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Ten Egyptian barley genotypes (2 commercial varieties and 8 breeding lines) were cultivated under normal condition at the Experimental Farm of Sakha Agricultural Research station and exposed to salinity stress condition at the Experimental Farm of El-hosainia plain Agricultural Research station, Elsharkia Governorate, Egypt, in an attempt to identify the relative salinity tolerant genotypes. A susceptibility index (SI) was used to estimate the relative stress loss because it accounted for variation in yield potential and stress intensity. Giza 123, Line-1, Line-5, Line-6 and Line-8 genotypes were considered as saline tolerant genotypes on the basis of their highly tolerance indices values. Barley genotypes were characterized by seven SSR markers and three SCoT primers in different combinations to discern the extent of genetic variation and develop a fingerprinting key. Normal SCoT reactions amplify single segments of DNA which are 15-to 19-mer long. A new strategy was used to increase SCoT potential in genetic diversity studies by using two and three different primer combinations per reaction. Amplification products scored a polymorphism percentage of 94.44% for Triple-SCoT and 90.91% for SSR, while the average no. of polymorphic fragments/primer was 17 and 7.14 in the two marker systems, respectively. On the other side, Triple-SCoT exhibited the highest average number of positive and negative genotype-specific markers. The cluster analysis of the studied genotypes using these different marker systems revealed four dendrograms varied in their topology. The dendrogram based on Triple-SCoT data exhibited the closest relationships to those illustrated by SSR dendrogram.

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