Dissection of genetic diversity and population structure patterns in Ferula assafoetida L. wild germplasms using SCoT and URP markers

Knowledge of genetic diversity is one of the most essential tasks for sustainable management of medicinal plants. In the present study, the molecular variability and population structure in a set of Ferula assafoetida accessions collected from different geographical regions of Iran were evaluated using start codon targeted polymorphism (SCoT) and universal rice primer (URP) markers. Based on results, SCoT (12 primers) and URP (12 primers) markers amplified 192 and 149 polymorphic fragments, respectively. The polymorphism information content (PIC) estimated by URP and SCoT ranged from 0.31 to 0.43, and 0.34 to 0.44, respectively. The analysis of molecular variance revealed the greater genetic variation within population compared to among them. The Kerman’s population showed the highest values for the heterozygosity (He), percentage of polymorphic bands (PPB), Shannon's information index (I), and effective number of alleles (Ne). The neighbor joining (NJ) clustering algorithm grouped all investigated accessions into six and five main groups based on URP and SCoT data, respectively. The results of structure analysis based on both marker systems showed that all accessions were divided into five subpopulations. Furthermore, principal coordinate analysis (PCoA) supported these findings. In conclusion, our results revealed a high level of genetic diversity and gene flow between F. assafoetida populations. Moreover, the SCoT markers were more effective than URP in detecting the genetic diversity in F. assafoetida populations. Hence, the use of SCoT markers in further genetic research such as genetic fingerprinting and association analysis would be recommended.