Assessment of diversity and genetic differentiation in polycross-derived populations of Thymus daenensis using ISSR and SCoT markers

Thymus daenensis is an important aromatic and medicinal plant endemic to Iran, with high biological and pharmacological properties. This study aimed to determine the genetic diversity and genetic differentiation pattern of 12 polycross-derived populations comprising 103 half-sib progenies of T. daenensis using inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) markers. Although both marker systems showed a high level of polymorphism, SCoT was more efficient in the detection of polymorphism for this species. The analysis of molecular variance (AMOVA) results of the two marker systems assigned higher genetic variation to progenies within in each population (88%) than among populations (12%). Based on diversity indices, the Arak and Isfahan2 populations exhibited the highest genetic variation. Furthermore, the Mantel test indicated that there were different patterns of polymorphism distribution between the ISSR and SCoT techniques, suggesting their complementary role in DNA fingerprinting of T. daenensis. Results highlight the reliability and informativeness of SCoT markers in assessing the genetic diversity and differentiation of this endangered plant species. In conclusion, the findings of this study provide a foundation for the establishment of more effective breeding and conservative programs for T. daenensis. The use of ISSR and SCoT markers could utilize the available genetic diversity for developing improved Thyme cultivars, and this meets the growing demands for this economically and ecologically important medicinal plant.