Genetic diversity in Ukrainian, Swedish, and Estonian apple germplasm revealed with SSR markers

Abstract Apple ( Malus domestica Borkh.) is one of Europe’s most significant fruit crops, and preserving its genetic diversity is critical for breeding and adaptation to climate change. This study presents a comprehensive molecular characterisation of apple germplasm collections from Ukraine, Sweden, and Estonia using 16 SSR markers to assess genetic identity, diversity, and structure. Genotyping data were harmonised using the Malus UNiQue genotype (MUNQ) system, enabling accurate cross-collection comparisons and clarification of mislabelled or synonymous accessions. In total, 422 unique diploid genotypes were analysed, representing both historical heirloom and modern cultivars from three national collections with diverse geographic and breeding origins. Structure analysis demonstrated clear genetic separation between Ukrainian and Northern European germplasm, with Swedish and Estonian cultivars clustering together, reflecting their shared breeding history and regional adaptation. Ukrainian heirloom cultivars formed a distinct genetic subgroup, whilst modern Ukrainian cultivars showed admixture with foreign germplasm, highlighting the underutilisation of the native gene pool in breeding programmes. These findings underscore the importance of preserving Ukrainian heirloom cultivars as valuable genetic resources for future breeding and conservation efforts, contribute to the global understanding of apple genetic resources, and demonstrate the utility of MUNQ harmonisation for curation and diversity studies in fruit tree collections.