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 (<i>ALX1</i>, <i>RASSF9</i> and <i>NTS</i>) 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.