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<p><i>Origanum rotundifolium</i> L. is a type of origanum that has been used in folk medicine since ancient times due to its immune system strengthening effect thanks to the antioxidant enzymes it contains. This study was carried out to determine the molecular and morphological variation of <i>Origanum rotundifolium</i>, revealing considerable differences among the genotypes in FHY (fresh herbage yield), DHY (dry herbage yield), DLY (dry leaf yield), LSR (leaf-to-stem ratio), NB (number of branches), CD (canopy diameter), plant height (PH), EOR (essential oil ratio), and CC (relative chlorophyll content; SPAD index) parameters and identifying G1, G2, G3, and G19 as superior genotypes; these morphological distinctions were further supported by the genetic diversity patterns obtained from 50 genotypes using start codon targeted (SCoT) polymorphism markers. Of the 25 SCoT primers tested, 10 successfully produced a total of 103 distinct and scorable bands. The number of bands generated per primer ranged from 7 to 14, with an average of 10.3 bands per primer. The mean polymorphism information content (PIC) value across the primers was 0.38. Additionally, the average effective number of alleles (ne), gene diversity (h), and Shannon’s information index (I) were 1.5128, 0.3333, and 0.5135, respectively. Cluster analysis was conducted using Dice's genetic distance and the unweighted pair group method with arithmetic mean (UPGMA), which grouped the genotypes into two main clusters. Genetic structure analysis further divided the origanum genotypes into five subpopulations, with an average expected heterozygosity of 0.3369. The population differentiation index (Fst) ranged from 0.0367 to 0.1281, with a mean value of 0.0839. This study is the first to investigate the genetic diversity and population structure of <i>Origanum rotundifolium</i> germplasm using the SCoT-retrotransposon marker system. The results highlight the effectiveness of SCoT markers in accurately assessing the genetic diversity of <i>Origanum rotundifolium</i> genotypes, offering an essential resource for future breeding and conservation strategies.</p>

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Exploring the genetic diversity and population structure of origanum (Origanum rotundifolium L.) genotypes through start codon targeted (SCoT) marker system

  • 期刊论文

  • 发表日期：

    2026年1月6日

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  • Halit Karagöz

摘要

Origanum rotundifolium L. is a type of origanum that has been used in folk medicine since ancient times due to its immune system strengthening effect thanks to the antioxidant enzymes it contains. This study was carried out to determine the molecular and morphological variation of Origanum rotundifolium, revealing considerable differences among the genotypes in FHY (fresh herbage yield), DHY (dry herbage yield), DLY (dry leaf yield), LSR (leaf-to-stem ratio), NB (number of branches), CD (canopy diameter), plant height (PH), EOR (essential oil ratio), and CC (relative chlorophyll content; SPAD index) parameters and identifying G1, G2, G3, and G19 as superior genotypes; these morphological distinctions were further supported by the genetic diversity patterns obtained from 50 genotypes using start codon targeted (SCoT) polymorphism markers. Of the 25 SCoT primers tested, 10 successfully produced a total of 103 distinct and scorable bands. The number of bands generated per primer ranged from 7 to 14, with an average of 10.3 bands per primer. The mean polymorphism information content (PIC) value across the primers was 0.38. Additionally, the average effective number of alleles (ne), gene diversity (h), and Shannon’s information index (I) were 1.5128, 0.3333, and 0.5135, respectively. Cluster analysis was conducted using Dice's genetic distance and the unweighted pair group method with arithmetic mean (UPGMA), which grouped the genotypes into two main clusters. Genetic structure analysis further divided the origanum genotypes into five subpopulations, with an average expected heterozygosity of 0.3369. The population differentiation index (Fst) ranged from 0.0367 to 0.1281, with a mean value of 0.0839. This study is the first to investigate the genetic diversity and population structure of Origanum rotundifolium germplasm using the SCoT-retrotransposon marker system. The results highlight the effectiveness of SCoT markers in accurately assessing the genetic diversity of Origanum rotundifolium genotypes, offering an essential resource for future breeding and conservation strategies.