![]() Furthermore, the positive selection of highland populations is related to the cardiovascular and respiratory system development, responses to the radiation, inflammation, DNA repair, and the immune responses 15. Recent evidences indicate that highland chickens are adapted based on factors including the small body size, the ability to outstand foraging, high hatchability, large organs (liver, heart and lungs), and higher hemoglobin concentration. Results of these studies show that hypoxia is involved in cerebral edema, tumorigenesis, myocardial ischemia and diabetes in human being, and some genes including Endothelin 1 ( EDN1), Erythropoietin ( EPO) and Aldosterone synthase ( CYP11B2) are reported as the key genes of hypoxia adaptation 11, 12, 13, 14. There are studies carried out in order to identify the genetic factors for high-altitude adaptation of Tibetan chickens, Yak, Tibetan pigs and Tibetan people 10. Thereby, understanding genetic factors that underlie adaptation to high-altitude conditions could lead to a new source of knowledge in order to understand the adaptation process 9. Hypoxia refers to the lack of oxygen 7, and the adaptation to hypoxia is a complex process contains biological pathways and gene networks 8. Usually, hypoxia occurs in high-attitude and pathological conditions. Investigating native chickens at the genomic level can clarify the genomic basis of their differences and the specific traits of indigenous chickens can also be precisely explored 6. The next generation sequencing (NGS) has become a tool to describe genomic features 5. However, there is no previous report on Iranian native chickens at the genomic level. Therefore, there is a remarkable genetic diversity of indigenous chickens in Iran 4. Iran is a large country that contains a special range of altitudes and climates. ![]() Therefore, farmers keep them and consequently, their morphology, behavior, physiology and adaptation to local environment conditions have been remarkably changed 3. Village chickens are also considered as important sources of food in Iran. They are used for different purposes including decoration, religions, cock fighting, and food production 2. Chickens have been domesticated in India and South-East of Asia 1. Whole-genome sequencing and variant discovery of native chickens provided novel insights about adaptation mechanisms and highlights the importance of valuable genomic variants in chickens.Ĭhickens ( Gallus gallus domesticus) are, domestically, considered as widespread birds. Finally, 3877 novel SNVs including the mtDNA ones, were submitted to EBI (PRJEB24944). The results of study suggest that MIR6644-2 is involved in hypoxia and high-altitude adaptations by regulation of embryo development. High-altitude associated with variant discovery highlighted the importance of COX3, a gene involved in cell respiration, in hypoxia adaptation. A total of 50 variants was detected in mtDNA for highland and lowland chickens. Cellular component analysis of variants showed that mitochondrion is the most important organelle for hypoxia adaptation. Amazingly, signature selection analysis demonstrated that differential variants are adaptive in response to hypoxia and are not due to other evolutionary pressures. ![]() We found that these adaptive variants are involved in DNA repair, organs development, immune response and histone binding. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of lowland and highland chickens. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. Native chickens are endangered genetic resources that are kept by farmers for different purposes.
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