title: Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens.
abstract: Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken and resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands.
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China University of Chinese Academy of Sciences, Beijing, China.
authors: Ming-Shan
authors: MS
authors: Wang
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors: Yan
authors: Y
authors: Li
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors: Min-Sheng
authors: MS
authors: Peng
authors: Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, China.
authors: Li
authors: L
authors: Zhong
authors: China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.
authors: Zong-Ji
authors: ZJ
authors: Wang
authors: China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.
authors: Qi-Ye
authors: QY
authors: Li
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China University of Chinese Academy of Sciences, Beijing, China.
authors: Xiao-Long
authors: XL
authors: Tu
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors: Yang
authors: Y
authors: Dong
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors: Chun-Ling
authors: CL
authors: Zhu
authors: Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, China.
authors: Lu
authors: L
authors: Wang
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors: Min-Min
authors: MM
authors: Yang
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors: Shi-Fang
authors: SF
authors: Wu
authors: Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
authors: Yong-Wang
authors: YW
authors: Miao
authors: Xishuangbanna Animal Husbandry and Veterinary Station of Yunnan Province, Jinghong, China.
authors: Jian-Ping
authors: JP
authors: Liu
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada.
authors: David M
authors: DM
authors: Irwin
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors: Wen
authors: W
authors: Wang
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors: Dong-Dong
authors: DD
authors: Wu
authors: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, China.
authors: Ya-Ping
authors: YP
authors: Zhang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000531:Altitude; D000818:Animals; D020013:Calcium Signaling / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D005828:Genetics, Population; D016678:Genome; D012641:Selection, Genetic; D018609:Tibet
keywords: calcium-signaling pathway; chicken domestication; hypoxia adaptation