Landscape Genomic Analyses Reveal Molecular Mechanisms of Local Environmental Adaptation in Asian‐ and European‐Origin Pig Groups

Domestic pigs independently originated from Asian and European wild boar populations, where long‐term parallel evolution under diverse ecological pressures has shaped distinct genomic architectures characterized by region‐specific genetic variants associated with local environmental adaptations. Here, we integrated publicly available genotype data from 1415 domestic pigs (777 of Asian origin, 638 of European origin) with geographic location and environmental information to investigate the genomic basis of environmental adaptation. Landscape genomics analyses were performed using imputed whole‐genome sequencing data combined with environmental variables. A global‐population genome‐wide association study (GWAS) detected 968 significant SNPs. Furthermore, a meta‐analysis using summary statistics from Asian‐ and European‐origin groups identified 427 SNPs. Multiancestry fine‐mapping analysis integrating summary statistics from both populations identified 57 shared causal SNPs. Of these, nine SNPs were consistently detected across both global and meta‐analyses. By integrating these variants with the transcriptomic database from the PigGTEx database, colocalization analysis prioritized candidate genes, including TCP11 , CRYAB , and DISC1 . Cross‐species phenome‐wide association analyses in pigs and humans linked these genes to traits associated with environmental adaptation, health, and immune function. Our findings provide insights into the genomic mechanisms underlying adaptive evolution in pigs and reveal conserved adaptive pathways across divergent populations.