Publications & COV

The last publication of the EcoFun team via Pubmed

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Caffier V, Shiller J, Bellanger MN, Collemare J, Expert P, Gladieux P, Pascouau C, Sannier M, Le Cam B. Hybridizations Between formae speciales of Venturia inaequalis Pave the Way for a New Biocontrol Strategy to Manage Fungal Plant Pathogens. Phytopathology. 2022 Jul;112(7):1401-1405. doi: 10.1094/PHYTO-05-21-0222-SC. Epub 2022 May 20.PMID: 35080437


Fontaine K, Fourrier-Jeandel C, Armitage AD, Boutigny AL, Crépet M, Caffier V, Gnide DC, Shiller J, Le Cam B, Giraud M, Ioos R, Aguayo J. Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards.PeerJ. 2021 Dec 1;9:e12496. doi: 10.7717/peerj.12496. eCollection 2021.PMID: 34917421 


  • Feurtey A, Guitton E., De Gracia Coquerel M, Duvaux L, Shiller J, Bellanger MN, Expert P, Sannier M, Caffier V, Giraud T, Le Cam B, Lemaire C. 2020. Asian wild apples threatened by gene flow from domesticated apples and by their pestified pathogen. Accepted in Molecular Ecology
  • Halkett F., Montarry J., Goyeau H., Le Cam B., Le May C., 2020. Contournements des résistances par les agents pathogènes - Une interaction évolutive : la course aux armements entre les plantes et leurs parasites. Immunité végétale. Edition quae


  • Le Cam B, Sargent D, Gouzy J, Amselem J, Bellanger MN, Bouchez O, Brown S, Caffier V, De Gracia M, Debuchy R, Duvaux L, Payen T, Sannier M, Shiller J, Collemare J, Lemaire C. 2019. Population genome sequencing of the scab fungal, species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata. G3 9: 2405-2414
  • Gossmann TI., Shanmugasundram A., Borno S., Duvaux L., Lemaire C, et al. 2019. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Current Biology 29 : 1712-1720.
  • Marolleau B, Petiteau A, Bellanger MN, Sannier M, Le Pocreau N, Porcher L, Paillard S, Foucher F, Thouroude T,  Serres-Giardi L, Aguileta G, Chastellier A,  Bonneau C,  Le Cam B, Soufflet-Freslon V, Hibrand-Saint Oyant L. 2020. Strong differentiation within Diplocarpon rosae strains based on microsatellite markers and greenhouse-based inoculation protocol on Rosa. Plant Pathology doi: 10.1111/ppa.13182.
  • Patocchi A, Wehrli A, Dubuis P.H,Auwerkerken A, Leida C, Cipriani G, Passey T, Staples M, Didelot F, et al. 2020 Ten years of VINQUEST: first insight for breeding new apple cultivars with durable apple scab resistance Plant Disease


  • Lasserre-Zuber P, Caffier V, Stievenard R, Lemarquand A, Le Cam B, Durel CED. 2018. Pyramiding Quantitative Resistance with a Major  Resistance Gene in Apple: from Ephemeral to Enduring Effectiveness in Controlling Apple Scab. Plant disease 102:2220-2223


  • Laloi G, Vergne E, Durel CE, Le Cam B, Caffier V. 2017. Efficiency of pyramiding of three quantitative resistance loci to apple scab. Plant Pathology, 66: 412-422
  • Le Guillou-Guillemette H., Pivert A., Bouthry E., Henquell C., Petsaris O., Ducancelle A., Veillon P., Vallet S., Payan C., Lunel-Fabiani F. & Lemaire C. 2017. Evolutionary history of V3 duplication in HCV 1b strains. Plos one 12 (4): e0174651
  • Pilet-Nayel ML, Moury B, Caffier V, Montarry J, Kerlan MC, Fournet S, Durel CE, Delourme R. 2017. Quantitative resistance to plant pathogens in pyramiding strategies for durable crop protection. Frontiers in Plant Science 8: 1838
  • Duvaux L, Shiller J, Vandeputte P, Duge de Bernonville T, Thornton C, Papon N, Le Cam B, Bouchara JP, Gastebois A. 2017. Draft Genome Sequence of the Human-Pathogenic Fungus Scedosporium boydii. Genome announcement doi:10.1128/genomeA.00871-17


