Genome-wide analysis reveals domestication selection signals in Bashang long-tail chickens

1. Using whole-genome comparative analysis, this study elucidated the genetic differentiation characteristics and domestication selection mechanisms between Bashang long-tail chickens and their wild ancestor, the red junglefowl.2. Linkage disequilibrium (LD) analysis investigated genome-wide recombination patterns, while population genetic structure analysis was conducted to assess the degree of differentiation between the two populations. Additionally, a multi-method selective sweep analysis was performed to identify genomic regions under selection.3. The LD decay rate in Bashang long-tail chickens was significantly slower than in red junglefowl, which indicated reduced genome recombination due to long-term artificial selection. Population structure analyses, including neighbour-joining trees, principal component analysis and admixture assessments consistently revealed significant genetic differentiation between the two groups.4. By integrating fixation index, Tajima’s D and nucleotide diversity ratio metrics, 102 high-confidence selective sweep regions were identified, encompassing 22 key candidate genes, including three genes (ALX1, RASSF9 and NTS) with potentially adaptive missense mutations, which exhibited strong selection signals. Functional enrichment analysis indicated that these genes were enriched in key biological pathways, including carbohydrate/protein metabolism and neural regulation.5. This data provided genomic signatures of domestication-driven adaptation variations accumulated during the domestication of Bashang long-tail chickens, offering new perspectives on the genetic mechanisms underlying chicken domestication. The study provided potential molecular markers for conserving local chicken genetic resources and molecular breeding.