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Open Access Research article

The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species

Thibault Leroy123, Christophe Lemaire123*, Frank Dunemann4 and Bruno Le Cam123*

Author Affiliations

1 Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Boulevard Lavoisier, Angers, 49045 France

2 INRA, IRHS, PRES UNAM, SFR QUASAV, Rue Georges Morel, Beaucouzé, 49071 France

3 Agrocampus Ouest, IRHS, PRES UNAM, SFR QUASAV, Rue Le Nôtre, F-49045 Angers, France

4 Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural and Fruit Crops, Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany

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BMC Evolutionary Biology 2013, 13:64  doi:10.1186/1471-2148-13-64

Published: 12 March 2013



Adaptation, which induces differentiation between populations in relation to environmental conditions, can initiate divergence. The balance between gene flow and selection determines the maintenance of such a structure in sympatry. Studying these two antagonistic forces in plant pathogens is made possible because of the high ability of pathogens to disperse and of the strong selective pressures exerted by their hosts. In this article, we analysed the genetic structure of the population of the apple scab fungus, Venturia inaequalis, in a heterogeneous environment composed of various Malus species. Inferences were drawn from microsatellite and AFLP data obtained from 114 strains sampled in a single orchard on nine different Malus species to determine the forces that shape the genetic structure of the pathogen.


Using clustering methods, we first identified two specialist subpopulations: (i) a virulent subpopulation sampled on Malus trees carrying the Rvi6 resistance gene; and (ii) a subpopulation infecting only Malus trees that did not carry this resistance gene. A genome scan of loci on these two subpopulations did not detect any locus under selection. Additionally, we did not detect any other particular substructure linked to different hosts. However, an isolation-by-distance (IBD) pattern at the orchard scale revealed free gene flow within each subpopulation.


Our work shows a rare example of a very strong effect of a resistance gene on pathogen populations. Despite the high diversity of Malus hosts, the presence of Rvi6 seems sufficient to explain the observed genetic structure. Moreover, detection of an IBD pattern at the orchard scale revealed a very low average dispersal distance that is particularly significant for epidemiologists and landscape managers for the design of scab control strategies

Gene flow; Isolation-by-distance (IBD); Apple scab; Adaptation; Spatial genetic structure