A compendium of genetic regulatory effects across pig tissues
The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in a...
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| Veröffentlicht in: | Nature genetics 2024-01, Vol.56 (1), p.112-123 |
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| creator | Teng, Jinyan Gao, Yahui Yin, Hongwei Bai, Zhonghao Liu, Shuli Zeng, Haonan Bai, Lijing Cai, Zexi Zhao, Bingru Li, Xiujin Xu, Zhiting Lin, Qing Pan, Zhangyuan Yang, Wenjing Yu, Xiaoshan Guan, Dailu Hou, Yali Keel, Brittney Rohrer, Gary Lindholm-Perry, Amanda Oliver, William Ballester, Maria Crespo-Piazuelo, Daniel Quintanilla, Raquel Canela-Xandri, Oriol Rawlik, Konrad Xia, Charley Yao, Yuelin Zhao, Qianyi Yao, Wenye Yang, Liu Li, Houcheng Zhang, Huicong Liao, Wang Chen, Tianshuo Karlskov-Mortensen, Peter Fredholm, Merete Amills, Marcel Clop, Alex Giuffra, Elisabetta Wu, Jun Cai, Xiaodian Diao, Shuqi Pan, Xiangchun Wei, Chen Li, Jinghui Cheng, Hao Wang, Sheng Su, Guosheng Sahana, Goutam Lund, Mogens Sandø Dekkers, Jack Kramer, Luke Tuggle, Christopher Corbett, Ryan Groenen, Martien Madsen, Ole Gòdia, Marta Rocha, Dominique Charles, Mathieu Li, Cong-Jun Pausch, Hubert Hu, Xiaoxiang Frantz, Laurent Luo, Yonglun Lin, Lin Zhou, Zhongyin Zhang, Zhe Chen, Zitao Cui, Leilei Xiang, Ruidong Shen, Xia Li, Pinghua Huang, Ruihua Tang, Guoqing Li, Mingzhou Zhao, Yunxiang Yi, Guoqiang Tang, Zhonglin Jiang, Jicai Zhao, Fuping Yuan, Xiaolong Liu, Xiaohong Chen, Yaosheng Xu, Xuewen Zhao, Shuhong Zhao, Pengju Haley, Chris Zhou, Huaijun Wang, Qishan Pan, Yuchun Ding, Xiangdong Ma, Li Li, Jiaqi Navarro, Pau Zhang, Qin Li, Bingjie Tenesa, Albert Li, Kui Liu, George |
| description | The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model. |
| doi_str_mv | 10.1038/s41588-023-01585-7 |
| format | Article |
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Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. 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Zhongyin</creatorcontrib><creatorcontrib>Zhang, Zhe</creatorcontrib><creatorcontrib>Chen, Zitao</creatorcontrib><creatorcontrib>Cui, Leilei</creatorcontrib><creatorcontrib>Xiang, Ruidong</creatorcontrib><creatorcontrib>Shen, Xia</creatorcontrib><creatorcontrib>Li, Pinghua</creatorcontrib><creatorcontrib>Huang, Ruihua</creatorcontrib><creatorcontrib>Tang, Guoqing</creatorcontrib><creatorcontrib>Li, Mingzhou</creatorcontrib><creatorcontrib>Zhao, Yunxiang</creatorcontrib><creatorcontrib>Yi, Guoqiang</creatorcontrib><creatorcontrib>Tang, Zhonglin</creatorcontrib><creatorcontrib>Jiang, Jicai</creatorcontrib><creatorcontrib>Zhao, Fuping</creatorcontrib><creatorcontrib>Yuan, Xiaolong</creatorcontrib><creatorcontrib>Liu, Xiaohong</creatorcontrib><creatorcontrib>Chen, Yaosheng</creatorcontrib><creatorcontrib>Xu, Xuewen</creatorcontrib><creatorcontrib>Zhao, Shuhong</creatorcontrib><creatorcontrib>Zhao, Pengju</creatorcontrib><creatorcontrib>Haley, Chris</creatorcontrib><creatorcontrib>Zhou, Huaijun</creatorcontrib><creatorcontrib>Wang, Qishan</creatorcontrib><creatorcontrib>Pan, Yuchun</creatorcontrib><creatorcontrib>Ding, Xiangdong</creatorcontrib><creatorcontrib>Ma, Li</creatorcontrib><creatorcontrib>Li, Jiaqi</creatorcontrib><creatorcontrib>Navarro, Pau</creatorcontrib><creatorcontrib>Zhang, Qin</creatorcontrib><creatorcontrib>Li, Bingjie</creatorcontrib><creatorcontrib>Tenesa, Albert</creatorcontrib><creatorcontrib>Li, Kui</creatorcontrib><creatorcontrib>Liu, George</creatorcontrib><title>A compendium of genetic regulatory effects across pig tissues</title><title>Nature genetics</title><description>The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.