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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Research themes - Quantitative Immunity in Plants

 RKS1 dependent immunity pathways

We recently identified in Arabidopsis thaliana by map-based cloning and Genome Wide Association (GWA) mapping, the RKS1 gene underlying a major QTL controlling resistance to most pathovars of Xcc originally identified on cruciferous cultivated plants. This gene encodes an atypical kinase. The functional analysis of this gene (and its molecular variants) and the characterization of the regulatory pathway(s) controlling and controlled by RKS1, are under investigation. RKS1 (and other candidate genes) will also be directly tested in a high throughput manner, and through a non-GMO approach, for their potential value (alleles or orthologs) to control pathogens in plants of agronomic interest (Brassica, tomato, pepper) in breeding programs

RSK1 dependent immunity pathways

Selected recent publications:

ZRK atypical kinases: emerging signaling components of plant immunity. Roux F, Noël L, Rivas S, Roby D. New Phytol. 2014 Aug;203(3):713-6.

Huard-Chauveau C, Perchepied L, Debieu M, Rivas S, Kroj T, Kars I, Bergelson J, Roux F, Roby D. An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis. PLoS Genet. 2013;9(9):e1003766. doi: 10.1371/journal.pgen.1003766. Epub 2013 Sep 12. PubMed PMID: 24068949; PubMed Central PMCID: PMC3772041.

Contact: Dominique Roby

Genetic and molecular bases of resistance in the natural pathosystem A. thaliana-Xanthomonas

Xanthomonas is one of a few known natural pathogens of A. thaliana, and is highly prevalent in natural populations of A. thaliana. In collaboration with Fabrice Roux (LIPM, Toulouse) and Joy Bergelson (University of Chicago), we identified strains of Xanthomonas in natural populations of Arabidopsis.  Now our research aims are to (i) finely map by GWA mapping genomic regions associated with natural variation of quantitative resistance to Xc, (ii) functionally validate candidate genes, and (iii) elucidate the ecological and evolutionary forces shaping the natural genetic diversity observed for these quantitative resistance genes.

Selected recent publications:

Debieu M, Huard-Chauveau C, Genissel A, Roux F, Roby D. Quantitative disease resistance to the bacterial pathogen Xanthomonas campestris involves an Arabidopsis immune receptor pair and a gene of unknown function. Mol Plant Pathol. 2016 May;17(4):510-20.

Le Roux C, Del Prete S, Boutet-Mercey S, Perreau F, Balagué C, Roby D, Fagard  M, Gaudin V. The hnRNP-Q protein LIF2 participates in the plant immune response.  PLoS One. 2014 Jun 10;9(6):e99343.

Contact: Dominique Roby

Characterization of molecular mechanisms underlying Arabidopsis quantitative immunity to the fungus Sclerotinia sclerotiorum

Using worldwide Arabidopsis thaliana populations, we documented extensive variation in quantitative immunity to S. sclerotiorum, opening the way to the molecular characterization of plant and pathogen determinants underlying this interaction. The overall objectives of this project are to identify which plant genes are involved in quantitative immunity to Sclerotinia and understand how they contribute to disease resistance? For this, we are developing notably genome wide association mapping, functional genetics, transcriptomics and high throughput quantitative phenotyping approaches.

Characterization of molecular mechanisms

Figure legend: A) The range of symptoms on Arabidopsis thaliana leaves inoculated by S. sclerotiorum with an illustration of image processing used to quantify disease. B) Molecular structure of a fungal protein predicted to facilitate host colonization. C) Genome wide association mapping of plant genes contributing to quantitative disease resistance, with a world map indicating the origin of plant accessions used. 

Selected recent publications:

Le Roux C, Huet G, Jauneau A, Camborde L, Trémousaygue D, Kraut A, Zhou B, Levaillant M, Adachi H, Yoshioka H, Raffaele S, Berthomé R, Couté Y, Parker JE, Deslandes L. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell. 2015 May 21;161(5):1074-88.

Roux F, Voisin D, Badet T, Balagué C, Barlet X, Huard-Chauveau C, Roby D, Raffaele S. Resistance to phytopathogens e tutti quanti: placing plant quantitative disease resistance on the map. Mol Plant Pathol. 2014 Jun;15(5):427-32.

Bozkurt TO, Richardson A, Dagdas YF, Mongrand S, Kamoun S, Raffaele S. The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans. Plant Physiol. 2014 May 7;165(3):1005-1018.

