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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 10 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.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1122-4) contains supplementary material, which is available to authorized users.

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