</description><subject>Computer Science</subject><subject>Life Sciences</subject><issn>1061-4036</issn><issn>1546-1718</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNqVirsKwjAUQIMovn_AKatD9F6TNlkcRBQHR_cSalojrSm5reDfq-APOJ3D4TC2QFghSLMmhYkxAjZSwMcSoXtsjIlKBWo0_Y9DikKBTEdsQnQHQKXADNlIGtRaKjVm2x3PQ924x9V3NQ8FL93DtT7n0ZVdZdsQX9wVhctb4jaPgYg3vuStJ-oczdigsBW5-Y9TtjweLvuTuNkqa6KvbXxlwfrstDtn3wZK4wY0PlH-874BnoNEaQ</recordid><startdate>20240104</startdate><enddate>20240104</enddate><creator>Teng, Jinyan</creator><creator>Gao, Yahui</creator><creator>Yin, Hongwei</creator><creator>Bai, Zhonghao</creator><creator>Liu, 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compendium of genetic regulatory effects across pig tissues</title><author>Teng, Jinyan ; Gao, Yahui ; Yin, Hongwei ; Bai, Zhonghao ; Liu, Shuli ; Zeng, Haonan ; Bai, Lijing ; Cai, Zexi ; Zhao, Bingru ; Li, Xiujin ; Xu, Zhiting ; Lin, Qing ; Pan, Zhangyuan ; Yang, Wenjing ; Yu, Xiaoshan ; Guan, Dailu ; Hou, Yali ; Keel, Brittney ; Rohrer, Gary ; Lindholm-Perry, Amanda ; Oliver, William ; Ballester, Maria ; Crespo-Piazuelo, Daniel ; Quintanilla, Raquel ; Canela-Xandri, Oriol ; Rawlik, Konrad ; Xia, Charley ; Yao, Yuelin ; Zhao, Qianyi ; Yao, Wenye ; Yang, Liu ; Li, Houcheng ; Zhang, Huicong ; Liao, Wang ; Chen, Tianshuo ; Karlskov-Mortensen, Peter ; Fredholm, Merete ; Amills, Marcel ; Clop, Alex ; Giuffra, Elisabetta ; Wu, Jun ; Cai, Xiaodian ; Diao, Shuqi ; Pan, Xiangchun ; Wei, Chen ; Li, Jinghui ; Cheng, Hao ; Wang, Sheng ; Su, Guosheng ; Sahana, Goutam ; Lund, Mogens Sandø ; Dekkers, Jack ; Kramer, Luke ; Tuggle, Christopher ; Corbett, Ryan ; Groenen, Martien ; Madsen, Ole ; Gòdia, Marta ; Rocha, Dominique ; Charles, Mathieu ; Li, Cong-Jun ; Pausch, Hubert ; Hu, Xiaoxiang ; Frantz, Laurent ; Luo, Yonglun ; Lin, Lin ; Zhou, Zhongyin ; Zhang, Zhe ; Chen, Zitao ; Cui, Leilei ; Xiang, Ruidong ; Shen, Xia ; Li, Pinghua ; Huang, Ruihua ; Tang, Guoqing ; Li, Mingzhou ; Zhao, Yunxiang ; Yi, Guoqiang ; Tang, Zhonglin ; Jiang, Jicai ; Zhao, Fuping ; Yuan, Xiaolong ; Liu, Xiaohong ; Chen, Yaosheng ; Xu, Xuewen ; Zhao, Shuhong ; Zhao, Pengju ; Haley, Chris ; Zhou, Huaijun ; Wang, Qishan ; Pan, Yuchun ; Ding, Xiangdong ; Ma, Li ; Li, Jiaqi ; Navarro, Pau ; Zhang, Qin ; Li, Bingjie ; Tenesa, Albert ; Li, Kui ; Liu, George</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-hal_primary_oai_HAL_hal_04712071v13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Computer Science</topic><topic>Life Sciences</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Teng, Jinyan</creatorcontrib><creatorcontrib>Gao, Yahui</creatorcontrib><creatorcontrib>Yin, Hongwei</creatorcontrib><creatorcontrib>Bai, Zhonghao</creatorcontrib><creatorcontrib>Liu, Shuli</creatorcontrib><creatorcontrib>Zeng, Haonan</creatorcontrib><creatorcontrib>Bai, Lijing</creatorcontrib><creatorcontrib>Cai, Zexi</creatorcontrib><creatorcontrib>Zhao, Bingru</creatorcontrib><creatorcontrib>Li, Xiujin</creatorcontrib><creatorcontrib>Xu, Zhiting</creatorcontrib><creatorcontrib>Lin, Qing</creatorcontrib><creatorcontrib>Pan, Zhangyuan</creatorcontrib><creatorcontrib>Yang, Wenjing</creatorcontrib><creatorcontrib>Yu, Xiaoshan</creatorcontrib><creatorcontrib>Guan, Dailu</creatorcontrib><creatorcontrib>Hou, Yali</creatorcontrib><creatorcontrib>Keel, Brittney</creatorcontrib><creatorcontrib>Rohrer, Gary</creatorcontrib><creatorcontrib>Lindholm-Perry, 