Supplementary files for the meta-analysis ：<b>Evidence that gene editing outperforms transgenesis in enhancing farmed animal traits</b>

Production traits such as growth, disease resistance, and fatty acid content in engineered animals are anticipated to be enhanced <i>via</i> transgenesis or genome editing. It is however unclear whether this expectation is upheld across taxa on a global comparison. Here, we conducted a meta-analysis of 154 studies involving 72 species and 55 genes to quantify and compare the effects of transgenesis and gene editing on production traits in farmed animals. While transgenesis is more commonly applied for trait enhancement, gene editing demonstrated more pronounced and widespread effects, particularly on growth and disease resistance traits, as reflected by larger effect sizes and broader impacts across trait parameters. Yet, we observed taxon-specific differences in patterns of trait enhancement. For instance, transgenesis reduced pathogen load in chickens and cattle but not in pigs, whereas gene editing lowered virus RNA levels in pigs but not in chickens or cattle. In contrast, both transgenesis and gene editing significantly increased growth rates in ray-finned fishes. Notably, although transgenes or edited genes remained highly expressed or repressed in F₁ offspring, the magnitude of trait improvement was diminished compared to the founder generations. This study offers important, evidence-based insights that can help researchers refine their approaches and guide future investigations into trait enhancement in genetically engineered animals.