  • Leroy T, Caffier V, Celton JM, Anger N, Durel CE, Lemaire C, Le Cam B. 2016. When virulence originates from non-agricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis. New Phytologist doi : 10.1111/nph.13873
  • Didelot F, Caffier V, Orain G, Lemarquand A, Parisi L. 2016. Sustainable management of scab control through the integration of apple resistant cultivars in a low-fungicide input system. Agriculture, Ecosystems and Environment 217: 41-48, doi: 10.1016/j.agee.2015.10.023
  • Caffier V, Le Cam B, Al Rifaï M, Bellanger MN, Comby M, Denancé C, Didelot F, Expert P, Kerdraon T, Lemarquand A, Ravon E, Durel CE.  2016. Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus. Infection Genetics and Evolution 44: 541-548
  • Merda D., Bonneau S., Guimbaud J-F., Durand K., Lemaire C., Jacques M-A. & Fischer-Le Saux M. 2016. Xanthomonas arboricola fits the epidemic bacterial population model with emergence of epidemic clones linked to acquisition of type three effectors upon a recombinant network. Environmental Microbiology Reports doi: 10.1111/1758-2229.12397.


  • Didelot F., Caffier V., Orain G., Lemarquand A., Parisi L. (2015) Sustainable management of scab control through the integration of apple resistant cultivars in a low-fungicide input system. Agriculture, Ecosystems and Environment, 217: 41-48, doi: 10.1016/j.agee.2015.10.023.
  • Lemaire C., de Gracia M., Leroy T., Michalecka M., Lindhard-Pedersen H., Guérin F., Gladieux P., Le Cam B. (2015) Emergence of new virulent populations of apple scab from non-agricultural disease reservoirs. New Phytologist, doi:10.1111/nph.13658.
  • Bourget R., Chaumont L., Durel C.E., Sapoukhina N. (2015). Sustainable deployment of QTLs conferring quantitative resistance to crops: first lessons from a stochastic model. New Phytologist. doi: 10.1111/nph.13295
  • Caffier V, Patocchi A, Expert P, Bellanger MN, Durel CE, Hilber-Bodmer M, Broggini GAL, Groenwold R, Bus VGM. (2015). Virulence Characterization of Venturia inaequalis Reference Isolates on the Differential Set of Malus Hosts. Plant Disease. doi:10.1111/ppa.12297
  • De Gracia M., Cascales M, Expert P, Bellanger MN, Le Cam B, Lemaire C. (2015). How did hosts domestication modify life history traits of its pathogens?  Plos One, doi:10.1371/journal.pone.0122909.
  • Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel, CE, Branca A (2015) Investigating the genomic bases of the differences between cider and dessert apple varieties. Evolutionary applications, doi:10.1111/eva.12270.
  • Le Guillou-Guillemette H , Ducancelle A, Bertrais S, Lemaire C, Pivert A, Veillon P, Bouthry E, Alain S, Thibault V, Abravanel F, Rosenberg AR, Henquell C, André-Garnier E, Petsaris O, Vallet S, Bour JB, Baazia Y, Trimoulet P, André P, Gaudy-Graffin C, Bettinger D, Larrat S, Signori-Schmuck A, Saoudin H, Pozzetto B, Lagathu G, Minjolle-Cha S, Stoll-Keller F, Pawlotsky JM, Izopet J, Payan C, Lunel-Fabiani F. (2015). Identification of a duplicated V3 domain in NS5A associated with cirrhosis and hepatocellular carcinoma in HCV-1b patients. Journal of clinical virology, 59:203-209.
  • Collemare J, Beenen HG, Crous PW, de Wit PJGM and van der Burgt A. .2015. Novel Introner-Like Elements in fungi are involved in parallel gains of spliceosomal introns. PLoS One. doi: 10.1371/journal.pone.0129302.
  • Karimi Jashni M, Dols IH, Iida Y, Boeren S, Beenen HG, Mehabi R, Collemare J, De Wit PJ. (2015) Synergistic action of serine- and metallo-proteases from Fusarium oxysporum f. sp. lycopersici cleaves chitin-binding tomato chitinases, reduces their antifungal activity and enhances fungal virulence. Molecular Plant-Microbe interactions, 28(9):996-1008. doi: 10.1094/MPMI-04-15-0074-R.
  • Song Z, W.Bakeer, J. Marshall, A. Yakasai, R. Mohd-Khalid, J. Collemare, E. Skellam, D. Tharreau, M. Lebrun, C. M. Lazarus, A. M. Bailey, T. J. Simpson and R. Cox. (2015). Heterologous Expression of the Avirulence gene ACE1 from the fungal rice pathogen Magnaporthe oryzae. Chemical Science. doi: 10.1039/C4SC03707C


