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

Abstract

BackgroundTracking 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.ResultsApplication 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.ConclusionsAmong 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 materialThe online version of this article (10.1186/s12862-018-1122-4) contains supplementary material, which is available to authorized users.

New Molecular Tool for a Quick and Easy Detection of Apple Scab in the Field

“…Most commercial apple varieties are susceptible to V. inaequalis [6,7], and the use of resistant apple varieties is highly recommended, though unfortunately, some scab-resistant cultivars are not appreciated by the consumers [8]. Consequently, management strategies such as chemical, physical and biological control as well as sanitation practices, leaf shredding and reduction of leaf litter, are applied to suppress the sexual stage during autumn [1,[9][10][11][12]. Several treatments with fungicides are applied during the cropping season to reduce the ascospore infection, leading, throughout the last decades, to the development of V. inaequalis populations resistant to benzimidazoles, demethylation inhibitors, quinone outside inhibitors and dodine [13].…”

Field apple scab susceptibility of a diverse Malus germplasm collection identifies potential sources of resistance for apple breeding

“…Congruent with this host distribution, V. inaequalis populations infecting domesticated apples originated from Central Asia and coevolved with M. sieversii during the domestication process (Gladieux et al 2008(Gladieux et al , 2010. Populations of the pathogen tend to show distinct genetic structure related to their original Malus host species, and the breakdown of resistance genes derived from wild Malus species might be caused by divergent pathogen populations emerging from wild apple reservoirs, as has been demonstrated in the case of Rvi6 resistance (Gladieux et al 2010;Lemaire et al 2016;Leroy et al 2016;Michalecka et al 2018). M. sieversii accessions (including the accession of M. kirghisorum syn.…”

Mycorrhiza: genotype assignment using phylogenetic networks

“…In this paper we present and evaluate a new machine learning algorithm for genetic assignment based in part on phylogenetic networks. Assignment methods have been used for a variety of applications, including wildlife forensics (Larraín et al, 2014;Schwartz and Karl, 2008;Glover et al, 2009;Lorenzini et al, 2011;Millions and Swanson, 2006), understanding migratory patterns and geographical boundaries for conservation efforts (Stewart et al, 2013) and the identification of hybrid individuals for the management of invasive species (Ibañez-Justicia et al, 2017;Johansson et al, 2018;Larraín et al, 2018;Michalecka et al, 2018; ✐ ✐ "main" -2020/10/20 -1:52 -page 2 -#2 ✐ ✐ ✐ ✐ ✐ ✐ 2…”