Abstract: 【Objective】Development of adequate molecular markers covering the whole genome of an alien species is becoming more and more important in identifying the homoeology and structure of the alien chromosomes, developing small segmental translocations, tracing target genes and physical mapping. Thinopyrum bessarabicum Löve is an important alien species with multiple beneficial genes for wheat breeding, 8 wheat alien lines involving seven chromosomes (arm) of Th. bessarabicum have been developed in Cytogenetics Institute, Nanjing Agricultural University, China. Recently, many small segmental translocations involving different chromosomes of Th. bessarabicum have been induced via irradiation, gametocidal chromosomes and ph1b system. However, the current markers are not enough to identify these translocations. To develop more specific markers, a transcriptome of Th. bessarabicum leaves at tillering stage was sequenced and assembled.【Method】The sequences were then used to blast against the D genome sequences of Aegilops tauschii and 4957 “no hits found” sequences probably representing Th.bessarabicum specific were used for primers development.【Result】Of 507 pairs of primers, 204 produced specific amplicons in Th. bessarabicum with a polymorphism (40.2%) quite higher than 12% showed in 134 primers developed based on wheat ESTs and 14% showed in 100 primers developed based on the transcriptome sequences of Th. bessarabicum. Of them, 64 pairs of primers had no amplification in wheat indicating species specific. Using 8 wheat alien lines involving seven chromosomes or arms of Th. bessarabicum, total 198 including 189 markers developed based on the transcriptome sequences of Th.bessarabicum were chromosomally mapped, which distributed on 1J, 2JS, 2JL, 3JS, 4JS, 4JL, 5J, 6JS, 6JL and 7JS, respectively, with a number of 31, 15, 26, 20, 12, 12, 27, 13, 22 and 20. Using these markers, three wheat alien translocations involved chromosomes 1J and 6J preliminarily designated as T1JS·1JL-W, T6JS·W, T6JS-W·W and one intercalary translocation with two specific markers were identified. After analysis on these translocations, 7 markers were mapped on the distal part of 1JL and 23 on the left part of 1J. For 6JS, 8 markers were mapped on the distal region and 4 on the pericentric region of 6JS. 【Conclusion】Blast against wheat D genome sequences with the transcriptome sequences of Th. bessarabicum, a high efficient way to develop markers specific for alien species of both wheat and other crops was developed. These markers facilitate both the identification of wheat alien translocations and physical mapping.

Key words: Thinopyrum bessarabicum, transcriptome, molecular markers, translocations