Integrative DNA Barcoding in Ficus Cultivars in Taif Highlands, Saudi Arabia: Complementary Roles of rbcL and trnH-psbA Markers

Abstract

The common fig (Ficus carica L.) is a commercially significant fruit crop in Saudi Arabia, with particular importance in the Al-Taif highland region. In this study, three DNA barcodes (rbcL, ITS, and trnH-psbA) were evaluated on eleven fig cultivars collected from various geographically distinct sites within the Al-Taif highlands. A combination of three plant DNA barcoding markers, rbcL, ITS, and trnH-psbA, alongside selected morphological traits of mature leaves and fruits, was used to assess the genetic and phenotypic diversity among Fig varieties. The integrative approach aimed to achieve reliable cultivar discrimination and enhance understanding of the genetic structure and potential lineage relationships within the local fig germplasm.The results revealed notable genetic variation among the cultivars, with The rbcL marker displaying a relatively elevated transition bias, contributing to higher apparent variability. The rbcL locus exhibited a high transition/transversion bias (R = 233.69) and the highest substitution rate (0.001) among the tested markers. Intraspecific distance analysis indicated that rbcL sequences had the greatest variation (0.0028), followed by the ITS+rbcL multilocus combination (0.0024). The rbcL marker also showed the highest percentage of variable points (79%), followed by the ITS+rbcL combination (55%). In contrast, the ITS region alone showed limited discriminatory power among closely related cultivars, and combinations excluding the rbcL marker (e.g., ITS + trnH-psbA, 10% variability) showed limited discriminatory capacity. In comparison, combinations including rbcL such as ITS + rbcL (79%), rbcL + trnH-psbA (31%), and ITS + rbcL + trnH-psbA (26%), revealed significantly higher genetic variability, underscoring the critical role of rbcL in improving resolution among closely related genotypes.