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Welcome to the ECOGEN lab!

The main objective of our team is to understand and predict biotic interactions with plants in the context of global changes by establishing a continuum from molecular biology and quantitative genetics to evolutionary ecology. This lofty goal requests (i) the identification of the main ecological factors acting as selective agents on plants, (ii) the description of the genetic architecture underlying adaptation in plants, and (iii) the identification and understanding of genetic and molecular determinants of adaptation, in particular the ones involved in plant-microbiota-pathobiota interactions and plant-plant interactions.


We work on the wild plant Arabidopsis thaliana as well as on the crop species wheat, rapeseed and tomato. To achieve our scientific goals, we promote interdisciplinarity and we developed strong collaborations at the local, national and international levels. We also offer an environment that favors training in complementary disciplines (ecology, molecular biology and quantitative genetics) and career development in an international spirit.


You like our research! You want to join the team!  Feel free to contact any member of the team to initiate discussion. We may have some money on current projects or we can help you to apply for some fellowships (ERC, Marie-Curie, EMBO…).

Stay connected and follow us on Twitter @EcogenLab

Nom equipe


Human activities generate numerous global changes, such as climate change, agricultural intensification, urbanization and landscape fragmentation. Global changes have major impacts on biodiversity. A potential lack of response of species to selection due to environmental changes would cause an erosion of biodiversity by disrupting ecosystems sustainably. This is especially important for plants whose dispersion is on average limited in comparison to animals. In this context, one of the main challenges in ecological genomics is to identify and understand the genetics of adaptation in plants. Adding ecology to the studies of adaptive genetics will help to estimate the adaptive dynamics of plants in response to natural selection and / or changes resulting from anthropogenic environments.


Establishing the causal relationship between adaptation and genetic changes is however extremely challenging in natural systems, largely due to the difficulties in identifying ecological factors acting as selective agents. In addition, we have to keep in mind that the adaptive potential response from a plant species to global changes will not only depend on its direct interactions with the abiotic environment, but also on the environmental effects on its biotic interactions (plant-microbiota-pathobiota interactions, plant-plant interactions…). In addition, our knowledge on adaptive dynamics of organism–organism interacting systems, and more precisely on co-evolution among several interacting species, remains surprisingly very limited. This is particularly relevant when studying the recruitment of mutations in biotic partners conferring the phenotypic variant likely to be retained by natural selection.

More precisely, we aim at answering to three key transversal questions:

  1. What are the main ecological factors (climate, soil physico-chemical properties, microbiota / pathobiota, plant communities…) acting as selection agents on plants?

  2. What are the genetic and molecular mechanisms of quantitative immunity, in ecologically relevant environments?

  3. What are the genetic and molecular mechanisms driving natural variation of plant-plant interactions, in particular competition and cooperation?

Questions scientifiques




Running projects

  • 2024-2025: Projet ANR SAPS-AI AssoCultures (Co-innovation agroécologique pour favoriser une production maraîchère durable). 150k€. Co-PIs: Mathieu Hanemian & Camille Dumat (in collaboration with La Milpa)

  • 2024-2025: Projet Métaprogramme METABIO CoCultures (Co-innovation agroécologique pour une production alimentaire durable dans les jardins et les exploitations maraîchères). 20k€. Co-PIs: Mathieu Hanemian, Camille Dumat & Sébastien Chalies

  • 2024-2025: Projet INRAE SPE D-P-CH (Diagnostic de Pathogènes, par Séquençage, au Champ ). 30k€. PI: J. Gouzy. Co-PI : B. Mayonade.

  • 2024-2025: Projet INRAE SPE SYM2PLANTS (Exploration of the impact of plant-plant interactions on the establishment of nitrogen-fixing root symbiosis in legumes). 20k€. Co-PIs: Mathieu Hanemian & Matthias Benoît

  • 2021-2027: Projet ERC Synergy PATHOCOM (Understanding and predicting pathogen communities). 10 M€. PIs: Detlef Weigel, Fabrice Roux & Joy Bergelson.

