Integrative multi-omics reveals regulators of oil accumulation in soybean seed

Seed oil content is a key agronomic trait that defines the quality and economic value of soybean. Although regulatory mechanisms of seed oil accumulation have been investigated using single-omics strategies, the metabolic dynamics during seed development remain poorly understood from a multi-omics perspective. Here, we performed an integrated analysis of metabolomics and transcriptomics across multiple seed developmental stages to dissect the regulatory landscape underlying oil biosynthesis and accumulation in soybean. In total, more than 1000 differential metabolites and 7000 differentially expressed genes (DEGs) were identified in nine soybean cultivars with contrasting oil contents. Through correlation analysis linking metabolic pathways, differential metabolites, and DEGs, we characterized 10 core DEGs significantly associated with seed oil content, which are involved in amino acid metabolism, flavonoid biosynthesis, lipid biosynthesis, and phenylpropanoid biosynthesis. Further integration of oil metabolism pathway analysis and natural population haplotype analysis verified that GmADH1 and GmCrRLK1L34 function as the core hub genes in the regulatory network governing soybean seed oil accumulation. Integrating multi-omics data, our study uncovers the core regulatory circuits controlling oil accumulation in soybean seeds and provides a valuable framework for investigating key agronomic traits across diverse crop species.