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Background  The tertiary gene pool of bread wheat, to which  Leymus racemosus  belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses.    Results  We generated de novo DNA and mRNA sequence information of  L. racemosus  and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat- L. racemosus  chromosome introgression lines, and  L. racemosus  chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species:  L. mollis, Psathyrostachys huashanica  and  Elymus ciliaris , indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes.    Conclusion  The efficiency of the markers in characterizing wheat- L. racemosus  chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from  L. racemosus  genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.    Electronic supplementary material  The online version of this article (10.1186/s12863-018-0603-1) contains supplementary material, which is available to authorized users.

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers