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

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 . According to the results of this study, the findings reveal considerable variation among the genotypes in terms of FHY, DHY, DLY, LSR, NB, PH, CD, CC, and EOR parameters. It was determined that the genotypes G1, G2, G3 and G19 had superior properties compared to other genotypes. This study also explores the genetic diversity among 50 Origanum rotundifolium L. genotypes using start codon targeted (SCoT) polymorphism markers. Of the 25 SCoT primers tested, 10 successfully produced a total of 382 distinct and scorable bands. The number of bands generated per primer ranged from 21 to 50, with an average of 38.2 bands per primer. The average number of bands per individual was found to be 7.64. The mean polymorphism information content (PIC) value across the primers was 0.448. 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 rotundifolium 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.