  • 2021-2027: Projet PPR DEEP-IMPACT (Deciphering plant-microbiota interactions to enhance crop defense to pests). 3 M€. PI: Christophe Mougel . Co-PIs: Fabrice Roux & Fabienne Vailleau (200k€).

  • 2021-2025: Projet ANR PATHOSYM. Understanding the frontiers between PATHOgenicity and legume-rhizobia SYMbiosis. 571.8 k€. PI: Pascal Ratet, IPS2. Co-PI: Fabienne Vailleau (237.8 k€).

  • 2019-2025: Réseau PLANTCOM INRAE-SPE-BAP-AgroEcoSys. The genetics of plant-plant interactions. 8k€/year. PI: Fabrice Roux.

Previous project (since 2013)

  • 2021-2023: Projet QuID. Département SPE - INRAE. Immunité quantitative chez Arabidopsis thaliana: dissection des voies de signalisation par l’analyse fonctionnelle d’un gène majeur, RKS1. 29 k€. Coordinatrice: C. Huard-Chauveau.

  • 2019-2022: Réseau PLANTCOM INRAE-SPE. The genetics of plant-plant interactions. 5k€/year. PI: F. Roux

  • 2021-2022: Projet PIPPIN. Département INRAE – SPE. Pathways involved in Plant-Plant interactions. 27k€. PI: M. Hanemian

  • 2020-2023: Projet de thèse - Interactions plante-plante : analyse fonctionnelle d'un gène de réponse à la compétition chez Arabidopsis thaliana. Co-financement INRAE Département Santé des Plantes et Environnement (47 k€) - Région Occitanie (55 k€). Co-PIs: D. Roby & M. Hanemian

  • 2020-2021: Projet CREA du métaprogramme SuMCrop (Sustainable Management of Crop Health). Collectif interdisciplinaire de réflexion sur l’utilisation des plantes de service pour la REgulation des bioAgresseurs en agriculture. 11.6 k€. PIs: A.-V. Lavoir & D. Moreau.  

  • 2020-2021: Projet Plant2Pro ALLELO. Bases génétiques des interactions plante-plante liées à l’exsudation dans la rhizosphère de métabolites spécialisés. 148 k€. Co-PIs: C.Rameau, F. Roux et A. Bouchereau.

  • 2020: Allocation d’arrivée jeune chercheur - INRAE Département Santé des Plantes et Environnement. M. Hanemian (10k€)

  • 2019-2021: Projet PLANTSYS. Innovation – Labex TULIP. Predicting plant phenotypes by systems biology. 134 k€. PI: F. Roux (50 k€). Partenaire industriel: startup iMean (94 k€).

  • 2019-2020: Projet de la FR Agrobiosciences, Interactions et Biodiversité (Toulouse). Diversité naturelle du mucilage de populations régionales d’A.thaliana en relation avec leurs spécificités écologiques. 8 k€. Co-PIs: C. Dunand & F. Roux. 

  • 2019-2020: Projet FACCTS. A genomic scan to dissect climate adaptation in phytopathogenic bacteria. 20 k$. Co-PIs: J. Bergelson & F. Roux. 

  • 2019-2020. Projet InterLabEx. Osmotic and pathogen crosstalks in roots: role of redOX signaling. 17.7 k€ LabEx TULIP. Co-PIs: F. Vailleau & L. Verdoucq.

  • 2018-2021: Projet STARTER. AAP Innovation LabEx TULIP / Partnership with SYNGENTA. Studying in field conditions the impact of the microbiota on the pathogenicity of Ralstonia solanacearum on tomato across two seasons. 100 k€. Co-PIs: F. Vailleau & R. Berthomé.

  • 2018-2020: Projet OPTIMA. New Frontiers – Labex TULIP. A citizen project for establishing a genomic map of local adaptation in Arabidopsis thaliana to climate, soil and microbiota. 88 k€. PI: F. Roux.

  • 2017-2020: Projet BURNED. Partnership with SYNGENTA, CIFRE PhD support. Identification of resistance mechanisms to Ralstonia solanaceraum and their characterization in Arabidopsis thaliana and tomato in a global warming context.105 k€. Co-PIs: R. Berthomé & F. Vailleau.

