Assessment of genetic variability in Ficus carica using SSR markers: a case study from the ‘Giardini di Pomona’

Fig (Ficus carica L.) is one of the earliest domesticated fruit trees, with a cultivation history spanning over 6,000 years across the Mediterranean basin. Despite its longstanding cultural and nutritional significance, fig remains a relatively understudied "minor fruit crop" in terms of genetic characterisation and conservation. In this study, we investigated the genetic variability and population structure of a fig germplasm collection maintained at the ‘Giardini di Pomona’ in Cisternino (Puglia region, Italy), which includes 235 fig genotypes originating from Italy, France, Albania, and caprifig accessions. The genotypes were characterised through 68 SSR markers previously validated for polymorphism and reproducibility. Genetic diversity parameters such as allele number, heterozygosity, and Shannon’s Information Index were calculated for each regional group. Genetic structure was further assessed using Principal Coordinate Analysis (PCoA), AMOVA, Neighbour-Joining phylogenetic clustering, and Bayesian clustering with the STRUCTURE software. The SSR markers revealed a total of 68 polymorphic alleles, with a moderate to high level of intra-population diversity. Shannon’s index values ranged from 0.25 (Albania) to 0.74 (Italy), and heterozygosity values from 0.12 to 0.43, indicating clear differences in genetic richness among regional groups. AMOVA analysis showed that 39% of total genetic variance was attributable to differences among populations (Fst = 0.386, p < 0.001), suggesting moderate genetic differentiation between geographic origins. The PCoA and phylogenetic tree analyses consistently grouped the genotypes into two major clusters. STRUCTURE analysis supported K = 2 as the most probable number of genetic clusters, further confirming the presence of two main subpopulations within the collection. This work highlights the significant genetic variation conserved within the Pomona Gardens fig germplasm and underlines the importance of safeguarding local fig varieties, particularly in light of climate change, agricultural diversification, and increased consumer interest in traditional and nutritionally valuable crops. The study also provides a molecular framework for future breeding efforts and germplasm conservation strategies in Ficus carica.