Identifying genomic regions under selection is crucial for comprehending the evolutionary history of the domestic chicken. The Arabian Peninsula (AP) indigenous chickens are mostly found outdoors, being reared by sheep and camel herders for secondary production purposes. These birds show high resilience to extreme temperatures (hot and cold), typical of the desert environment. The selection pressures responsible for unique local adaptations in these birds remain largely unidentified. Here, we aimed to investigate the genome diversity and structure of fifteen indigenous chicken populations including thirteen indigenous populations from the AP(n = 5), Ethiopia (n = 6), and China (n = 2). We also included two commercial chicken populations, Fayoumi (selected for heat tolerance) and Chantecler (known for cold resistance). A PCA separated all populations based on their geographic areas of origin. PC1 separates the Ethiopian populations from the Chinese and AP populations, while PC2 separates the AP populations from the Chantecler population, as well as the Ethiopian populations from the Dulong and Chantecler populations. Genome-wide selection analysis identified different regions spanning genes that appear to be relevant for tolerance to environmental challenges, for example, balance metabolism energy (SUGCT, HECW1, MMADHC), behaviour (CNTNAP2), cells apoptosis (APP, SRBD1, NTN1, PUF60, SLC26A8, DAP, SUGCT), angiogenesis (RYR2, LDB2, SOX5), protected skin associated with melanin and solar radiation (FZD10, BCO2, WNT5B, COL6A2 and SIRT1) and growth or production (NELL1). Our findings suggest that Arabian chicken populations represent a uniquely distinct gene pool of adaptation to harsh environments, including the control of adrenergic signaling in cardiomyocytes, melanogenesis, behaviour, growth, and cell apoptosis.
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