Combined analysis of the metabolome and transcriptome provides insight into seed oil accumulation in soybean

Background: Soybean ( Glycine max (L.) Merr) is an important source of human food, animal feed, and bio-energy. Although the genetic network of lipid metabolism is clear in Arabidopsis , the understanding of lipid metabolism in soybean is limited. Results: In this study, 30 soybean varieties were subjected to transcriptome and metabolome analysis. In total, 98 lipid-related metabolites were identified, including glycerophospholipid, alpha-linolenic acid, linoleic acid, glycolysis, pyruvate, and the sphingolipid pathway. Of these, glycerophospholipid pathway metabolites accounted for the majority of total lipids. Combining the transcriptomic and metabolomic analyses, we found that 33 lipid-related metabolites and 83 lipid-related genes, 14 lipid-related metabolites and 17 lipid-related genes, and 12 lipid-related metabolites and 25 lipid-related genes were significantly correlated in FHO (five high oil varieties) vs. FLO (five low oil varieties), THO (10 high oil varieties) vs. TLO (10 low oil varieties), and HO (15 high oil varieties) vs. LO (15 low oil varieties), respectively. Conclusions: The GmGAPDH and GmPDAT genes were significantly correlated with lipid metabolism genes, and the result revealed the regulatory relationship between glycolysis and oil synthesis. These results improve our understanding of the regulatory mechanism of soybean seed oil improvement.