Genetic Variability in Fig Germplasm Repository from a Pomological Garden, the ‘Giardini di Pomona’

Fig (Ficus carica L.) is an ancient Mediterranean fruit species characterized by extensive clonal propagation, high phenotypic variability, and a complex domestication history. However, the relationships between genetic structure, phenotypic diversity, and agronomically relevant traits remain insufficiently understood, limiting the efficient use of germplasm resources in breeding programs. To address this gap, we integrated molecular, phenotypic, and association analyses to characterize 235 fig genotypes conserved in the “Giardini di Pomona” repository. Genetic diversity was assessed using 66 polymorphic SSR alleles, while a representative subset of 83 genotypes was evaluated for 27 morphological, fruit, tree, and phenological traits. Population analyses revealed a structured but highly admixed genetic organization, with two major genetic groups identified by Bayesian clustering. Principal Coordinate Analysis explained 44.4% of the total molecular variation, and STRUCTURE analysis assigned 105 and 130 genotypes to the two groups, respectively. Despite this genetic structure, Shannon diversity and AMOVA indicated that most diversity was maintained within geographic groups (93.2% and 61% of total variation, respectively), highlighting the importance of historical germplasm exchange and vegetative propagation in shaping Mediterranean fig diversity. Phenotypic analyses revealed broad but continuous variation across all trait categories, with several cultivars displaying distinctive combinations of tree, fruit, and phenological characteristics. Association mapping identified significant SSR–trait relationships involving leaf morphology, tree growth habit and vigor, fruit weight and pigmentation, cropping type, and ripening time, identifying candidate markers with potential utility for early selection. By combining population genetics, phenotypic characterization, and marker–trait associations within a single germplasm collection, this study provides a comprehensive framework for cultivar identification, conservation prioritization, and marker-assisted breeding in fig.