title: Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.
abstract: Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Yang
authors.affiliation: Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China.
authors.forename: Wen-Rong
authors.initials: WR
authors.lastname: Li
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.
authors.forename: Feng-Hua
authors.initials: FH
authors.lastname: Lv
authors.affiliation: Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China.
authors.forename: San-Gang
authors.initials: SG
authors.lastname: He
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Shi-Lin
authors.initials: SL
authors.lastname: Tian
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China.
authors.forename: Wei-Feng
authors.initials: WF
authors.lastname: Peng
authors.affiliation: Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China College of Animal Science and Technology, Shihezi University, Shihezi, China.
authors.forename: Ya-Wei
authors.initials: YW
authors.lastname: Sun
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China.
authors.forename: Yong-Xin
authors.initials: YX
authors.lastname: Zhao
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Xiao-Long
authors.initials: XL
authors.lastname: Tu
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China School of Life Sciences, University of Science and Technology of China, Hefei, China.
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China.
authors.forename: Xing-Long
authors.initials: XL
authors.lastname: Xie
authors.affiliation: College of Biological and Geographic Sciences, Kashgar University, Kashgar, China.
authors.forename: Yu-Tao
authors.initials: YT
authors.lastname: Wang
authors.affiliation: College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
authors.forename: Jin-Quan
authors.initials: JQ
authors.lastname: Li
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
authors.forename: Yong-Gang
authors.initials: YG
authors.lastname: Liu
authors.affiliation: Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China.
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Shen
authors.affiliation: Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Guang-Jian
authors.initials: GJ
authors.lastname: Liu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, China.
authors.forename: Hong-Feng
authors.initials: HF
authors.lastname: Lu
authors.affiliation: Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Kantanen
authors.affiliation: CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya.
authors.forename: Jian-Lin
authors.initials: JL
authors.lastname: Han
authors.affiliation: CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China menghua.li@ioz.ac.cn xjlmj2004@aliyun.com.
authors.forename: Meng-Hua
authors.initials: MH
authors.lastname: Li
authors.affiliation: Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China menghua.li@ioz.ac.cn xjlmj2004@aliyun.com.
authors.forename: Ming-Jun
authors.initials: MJ
authors.lastname: Liu
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D001947:Breeding; D002980:Climate; D004777:Environment; D000071251:Extreme Environments; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods; D012756:Sheep / Q000235:genetics*
keywords: Ovis aries; climate change.; extreme environment; rapid adaptation; whole-genome sequencing