Genomic Insights into Genetic Diversity and Adaptation of Nanyang Cattle: Implications for Conservation and Breeding

The conservation of agricultural animal resources holds significant importance for addressing future breeding demands and promoting sustainable utilization of regional livestock genetic resources. As one of China's five major fine cattle breeds, Nanyang cattle exhibit notable characteristics, including strong adaptability and a docile temperament. Through whole-genome comparative analysis of the Nanyang cattle core conservation population and free-ranging populations in mountainous areas, this study systematically investigated the genetic diversity, population structure, and adaptive evolutionary mechanisms of this indigenous Chinese cattle breed. Population structure analysis revealed that both groups belong to a single genetic lineage of Nanyang cattle without significant genetic differentiation; however, the free-ranging population demonstrated a slower linkage disequilibrium decay rate. Combined <i>F</i>_ST and θπ ratio analyses identified 170 positively selected genes, with KEGG enrichment highlighting glutamatergic synapse and African trypanosomiasis immune pathways. PLCB4, as a shared gene across both pathways, may exert pleiotropic functions in environmental adaptation. The core conservation population likely exhibits reduced diversity in neuroplasticity-related genes under artificial selection, whereas the free-ranging population retained more genes associated with environmental adaptation and immune response. These findings provide genomic evidence for formulating differentiated conservation strategies for Nanyang cattle, necessitating balanced co-optimization of production trait breeding and natural adaptability preservation.