Comparison of DNA methylation in the developing seeds of yellow- and black-seeded Brassica napus through MSAP analysis

DNA methylation is a crucial modification process implicated in the epigenetic regulation of gene expression, which may be responsible for agronomic trait variation. However, the epigenetic regulation of the yellow- and black-seeded characters of Brassica napus has yet to be reported. In this study, methylation-sensitive amplification polymorphism (MSAP) analysis was performed to investigate the target regions of seed coat variation in B. napus. The yellow-seeded rapeseed line derived from the somatic hybrids of B. napus–Sinapis alba and the black-seeded rapeseed line were used as experimental materials. Extensive methylation changes were observed between yellow- and black-seeded B. napus. In particular, 10 % of demethylation and 5 % of hypermethylation were detected in yellow rapeseeds compared with black rapeseeds. Nonetheless, this variation was barely identified in different developmental stages. The relative expression levels of polymorphic fragments in MSAP profiles were also analyzed. The gene expression of the demethylated fragments in the yellow rapeseeds was upregulated. For instance, bHLH, a transcription factor regulating flavonoid biosynthesis, was upregulated at 3–5 weeks after flowering of yellow seeds. Therefore, epigenetic changes among rapeseed lines with different seed colors help elucidate the formation of the yellow seed character.