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Background  Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of  B. napus  (AnAnCnCn) and  B. rapa  (ArAr) have been reported.    Results  Here, we apply small RNA sequencing to explore miRNA expression patterns between  B. napus ,  B. rapa  and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in  B. napus ,  B. rapa  and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between  B. napus ,  B. rapa  and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of  B. napus ,  B. rapa  and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid.    Conclusions  This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of  Brassica  allopolyploids.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-6001-x) contains supplementary material, which is available to authorized users.

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa