Selection Signatures and Genetic Divergence in Hotan Black and F2 Yeonsan Ogye Chickens

Local chicken breeds have long been subjected to unique geographical isolation and extreme environmental pressures, which have led to significant environmental adaptation. This provides a valuable opportunity to explore the mechanisms of adaptive evolution in domestic chickens and to develop rare genetic resources. However, the molecular genetic basis of these local breeds remains inadequately studied. In this research, we systematically compared the population genetic structure and selection signals between the Hotan Black Chicken (HT) from Xinjiang and the F2 hybrid population of Yeonsan Ogye × White Leghorn chickens (OLF) based on medium-density SNP chip data. Principal Component Analysis (PCA), Neighbor-Joining (NJ) phylogenetic trees, and ancestry inference methods revealed significant genetic differentiation between the two populations. HT exhibited a relatively homogeneous genetic background, while the F2 population showed a more complex genomic structure. By combining a sliding window approach with population differentiation index (F_ST), nucleotide diversity (π), and the ratio log2(π_HT/π_OLF), we identified selection signal regions across the whole genome, with 99 candidate genes for the OLF population and 36 for the HT population. The candidate regions in the HT population were enriched in pathways related to environmental adaptation, including cell adhesion, neurodevelopment, and immune regulation, while the F2 population showed significant enrichment in PI3K/AKT signaling and protein phosphorylation pathways related to production performance. This study not only elucidates the adaptive genomic features of local chicken breeds in extreme environments but also provides a genomic basis for the conservation and molecular breeding of local chicken genetic resources.