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Background   Aegilops umbellulata  Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of  Ae. umbellulata , however, has not been well studied and the genomic information in this species is limited.    Results  To develop novel genetic markers distributed over all chromosomes of  Ae. umbellulata  and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of  Ae. tauschii  and barley ( Hordeum vulgare  L.), which were regarded as virtual chromosomes of  Ae. umbellulata . Interestingly, genetic diversity in  Ae. umbellulata  was higher than in  Ae. tauschii,  despite the narrow habitat of  Ae. umbellulata . Comparative analyses of nucleotide polymorphisms between  Ae. umbellulata  and  Ae. tauschii  revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in  Ae. umbellulata , with patterns clearly distinct from those in  Ae. tauschii .    Conclusions  The anchored SNPs, covering all chromosomes, provide sufficient genetic markers between  Ae. umbellulata  accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in  Ae. umbellulata .    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1498-8) contains supplementary material, which is available to authorized users.

bmc plant biology

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata