Integrating Longitudinal Metabolite Profiles Improves Trait Prediction in Pigs in a Trait- and Timepoint-Dependent Manner

Across all traits, models combining genotype data with metabolite profiles from one or multiple timepoints achieved the highest or equally high prediction accuracies compared to the genotype-only model, reflecting complementary biological insights captured by metabolite profiles. These findings highlight the potential value of metabolite-profile data as an intermediate omics layer to enhance genomic prediction, particularly when integration strategies are tailored to trait-specific biology and sampling timepoints.