  • Caffier V., Lasserre–Zuber P., Giraud M., Lacostes M., Stievenard R., Lemarquand., van de Weg E., Expert P., Denancé C., Le Cam B., Durel CE. (2014). Erosion of quantitative host resistance in relation to aggressiveness levels in pathogen populations : a case study in the apple x Venturia inaequalis pathosystem. Infection Genetics and Evolution.
  • Leroy T., Le Cam B., Lemaire C. (2014). When virulence origins from the wild : New Insights for plant breeding. Infection Genetics and Evolution.
  • Tellier A, Lemaire C. (2014). Coalescence 2.0: a multiple branching of recent theoretical developments and their applications. Molecular Ecology. doi: 10.1111/mec.12755.
  • Bourget R, Chaumont L, Sapoukhina N. (2014). Exponentiality of First Passage Times of Continuous Time Markov Chains. Acta Applicandae Mathematicae. 131, 197-212.
  • Cunty A, Poliakoff F, Rivoal C, Cesbron S, Fischer-Le Saux M, Lemaire C, Jacques M-A, Manceau C and Vanneste JL.(2014). Characterization of Pseudomonas syringae pv. actinidiae (Psa) isolated from France and assignment of Psa biovar 4 to a de novo pathovar: Pseudomonas syringae pv. actinidifoliorum pv. nov.Plant Pathology. doi:10.1111/ppa.12297.


  • Crété R., Pumo B., Soubeyrand S., Didelot F., Caffier V.(2013). A Continuous Time-and-State Epidemic Model Fitted to Ordinal Categorical Data Observed  on a Lattice at Discrete Times. Journal of Agricultural, Biological, and Environmental Statistics 18, 538-555.
  • Belin E, Rousseau D, Boureau T, Caffier V. 2013. Thermography versus chlorophyll fluorescence imaging for detection and quantification of apple scab. Computers and Electronics in Agriculture, 90: 159-163
  • Bourget R, Chaumont L, Sapoukhina N 2013 .Timing of pathogen adaptation to a multicomponent Treatment.PLoS One,8(8): e71926. doi:10.1371
  • Cornille A., Giraud T., Bellard C., Tellier A., Le Cam B., Smulders R., Kleinschmit J., Roldan-Ruiz I., Gladieux P 2013 .Post-glacial recolonization of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple.Molecular ecology,22,  2249–2263
  • Fourcade Y., Chaput-Bardy A., Secondi J., Fleurant C. and Lemaire C. 2013 .Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection.Molecular ecology, 22, 2065–2073
  • Leroy T., Lemaire C., Dunemann F., Le Cam B 2013 .Fine-scale spatial genetic structure of fungal pathogen populations in a heterogenous habitat..BMC Evolutionary Biology ,13: 64.  doi:10.1186/1471-2148-13-64
  • Lê Van A, Caffier V, Lasserre-Zuber P, Chauveau A, Brunel D, Le Cam B, Durel CE. 2013. Differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population: a case study in an apple x Venturia inaequalis pathosystem. New Phytologist, 197:899-908
  • Mhedbi-Hajri N., Hajri A, Boureau T., Darrasse A., Durand K., Brin C., Fischer-Lesaux M., Manceau C., Poussier S., Pruvost O., Lemaire C., Jacques M-A. 2013 .Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis.PLoS One,8(3):e58474
  • Sapoukhina N., Paillard S., Dedryver F., Vallavieille-Pope C 2013 .Quantitative plant resistance in cultivar mixtures: Wheat stripe rust as a modeling case study.New Phytologist,doi: 10.1111/nph.12413.


