title: Emergence of new virulent populations of apple scab from nonagricultural disease reservoirs.
abstract: Plant pathogens adapt readily to new crop varieties in agrosystems, and it is crucial to understand the factors underlying the epidemic spread of new virulent strains if we are to develop more efficient strategies to control them. In this study we used multilocus microsatellite typing, molecular epidemiology tools and a large collection of isolates from cultivated, wild and ornamental apples to investigate the origin of new virulent populations of Venturia inaequalis, an ascomycete fungus causing apple scab on varieties carrying the Rvi6 resistance gene. We demonstrated a common origin at the European scale of populations infecting apples (Malus × domestica) carrying the Rvi6 resistance and Malus floribunda, the progenitor of the Rvi6 resistance. Demographic modeling indicated that the Rvi6-virulent lineage separated several thousands of years ago from populations infecting non-Rvi6 hosts, without detectable gene flow between the two lineages. These findings show that 'breakdowns' of plant resistance genes can be caused by the selection and migration of virulent genotypes from standing genetic variation maintained in environmental disease reservoirs, here ornamental crabapples. This work stresses the need to take better account of pathogen diversity in resistance screenings of breeding lines and in resistance deployment strategies, in order to enhance sustainable disease management.
authors.affiliation: Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES L'UNAM, Angers, 49075, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Lemaire
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France.
authors.forename: Marie
authors.initials: M
authors.lastname: De Gracia
authors.affiliation: Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES L'UNAM, Angers, 49075, France.|INRA, UMR 1202 BIOGECO, Cestas, 33612, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: Leroy
authors.affiliation: Department of Plant Pathology, Institute of Horticulture, Skierniewice, 96-100, Poland.
authors.forename: Monika
authors.initials: M
authors.lastname: Michalecka
authors.affiliation: Department of Food Science, Aarhus University, Aarslev, 5792, Denmark.
authors.forename: Hanne
authors.initials: H
authors.lastname: Lindhard-Pedersen
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France.|Université de la Réunion, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, 97715, La Réunion, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Guerin
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France.|INRA, UMR BGPI, Montpellier, 34398, France.|CIRAD, UMR BGPI, Montpellier, 34398, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gladieux
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Le Cam
mesh_terms: D000383:Agriculture; D001203:Ascomycota / Q000235:genetics / Q000472:pathogenicity*; D001499:Bayes Theorem; D005075:Biological Evolution; D016002:Discriminant Analysis; D004197:Disease Reservoirs / Q000382:microbiology*; D051456:Gene Flow; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D027845:Malus / Q000382:microbiology*; D018895:Microsatellite Repeats / Q000235:genetics; D015999:Multivariate Analysis; D009154:Mutation / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology*; D025341:Principal Component Analysis; D014774:Virulence
keywords: Malus × domestica; Venturia inaequalis; approximate Bayesian computation; environmental reservoirs; evolutionary epidemiology; microsatellites