Comparative assessment of SCoT and ISSR markers for analysis of genetic diversity and population structure in some Aegilops tauschii Coss. accessions

Aegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCOT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (H-t) and genetic diversity within populations (H-s) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCOT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCOT (2.13 versus 8.62). Cluster analysis and population structure of SCOT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCOT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.