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    Analysis of genetic variation and population structure among of oregano (Origanum acutidens L.) accessions revealed by agro-morphological traits, oil constituents and retrotransposon-based inter-primer binding sites (iPBS) markers
    (Springer, 2020) Karagoz, Halit; Cakmakci, Ramazan; Hosseinpour, Arash; Ozkan, Gutter; Haliloglu, Kamil
    The genetic associations among 31 oregano (Origanum acutidens (Hand.-Mazz.) Ietswaart) genotypes collected from different provinces of Turkey were determined by comparing their agro-morphological traits, essential oil components and molecular traits. In order to assess the genetic diversity in 9 agro-morphological traits and 9 essential oil components, 10 polymorphic iPBS primers were used. Principle component analysis (PCA) for agro-morphological traits had two axes explaining 81.35% of total variation and PCA for essential oil components had 4 axes explaining 89.67% of total variation. Cluster analysis yielded two main clusters for agro-morphological traits and four main clusters for essential oil components. Present iPBS primers generated 289 alleles. Number of alleles per polymorphic locus varied between 25 and 36 with an average value of 28.40. The average polymorphism ratio was as 98.36%. Polymorphic information content values varied between 0.28 and 0.42. The average number of alleles (ne), Nei's genetic diversity (h) and Shannon's information index (I) were obtained 1.61, 0.37 and 0.55, respectively. The 31 accessions were assembled into three main clusters according to the unweighted pair-group mean average based on iPBS markers. Similarity index value varied between 0.51 and 0.81. Moreover, population structure analysis using Bayesian method showed that all genotypes formed eight sub-population (K = 8) with an average value of 0.3544 for expected heterozygosity and 0.0400 for population differentiation measurements (F-st value). In present study, population structure of 31 oregano genotypes collected from different provinces of Turkey were successfully characterized with the aid of iPBS markers and model-based clustering. It was concluded based on present findings that iPBS markers could reliably be used in genetic diversity and molecular analysis of oregano genotypes.
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    Öğe
    Dissection of genetic diversity and population structure in oregano (Origanum acutidens L.) genotypes based on agro-morphological properties and start codon targeted (SCoT) markers
    (Springer, 2022) Karagoz, Halit; Hosseinpour, Arash; Karagoz, Fazilet Parlakova; Cakmakci, Ramazan; Haliloglu, Kamil
    Besides aromatic characteristics of the other oregano species, essential oil of Origanum acutidens has lethal effects on some cancer lines. This study was performed to determine genetic diversity in the 70 oregano (Odostomia acutidens) genotypes based on several agro-morphological traits and start codon targeted (SCoT) markers in the endemic spread zone of O. acutidens. The result of principal component analysis (PCA) revealed that the first two components accounted for 79.56% of the total agro-morphological variation. Cluster analysis based on phenotypic data grouped all investigated genotypes into three main clusters. GGE Biplot analysis indicated that genotype numbers as G35, G11, G24, G10, and G22 with the lowest interaction with different environments were more stable than the others ones. Taking into account all analyses, genotype numbers G36, G12, G10, and G33 were selected as ideal materials. In the molecular section, 10 SCoT primers generated 109 polymorphic fragments. The mean value of polymorphic information content (PIC) was 0.36. The mean number of effective alleles (Ne), Nei's genetic diversity (H), and Shannon's information index (I) were 1.63, 0.38, and 0.57, respectively. The unweighted pair-group method with arithmetic mean (UPGMA) algorithm grouped the 70 investigated genotypes into three main clusters. Mantel test showed no correlation between genetic distance and geographical distance in these individual (r = 0.01, p = 0.69). Moreover, population structure analysis showed that all genotypes formed three sub-populations. In general, population structure of the 70 investigated oregano genotypes collected from different origins of Turkey were successfully characterized with the aid of SCoT markers. Our results suggest that evaluation of genetic diversity and structure analysis in the natural populations could efficiently provide comprehensive information for conservation of endemic and endangered species that can be used in future breeding programs.