Pomegranate Germplasm Collections from Elche (Spain) and Bari (Italy): Genetic Resources Characterization for Emerging Mediterranean Challenges

Pomegranate (Punica granatum L.) is a strategic crop for Mediterranean agriculture due to its adaptability to arid environments—an increasingly important trait in the context of climate change—and its rising market demand driven by nutritional and medicinal properties. To support breeding and conservation efforts, this study evaluated the genetic diversity and phenotypic traits of two Mediterranean germplasm collections from Elche (Spain) and Bari (Italy). A total of 184 accessions were analyzed using SSR markers and evaluated for key pomological and phenological traits, including fruit weight, skin and aril color, seed hardness, aril weight, titratable acidity, soluble solids content, and harvest time. Genetic analyses revealed high levels of diversity within and between collections, with clear population structure influenced by geographic origin. Phenotypic evaluation revealed considerable variation in agronomic and quality traits, and several accessions with notably desirable characteristics were identified. For example, Ovadan and Molla Nepes displayed very high soluble solids content (>19 °Bx), Sanrà Nero, Sanrà Rosso, and Tajikistan Dark Red exhibited titratable acidity exceeding 40 g/L citric acid, and De Marco reached aril weights of up to 0.60 g. The integration of molecular and morphological data provided valuable insights into the distinctiveness and breeding potential of the studied genotypes. Misclassifications were identified, as well as phenotypic differences attributable to environmental influences. These findings highlight the importance of characterizing regional germplasm to preserve local adaptations and support development of new cultivars adapted to changing environmental conditions. This work reinforces the role of European pomegranate collections as reservoirs of genetic resources for sustainable cultivation and future breeding programs.