 7 years on meat quality, and then 14 years on the characterization of the microbiota of farm animal digestive ecosystems by preparing samples for sequencing (DNA extraction, PCR, qPCR, microbiology).

Then she wanted to work with plants and joined the ECOGEN team in September 2020 (part-time 50%) to monitor plants grown in the field or in the greenhouse, and to perform the molecular characterization of interspecific plant-plant interactions (Arabidopsis thaliana with 4 associated species).

During her other half of the part-time, she works on the Plant Production and Experimentation platform of the LIPME.

Key words

 
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Rémy ZAMAR

Technician INRAE

ECOGEN

RESEARCH SUBJECTS

After achieving a BEP in horticultural production, Rémy obtained a BAC Pro degree in landscaping. Since July 2018, Rémy has been using his multiple skills in experimentation and plant production on the following successive projects: OPTIMA (Testing local adaptation to climate, soil and microbiota in Arabidopsis thaliana), PLANTSYS (Predicting plant phenotype using systems biology in Arabidopsis thaliana) and DEEP-IMPACT (Analysis of plant-microbiota interactions to promote plant defense against pests and diseases in canola and wheat).

Key words

 
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Choghag DEMIRJIAN

PhD student

ECOGEN

RESEARCH SUBJECTS

Choghag Demirjian obtained her master degree specialized in plant production from the Lebanese University in 2016. She did her master internship at the International Center for Agricultural Research in the Dry Areas (ICARDA), where she worked on the identification of drought tolerance QTLs in cultivated wheat. Choghag joined LIPME as a PhD student in January 2019, under the co-supervision of Fabienne Vailleau and Richard Berthomé on the project entitled “Deciphering Arabidopsis thaliana responses to Ralstonia solanacearum virulence factors through the study of plant natural variation”. The aim of her Ph.D. project is to study interesting type III effectors of Ralstonia solanacearum and to characterize their role in plant response using natural plant variation.

Key words

 
 
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Daniela RAMIREZ-SANCHEZ

PhD student

ECOGEN

RESEARCH SUBJECTS

Daniela obtained a Bachelor degree in Biotechnology Engineering in 2013, then she obtained her Master’s degree in Genetics and Molecular Biology in the center for research and advanced studies (Cinvestav) in Mexico City in 2016, where she studied the microbiota functionality of the distal colon of Mexican population. In 2017 she worked in a Pharmaceutical Product Development (PPD) company in Mexico as a Clinical Trial Coordinator. She joined the LIPME in October 2019 to start her PhD under the supervision of Fabrice Roux and Fabienne Vailleau aiming to establish  in Arabidopsis thaliana a genomic map of local adaptation to the most common leaf bacterial species in southwest France.

Key words

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Marie INVERNIZZI

PhD student

ECOGEN

RESEARCH SUBJECTS

Marie Invernizzi joined the ECOGEN team in October 2020 to start a PhD thesis under the direction of Dominique Roby and Mathieu Hanemian. Her project seeks to understand plant-plant interactions and more particularly, the pathways leading to Arabidopsis thaliana response to plant competition.

TRAINING

She obtained her Population and organisms Biology licence at the University of Toulouse in 2017. Then, she did a master’s degree in plant sciences at the University of Toulouse in 2019. In this context, she did two internships in Dominique Roby's team at the LIPM on the understanding of the molecular pathways leading to quantitative disease resistance to Xanthomonas campestris pv. campestris in Arabidopsis thaliana. After her Master, she work 1 year for Syngenta as a project leader in the Europe Corn Patholgy team. She studied mycotoxins and the corn genomic response to Fusarium Wilt.

RECENT FUNDING

Her PhD is funded by INRAe and Occitanie region.

COMMITTEE MEMBER

  • Marie is a member of the Sustainable development committee, and of the Health and safety committee.

CONNECTIONS

HOBBY

« I love plants, and my cats. I draw; I read a lot, especially about History or sciences like Astronomy. And in case you were wondering, my favorite dinosaur is the Triceratops.»

 
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Rémi DUFLOS

PhD student

ECOGEN

RESEARCH SUBJECTS

Rémi Duflos obtained two master degrees in 2021, the first one at INP-ENSAT University (Toulouse, France) in AgroBiosciences and the second one at Paul Sabatier University (Toulouse, France) in Plant Biology. He performed his Master internship in the ECOGEN team, under the supervision of Fabienne Vailleau and Fabrice Roux. The goal of this project was the establishment of a genomic map of local adaptation in Arabidopsis thaliana to its most abundant bacterial species in the leaf compartment in south-west of France. His PhD   project follows this internship with (i) the functional validation of candidates genes underlying QTLs identified in A. thaliana during his Master internship, and (ii) the identification, in Pseudomonas koreensis, of genes that mediate the genetic and molecular dialog with A. thaliana.

Key words

 
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Former members

Post-docs

Claudia Bartoli - post-doc (2014-2016)

Ullrich Dubiella - post-doc (2015-2018)

Tatiana Vernié- post-doc (2017-2018)

Florent Delplace - post-doc (2020-2021)

 

PhD students

Romain Villoutreix (2010-2013)

Etienne Baron (2011-2014)

Lea Frachon (2014-2017)

Cyril Libourel (2015-2019)

Nathalie Aoun (2016-2019)

Lorenzo Favale (2017)

Jaishree Subrahmaniam (2017-2020)

Florent Delplace (2017-2020)

Nargess Razavi (2017-2021)


 

Students

Cyril Libourel - Master 2 (2015)

Eve Coutant - Master 1 (2015)

Arnaud Chevalier-Mairet - Master 1 (2016)

Wijmer Taeken - Master 1 (2016)

Thomas Dussarat - Master 1 (2017)

Arnaud Chevalier-Mairet - Master 2 (2018)

Laurie Thailades - Master 1 (2019)

Alexandre Boubegtitène - Master 2 (2021)

Rémi Duflos - Master 2 (2021)

Paul Baumet - Master 1 (2021)

Manon Pradel - Master 1 (2021)