DNA methylation, metabolome, and transcriptome analysis reveal epigenomic differences between diploid Chinese cabbage seeds and tetraploid Chinese cabbage seeds.

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.