Unintended omics changes in two gene-edited wheat lines exhibit less variation than in conventional lines and show no detectable adverse effects on the aphid Schizaphis graminum.

A key safety concern for gene-edited (GE) crops is whether unintended molecular changes associated with gene editing pose risks to non-target organisms (NTO). Here, we combined proteomic and metabolomic profiling with insect bioassays to assess the effects of two GE wheat lines (mildew resistance Locus O (MLO)- and Triticum aestivum acetolactate synthase (TaALS)-edited) on the aphid Schizaphis graminum, benchmarking the two lines against their parental lines and five conventional wheat varieties. Our results show that among 11,748 identified proteins, differentially expressed proteins (DEPs) in GE/parental comparisons (104-132) were lower than those found among conventional varieties (243-469). Similarly, among 3044 detected metabolites, the differential metabolites (DMs) in GE lines (153-332) were comparable to or lower than the variation observed in conventional lines (390-863). Notably, all unique proteins detected in GE lines but absent in the parental lines were detected in at least one conventional variety. Aphid bioassays revealed no significant differences in key life-history traits including survival, lifespan, and fecundity between insects reared on GE wheat and those on parental controls (all P > 0.05). We conclude that, when compared to conventional variety comparisons, the unintended omics changes in the two tested GE wheat lines exhibit less variation and show no statistically detectable effects on the aphid S. graminum under controlled laboratory conditions. This integrated approach offers a powerful paradigm for environmental risk assessment of future GE crops.