Population genomics and transcriptomics identify patterns of selection in two Liangshan chicken breeds

1. The global diversity of domestic chicken breeds, each exhibiting unique and specialised traits, offers a compelling context to explore how selection influences genetic variation patterns. China, with its myriad local chicken breeds, contributes significantly to this diversity. 2. This study presents a population genome overview of genetic variations in 35 domestic chickens encompassing two distinct breeds from the Liangshan Prefecture in Sichuan Province. Through comparative genomic analysis of 17 red jungle fowls (RJF), genes associated with artificial selection in the Yanying and Luning chickens were identified. Further transcriptome comparison between these two breeds with Lohmann layers identified expression profiles of genes under selection. 3. In total, 1,006 and 982 selected genes were identified in Yanying and Luning chickens, respectively, with 326 shared genes. These genes were primarily involved in immunity, energy metabolism, body size maintenance, and fertility. Transcriptomic analysis revealed tissue-specific gene expression, with Yanying showing immunity-related gene upregulation in ovaries compared to Lohmann chickens. 4. These findings provide valuable insights into the genetic basis of breed-specific traits, offering potential targets for future breeding programmes to enhance chicken productivity and adaptability.