Introduction: Molecular markers are the examples of the contribution of genome technology to medicinal plant breeding through marker-assisted selection (MAS) for pharmaceutical quality. Objective: Forty-two accessions of origanum vulgare L. originating from Europe were evaluated to detect genomic and chemotypic polymorphisms and to discover possible associations between them. Methods: A total of 477 molecular polymorphisms including 214 AFLP (Amplified Fragment Length Polymorphism) and 263 SAMPL (Selectively Amplified Microsatellite Polymorphic Loci) were used for genotyping. Components in the essential oils were identified and quantified by gas chromatography (GC) and two major compounds (two economically important monoterpenes: carvacrol and thymol) were investigated. Results: Based on results, a relatively high correlation between chemotypic patterns and genetic markers was identified. Associations between traits of interest foressential oils (carvacrol and thymol content) and genetic markers were tested using five statistical methods including three General Linear Model (GLM) and two unified Mixed Linear Model (MLM) approaches. Significant associations were found for 3 AFLP and 20 SAMPL with three key traits including essential oil yield, carvacrol and thymol content. Conclusion: These associations can constitute a useful starting point for marker-assisted selection. Therefore, the results provide the basis for molecular breeding of o. vulgare for pharmaceutical purposes.
