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Durum wheat (Triticum turgidumvar. durum) is one of the most important cereal crops widely cultivated all over the world with high economic value. In the present study, genetic variation in a mini-core collection of durum wheat germplasm, including 25 breeding lines and 18 landraces, was evaluated using 15 inter-simple sequence repeat (ISSR) and six start codon targeted (SCoT) markers. High levels of polymorphism were observed; 98.70% (ISSR) and 100% (SCoT), which indicated that these markers are useful tools for detection of genetic variation in the collection. Analysis of molecular variance revealed that the major part of genetic variations (90% and 93% for ISSR and SCoT, respectively) occurred within genotypes set. Comparing the genetic variation of breeding lines and landraces based on genetic parameters showed that effective number of alleles (Ne), Nei's gene diversity (He) and Shannon's Information index (I) in landraces were higher than in breeding lines. Although cluster analysis, based on both markers, separated the genotypes in five groups, the dendrogram obtained from SCoT provided the best clustering pattern. Inter-population differentiation (Gst) estimated on the basis of two marker systems representing that a vast portion of the total genetic diversity refers to variation within two sets of genotypes. In conclusion, the results verified a high level of genetic variation among the durum wheat mini-core collection, particularly among landraces, which can be interesting for future breeding programmes. [ABSTRACT FROM PUBLISHER]