SummaryWe evaluated the genome structure and salt stress response of BC 1 F 6 lines derived from a cross between an Iranian salt tolerant bread wheat cultivar Roushan (2n=6x=42, AABBDD) and a synthetic allohexaploid Tritipyrum (2n=6x=42, AABBE b E b ). Sixteen lines (L1 to L16) and their parents were studied for their chromosome composition, K + : Na + ratio, and relative dry mass (RDM) by growing them in nutrient solution containing 0 (control) or 100 mM NaCl (treatment). Among the studied lines, eight wheat Thinopyrum bessarabicum (E b genome) disomic substitution lines were identified using PCR-based Landmark Unique Gene (PLUG) markers and cytogenetic analysis. Ten (37%) of 27 PLUG markers used were informative for E b chromosomes 1, 2, 3, 4, and 6 in a wheat background. PLUG markers also revealed that one line, L9, was a disomic substitution line DS2E b (2B), and that seven lines, L3, L4, L7, L8, L14, L15, and L16, were DS6E b (6D). There were large differences in morphological traits and salinity tolerance even among DS6E b (6D) substitutions or untranslocated lines, due perhaps to unidentified rearrangements or small introgressions.Key words Disomic substitution line, EST-based marker, Thinopyrum bessarabicum, Wheat. Domestication and modern plant breeding have narrowed the genetic base of bread wheat (Triticum aestivum; 2n=6x=42, AABBDD), which could restrict future crop improvement (Reif et al. 2005). Plants are constantly exposed to environmental stresses that limit their growth and productivity. Seven percent of the land in Iran contain salt either in the irrigation water or in soil (Zohary 1973). Wheat (Triticum aestivum L.) is the most important and widely adapted cereal in this country, and breeding for salt tolerance is one of the most efficient ways to increase its yield.To increase the salt tolerance of wheat, most of the attention has been focused on identifying genetic sources with low rates of transport of Na + to leaves, high selectivity for K + over Na + (i.e. Na + exclusion ), and higher performance . Wide hybridization of some halophytic wild species in the Triticeae with wheat has been proposed as a strategy to increase salt tolerance beyond the existing cultivated wheat gene pool (Colmer et al. 2006). Amongst the wild relatives, tall wheatgrass species, e.g. Thinopyrum bessarabicum (Save ex Rayss) A Löve (2n=2x=14,and Lophopyrum elongatum (Host) A. Löve (2n=2x=14, EE), are important sources of genes for agronomically desirable traits, particularly salt tolerance (Dvorak and Ross 1986). Wheat Th. bessarabicum amphiploids (Tritipyrums) have been produced and one such amphiploid was shown to survive in 250 mM NaCl, equivalent to halfstrength sea water (Forster et al. 1988). The salt tolerance potential of Tritipyrum and some of the disomic addition and substitution lines derived from a cross between wheat and Tritipyrum have been evaluated, and the positive contribution of 5E b addition lines has been reported (King et al. 1997a).Cytogenetic methods and molecular markers have been used in s...