Intraspecific diversity and relationship between subspecies of Origanum vulgare revealed by comparative AFLP and SAMPL marker analysis

The genus Origanum is often referred to as an under-utilized taxon because of its complex taxonomy. Origanum vulgare L., the most variable species of the genus, is a spice and medicinal herb that is characterized by high morphological diversity (six subspecies). In this study, the relative efficiencies of two PCR-based marker approaches, amplified fragment length polymorphism (AFLP) and selectively amplified microsatellite polymorphic loci (SAMPL), were used for comparable genetic diversity surveys and subspecies discrimination among 42 oregano accessions. Seven assays each of AFLP and SAMPL markers were utilized. Effective multiplex ratio (EMR), average heterozygosity (Hav-p), marker index (MI), and resolving power (RP) of the primer combinations were calculated for the two marker systems. UPGMA and Structure analysis along with PCoA plots derived from the binary data matrices of the two markers depicted the genetic distinction of accessions. Our results indicate that both marker systems are suitable but SAMPL markers are slightly more efficient in differentiating accessions and subspecies than AFLPs.