Meng Chuan, Liu Xiaodong, Wu Fang, Ma Xiaochao, Ma Lei, Wang Qingfeng, Wang Mingqiu
Institute of Economic Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei 050051, China.
Institute of Economic Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei 050051, China.
Genomics. 2025 Sep;117(5):111088. doi: 10.1016/j.ygeno.2025.111088. Epub 2025 Jul 17.
This study aimed to elucidate the epigenomic differences between diploid and tetraploid Chinese cabbage seeds and preliminarily explore the mechanisms underlying the reduced seed vigor in tetraploid seeds. We comprehensively analyzed the transcriptome, metabolome, and whole-genome bisulfite sequencing (WGBS) to investigate gene expression, metabolite profiles, and DNA methylation patterns in diploid and tetraploid Chinese cabbage seeds from different years. Results showed that tetraploid seeds exhibited lower DNA methylation levels and fewer methylated cytosines than diploid seeds across all sequence contexts (CG, CHG, and CHH). Differentially methylated regions (DMRs) were predominantly enriched in upstream and downstream regions of genes, with a higher number of hypermethylated regions in diploid seeds. Transcriptomic analysis revealed significant changes in gene expression before and after germination, with more genes downregulated post-germination. KEGG enrichment analysis indicated that differentially expressed genes were mainly involved in carbohydrate metabolism, amino acid metabolism, and signal transduction pathways. Metabolome analysis identified 1346 metabolites, with flavonoids and plant hormone signal transduction pathways being the most prominent. Notably, ABA-related genes, including seven ABF genes, 18 PYR/PYL genes, six SRK genes, and two PP2C genes, exhibited differential methylation and expression patterns between diploid and tetraploid seeds. These genes were enriched in pathways related to secondary metabolite biosynthesis and plant hormone signaling, suggesting a potential role in the reduced seed vigor of tetraploid seeds. In conclusion, our study provides a comprehensive understanding of the epigenetic and transcriptional characteristics underlying the differences in seed vigor between diploid and tetraploid Chinese cabbage seeds. The findings highlight the importance of DNA methylation and ABA signaling in regulating seed development and vigor.
本研究旨在阐明二倍体和四倍体大白菜种子之间的表观基因组差异，并初步探究四倍体种子活力降低的潜在机制。我们综合分析了转录组、代谢组和全基因组亚硫酸氢盐测序（WGBS），以研究不同年份的二倍体和四倍体大白菜种子中的基因表达、代谢物谱和DNA甲基化模式。结果表明，在所有序列背景（CG、CHG和CHH）下，四倍体种子的DNA甲基化水平低于二倍体种子，甲基化胞嘧啶数量也更少。差异甲基化区域（DMRs）主要富集在基因的上游和下游区域，二倍体种子中高甲基化区域的数量更多。转录组分析显示，发芽前后基因表达发生了显著变化，发芽后更多基因下调。KEGG富集分析表明，差异表达基因主要参与碳水化合物代谢、氨基酸代谢和信号转导途径。代谢组分析鉴定出1346种代谢物，其中黄酮类化合物和植物激素信号转导途径最为突出。值得注意的是，包括7个ABF基因、18个PYR/PYL基因、6个SRK基因和2个PP2C基因在内的与脱落酸（ABA）相关的基因，在二倍体和四倍体种子之间表现出不同的甲基化和表达模式。这些基因富集在与次生代谢物生物合成和植物激素信号相关的途径中，表明它们在四倍体种子活力降低中可能发挥作用。总之，我们的研究全面了解了二倍体和四倍体大白菜种子活力差异背后的表观遗传和转录特征。研究结果突出了DNA甲基化和ABA信号在调节种子发育和活力方面的重要性。
