Large-Scale Comparative Genomics of European and Chinese Cattle Breeds Reveals Population Structure, Breeding History, and Adaptive Divergence

Abstract

Chinese native cattle represent a diverse genetic resource that has evolved under localized natural and anthropogenic selection pressures, giving rise to genomic characteristics that are markedly distinct from those of globally commercialized breeds. Through comprehensive genomic analysis, we investigated the contrasting evolutionary trajectories of the native and European commercial cattle breeds. We found that Chinese native cattle maintain higher genetic diversity and a more complex admixed ancestry shaped by geography. Their genomes bear strong selection signals related to nervous system regulation and environmental adaptation, rather than traits for high yield. In contrast, European commercial breeds show selection on coordinated networks for production efficiency but carry a higher burden of potentially harmful mutations. This study provides a genetic basis for conserving the unique adaptive potential of Chinese native cattle and utilizing their resilience genes in future breeding. Keywords: population genomics, genetic diversity, adaptive evolution, selection signatures, deleterious mutation load