  • 2017-2020: Projet RETHINK. AAP Innovation LabEx TULIP / Partnership with SYNGENTA. Search for Sustainable Bacterial Wilt Resistance in Tomato using Host Natural Variability in a Global Warming Context. 68 k€. Co-PIs: R. Berthomé & F. Vailleau.

  • 2017-2021: Projet de thèse - Deciphering Arabidopsis thaliana responses to bacterial virulence factors of Ralstonia solanacearum through the study of natural variation of both biotic partners. Co-financement INRAE Département Santé des Plantes et Environnement (47 k€) - Région Occitanie (55 k€). Co-PIs: F. Vailleau & R. Berthomé

  • 2017: Projet de la FR Agrobiosciences, Interactions et Biodiversité (Toulouse). Identification des bases génétiques de la réponse d’Arabidopsis thaliana à la présence de légumineuses. 4k€. Co-PIs: F. Roux & A. Niebel.

  • 2017-2018: Projet France and Chicago Collaborating in The Sciences (FACCTS). Evolution of R genes in plants. 20 k$. Co-PIs: J. Bergelson & F. Roux. 

  • 2017-2020: Projet de thèse - Analyse éco-fonctionnelle d’une kinase atypique conférence une résistance quantitative à la bactérie phytopathogène Xanthomonas campestris. Co-financement INRAE Département Santé des Plantes et Environnement (47 k€) - Région Occitanie (55 k€). Co-PIs: D. Roby & F. Roux.

  • 2016-2019: Projet de thèse - Identification chez Arabidopsis thaliana des bases génétiques de la résistance à Ralstonia solanacearum dans un contexte de réchauffement climatique. Cofinancement INRAE Département Santé des Plantes et Environnement (47 k€) - Région Occitanie (55 k€). Co-PIs: R. Berthomé & F. Roux.

  • 2016–2018: Projet ADORABLE. Département INRAE – SPE. Identification of genetic factors underlying potential disease outbreaks of the bacterial pathogen Xanthomonas campestris. 40 k€. PI: F. Roux. 

  • 2016–2017: Projet de la FR Agrobiosciences, Interactions et Biodiversité (Toulouse). Effet de changements climatiques sur le trade-off croissance/réponse aux bioagresseurs chez Arabidopsis thaliana. 10 k€. PI: F. Roux. 

  • 2014-2019: Projet ANR RIPOSTE. Exploitation of pathogen quantitative resistance diversity to improve disease resistance tolerance in crops. 496 k€. PI: D. Roby (191 k€). Co-PI: F. (248 k€).

  • 2014-2015: Projet RESURRECTION. Département INRAE – SPE. Une étude de résurrection pour étudier l’évolution phénotypique et génomique d’une population naturelle d’Arabidopsis thaliana face à la compétition interspécifique d’une graminée adventice. PI : F. Roux. 30k€.

  • 2014-2017: Projet CLIMARES. Région Midi-Pyrénées, programme « Accueil de nouvelles équipes d’excellence ». Étudier le potentiel des populations naturelles végétales face au changement climatique en identifiant les gènes associés à la résistance aux pathogènes. PI : F. Roux. 236k€.

  • 2013-2018 : Starting grant Labex TULIP. Ecological genomics of organism – organism interactions: cases of plant – pathogen and plant – plant interactions. PI : F. Roux. 250 k€.

  • 2012-2016 : Projet CYTOPHENO. ANR BIOADAPT. Cyto-nuclear co-adaptation and plant adaptive phenotypes. 500 k€. PI : F. Budar (INRA IJPB, Versailles). Co-PI: F. Roux (25 k€). 

  • 2011-2019 : Contrat ANR-Investissement d’Avenir LabEx TULIP "Towards a Unified Theory of biotic Interactions: roLe of Environmental Perturbations"  Coordinators  D. Roby / E. Danchin, 9 000 k€

  • 2009-2014 : ANR Blanc, projet QUANTIREX. Identification of key genes underlying quantitative resistance to Xanthomonas campestris in Arabidopsis thaliana by Genome Wide Association mapping and QTL analysis. 395 k€. PI : D. Roby  (240 k€). Co-PI : F. Roux (155 k€).




