Genetic and Evolutionary Analysis of Ake Chicken: New Insights into China’s Sole Indigenous Naked-Neck Chicken Breed

Heat-stress resilience is vital for poultry in tropical/subtropical regions where high temperatures impair productivity. Ake chickens, as the only naked-neck chicken breed in China, exhibit robust resistance to heat stress, but this breed lacks clarity in its genetic origins. This study utilized the next-generation sequencing data from 22 chicken breeds to conduct phylogenetic and population analyses. Gene flow analysis revealed a gene migration event from Iranian naked-neck chickens and Indian local breeds to Ake chickens, and population separation estimates suggested that the naked-neck gene was introduced to China around 500–600 years ago. NJ-tree, PCA, and population structure analyses showed that Ake chickens cluster with Yunnan native breeds, which diverged only 100–200 years ago. A selective sweep in the candidate region on chromosome 3 (97.0–97.37 Mb) showed elevated genetic differentiation (FST) and reduced nucleotide diversity (π) compared to the genome-wide average, indicating rapid fixation of the trait under natural/artificial selection. Demographic reconstruction indicated that the current effective size of Ake chickens is stable at 2000–3000 individuals. These findings deepen our understanding of Ake chicken evolution and provide valuable insights for conservation and the development of heat-stress-resistant poultry breeds.