MiRNA identification, characterization and integrated network analysis for flavonoid biosynthesis in Brassicacoraphanus

Brassica rapa (AA, 2n = 20) and Raphanus sativus (RR, 2n = 18) are popular vegetables containing multiple secondary metabolites, such as flavonoids and anthocyanins. Nevertheless, few studies on miRNA expression profiles and potential regulatory network of flavonoid metabolism have been reported in the intergeneric hybrid of B. rapa and R. sativus (Brassicacoraphanus, AARR, 2n = 38). Here, the miRNAs of Brassicacoraphanus and its parents were first identified by small RNA sequencing. It was revealed that 315 conserved miRNAs and 193 novel miRNAs were found in Brassicacoraphanus and its parents. Moreover, the miRNA expression profiles were characterized and 204 miRNAs with differential expression were obtained. Further analysis showed that 184 miRNAs were non-additively expressed in Brassicacoraphanus. At last, the potential regulatory network of flavonoid metabolism in Brassicacoraphanus was analyzed by multi-omics data, suggesting possible roles of miR858a and miR157a in regulating flavonoid synthesis pathway in Brassicacoraphanus. Taken together, this study provides useful resources for probing global miRNA ex-pression patterns in Brassicacoraphanus, which facilitates regulatory mechanism research on the biosynthesis pathway of secondary metabolites in Brassicacoraphanus.