​2024

• Magne, K., Massot, S., Folletti, T., Sauviac, L., Ait-Salem, E., Pires, I., Saad, M.M., Eida, A.A., Bougouffa, S., Jugan, A., Rolli, E., Forquet, R., Puech-Pages, V., Maillet, F., Bernal, G., Gibelin-Viala, C., Hirt, H., Gruber, V., Peyraud, R., Vailleau, F., Gourion, B., Ratet, P. Atypical rhizobia trigger nodulation and pathogenesis on the same legume hosts. Nat Commun. 2024 Oct 26;15(1):9246. doi: 10.1038/s41467-024-53388-x.

• Whiting, J.R., T.R. Booker, C. Rougeux, B.M. Lind, P. Singh, M. Lu, K. Huang, M.C. Whitlock, S.N. Aitken, R.L. Andrew, J.O. Borevitz, J.J. Burhl, T. Collins, M.C. Fischer, K.A. Hodgins, J.A. Holliday, P.K. Ingvarsson, J.K. Janes, M. Khandaker, D. Koenig, J.M. Kreiner, A. Kremer, M. Lascoux, T. Leroy, P. Milesi, K.D. Murray, T. Pyhäjärvi, C. Rellstab, L.H. Rieseberg, F. Roux, J.R. Stinchcombe, I.R.H. Telford, M. Todesco, J. Tyrmi, B. Wang, D. Weigel, Y. Willi, S.I. Wright, L. Zhou and S. Yeaman. 2024. Core gene driving climate adaptation in plants. Nature Ecology & Evolution (https://doi.org/10.1038/s41559-024-02514-5).

• Desaint H., Gigli A., Belny A., Cassan-Wang H., Martinez Y., Vailleau F., Mounet F., Vernhettes S., Berthomé R., Marchetti M. 2024. Reshaping the primary cell wall: dual effects on plant resistance to Ralstonia solanacearum and heat stress response. Mol Plant Microbe Interact. Aug;37(8):619-634. doi: 10.1094/MPMI-05-24-0059-R.

• Ramirez-Sanchez D*, Duflos R*, Gibelin-Viala C, Zamar R, Vailleau F†, Roux F†. 2024. The genetic architecture of Arabidopsis thaliana in response to native non-pathogenic bacterial species revealed by GWA mapping in field conditions. Phytobiomes J. https://doi.org/10.1094/PBIOMES-01-24-0010-. *Authors contributed equally to this work. †The authors share senior authorship.

• Cassan, O., Pimparé L.-L., Mozzanino T., Fizames C., Devidal S., Roux F., Milcu A., Lèbre S., Gojon A. and Martin A. 2024. Natural genetic variation underlying the negative effect of elevated CO2 on ionome composition in Arabidopsis thaliana. eLife 12:RP90170. https://doi.org/10.7554/eLife.90170.2.

• Chauveau C. and Roby D. 2024. Molecular complexity of quantitative immunity in plants: from QTL mapping to functional and systems biology. Académie des Sciences. Comptes Rendus. Biologies 347:35-44. https;//doi.org/10.5802/crbiol.153.

• Xue M., Sofer L., Simon V., Arvy N., Diop M., Lion R., Beucher G., Bordat A., Tilsner J., Gallois J.-L. and German-Retana S. 2024. AtHVA22a, a plant-specific homologue of Reep/DP1/Yop1 family proteins is involved in turnip mosaic virus propagation. Mol Plant Pathol.25:e13466. https://doi.org/10.1111/mpp.13466.

• 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. https://doi.org/10.1038/s41588-024-01715-9.

• 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. https://doi.org/10.1111/ppa.13849.

• 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. https://doi.org/10.1016/j.plaphy.2024.108375. 

• Duran P. 2024. The core microbiota across the green lineage. Current Opinion in Plant Biology. 77 : 102487. https://doi.org/10.1016/j.pbi.2023.102487.

• 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. https://doi.org/10.1002/ggn2.202300210

• 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. https://doi.org/10.1016/j.chom.2024.02.014. *Authors contributed equally to this work.

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2023

• 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.

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2022

• 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.

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2021

• 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.

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2020

• 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.

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2019

• 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.

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2018

• 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.

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2017

• 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.

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2016

• 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.

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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.