Genetic variation and population differentiation in North American, central Asian and European isolates of Venturia inaequalis

Abstract

Venturia inaequalis, the causal fungal pathogen of apple scab, has evolved with its Malus hosts during apple domestication. This co‐evolution has resulted in a genetic structure in V. inaequalis populations from Europe and central Asia based on host species and geographic isolation. However, it is not yet clear if geographic isolation has led to population differentiation in North American isolates. We resequenced the genomes of 54 V. inaequalis isolates from North America and analysed them with publicly available genome sequences of 90 European and central Asian isolates for variant discovery and population structure. A total of 204,566 high‐quality single‐nucleotide polymorphisms (SNPs) were identified and used to assess population genetic structure and genomic diversity across 123 Venturia spp. isolates from around the world. Population genetic analysis identified four clusters based on Malus and non‐Malus hosts and Venturia species; this differentiation was supported by genetic diversity parameters including FST, Nei's π and Tajima's D. Genetic structure analysis did not reveal a distinct subpopulation of North American V. inaequalis isolates within the global isolates. Additionally, structure was not observed in V. inaequalis isolates collected on M. × domestica between North America and Europe. These observations indicate that geographical isolation has not contributed to the population differentiation between North America and Europe/central Asia. These results will enhance our understanding of the evolution of V. inaequalis, the emergence of virulent isolates and their implications for managing apple scab effectively.