  • Lian, Q., Huettel, B., Walkemeier, B., Mayonade B., Lopez-Roques C., Gil L., Roux F., Schneeberger K. and Mercier R. 2024. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nature Genetics.

  • Bartoli C., Rigal, M., Huard-Chauveau C., Mayjonade B. and Roux F. 2024. The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south-west of France. Plant Pathology 73:884-897.

  • Viudes S., Zamar R., Burlat V., Roux F., and Dunand C. 2024.Genome wide association study of Arabidopsis seed mucilage layers at a regional scale. Plant Physiology and Biochemistry 207 : 108375. 

  • Duran P. 2024. The core microbiota across the green lineage. Current Opinion in Plant Biology. 77 : 102487.

  • Duflos R., Vailleau F. and Roux F. 2024. Toward ecologically relevant genetics of interactions between host plants and Plant growth-Promoting Bacteria. Advances genetics 2300210.

  • Loo E.P.I.*, Duran P.*, Pang T.Y., Westhoff P., Deng C., Duran C., Lercher M., Garrido-Oter R. and Frommer W.B. 2024. Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis.  Cell Host & Microbe 32, 1–14. *Authors contributed equally to this work.


  • Gawra, J., Valdivieso A., Roux F., Laporte M., de Lorgeril J., Gueguen Y., Saccas Y., Escoubas J.-M., Montagnani C., Destoumieux-Garzon D., Lagarde F., Leroy M.A., Haffner P., Lamy J.-B., Petton B., Cosseau C., Morga B., Dégremont L., Mitta G., Grunau C. and Vidal-Dupiol J.. 2023. Epigenetic variations are more substantial than genetic variations in rapid adaptation of oyster to Pacific Oyster Mortality Syndrome. Science Advances 9:eadh8990. 

  • Ramirez-Sanchez, D., Gibelin-Viala C., Roux F.† and Vailleau F.†. 2023. Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain. Frontiers in Plant Science 14:1266032. †The authors share senior authorship.

  • Vailleau F. and Genin S. 2023. Ralstonia solanacearum: An Arsenal of Virulence Strategies and Prospects for Resistance. Annu Rev Phytopathol. 5;61:25-47.

  • Demirjian C.*, Razavi N.*, Yu G., Mayjonade B., Zhang L., Lonjon F., Chardon F., Carrere S., Gouzy J., Genin S., Macho A.P., Roux F., Berthomé R.† and Vailleau F.†. 2023. An atypical NLR gene confers bacterial wilt susceptibility in Arabidopsis. Plant Commun. 4, 100607.*Authors contributed equally to this work. †The authors share senior authorship.

  • Wlodzimieriez, P.*, Rabanal F.A.*, Burns R.*, Naish M., Primetis E., Scott A., Mandakova T., Gorringe N., Tock A.J., Holland D., Fritschi K., Habring A., Lanz C., Patel C., Schlegel T., Collenberg M., Mielke M., Nordborg M., Roux F., Shirsekar G., Alonso-Blanco C., Lysak M.A., Novikova P., Bousios A.✝, Weigel D.✝ and Henderson I.R.✝. 2023. Cycles of satellite and transposon evolution in Arabidopsis pancentromere. Nature 557-565. *Authors contributed equally to this work. †The authors share senior authorship.

  • Li C., Binaghi M., Pichon V., Cannarozzi G., Brandão de Freitas L., Hanemian M.† and Kuhlemeier C.†. 2023. Tight genetic linkage of genes causing hybrid necrosis and pollinator isolation between young species. Nature Plants. 9(3):420-432.†The authors share senior authorship.

  • Demirjian C. Vailleau F., Berthomé R. and Roux F. 2023. Genome-wide association studies in plant-pathosystems: success or failure? Trends in Plant Science 28(4): 471-485.

  • Huang K., Jahani M.,  Gouzy J., Legendre A., Carrere S., Lázaro-Guevara J.M., González Segovia E.G., Todesco M.,  Mayjonade B, Rodde N., Cauet S., Dufau I., Staton S. E. , Pouilly N., Boniface M.C., Tapy C.,  Mangin B., Duhnen A., Gautier V., Poncet C., Donnadieu C., Mandel T., Hübner S., Burke J.M., Vautrin S., Bellec A., Owens G.L., Langlade N., Muños S., and Rieseberg L.H. 2023. The genomics of linkage drag in inbred lines of sunflower. PNAS 120 (14) e2205783119

  • Carrère S., Mayjonade B., Lalanne D., Gaillard S., Verdier J. and Chen WG N. 2023. First Whole Genome Assembly and Annotation of a European Common Bean Cultivar Using PacBio HiFi and Iso-Seq Data. 

  • Roux, F., Frachon L. and Bartoli C.. 2023. The genetic architecture of adaptation to leaf and root bacterial microbiota in Arabidopsis thaliana. Molecular Biology & Evolution 40(5):msad093.

  • The International PLANTCOM network, Becker C., Berthomé R., Delavault P., Flûtre T., Fréville H., Giboy-Leclerc S., Le Corre V., Morel J.-B., Moutier N., Munos S., Richard-Molard C., Westwood J., Courty P.-E.†, de Saint-Germain A.†, Louarn G.† and Roux F.†. 2023. The ecologically relevant genetics of plant-plant interactions. Trends in Plant Science 28(1): 31-42. †The authors share senior authorship.


  • Simon M., Durand S., Ricou A., Vrielynkc N., Mayjonade B., Gouzy J., Boyer R., Roux F., Camilleri C. and Budar F. 2022. APOK3, a pollen killer antidote that emerged in Arabidopsis thaliana. Genetics 221(4), iyac089. 

  • Durán P., Ellis T.J., Thiergart, T., ÅgrenJ. and Hacquard, S. 2022. Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations. The New Phytologist; 236(2):608-621.

  • Roux, F. and Frachon L. 2022. A Genome-Wide Association study in Arabidopsis thaliana to decipher the adaptive genetics of quantitative disease resistance in a native heterogeneous environment. PLoS One 17(10): e0274561.

  • Ramirez-Sanchez D.*, Gibelin-Viala C.*, Mayjonade B.*, Duflos R., Belmonte E., Pailler V., Carrere S., Vailleau F.† and Roux F.†. 2022. Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats. Frontiers in Microbiology 13:984832. *Authors contributed equally to this work. †The authors share senior authorship.

  • Gloss D.A., Vergnol A., Morton T.C., Laurin P.J., Roux F. and Bergelson J. 2022. Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity. Philosophical Transactions of the Royal Society B-Biological Sciences 377:20200512. 

  • Russo A., Mayjonade B., Frei D., Potente G., Kellenberger R.T., Frachon L., Copetti D., Studer B., Frey J.E., Grossniklaus U. and Schlüter P.M.. 2022. Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families, Front. Plant Sci., 13:883897.

  • Zavala D.*, Fuenzalida I.*, Gangas M.V., Margutti M.P., Bartoli C., Roux F., Herrera-Vasquez A., Meneses C. and Blanco-Herrera F. 2022. Molecular and genomic characterization of Pseudomonas syringae RAYR-BL, a newly discovered pathogen of Arabidopsis thaliana and Nicotiana benthamiana plants. Microorganisms 10:707. *Authors contributed equally to this work.

  • Fulgione A.*, Neto C.*, Elfarargi A.F., Tergemina E., Göktay M., Dinis H., Döring N., Flood P.J., Rodriguez-Pacheco S., Walden N., Koc M., Roux F., Hermisson J. and Hancock A.M.. 2022. Parallel reduction in flowering time enabled evolutionary rescue and establishment in a colonizing Arabidopsis lineage. Nature Communications 13:1461. *Authors contributed equally to this work.

  • Fuenzalida-Valdivia, I., Gangas M.V., Zavala D., Herrera-Vasquez A., Roux F., Meneses C. and Blanco-Herrera F. 2022. Draft genome of Pseudomona syringae RAYR-BL, a strain isolated from natural accessions of Arabidopsis thaliana plants. Microbiology Resource Announcements 1:e01001-21.

