Genetic architecture of two novel chicken breeds from Xinjiang: A whole-genome sequencing study on Ili gamecock and Yemili Chicken

Indigenous poultry genetic resources are crucial for breeding and food security. In Xinjiang, China, the Ili gamecock and Yemili chicken represent two indigenous breeds with distinct and valuable traits. The Ili gamecock is prized for its large body size and aggressive behavior, whereas the Yemili chicken shows remarkable adaptation to the cold environment of the Tacheng area, with strong disease resistance, and foraging ability suited to free-range grazing. As understanding their genetic basis is key to their conservation and sustainable use, we conducted whole-genome sequencing of 22 individuals from both breeds and integrated the data with 83 publicly available genomes to construct a comprehensive dataset of 12 global chicken populations. After identifying over 11.3 million high-quality SNPs, we assessed genetic diversity and population structure. Analyses revealed that the Ili gamecock is closely related to the Turpan gamecock, forming a distinct cluster. Selection signature analyses based on fixation index (FST) and nucleotide diversity ratio (π ratio) identified genomic regions under positive selection associated with aggressiveness and muscularity in gamecocks (e.g., NELL1, SOX5, SEMA3A, KCNMA1) and with stress response, intestinal integrity, and energy homeostasis in Yemili chickens (e.g.,MAPK8IP3, HBEGF, PARD3, ATP6V1B2, ATP5PD). This study provides a comprehensive genomic landscape of these two emerging Xinjiang breeds, elucidates their unique evolutionary histories, and offers valuable genetic resources for future conservation and breeding programs.