Metabolite profiling of a high protein fast neutron soybean mutant revealed increased storage of methionine and flavonoids

In this study, we used mass spectrometry (MS)‐based techniques to assess the metabolic profile of fast neutron–radiated soybean (Glycine max) seeds that had higher protein content. This mutant showed 1743 gene duplication compared to its non‐mutated counterpart. The metabolic profiling of soybean seeds identified 629 metabolites, of which 95 exhibited increased abundance and 127 exhibited decreased abundance in the mutant. The mutant showed an increase in several sulfur (S)‐containing metabolites, such as S‐methymethionine, methionine, and cysteine. Additionally, several secondary metabolites, such as cosmosiin and apigenin, increased significantly. The integration of metabolomics data and the duplicated genes on the global metabolic pathways revealed several duplicated genes on glycolytic, aspartate, and methionine metabolic pathways that might have contributed to the increased S‐metabolites in the seeds. We anticipate that the cascade effect of gene duplication discovered by metabolic profiling, along with information gleaned from gene expression, can be used to produce functional traits for soybean that add value to the soybean seeds. Core Ideas Metabolic engineering is being sought to improve sulfur (S)‐containing amino acids in soybean seeds. Metabolic profiling of a gene‐duplicated mutant was conducted, and global metabolic pathways were analyzed. Metabolic pathway analyses revealed the possible mechanism of increased S‐containing amino acids. The results can be used in manipulating S‐ metabolism to improve the nutritional value of soybean seed.