Evaluation of the Unintended Effects of fad2-1-Gene-Edited Soybean Line AE15 Seeds

A data-independent acquisition (DIA)-based proteomic analysis was performed to evaluate the unintended effects of <i>fad2-1</i>-gene-edited soybean line AE15 seeds. A total of 561, 269, and 227 differentially expressed proteins (DEPs) were identified in seeds from three consecutive generations of AE15 soybean, respectively, and were primarily enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbon metabolism, protein processing in the endoplasmic reticulum, and proteasome function. Furthermore, eight commonly differentially expressed proteins (co-DEPs) were detected across all three generations of AE15 soybean seeds, among which two-beta-amylase and endoplasmic reticulum (ER) lumen protein-retaining receptor-exhibited consistently upregulated expression. In the wild-type soybean control groups, 1063, 989, and 671 DEPs were identified across the three comparisons (ZhH302E3/ZhH10, ZhH10/ZhH42, and ZhH42/ZhH302E3), among which 71 co-DEPs were observed. These findings indicate that the protein expression profile alterations resulting from <i>fad2-1</i> gene editing are considerably less pronounced compared to those caused by natural genetic variation among soybean seeds.