Differential Allelic Richness between Malus sylvestris L. and Malus × domestica Borkh. from Finland as a Measure of Genetic Loss

European wild apple (Malus sylvestris L.) is the only Malus wild species native to Europe which is a relative of cultivated apples (Malus × domestica Borkh.). It grows on forests’ edges, farmland hedges, and marginal sites; by living in those scattered meta-populations, it is exposed to genetic erosion in relation to hybridization and habitat degradation. In Finland, it grows at the northern edge of its distribution in Europe and is considered as a near-threatened taxon requiring urgent conservation. In order to evaluate the molecular genetic diversity of M. sylvestris, five populations including 43 trees were analyzed using 15 microsatellite markers. Additionally, a similar number of samples from cultivated apples, which are common to the same region, was included in order to estimate gene diversity gaps and give an insight into putative hybridization. European wild apple in Finland proved to be populationally structured, and seems not to be threatened by introgression events from its cultivated relative. They were all separated into different clusters, except for one individual. However, urgent conservation is indeed needed, especially due to the very low total number of trees (four) in some of the analyzed populations. These populations should be restored in order to enable permanent access to the wild relatives’ diversity, as they might be a critical source of gene variants for future needs.