Germplasm Mining of Prunus domestica L.: Multi-Year Assessment of Pomological Characters to Identify Candidate Elite Donor Parents for European Plum Breeding and Their Genetic Evaluation

European plum (Prunus domestica L.) breeding for competitive production increasingly requires donor parents that combine attractive, market-oriented fruit quality with stable trait expression. This study evaluated a set of 36 phenotypically highly different cultivars from the germplasm collection maintained at the Research and Breeding Institute of Pomology Holovousy Ltd. (the Czech Republic). First, genetic analyses based on SSR marker data were performed to assess the diversity and kinship relationships within the selected collection of plum varieties. Several parentage combinations were successfully identified for cultivars with previously undocumented origins. Population-level analyses confirmed broad genetic diversity and separated the collection into four genetically distinct groups. Phenotypes were obtained on fruits ripened on trees from a non-irrigated orchard on myrobalan rootstock over five consecutive years (2019–2023). Pomological and related quality traits were recorded using nine-point UPOV-based rating scales together with instrumental measurements. The dataset included fruit size and shape descriptors, skin and flesh color, wax bloom, soluble solids (°Brix), firmness, bruising resistance, stone separability, and sensory attributes (flavor, aroma, juiciness, texture, and acidity). Interannual variability was quantified using coefficients of variation, and relationships among traits were explored using Pearson correlations. The results revealed broad phenotypic diversity among the individual varieties and also their genetic groups. Finally, phenotypes were associated with genotypes, and the most genetically determined traits were identified. Multi-year stability profiling supported the identification of candidate elite donor cultivars that combine favorable attributes for the fresh market and/or traits relevant to processing. These findings provide a practical pre-breeding shortlist and quantitative trait targets to support crossing design and selection under central European conditions.