Comprehensive Analysis of Protein Expression Profiles in Seeds of the Gene-Edited High Oleic Acid Soybean Variety P16

This study systematically characterized seed proteome dynamics across three consecutive generations (T5–T7) of the fad2-1 (encoding Δ-12 fatty acid desaturase, catalyzing the conversion of oleic acid to linoleic acid) gene-edited high-oleic acid soybean variety P16 using data-independent acquisition (DIA)-based quantitative proteomics. Compared with the wild-type control soybean cultivar ZH42, different numbers (234, 112, and 131) of differentially expressed proteins (DEPs) were screened from soybean seeds of the P16 T5, T6, and T7 generations. Functional enrichment analysis revealed significant representation of these DEPs in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to “protein processing in endoplasmic reticulum (ER)” and/or “peroxisome.” Furthermore, eight proteins were consistently differentially expressed across all three generations—hereafter referred to as consistently differentially expressed proteins (coDEPs). The preliminary in silico evaluation of the toxicity, anti-nutritional properties, and allergenicity of the coDEPs indicated that all identified coDEPs were predicted to be non-toxic and non-allergenic, and to lack anti-nutritional activity—except for the STI1 domain-containing protein, which was computationally predicted to exhibit allergenic potential. Mass spectrometry (MS) analysis demonstrated a significant and consistent decrease in the abundance of the FAD2-1-associated peptide in P16 seeds across all three generations relative to the wild-type soybean cultivar ZH42.