Rapeseed (Brassica napus) supplies about half of the vegetable oil in China. Increasing oil production and searching for genes that control oil content in the crop are research goals. In our previous studies, four major QTL for oil content located on A08, A09, C03 and C06 in the KenC-8 × N53-2 (KN DH) mapping population were detected. The parental lines were resequenced to identify structural variations and candidate genes affecting oil content in these four major QTL regions. Insertion-deletion (InDel) markers were developed and used to narrow the regions. Differentially expressed genes located in the regions were investigated. GO and KEGG analysis showed that several genes were associated with lipid metabolism. Several transcription factors with higher expression in N53-2 than in KenC-8 were identified. These results shed light on the genetic control of oil content and may be helpful for the development of high-oil-content cultivars.

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 expression patterns in Brassicacoraphanus, which facilitates regulatory mechanism research on the biosynthesis pathway of secondary metabolites in Brassicacoraphanus.