  • Demirjian, C.*, Razavi N.*, Desaint H., Lonjon F., Génin S., Roux F., Berthomé R.* and Vailleau F.*. 2022. Study of natural diversity in response to a key pathogenicity regulator of Ralstonia solanacearum reveals new susceptible genes in Arabidopsis thaliana. Molecular Plant Pathology 23:321-338. *Authors contributed equally to this work.

  • Invernizzi M., Hanemian M., Keller J., Libourel C., and Roby D. 2022. PERKing up our understanding of the proline-rich extensin-like receptor kinases, a forgotten plant receptor kinase family. New Phytologist  235(3):875-884.

  • Delplace F., Huard-Chauveau C., Berthomé R.† and Roby D.†. 2021. Network organization of the plant immune system: from pathogen perception to robust defense induction. The Plant Journal 109(2):447-470.  †The authors share senior authorship.


  • Libourel C., Baron E., Lenglet J., Amsellem L., Roby D. and Roux F. 2021. The genomic architecture of competitive response of Arabidopsis thaliana is highly flexible between monospecific and plurispecific neighborhoods. Frontiers in Plant Science 12:741122.

  • Subrahmaniam J., Roby D. and Roux F.. 2021. Towards unifying evolutionary ecology and genomics to understand positive plant-plant interactions within wild species. Frontiers in Plant Science 12:683373.

  • Bergelson J.*, Brachi B.*, Roux F.* and Vailleau F.*. 2021. Assessing the potential to harness the microbiome through plant genetics. Current Opinion in Biotechnology 70:167-173. *Authors contributed equally to this work.

  • Lannou C., Roby D., Ravigné V., Hannachi M. and Moury, B. 2021. L'immunité des plantes: Pour des cultures résistantes aux maladies. Editions Quae.

  • Rubio B., Fernandez O., Cosson P., Breton T., Caballero M., Lion R., Roux F., Bergelson J., Gibon Y. and Schurdi-Levraud V. 2021. Metabolic profile discriminates and predicts Arabidopsis susceptibility under field conditions. Metabolites 11:230.

  • Desaint H.*, Aoun N.*, Deslandes L., Vailleau F., Roux F. and Berthomé R.. 2021. Fight hard or die trying: when plants face pathogens under heat stress. New Phytologist 229:712-734. *Authors contributed equally to this work.


  • 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 104:289-301. *Authors contributed equally to this work.

  • Aoun N., Desaint H., Boyrie L., Bonhomme M., Deslandes L., Berthomé R. and Roux F.. 2020. A complex network of additive and epistatic QTLs underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress. Molecular Plant Pathology 21:1405-1420. 

  • Delplace F.*, Huard-Chauveau C.*, Dubiella U., Khafif M., Alvarez E., G. Langin G., Roux F., Peyraud R. and Roby D. 2020. Robustness of plant quantitative disease resistance is provided by a decentralized immune network. Proc. Natl. Acad. Sci. USA 117(30):18099-18109. *Authors contributed equally to this work.

  • Lonjon F., Rengel D., Roux F., Henry C., Turner M., Le Ru A., Razavi N., Sabbagh C.R.R, Génin S. and Vailleau F. 2020. HpaP guards HrpJ, an essential component of Ralstonia solanacearum virulence, able to trigger necrosis in Arabidopsis. Molecular Plant-Microbe Interactions 33(2): 200-211.

  • Thiergart T.*, Duran P.*, Ellis T.*, Garrido-Oter R., Kemen E., Roux F., Alonso-Blanco C., Agren J., Schulze-Lefert P. and Hacquard S. 2020. Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature Ecology and Evolution 4: 122-131. *Authors contributed equally to this work.


  • Frachon L.*, Mayjonade B.*, Bartoli C.*, Hautekèete N.C. and Roux F. 2019. Adaptation to plant communities across the genome of Arabidopsis thaliana. Molecular Biology and Evolution 36(7):1442-1456. *Authors contributed equally to this work.

  • Rubio B., Cosson P., Caballero M., Revers F., Bergelson J., Roux F. and Schurdi-Levraud V. 2019. Genome-wide association study reveals new loci involved in Arabidopsis thaliana and Turnip mosaic virus (TuLM) interactions in the field. New Phytologist 221:2026-2038.


  • Wang M.*, Roux F.*, Bartoli C., Huard-Chauveau C., Lee H., Meyer C., Roby D., McPeek M.S. and Bergelson J. 2018. Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes. Proc. Natl. Acad. Sci. USA 115(24):E5440-E5449. *Authors contributed equally to this work.

  • Bartoli C.*, Frachon L.*, Barret M., Rigal M., Huard-Chauveau C., Mayjonade B., Zanchetta C., Bouchez O., Roby D., Carrère S. and Roux F. 2018. In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana. The ISME Journal 12:2024-2038. *Authors contributed equally to this work.

  • Pujol B., S. Blanchet S., Charmantier A., Danchin E., Facon B., Marrot P., Roux F., Scotti I., Téplitsky C., Thomson C.E. and Winney I. 2018. The missing response to selection in the wild. Trends in Ecology and Evolution 33(5): 337-346.

  • Fulgione A., Koornneef M., Roux F., Hermisson J. and Hancock A. 2018. Evolutionary dynamics of island colonization: Arabidopsis thaliana from the island of Madeira. Molecular Biology and Evolution 35(3): 564-574.

  • Subrahmaniam J., Libourel C., Journet E.-P., Morel J.-B., Muños S., Niebel A., Raffaele S. and Roux F. 2018. The genetics underlying natural variation of plant-plant interactions: a beloved but forgotten member of the family of biotic interactions. The Plant Journal 93: 747-770.


  • Frachon L.*, Libourel C.*, Villoutreix R., Carrère S., Glorieux C., Huard-Chauveau C., Navascués M., Gay L., Vitalis R., Baron E., Amsellem L., Bouchez O., Vidal M., Le Corre V., Roby D., Bergelson J. and Roux F. 2017. Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nature Ecology & Evolution 1: 1551-1561. *Authors contributed equally to this work.

  • Aoun N., Tauleigne L., Lonjon F., Deslandes L.,  Vailleau F., Roux F. and Berthomé R.. 2017. Quantitative disease resistance under elevated temperature: genetic basis of new resistance mechanisms to Ralstonia solanacearum. Frontiers in Plant Science 8:1387.

  • Bartoli C. and Roux F. 2017. Genome-Wide Association studies in plant pathosystems: towards an ecological genomics approach. Frontiers in Plant Science 8: article 763.


  • Gascuel Q., Bordat A., Sallet E., Pouilly N., Carrère S., Roux F., Vincourt P. and Godiard L. 2016. Polymorphic effectors of the sunflower downy mildew pathogen Plasmopara halstedii, used as a tool for identifying field isolates, suggest an on-going adaptive dynamics of pathogen virulence. PLoS One 11(2): e0148513.

  • Roux F. and Bergelson J. 2016. The genetics underlying natural variation in the biotic interactions of Arabidopsis thaliana: the challenges of linking evolutionary genetics and community ecology. Current Topics in Developmental Biology 119: 111-156.

  • Debieu M., Huard-Chauveau C., Génissel A., Roux F. and Roby D. 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 17(4): 510-520.

  • Roux F., Mary-Huard T., Barillot E., Wenes E., Botran L., Durand S., Villoutreix R., Martin-Magniette M.L., Camilleri C. and Budar F. 2016. Cytonuclear interactions affect adaptive phenotypic traits of the annual plant Arabidopsis thaliana in the field. Proc. Natl. Acad. Sci. USA 113(13): 3687-3692.

  • Bartoli C., Roux F. and Lamichhane J.-R. 2016. Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective. Molecular Plant Pathology 16(8): 860-869.

2015 and before

  • Baron E., Richirt J., Villoutreix R., Amsellem L. and Roux F. 2015. The genetics of intra- and interspecific competitive response and effect in a local population of an annual plant species. Functional Ecology 29: 1361-1370.

  • Brachi B., Meyer C., Villoutreix R., Platt A., Roux F. and Bergelson J. 2015. Co-selected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana. PNAS 112(3): 4032-4037.

