Integrated metabolomic and transcriptomic analyses of the role of DNA methylation in shaping soybean seed quality

Soybean is a major oilseed crop, yet how DNA methylation regulates its seed quality remains unclear. Therefore, This study leveraged mutants of distinct DNA methyltransferases (CMT, MET1 and DRM) to elucidate their impact on soybean quality. Notably, the Gmdrm2c3a3b mutant exhibited the highest oil content (22.60%), whereas the Gmcmt mutant showed the highest protein content (44.10%). Concurrently, the fatty acid composition underwent significant remodeling across the different mutants. Metabolomic profiling indicated that the metabolic composition was divergently remodeled with pathway-specific enrichment in lipid, amino acid, and glycerophospholipid metabolism, as well as alterations in essential amino acid profiles. Transcriptomic analysis of high-oil mutants at the R5.5–R6 stages showed differential expression of fatty acid synthesis and carbon-nitrogen metabolism. Transgenic validation confirmed that the candidate gene ( Glyma.20G044500 ) promoted oil accumulation. Overall, DNA methylation pathways collectively modulate oil accumulation and seed quality through genome-wide methylation, transcriptional reprogramming, and metabolic network rewiring during seed development.