  • Caffier, V; Le Cam, B; Expert, P; Tellier, M; Devaux, M; Giraud, M; Chevalier, C. 2012. A new scab-like disease on apple caused by the formerly saprotrophic fungus Venturia asperata. PLANT PATHOLOGY, 61: 915-924
  • Chene, Y; Rousseau, D; Lucidarme, P; Bertheloot, J; Caffier, V; Morel, P; Belin, E; Chapeau-Blondeau, F. 2012. On the use of depth camera for 3D phenotyping of entire plants. COMPUTERS AND ELECTRONICS IN AGRICULTURE, 82: 122-127
  • Cornille, A; Gladieux, P; Smulders, MJM; Roldan-Ruiz, I; Laurens, F; Le Cam, B; Nersesyan, A; Clavel, J; Olonova, M; Feugey, L; Gabrielyan, I; Zhang, XG; Tenaillon, MI; Giraud, T. 2012. New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties. PLOS GENETICS, 8:e1002703
  • Lê Van A., Gladieux P., Lemaire C., Cornille A., Giraud T., Durel C.E., Caffier V., Le Cam B. 2012. Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host. Evolutionnary Applications,doi:10.1111/j.1752-4571.2012.00246.x


  • Revision of Nomenclature of the Differential Host-Pathogen Interactions of Venturia inaequalis and Malus. Bus VGM, Rikkerink EHA, Caffier V, Durel CE, Plummers KM.  Annual Review of Phytopathology 49, 391-413.
  • Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants. Gladieux P., Guérin F., Giraud T., Caffier V., Parisi L., Didelot F., Lemaire C., Le Cam B. Molecular Ecology 20, 4521-4532.
  • The threat of wild habitat to scab resistant apple cultivars. Lê Van A., Durel C. E., Le Cam B., Caffier V. Plant Pathology 60, 621-630.
  • Contrasting recombination patterns and demographic histories of the model plant pathogen Ralstonia solanacearum inferred from MLSA. Wicker E, Lefeuvre P, de Cambiaire JC, Lemaire C, Poussier S, Prior P. ISME Journal. doi: 10.1038/ismej.2011.160.
  • Sensing and adhesion are adaptive functions in the plant pathogenic xanthomonads. Mhedbi-Hajri N., A. Darrasse, S. Pigné, K. Durand, S. Fouteau, V. Barbe, C. Manceau, C. Lemaire and M.-A. Jacques. BMC Evolutionary Biology, 11:67.
  • Widespread introgression does not leak into allotopy in a broad sympatric zone. Johanet A., Secondi J. & Lemaire C. Heredity 106, 962-972.
  • La combinaison de méthodes, fondement de la protection intégrée. Munier-Jolain N., Parisi L., Alaphilippe A., Brun L., Caffier V., Deytieux V., Didelot F., Lemarquand A., Simon S. In : Ricci P, Bui S., Lamine C. Repenser la protection des cultures – Innovations et transitions. Educagri Editions/Editions Quæ, 57-80


