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

Abstract The global diversity of domestic chicken breeds or lines, each exhibiting unique and specialized 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. 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 with 17 red jungle fowls (RJFs), genes associated with natural selection in the Yanying and Luning Chickens were identified. Notably, selected genes in Yanying Chickens primarily affect energy metabolism, body size maintenance, and available food sources, mirroring similar trends in Luning Chickens. Transcriptomic analysis further validated the potential roles of these genes in the domestication of both breeds. This research sheds light on the unique evolutionary trajectories shaped by artificial selection for agricultural purposes and natural selection for high-altitude chickens. The study identified specific genes as potential candidates for influencing economic traits and other phenotypic characteristics in chickens