Conserved DNA-derived polymorphism as a useful molecular marker to explore genetic diversity and relationships of wild and cultivated Tunisian figs (Ficus carica L.)

Key message The first insight into the genome of Ficus carica L. with a gene target marker (conserved DNA-derived polymorphism (CDDP)) and assessment of genetic diversity mostly related to functional domains of plant genes. To improve the molecular database of Ficus carica L. species, we report for the first time the use of conserved DNA-derived polymorphism (CDDP) as a gene-targeted marker to assess molecular diversity, and establish relationships among 62 Tunisian cultivated and wild fig trees. The mapping process for the in silico analysis of CDDP primers against the whole F. carica genome cv Dottato verified the specificity of the CDDPs and the stringency of PCR conditions. Overall, a set of twelve CDDP primers were tested revealing 200 markers. Based on the polymorphic information content (PIC = 0.90), resolving power (Rp = 8.13) and the level of polymorphisms (98.04%) CDDP markers were found to highly discriminant and informative compared to other non-targeted methods. The UPGMA dendrogram revealed that Tunisian figs could be differentiated into three main groups, which was also supported by the principal coordinate analysis. The analysis of molecular variance (AMOVA) suggested that the maximum genetic variation was within groups (86.10%) with less variation among groups (19%) indicating that there is a limited diversity that distinguishes fig groups. Here, we present the first report in which a targeted DNA region molecular marker successfully clustered the Tunisian fig germplasm depending on the sex, the botanical classification of figs and consistently in agreement, with their geographic origin). The results highlight that the CDDP markers are able to characterize wild and cultivated Ficus carica L. species and provide a new valuable tool for further genome investigation and will guide the development of conservation and management strategies for existing fig tree germplasm.

Automated summary

The study used gene-targeted markers (CDDP) to assess the genetic diversity of cultivated and wild fig trees in Tunisia, and found that CDDP markers were more discriminating and informative compared to other non-targeted methods. The results showed that Tunisian figs could be differentiated into three main groups, which was supported by principal coordinate analysis. CDDP markers can effectively distinguish different fig groups.