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

Background: 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. Results: Using clustering methods, we first identified two specialist subpopulations: (i) a virulent subpopulation sampled on Malus trees carrying the Rvi6 resistance gene; and (ii) an avirulent 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. Conclusions: 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.背景：适应性可通过使种群随环境条件产生分化，进而启动种群趋异演化。基因流与选择之间的平衡决定了这类种群结构在同域环境中的维持。针对植物病原体开展这两种拮抗力量的研究具备可行性，这得益于病原体极强的扩散能力，以及宿主施加的强烈选择压力。本文针对由多种苹果属（Malus）植物构成的异质生境，分析了苹果黑星病菌（Venturia inaequalis）的种群遗传结构。研究基于从单一果园内9种不同苹果属植物上采集的114株菌株获得的微卫星（microsatellite）与扩增片段长度多态性（AFLP）数据展开推演，以明确塑造该病原体遗传结构的关键因子。 结果：通过聚类分析方法，本研究首先鉴定出两个特化亚种群：其一为在携带Rvi6抗病基因的苹果属植株上采样得到的毒力型亚种群；其二为仅能侵染不携带该抗病基因的苹果属植株的无毒型亚种群。对这两个亚种群开展的全基因组位点扫描未检测到受选择的位点。此外，未发现与其他宿主种类相关的特殊种群亚结构。不过，在果园尺度下检测到的距离隔离（IBD）模式表明，每个亚种群内部存在自由的基因流。 结论：本研究揭示了抗病基因对病原体种群产生极强影响的罕见案例。尽管宿主苹果属植物具有高度多样性，但Rvi6基因的存在似乎足以解释本次观测到的种群遗传结构。此外，果园尺度下距离隔离模式的检测结果显示病原体的平均扩散距离极短，这一发现对于流行病学家与景观管理者制定黑星病防控策略具有重要参考价值。