本研究通过RNA-seq分析比较了甘蓝型油菜-白芥属间杂种后代的黄籽材料及其褐籽亲本间的基因表达差异，并与类黄酮和脂肪酸含量变化进行关联分析。通过HPLC-PDA-ESI(−)/MSⁿ分析，我们发现黄籽中苯丙烷和类黄酮类物质（如异鼠李素、表儿茶素、山奈酚和其它衍生物）的含量显著低于褐籽材料。黄籽材料的脂肪酸含量较褐籽高，主要是由于C16:0、C18:0、C18:1、C18:2和C18:3的含量变化所导致。通过授粉后4周（4 WAF）和5周种子的RNA-seq分析，我们发现黄、褐籽间的差异表达基因（DEGs）主要富集于类黄酮和脂肪酸合成相关的路径，包括BnTT3、BnTT4、BnTT18和BnFAD2。此外，我们发现黄籽中脂肪酸合成、去饱和、延伸相关的基因（FAD3、LEC1、FUS3、LPAT2）较褐籽上调表达，而与β氧化相关的基因（AIM1和KAT2）在黄籽中下调表达。这些与类黄酮、苯丙烷、脂肪酸含量变化相关的DEGs将有助于解释黄籽甘蓝型油菜的表型变化，且对于油菜的遗传改良也具有一定的意义。

    DNA methylation, an important epigenetic modification, serves as a key function in the polyploidization of numerous crops. In this study, early generations of resynthesized Brassica napus (F₁, S₁–S₃), ancestral parents B. rapa and B. oleracea were analyzed to characterize their DNA methylation status during polyploidization, applying DNA methylation-sensitive amplification polymorphism (MSAP) and high-performance liquid chromatography methods. In F₁, 53.4% fragments were inherited from both A- and C-genomes. Besides, 5.04 and 8.87% fragments in F₁ were inherited from A- and C- genome, respectively. 5.85 and 0.8% fragments were newly appeared and disappeared in resynthesized B. napus, respectively. 13.1% of these gene sites were identified with methylation changes in F₁, namely, hypermethylation (7.86%) and hypomethylation (5.24%). The lowest methylation status was detected in F₁ (38.7%) compared with in S₁–S₃. In S₃, 40.32% genes were methylated according to MSAP analysis. Sequencing of methylated fragments indicated that genes involved in multiple biological processes were modified, including transcription factors, protein modification, and transporters. Expression ananlysis of DNA methyltransferase 1 and DNA methyltransferase chromomethylase 3 in different materials was consistent to the DNA methylation status. These results can generally facilitate dissection of how DNA methylation contributes to genetic stability and improvement of B. napus during polyploidization.