Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments
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 we...
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| Veröffentlicht in: | Molecular biology and evolution 2016-10, Vol.33 (10), p.2576-2592 |
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| creator | Yang, Ji Li, Wen-Rong Lv, Feng-Hua He, San-Gang Tian, Shi-Lin Peng, Wei-Feng Sun, Ya-Wei Zhao, Yong-Xin Tu, Xiao-Long Zhang, Min Xie, Xing-Long Wang, Yu-Tao Li, Jin-Quan Liu, Yong-Gang Shen, Zhi-Qiang Wang, Feng Liu, Guang-Jian Lu, Hong-Feng Kantanen, Juha Han, Jian-Lin Li, Meng-Hua Liu, Ming-Jun |
| description | 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 (1500 m) versus low-altitude region ( |
| doi_str_mv | 10.1093/molbev/msw129 |
| format | Article |
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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.</description><identifier>ISSN: 0737-4038</identifier><identifier>EISSN: 1537-1719</identifier><identifier>DOI: 10.1093/molbev/msw129</identifier><identifier>PMID: 27401233</identifier><language>eng</language><publisher>United States: Oxford University Press</publisher><subject>Acclimatization - genetics ; Adaptation, Physiological - genetics ; Animals ; Breeding ; Climate ; Discoveries ; Environment ; Extreme Environments ; Genome ; Genomics ; High-Throughput Nucleotide Sequencing - methods ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA - methods ; Sheep - genetics</subject><ispartof>Molecular biology and evolution, 2016-10, Vol.33 (10), p.2576-2592</ispartof><rights>The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2016</rights><rights>The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c490t-f5f0ed23d64f481956904ebcf6b8b326ae09e9283d2242c77fbe2f165a08e72d3</citedby><cites>FETCH-LOGICAL-c490t-f5f0ed23d64f481956904ebcf6b8b326ae09e9283d2242c77fbe2f165a08e72d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026255/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026255/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27401233$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Ji</creatorcontrib><creatorcontrib>Li, Wen-Rong</creatorcontrib><creatorcontrib>Lv, Feng-Hua</creatorcontrib><creatorcontrib>He, San-Gang</creatorcontrib><creatorcontrib>Tian, Shi-Lin</creatorcontrib><creatorcontrib>Peng, Wei-Feng</creatorcontrib><creatorcontrib>Sun, Ya-Wei</creatorcontrib><creatorcontrib>Zhao, Yong-Xin</creatorcontrib><creatorcontrib>Tu, Xiao-Long</creatorcontrib><creatorcontrib>Zhang, Min</creatorcontrib><creatorcontrib>Xie, Xing-Long</creatorcontrib><creatorcontrib>Wang, Yu-Tao</creatorcontrib><creatorcontrib>Li, Jin-Quan</creatorcontrib><creatorcontrib>Liu, Yong-Gang</creatorcontrib><creatorcontrib>Shen, Zhi-Qiang</creatorcontrib><creatorcontrib>Wang, Feng</creatorcontrib><creatorcontrib>Liu, Guang-Jian</creatorcontrib><creatorcontrib>Lu, Hong-Feng</creatorcontrib><creatorcontrib>Kantanen, Juha</creatorcontrib><creatorcontrib>Han, Jian-Lin</creatorcontrib><creatorcontrib>Li, Meng-Hua</creatorcontrib><creatorcontrib>Liu, Ming-Jun</creatorcontrib><title>Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments</title><title>Molecular biology and evolution</title><addtitle>Mol Biol Evol</addtitle><description>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.</description><subject>Acclimatization - genetics</subject><subject>Adaptation, Physiological - genetics</subject><subject>Animals</subject><subject>Breeding</subject><subject>Climate</subject><subject>Discoveries</subject><subject>Environment</subject><subject>Extreme Environments</subject><subject>Genome</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Phylogeny</subject><subject>Selection, Genetic</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Sheep - genetics</subject><issn>0737-4038</issn><issn>1537-1719</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqFkUtP3DAURi0EgoF2ybbykk3ArzjJphJCU0BCgGirLi0nuZ64SuzUzoTy7zEanitWtq6PznflD6FDSo4pqfjJ4Psa5pMh3lNWbaEFzXmR0YJW22hBinQXhJd7aD_Gv4RQIaTcRXusEIQyzheo-9P5HrJzcH4A_BP-rcE11q2wN_haT3ZOww5gxLfBz7aFiC9dtKtuiti6yeM7PdoWn7Z6nBLtXcRpuPw_BUi6pZtt8G4AN8UvaMfoPsLX5_MA_f6x_HV2kV3dnF-enV5ljajIlJncEGgZb6UwoqRVLisioG6MrMuaM6mBVFCxkreMCdYUhamBGSpzTUooWMsP0PeNd1zXA7RNyg66V2Owgw4PymurPr4426mVn1VOmGR5ngRHz4Lg02_ESQ02NtD32oFfR0VLRiShOS0Smm3QJvgYA5jXGErUUztq047atJP4b-93e6Vf6njL9uvxE9cj-mid5Q</recordid><startdate>20161001</startdate><enddate>20161001</enddate><creator>Yang, Ji</creator><creator>Li, Wen-Rong</creator><creator>Lv, Feng-Hua</creator><creator>He, San-Gang</creator><creator>Tian, Shi-Lin</creator><creator>Peng, Wei-Feng</creator><creator>Sun, Ya-Wei</creator><creator>Zhao, Yong-Xin</creator><creator>Tu, Xiao-Long</creator><creator>Zhang, Min</creator><creator>Xie, Xing-Long</creator><creator>Wang, Yu-Tao</creator><creator>Li, Jin-Quan</creator><creator>Liu, Yong-Gang</creator><creator>Shen, Zhi-Qiang</creator><creator>Wang, Feng</creator><creator>Liu, Guang-Jian</creator><creator>Lu, Hong-Feng</creator><creator>Kantanen, Juha</creator><creator>Han, Jian-Lin</creator><creator>Li, Meng-Hua</creator><creator>Liu, Ming-Jun</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20161001</creationdate><title>Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments</title><author>Yang, Ji ; Li, Wen-Rong ; Lv, Feng-Hua ; He, San-Gang ; Tian, Shi-Lin ; Peng, Wei-Feng ; Sun, Ya-Wei ; Zhao, Yong-Xin ; Tu, Xiao-Long ; Zhang, Min ; Xie, Xing-Long ; Wang, Yu-Tao ; Li, Jin-Quan ; Liu, Yong-Gang ; Shen, Zhi-Qiang ; Wang, Feng ; Liu, Guang-Jian ; Lu, Hong-Feng ; Kantanen, Juha ; Han, Jian-Lin ; Li, Meng-Hua ; Liu, Ming-Jun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c490t-f5f0ed23d64f481956904ebcf6b8b326ae09e9283d2242c77fbe2f165a08e72d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Acclimatization - genetics</topic><topic>Adaptation, Physiological - genetics</topic><topic>Animals</topic><topic>Breeding</topic><topic>Climate</topic><topic>Discoveries</topic><topic>Environment</topic><topic>Extreme Environments</topic><topic>Genome</topic><topic>Genomics</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Phylogeny</topic><topic>Selection, Genetic</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Sheep - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yang, Ji</creatorcontrib><creatorcontrib>Li, Wen-Rong</creatorcontrib><creatorcontrib>Lv, Feng-Hua</creatorcontrib><creatorcontrib>He, San-Gang</creatorcontrib><creatorcontrib>Tian, Shi-Lin</creatorcontrib><creatorcontrib>Peng, Wei-Feng</creatorcontrib><creatorcontrib>Sun, Ya-Wei</creatorcontrib><creatorcontrib>Zhao, Yong-Xin</creatorcontrib><creatorcontrib>Tu, Xiao-Long</creatorcontrib><creatorcontrib>Zhang, Min</creatorcontrib><creatorcontrib>Xie, Xing-Long</creatorcontrib><creatorcontrib>Wang, Yu-Tao</creatorcontrib><creatorcontrib>Li, Jin-Quan</creatorcontrib><creatorcontrib>Liu, Yong-Gang</creatorcontrib><creatorcontrib>Shen, Zhi-Qiang</creatorcontrib><creatorcontrib>Wang, Feng</creatorcontrib><creatorcontrib>Liu, Guang-Jian</creatorcontrib><creatorcontrib>Lu, Hong-Feng</creatorcontrib><creatorcontrib>Kantanen, Juha</creatorcontrib><creatorcontrib>Han, Jian-Lin</creatorcontrib><creatorcontrib>Li, Meng-Hua</creatorcontrib><creatorcontrib>Liu, Ming-Jun</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Ji</au><au>Li, Wen-Rong</au><au>Lv, Feng-Hua</au><au>He, San-Gang</au><au>Tian, Shi-Lin</au><au>Peng, Wei-Feng</au><au>Sun, Ya-Wei</au><au>Zhao, Yong-Xin</au><au>Tu, Xiao-Long</au><au>Zhang, Min</au><au>Xie, Xing-Long</au><au>Wang, Yu-Tao</au><au>Li, Jin-Quan</au><au>Liu, Yong-Gang</au><au>Shen, Zhi-Qiang</au><au>Wang, Feng</au><au>Liu, Guang-Jian</au><au>Lu, Hong-Feng</au><au>Kantanen, Juha</au><au>Han, Jian-Lin</au><au>Li, Meng-Hua</au><au>Liu, Ming-Jun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments</atitle><jtitle>Molecular biology and evolution</jtitle><addtitle>Mol Biol Evol</addtitle><date>2016-10-01</date><risdate>2016</risdate><volume>33</volume><issue>10</issue><spage>2576</spage><epage>2592</epage><pages>2576-2592</pages><issn>0737-4038</issn><eissn>1537-1719</eissn><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.</abstract><cop>United States</cop><pub>Oxford University Press</pub><pmid>27401233</pmid><doi>10.1093/molbev/msw129</doi><tpages>17</tpages><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | Acclimatization - genetics Adaptation, Physiological - genetics Animals Breeding Climate Discoveries Environment Extreme Environments Genome Genomics High-Throughput Nucleotide Sequencing - methods Phylogeny Selection, Genetic Sequence Analysis, DNA - methods Sheep - genetics |
| title | Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments |
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