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 educed 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.

Naked-neck chickens are distributed across tropical and subtropical regions and exhibit notable resistance to heatstress. The naked-neck trait in chickens is an incompletely dominant characteristic determined by the Na gene, and significant differences in feather quantity and distribution have been observed between homozygous and heterozygous individuals. The Ake chicken, a native Chinese breed originating from southwestern Yunnan Province, is the only breed in China that possesses the naked-neck trait. The Ake chicken was developed in a relatively isolated mountain area, and the genetic basis for the determinants of the naked-neck trait in this breed remains unclear. In this study, we utilized Oxford Nanopore Technologies and next-generation sequencing to obtain genomic data from Ake chickens and other naked-neck chicken breeds from Iran and Egypt. Genome sequence alignments revealed that the mutation responsible for the naked-neck trait in Ake chickens was the same as that in naked-neck chickens from other regions, specifically, a 73-kb insertion at the end of chromosome 3. We further demonstrated that the insertion fragment was homologous to the intergenic region between the WNT11 and UVRAG genes at 198 Mb on chromosome 1. The original sequence on chr 1 remained intact without any mutation. This study provides a genetic foundation for the naked-neck trait in chickens and provides a reliable molecular marker for the future breeding of heat stress-resistant chicken breeds.