Multiplexed SSR marker analysis of Diplocarpon coronariae reveals clonality within samples from Middle Europe and genetic distance from Asian and North American isolates

Abstract

Background Apple blotch (AB) caused by Diplocarpon coronariae (Dc) has been established in Europe since 2010. AB is a serious apple disease, mostly in low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. However, the epidemiology and population genetic structure of this pathogen is unknown. Methods We developed twelve Dc-specific microsatellite markers and screened DNA of both pure fungal isolates and infected apple leaves. The marker data of 313 European samples of Dc were compared to Dc isolates from Asia (n = 7) and the USA (n = 3). Results We found 31 distinct multilocus genotypes (MLGs) in European samples, and seven additional MLGs in the Asian and USA samples. The European samples had the typical genetic signature of a recently introduced species including high clonality, a low number of private alleles and one dominant MLG across all the sampling sites. All European MLGs were genetically distant from those MLGs of Asian and USA origin. Based on the lack of linkage disequilibrium observed, there is evidence that Dc undergoes regular cycles of sexual recombination in the European population, although the sexual stage (apothecia) has not been observed in Europe. Conclusions The twelve newly developed SSR markers reported here provide a useful tool to characterize the population genetic diversity and structure of Dc in Europe. Our study supports the hypothesis that Dc is a recently introduced pathogen in Europe, but of currently unknown origin. Dc has a large effective population size during field epidemics, so we believe that the pathogen has substantial evolutionary potential. Application of the SSR markers to large-scale and diverse Dc samples will help to better understand the epidemiology of AB, which has become a global apple disease, and will help guide effective mitigation strategies based on disease management and resistance breeding.

Monitoring Spore Dispersal and Early Infections of Diplocarpon coronariae Causing Apple Blotch Using Spore Traps and a New qPCR Method

“…The fact that we could not cause leaf infections from bud, bark or fruit mummy tissues may be due to technical issues, and the role of the various apple tree organs for overwintering of Dc requires further investigation. Dc present on buds and wood in propagation material could be exchanged between nurseries across Europe and may explain the rapid spread of this disease to many European apple production areas since its first detection in Northern Italy (Oberhänsli et al 2021). Our observation that conidia produced on fruits after six months in storage at 4°C are able to infect apple leaves provides an indication that fruit-derived conidia might represent an additional source of primary inoculum at least on a local scale.…”

“…have not yet been observed in Europe(Wöhner and Emeriewen 2019), indicating it is unlikely they were the spore type captured.Although not yet observed, the importance of ascospores as primary inoculum in Europe should be subject to further research. A recent population genetic study suggested a mixed sexual and asexual reproduction of Dc in Europe, although Dc populations in Europe are genetically homogenous, clonal and dominated by a few multi-locus genotypes(Oberhänsli et al 2021). …”