Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan Capsicum annuum germplasm

Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. The Balkans, including Bulgaria, are considered as the secondary centre of pepper diversity especially for C. annuum, where local forms with diverse phenotypes and qualities have formed due to the specific agro-climatic conditions and breeding traditions. Evaluation of the genetic diversity and structure of a pepper collection is an important tool for further development of new varieties and the maintenance of sustainable agriculture. In this study, a set of 179 C. annuum accessions collected from different locations in the Balkan Peninsula was genotyped with 21 simple sequence repeat (SSR; microsatellite) markers. In total, 146 alleles were amplified among which the majority were with low frequencies (