Evaluation of the Unintended Effects of Herbicide-Resistant Soybean Seeds via TMT Quantitative Proteomics and Flavonoid-Targeted Metabolomics

Tandem mass tag (TMT) quantitative proteomic and flavonoid-targeted metabolomic analyses were applied to evaluate the unintended effects of five herbicide-resistant soybean varieties, in addition to three natural genotypic soybean varieties. A total of 65, 29, 56, 38, and 26 differentially expressed proteins (DEPs) were identified in ZLD6010, FD3003, JY2812, ZLD8001, and ZLD2426, respectively, compared with ZH13. Twenty-four and 16 DEPs were identified in ZLD2426 compared with JD12 and KS1, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that most of the DEPs were involved in ribosome, protein processing in the endoplasmic reticulum, and tropane, piperidine, and pyridine alkaloid biosynthesis. Proteomic analysis of the studied soybean seeds revealed no significant changes in herbicide-resistant soybean varieties compared with natural genotypic soybean varieties. Flavonoid-targeted metabolomics analysis detected and quantified 12 flavonoids. Daidzein, genistein/apigenin, taxifolin, and luteolin contents in the herbicide-resistant soybean variety seeds were significantly greater than those in the natural genotypic soybean variety seeds. Their contents in the seeds of three natural genotypic soybean varieties also significantly differed according to pairwise reciprocal comparisons. The introduction of 3-phosphoshikimate 1-carboxyvinyltransferase (EPSPS) might affect flavonoid accumulation of herbicide-resistant soybean varieties. The genetic background of soybean also influences its flavonoid metabolomic profile.