  • Evolution of the population structure of Venturia inaequalis, the apple scab fungus, associated with the domestication of its host. Gladieux P, Zhang X-G, Roldan Ruiz I., Caffier V., Leroy T., Devaux M., Van Glabeke S., Coart E., Le Cam B. Molecular Ecology 19, 658-674.
  • Aggressiveness of eight Venturia inaequalis isolates virulent or avirulent to the major resistance gene Rvi6 on a non-Rvi6 apple cultivar. Caffier V,  Didelot F, Pumo B, Causeur D, Durel CE, Parisi L. Plant Pathology 59, 1072-1080.
  • Host-specific differentiation among populations of Venturia inaequalis causing scab on apple, pyracantha and loquat. Gladieux P, Caffier V, Devaux M, Le Cam B. Fungal Genetics and Biology. 47, 511-521.
  • Spatially mixed crops to control the stratified dispersal of airborne fungal diseases. Sapoukhina, N,  Tyutyunov, Y Sache, I, Arditi, R. Ecological Modelling 221, 2793-2800.
  • Integrating scab control methods with partial effects in apple orchards: the association of cultivar resistance, sanitation and reduced fungicide schedules. Didelot F, Caffier V, Baudin M, Orain G, Lemarquand A, Parisi L. IOBC wprs Bulletin, 54: 525-528.
  • Efficiency of association of scab control methods on resistance durability of apple: the case study of cultivar Ariane. Caffier V, Didelot F, Orain G, Lemarquand A, Parisi L. IOBC wprs Bulletin, 54: 327-330.
  • Olfactory and visual species recognition and their role in hybridization. Secondi J, Johanet A, Pays O, Cazimajou F, Djalout Z, Lemaire C. Behaviour. 147, 1693-1712.


  • Spatial deployment of gene-for-gene resistance governs evolution and spread of pathogen populations. Sapoukhina N, Durel CE, Le Cam B. Theoretical Ecology 2, 229–238.
  • The discovery of a novel sodium channel in the cockroach Periplaneta americana: Evidence for an early duplication of the para-like gene. Moignot B., Lemaire C., Quinchard S., Lapied B. & Legros C. Insect Biochemistry and Molecular Biology 39, 814-823.
  • A «Repertoire for Repertoire» Hypothesis: Repertoires of Type Three Effectors are Candidate Determinants of Host Specificity in Xanthomonas. Hajri A., Brin C., Hunault G., Lardeux F., Lemaire C., Manceau C., Boureau T. & Poussier S. PLoS ONE. 4: e6632. doi:10.1371/journal.pone.0006632
  • Situation actuelle en France du contournement de la résistance Vf par Venturia inaequalis - propositions de méthodes de lutte adaptées. Didelot F, Parisi L, Orain G, Lemarquand A, Le Cam B, Laurens F, Caffier V.In: Sinoir N, Coulombel A, eds. Journées Techniques Nationales Fruits et Légumes Biologiques. Paris, France : ITAB [],  65-8.


  • On the Origin and Spread of the Scab Disease of Apple: Out of Central Asia. Gladieux P., Zhang X-G., Afoufa-Bastien D., Valdebenito Sanhueza R-M., Sbaghi M., Le Cam B. PLoS ONE 3 (1): e1455. doi:10.1371/journal.pone.0001455.
  • Effects of apple cultivar susceptibility to Venturia inaequalis on scab epidemics in apple orchards. Brun, L., Didelot, F., Parisi, L. Crop Protection 27, 1009-1019.
  • Two new species of Ulocladium from Southwest China. Wang Y., Le Cam B., Zhang X. G.  Mycologia 100, 455–459.

See also

L'ensemble des publications de l'IRHS

Modification date: 26 February 2024 | Publication date: 11 May 2011 | By: Maël Baudin