Universal Rice Primer (URP) and Start Codon Target (SCoT) Markers in Studying Population Structures and Genetic Variation in Ferula AssafoetidaL. Accessions

Ferula assafoetidais an herbaceous, annual and monocarpic genus of the Apiaceae family. So far, there has been common usage of Ferula oleo resinous gum in food and herbal medicines.The origin of F.assafoetidais can be traced back into the steppes of Iran and some reigns of Afghanistan with an extended distribution. Despite the economic value and therapeutic importance of F.assafoetida, only a few studies have reported on the genetic capacity of this herb.The present study was carried out on a set of 90 individual plants belonging to different populations of Ferula assafoetida L. via the start codon target marker (SCoT) and the universal rice primer (URP) markers. Twelve SCoT and twelve URP primers generated 192 and 149 polymorphic fragments, while having 16 and 12.41 fragments respectively on average per primer. The Polymorphism information content (PIC) for URP primers and ScoT ranged from 0.31 to 0.43 and 0.34 to 0.44 respectively, which indicated a good efficiency forboth markers. The diversity indices including heterozygosity (He), percentage of polymorphic bands (PPB), Shannon’s information index (I) and marker index (MI) were calculated based on the SCoT and URP data.The results revealed that SCoT primers were more efficient than URP primers in identifying genetic diversity within populations. Neighbor joining (Nj), as a base for clustering, classified 90 accessions into 5 and 6 groups using SCoT and URP data respectively. Moreover, the combined data (SCoT+URP) succeeded in classifying all accessions into 6 groups, although this did not correspond with the geographical distribution of accessions. Structure analysis divided 90 genotypesinto 5 subpopulations using SCoT and URP markers, whereas the combined data (SCoT+URP) divided the accessions into 6 subpopulations, which confirmed the classification achieved by the Nj method. Principal coordinate analysis (PCoA) corroborated these conclusions. According to the analysis of molecular variance) AMOVA(, a high percentage of genetic diversity was found within the species, suggesting a rich diversity of germplasm for breeding plans. The assessment of population structure demonstrated a high rate of gene flow and the mixture of populations. Taken together, our findings suggest SCoT markers are more efficient than URP markers in assessing genetic diversity among F.assafoetida genotypes. All in all, genetic diversity could help the selection of appropriate markers and special genotypes for breeding plans.