Exploring Genetic Diversity in a Core Collection of Aegilops tauschii Coss. Populations Using iPBS and SCoT Markers

Evaluation of population structure and genetic diversity is one of the primary steps in any plant breeding program. Wheat (Triticum aestivum L.) is a key staple cereal crop that plays an important role in global food security. The development of improved wheat varieties and the broadening of their genetic base depends on identifying novel allelic variations within germplasm resources. Hence, this study aimed to analyze the genetic diversity and population structure of 111 selected Aegilops tauschii Coss. accessions—the donor of the D-genome in bread wheat—collected from different countries, using Start Codon Targeted (SCoT) and inter-Primer Binding Site (iPBS) molecular markers. Ten selected primers from the SCoT and iPBS marker systems amplified a total of 108 and 147 fragments, respectively. Key informativeness parameters, including the number of polymorphic fragments (NPF), polymorphic information content (PIC), marker index (MI), and resolving power (Rp), were estimated as 10.80/14.70, 0.38/0.41, 4.12/6.13, and 12.90/16.31 for SCoT and iPBS primers, respectively. Analysis of molecular variance (AMOVA) indicated that genetic variation within regions was greater than variation among them. Among the studied populations, those from Iran and Afghanistan exhibited the highest levels of genetic diversity. Multivariate analyses showed that grouping patterns largely corresponded to the geographical origins of the accessions. These results were further validated by population structure analysis, which confirmed distinct genetic classifications based on SCoT, iPBS, and combined marker data. In conclusion, our results highlight that the combining SCoT and iPBS markers can be a robust approach for genotyping and assessing genetic diversity in plant germplasms. These insights are valuable for wheat breeding programs, aiding in the identification and utilization of diverse germplasm and managing it for crop improvement.