Multiomics analysis uncovers host-microbiota interactions regulate hybrid vigor traits in geese

Economic hybridization represents a predominant breeding strategy for enhancing poultry quality. In this study, we bred hybrid geese (ZF) by crossing Xianghai Flying geese (FG) as paternal lines with Zi geese (ZG) as maternal lines. ZF exhibited integrated superior traits, including increased body weight and breast muscle index, reduced abdominal fat, and improved meat quality (enhanced tenderness, deeper red meat color), with notably higher ileal villus height than parental lines. Integrated phenotypic, transcriptomic, gut microbiome and metabolomic analyses systematically revealed regulatory mechanisms underlying heterosis. The analysis showed 87 differentially expressed genes common between ZF and both parents, mainly enriched in energy metabolism and cytoskeletal and cell adhesion-related pathways. Protein-protein interaction networks revealed KDR, CS, PDHA1, IDH2, and GAPDH as key candidate genes (fold change > 2 and P < 0.0001) regulating the host phenotype. Meanwhile, ZF exhibited microbiome reconfiguration, characterized by the dominance of Bacteroides producing short-chain fatty acids (SCFAs), along with beneficial genera such as Megamonas, Romboutsia, and Subdoligranulum. Additionally, there was a depletion of the pathogenic genus Desulfovibrio. Integrated multi-omics analyses demonstrated that host genes and microbiota interact closely, synergistically governing hybrid vigor traits. The findings provide the first theoretical basis for revealing the potential molecular mechanisms by which the host-gut microbiota interactions regulate hybrid vigor traits in geese.