Abstract
BackgroundAdaptation, 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.ResultsUsing 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.ConclusionsOur 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
Highlights
Adaptation, which induces differentiation between populations in relation to environmental conditions, can initiate divergence
The presence of the Rvi6 resistance gene in Malus accessions divides the V. inaequalis population into two subpopulations Among the 114 strains analysed, we observed 106 unique haplotypes based on 11 microsatellite loci and 79 AFLP markers (Additional file 1: Tables S2)
Because the major resistance gene Rvi6, introgressed from the clone Malus x floribunda 821, is known to exert a high selective pressure on V. inaequalis populations [18], we evaluated the presence of this gene in all hosts sampled in this study (Additional file 1: Table S1)
Summary
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 agro-ecosystems, higher homogeneity and density of hosts, coupled with a low host species diversity, are expected to induce quick cultivars carrying different resistance traits, both adaptation and gene flow processes are expected to shape the genetic structure of pathogen populations. An IBD pattern over a heterogeneous landscape of host species would indicate that strains are generalists Under this hypothesis, two strains isolated from neighbour demes that infect different host species are expected to be more closely related than two strains isolated from two distant demes, even if they infect the same host. We could question whether it remains possible to maintain pathogen differentiations related to hosts in a heterogeneous environment
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