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Diploid Thinopyrum elongatum, a wild relative  of wheat, contains many agronomically desirable traits and has potential for  increasing genetic variability and introducing desirable characters in this  crop. Few molecular markers are available for rapid screening of T.  elongatum genome segments in the wheat genetic background. We used 36 RAPD  primers and 33 ISSR primers to screen for polymorphisms in the common wheat  variety Chinese Spring and in T. elongatum. Two RAPD markers and one  ISSR marker, designated OPF03(1407),  LW10(1487)  and UBC841(701), were identified and were specific for the T.  elongatum E genome. Three pairs of primers flanking these specific sequences  were designed to produce SCAR markers. All three SCAR markers were T.  elongatum E genome-specific. Two of these SCAR markers, SCAR(807) and SCAR(577),  were present in all seven T. elongatum chromosomes, while SCAR(839) was specific for T. elongatum chromosomes 2E  and 3E. These newly developed SCAR markers should be useful for detecting alien  genome chromatin or chromosome segments in the genetic background of common  wheat.

RAPD and ISSR-assisted identification and development of three new SCAR markers specific for the Thinopyrum elongatum E (Poaceae) genome