Contact: Sylvain Raffaele

Thigmoimmunity: contribution of mechanical signal perception to quantitative immunity against Sclerotinia

During their interaction with plants, and prior to plant tissue penetration or degradation, fungal pathogens develop important mechanical loads susceptible to emit Mechanical loads are due to the tremendous turgor pressure created by water in the vacuole of appressoria and fungal cell wall mechanical preperties. This mechanical stress is generally sufficient to penetrte plant cells. Mechanosensing occurs at the plant cell level and relies on the internal mechanical state of the cell.

Recent studies demonstrated the link between mechanosensing and plant immune response to B. cinerea in Arabidopsis thaliana: plants submitted to MS exhibited higher resistance to fungal infection suggesting a priming effect operated by sterile mechanosensing. Future work should aim at addressing whether mechanosensing for fungal contact or penetration per se, in addition to PAMP perception, leads to enhanced plant immunity.


Mechanoperception and thigmomorphogenesis at INRA

Selected recent publications:

Mbengue M, Navaud O, Peyraud R, Barascud M, Badet T, Vincent R, Barbacci A, Raffaele S. Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum.  Front Plant Sci. 2016 Mar 31;7:422.

Barbacci A, Magnenet V, Lahaye M. Thermodynamical journey in plant biology. Front Plant Sci. 2015 Jun 30;6:481.

Contact: Adelin Barbacci

Fungal adaptations to plant quantitative immunity

Fungal plant pathogens are major and rising threats for global food security and environment sustainability. Generalist fungal pathogens such as S. sclerotiorum, infecting a broad range of host species in nature, are among the most devastating plant pathogens worldwide. The range of hosts that pathogens can infect in nature is a key determinant of the emergence and spread of diseases. How pathogens evolve the ability to infect many diverse hosts remains enigmatic. Through this project, we are addressing the following questions: What are the mechanisms used by Sclerotinia to colonize its hosts? What are the evolutionary processes that shaped the extent fungal virulence and plant immunity processes? This work relies mostly on comparative genomics, transcriptomics, phylogeny, and systems biology approaches.

Fungal adaptations to plant quantitative immunity

Figure legend: A) S. sclerotiorum colonizing an Arabidopsis leaf imaged using a strain expressing the green fluorescent protein. B) A Circos diagram illustrating comparative genomics of fungal species related to S. sclerotiorum. C) A phylogenetic tree of fungi from the Sclerotiniaceae family.

Selected recent publications:

Dong S, Raffaele S, Kamoun S. The two-speed genomes of filamentous pathogens:  waltz with plants. Curr Opin Genet Dev. 2015 Dec;35:57-65. doi: 10.1016/j.gde.2015.09.001.

Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. Front Plant Sci. 2015 Sep 24;6:776.

Guyon K, Balagué C, Roby D, Raffaele S. Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum. BMC Genomics. 2014 May 4;15:336.

Contact: Sylvain Raffaele


  • Bruno Grezes-Besset; Biogemma Mondonville
  • Fabrice Roux; LIPM Toulouse
  • Sébastien Mongrand; LBM Bordeaux
  • John P. Clarkson; University of Warwick (UK)
  • Richard P. Oliver, Mark Derbyshire, Matthew Denton-Giles; Curtin University (Aus)
  • Lone Buschwaldt; University of Saskatchewan (Can)
  • Jan van Kan, Michael Siedl; Wageningen University (NL)
  • Sophien Kamoun; The Sainsbury Laboratory Norwich (UK)
  • Jean-Charles Portais, Pierre Millard; LISBP Toulouse
  • Ludovic Cottret, Lucas Marmiesse; LIPM Toulouse


  • Contract ANR-Investissement d’Avenir LabEx TULIP, 2011-2020, Coordinators ROBY Dominique /Danchin Etienne, 9 000 k€
  • Contract Marie Curie CIG grant – European commission FP7, « Identification of Sclerotinia sclerotiorum Effector Proteins mediating virulence on Arabidopsis thaliana ecotypes (SEPAraTE) », 2013-17, Coordinator Sylvain Raffaele, 100 k€
  • Contract ERC Starting Grant Conseil Européen « Understanding White mold disease quantitative resistance using natural variation (VariWhiM) », scientific coordinator Sylvain Raffaele, 2013-2018, 1500 k€.
  • TULIP “New Frontiers” project “Virulence function and evolution of Sclerotinia signals manipulating plant RNA silencing pathways (ScleRNAi)”, Coordinator S. Raffaele, 2014-16, 119 k€.
  • Contract ANR RIPOSTE “Exploitation of pathogen quantitative resistance diversity to improve disease tolerance in crops”, Coordinator D. Roby, 2014-2018, 248 k€.
  • Project Plant Health & Environment Division INRA – SPE. “Identification of genetic factors underlying potential disease outbreaks of the bacterial pathogen Xanthomonas campestris” PI : Fabrice Roux, 2016 – 2017, 40k€.