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Raphanobrassica  is an allopolyploid species derived from inter-generic hybridization that combines the R genome from  R. sativus  and the C genome from  B. oleracea  var.  alboglabra . In the present study, we used a high-throughput sequencing method to identify the mRNA and miRNA profiles in  Raphanobrassica  and its parents. A total of 33,561 mRNAs and 283 miRNAs were detected, 9,209 mRNAs and 134 miRNAs were differentially expressed respectively, 7,633 mRNAs and 39 miRNAs showed ELD expression, 5,219 mRNAs and 57 miRNAs were non-additively expressed in  Raphanobrassica . Remarkably, differentially expressed genes (DEGs) were up-regulated and maternal bias was detected in  Raphanobrassica . In addition, a miRNA-mRNA interaction network was constructed based on reverse regulated miRNA-mRNAs, which included 75 miRNAs and 178 mRNAs, 31 miRNAs were non-additively expressed target by 13 miRNAs. The related target genes were significantly enriched in the GO term ‘metabolic processes’. Non-additive related target genes regulation is involved in a range of biological pathways, like providing a driving force for variation and adaption in this allopolyploid. The integrative analysis of mRNA and miRNA profiling provides more information to elucidate gene expression mechanism and may supply a comprehensive and corresponding method to study genetic and transcription variation of allopolyploid.

Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica