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Background   Brassica napus  L. (2n = 38, AACC) is one of the most important oil crops and sources of protein for animal feed worldwide. Lignin is a large molecule aromatic polymer and a major cell wall component. However, lignin in the seed coat reduces the availability and restricts the development of rapeseed cake. Therefore, it is critical to reduce the lignin content of the seed coat. Here, high-lignin (H-lignin) and low-lignin (L-lignin) content recombinant inbred lines (RILs) were selected from an RIL population for analysis.    Results  The cross-section results indicated that the seed coat of the H-lignin lines was thicker than that of the L-lignin lines, especially the palisade layer. The seed coats and embryos at 35, 40 and 46 days after flowering (DAF) were subjected to RNA sequencing (RNA-Seq), and the expression of the  BnPAL  and  BnC4H  gene families in the lignin pathway was significantly higher in the H-lignin seed coat than in the L-lignin seed coat. The  Bn4CL  gene family also showed this trend. In addition, among the genes related to plant hormone synthesis,  BnaC02g01710D  was upregulated and  BnaA07g11700D  and  BnaC09g00190D  were downregulated in H-lignin lines. Some transcription factors were upregulated, such as  BnNAC080 ,  BnNAC083 ,  BnMYB9 ,  BnMYB9-1 ,  BnMYB60  and  BnMYB60-1 , while  BnMYB91  was downregulated in H-lignin lines. Moreover, most genes of the flavonoid pathway, such as  BnCHS  and  BnDFR , were strongly expressed in H-lignin seed coat.    Conclusions  In Our study, some key genes such as hormone synthesis genes, transcription factors and miRNAs related to lignin and flavonoid biosynthesis were identified. A regulatory model of  B. napus  seed coat lignin was proposed. These results provide new insight into lignin and flavonoid biosynthesis in  B. napus .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03030-5.

Comparative transcriptomic analysis of seed coats with high and low lignin contents reveals lignin and flavonoid biosynthesis in Brassica napus