Multi-Omics Revealed Key Pathways Related to Soybean (Glycine max [L.] Merr.) Seed Hardness

Soybean (Glycine max [L.] Merr.) seed hardness is a critical physical trait that dictates processing efficiency and end-product quality, yet the underlying genetic and metabolic regulatory networks remain poorly elucidated. To systematically decipher the mechanisms governing this complex quantitative trait, a multi-omics approach integrating a genome-wide association study (GWAS), transcriptomics, and metabolomics was conducted on a panel of 162 soybean germplasm accessions from Northeast China. Four significant quantitative trait nucleotides (QTNs) on chromosomes 15 and 19 were identified by GWAS. Subsequent RNA-seq and liquid chromatography-mass spectrometry (LC-MS) analyses comparing extreme phenotypes identified 573 differentially expressed genes (DEGs) and 784 differentially accumulated metabolites (DAMs). Joint multi-omics analysis revealed 14 consistently enriched pathways, highlighting the crucial role of secondary metabolite biosynthesis. Notably, Glyma.19G030500, which encodes an isoflavone malonyltransferase, was identified as the primary hub gene. These findings offer valuable genomic targets for the marker-assisted breeding of soybean varieties with optimized processing qualities.