  • Karasov T.L., Kniskern J.M., Gao L., DeYoung B.J., Ding J., Dubiella U., Lastra R., Nallu S., Roux F., Innes R.W., Barrett L.G., Hudson R.R. and Bergelson J. 2014. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature 512: 436-440.

  • Roux F., Noel L., Rivas S. and Roby D. 2014. Atypical kinases: emerging signaling components of plant immunity. New Phytologist 203: 713-716.

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

  • Brachi B., Faure N., Bergelson J., Cuguen J. and Roux F. 2013. Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years. Acta Botanica Gallica – Botany Letters 160: 205-218. Special Issue ‘Quantitative genetics in natural populations’.

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

  • Brachi B., Villoutreix R., Faure N., Hautekèete N., Piquot Y., Pauwels M., Roby D., Cuguen J., Bergelson J. and Roux F. 2013. Investigation of the geographical scale of adaptive phenological variation and its underlying genetic bases in Arabidopsis thaliana. Molecular Ecology 22: 4222-4240.


  • Local collaborations : Richard Berthomé, Laurent Deslandes, Benjamin Gourion, Andreas Niebel, Stéphane Munos (LIPME, INRAE, Toulouse); Maxime Bonhomme, Pierre-Marc Delaux & Christophe Dunand (LRSV, Toulouse), startup iMean.

  • National collaborations: Claudia Bartoli & Christophe Mougel (IGEPP, Rennes);  Lionel Verdoucq (LBPMP, Montpellier); Jean-Philippe Reichheld (LGDP, Perpignan); Pascal Ratet (ISP2, Saclay); Françoise Budar, Christine Camilleri, Alexandre de Saint-Germain & Catherine Rameau (IJPB, Versailles); Mathieu Gautier (CBGP, Montpellier); Valérie Schurdi-Levraud (BFP, Bordeaux).

  • International collaborations: Joy Bergelson (New-York University, USA); Detlef Weigel (MPI Tübingen, Germany); Angela Hancock, Stéphane Hacquard & Paul Schulze-Lefert (MPI Cologne, Germany); Léa Frachon (University of Zurich, Suisse); Alberto Macho (Shanghai Center of Plant Stress Biology, China).



  • Mise en place du projet de science participative OPTIMA visant à tester l’adaptation d’Arabidopsis thaliana aux communautés microbiennes du sol. Ce projet a reposé sur la mise à disposition de jardins de 47 participants (retraités, école, conservatoire botanique, réserves naturelles…) qui ont effectué des prises de photos de plantes pendant l’hiver 2018-2019.

  • Intervention lors d’une rencontre-échange scientifique Exploreur sur le thème ‘Quand les citoyens se mobilisent pour étudier l’adaptation des plantes à leur environnement !’ au Quai des Savoirs. Juin 2021. Toulouse France.

  • Séminaire de vulgarisation dans le cadre du ‘Jeudi Sciences’ organisé par la FR AIB. Comment les espèces s’adaptent à leur environnement ? Octobre 2019. Toulouse, France.

  • Restitution des premiers résultats du projet de science participative OPTIMA aux élèves de CM1 et de CM2 de l’école de Tarabel. Juin 2019. Tarabel, France.

  • Participation de l’équipe ECOGEN aux trois premières journées du Salon International de l’Agriculture. Février 2019. Paris, France.

  • Participation de l’équipe ECOGEN aux deux journées ‘Accueil Portes ouvertes Inra Toulouse’. Octobre 2016. Toulouse, France.

  • Participation de l’équipe ‘Génomique écologique de l’adaptation dans les communautés végétales’ au kiosque Museum ‘De la graine à la plante’. Juin 2016. Toulouse, France.

  • Participation de l’équipe ‘Génomique écologique de l’adaptation dans les communautés végétales’ au kiosque Museum ‘Des petits pois de Mendel à l’épigénétique, 150 ans de révolutions en génétique’. Février 2016. Toulouse, France.


  • Forum des métiers, collège Montesquieu Cugnaux (2019-2023-2024)

  • European Science Open Forum (2018)

  • Fête de la Science (2006, 2010, 2013, 2023)

Sciences et Société
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