Evaluation and comparison of SSR, ISSR, and retrotransposon molecular markers in the study of genetic diversity of Aegilops tauschii as wild ancestor of wheat

Abstract Wheat is an annual plant from the cereal family, this plant is the most important agricultural plant used in the human food chain. In plant breeding programs, identifying genes resistant to biotic and non-biotic stresses is of particular importance to transfer them to crop species to increase production. The most important goal in breeding programs is the existence or creation of diversity to select superior plants. One of the ways to enrich genetic resources is to know the level of diversity in germplasm and genetic treasures, which is one of the important sources of diversity and identification of useful genes in wild relatives. In this research, the genetic diversity of 125 Aegilops tauschii genotypes was investigated using SSR, ISSR, and retrotransposon markers. In this research, based on the presented results and the changes in ΔK and its maximum curve at K = 7, the number of 125 studied Aegilops tauschii genotypes were divided into 7 subpopulations with a probability of more than 70%. In general, the results obtained from this study showed that retrotransposon markers were better markers than SSR and ISSR in terms of useful indicators. However, the average PIC index in the other two systems was higher than retrotransposon, but they did not differ much from each other. Among the three marker systems, retrotransposons and SSRs were able to show a high level of intraspecies diversity.