Genetic structure of wild raspberry populations in the Central Balkans depends on their location and on their relationship to commercial cultivars

•Genetic variability of wild red raspberry populations.•Relationship with the most common cultivated cultivars.•Amplified fragment length polymorphism (AFLP) markers.•AFLP markers show that the cultivars are clearly distinct from wild populations.•The most of the genetic diversity is attributable to differences between individuals. The red raspberry (Rubus idaeus L.) is one of the most important fruit species in Serbia; there are currently approximately 11000 ha under cultivation. Wild red raspberry populations can be an important source of genes for breeding new raspberry varieties. This study was carried out to determine the genetic variability of wild populations, as well as their relationship with the most common cultivated cultivars using amplified fragment length polymorphism (AFLP) markers. In this study were included 128 individuals from seven wild populations and seven cultivar specimens from a nursery ('Mekeer', 'Willamette', 'Polka', 'Polana', 'Loganberry', 'Tayberry', 'Black Jewel'). Four AFLP combinations yielded a total of 247 polymorphic bands in 135 R. idaeus specimens. Analysis of AFLP markers showed that the cultivars are clearly distinct from wild populations. Population P4 (Mt. Ozren) had the highest gene diversity, the highest number of private markers and the highest rarity index. Analysis of molecular variance among and within wild populations showed that the most of the genetic diversity was attributable to differences between individuals within populations. A Mantel test showed that differences in altitude play the crucial role in structuring of the genetic diversity of red raspberry populations. Altitude contributed more to the population differentiation than spatial distance. Populations of wild raspberry from the territory of Serbia are characterized by high diversity, and should be protected and used as a resource in selection and breeding processes for the production of new varieties, with improved properties in terms of better yield and stronger resistance to external factors.