Data from: Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation

Background: Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards. For this purpose, we investigated the genetic structure of populations of the apple scab fungus, occurring on apple tree cultivars containing Rvi6, Rvi1 or Rvi17 resistance gene or no resistance at all, based on microsatellite data obtained from 606 strains sampled in 11 orchards composed of various host cultivars. Results: Application of genetic distance inferring and clustering methods allowed us to observe clear genetic distinctness of the populations virulent towards cultivars carrying Rvi6 gene from the Rvi6-avirulent populations and substructures within the Rvi6-group as a consequence of independent immigration events followed by rare, long-distance dispersals. We did not observe such a structuring effect of other genes determining apple scab resistance on any other populations, which in turn were genetically homogenous. However, in two orchards the co-occurrence of strains of different virulence pattern on the same trees was detected, blurring the genetic boundaries between populations. Conclusions: Among several resistance genes studied, only Rvi6 exerted selective pressure on pathogens populations: those virulent toward Rvi6 hosts show unique and clear genetic and virulence pattern. For the first time in commercial Malus x domestica orchards, we reported secondary contacts between populations virulent and avirulent toward Rvi6 hosts. These two populations, first diverged in allopatry, second came into contact and subsequently began interbreeding, in such way that they show unambiguous footprints of gene flow today.研究背景：追踪农业生态系统中新兴的致病力种群，有助于深化我们对病原菌与其宿主协同演化动态的认知。一方面，宿主植物对病原菌种群施加选择压力，将其划分为不同致病力的亚种群；另一方面，也为同一植株上两个分化种群的二次接触创造了条件。本研究的主要目标为：探究在波兰首次出现新型致病力菌株数年后，此前报道的、针对携带Rvi6基因（Rvi6）的栽培苹果（Malus × domestica）品种具有致病力或无致病力的两种苹果黑星菌（Venturia inaequalis）种群类型间的遗传结构，是否仍维持或已被打破；同时分析源自同一商业果园的“新兴”与“本土”种群间的关联。为此，本研究基于从11个种植不同宿主苹果品种的果园中采集的606株菌株的微卫星（microsatellite）数据，对携带Rvi6、Rvi1或Rvi17抗性基因，或完全不携带抗性基因的苹果品种上的苹果黑星菌种群的遗传结构展开了分析。 研究结果：通过遗传距离推断与聚类分析方法，我们发现：针对携带Rvi6基因品种具有致病力的种群，与无Rvi6致病力的种群间存在显著遗传分化；且Rvi6致病种群组内存在亚结构，这一现象源于独立的迁入事件以及罕见的长距离扩散。针对其他决定苹果黑星病抗性的基因，我们未在对应种群中观察到此类结构化效应，这些种群的遗传背景均一。但在两个果园中，我们检测到同一植株上共存有不同致病力模式的菌株，这使得种群间的遗传边界变得模糊。 研究结论：在本研究涉及的多个抗性基因中，仅Rvi6对病原菌种群施加了选择压力：针对Rvi6宿主具有致病力的菌株呈现出独特且清晰的遗传与致病力模式。本研究首次在商业栽培苹果园中报道了针对Rvi6宿主具有致病力与无致病力的种群间的二次接触。这两个种群最初以异域方式分化，随后发生接触并开始杂交，时至今日仍能观察到明确的基因交流痕迹。