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Jun</creatorcontrib><creatorcontrib>Cai, Xiaodian</creatorcontrib><creatorcontrib>Diao, Shuqi</creatorcontrib><creatorcontrib>Pan, Xiangchun</creatorcontrib><creatorcontrib>Wei, Chen</creatorcontrib><creatorcontrib>Li, Jinghui</creatorcontrib><creatorcontrib>Cheng, Hao</creatorcontrib><creatorcontrib>Wang, Sheng</creatorcontrib><creatorcontrib>Su, Guosheng</creatorcontrib><creatorcontrib>Sahana, Goutam</creatorcontrib><creatorcontrib>Lund, Mogens Sandø</creatorcontrib><creatorcontrib>Dekkers, Jack</creatorcontrib><creatorcontrib>Kramer, Luke</creatorcontrib><creatorcontrib>Tuggle, Christopher</creatorcontrib><creatorcontrib>Corbett, Ryan</creatorcontrib><creatorcontrib>Groenen, Martien</creatorcontrib><creatorcontrib>Madsen, Ole</creatorcontrib><creatorcontrib>Gòdia, Marta</creatorcontrib><creatorcontrib>Rocha, Dominique</creatorcontrib><creatorcontrib>Charles, Mathieu</creatorcontrib><creatorcontrib>Li, Cong-Jun</creatorcontrib><creatorcontrib>Pausch, Hubert</creatorcontrib><creatorcontrib>Hu, Xiaoxiang</creatorcontrib><creatorcontrib>Frantz, Laurent</creatorcontrib><creatorcontrib>Luo, Yonglun</creatorcontrib><creatorcontrib>Lin, Lin</creatorcontrib><creatorcontrib>Zhou, Zhongyin</creatorcontrib><creatorcontrib>Zhang, Zhe</creatorcontrib><creatorcontrib>Chen, Zitao</creatorcontrib><creatorcontrib>Cui, Leilei</creatorcontrib><creatorcontrib>Xiang, Ruidong</creatorcontrib><creatorcontrib>Shen, Xia</creatorcontrib><creatorcontrib>Li, Pinghua</creatorcontrib><creatorcontrib>Huang, Ruihua</creatorcontrib><creatorcontrib>Tang, Guoqing</creatorcontrib><creatorcontrib>Li, Mingzhou</creatorcontrib><creatorcontrib>Zhao, Yunxiang</creatorcontrib><creatorcontrib>Yi, Guoqiang</creatorcontrib><creatorcontrib>Tang, Zhonglin</creatorcontrib><creatorcontrib>Jiang, Jicai</creatorcontrib><creatorcontrib>Zhao, Fuping</creatorcontrib><creatorcontrib>Yuan, Xiaolong</creatorcontrib><creatorcontrib>Liu, Xiaohong</creatorcontrib><creatorcontrib>Chen, Yaosheng</creatorcontrib><creatorcontrib>Xu, Xuewen</creatorcontrib><creatorcontrib>Zhao, Shuhong</creatorcontrib><creatorcontrib>Zhao, Pengju</creatorcontrib><creatorcontrib>Haley, Chris</creatorcontrib><creatorcontrib>Zhou, Huaijun</creatorcontrib><creatorcontrib>Wang, Qishan</creatorcontrib><creatorcontrib>Pan, Yuchun</creatorcontrib><creatorcontrib>Ding, Xiangdong</creatorcontrib><creatorcontrib>Ma, Li</creatorcontrib><creatorcontrib>Li, Jiaqi</creatorcontrib><creatorcontrib>Navarro, Pau</creatorcontrib><creatorcontrib>Zhang, Qin</creatorcontrib><creatorcontrib>Li, Bingjie</creatorcontrib><creatorcontrib>Tenesa, Albert</creatorcontrib><creatorcontrib>Li, Kui</creatorcontrib><creatorcontrib>Liu, George</creatorcontrib><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Nature genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Teng, Jinyan</au><au>Gao, Yahui</au><au>Yin, Hongwei</au><au>Bai, Zhonghao</au><au>Liu, Shuli</au><au>Zeng, Haonan</au><au>Bai, Lijing</au><au>Cai, Zexi</au><au>Zhao, Bingru</au><au>Li, Xiujin</au><au>Xu, Zhiting</au><au>Lin, Qing</au><au>Pan, Zhangyuan</au><au>Yang, Wenjing</au><au>Yu, Xiaoshan</au><au>Guan, Dailu</au><au>Hou, Yali</au><au>Keel, Brittney</au><au>Rohrer, Gary</au><au>Lindholm-Perry, Amanda</au><au>Oliver, William</au><au>Ballester, Maria</au><au>Crespo-Piazuelo, Daniel</au><au>Quintanilla, Raquel</au><au>Canela-Xandri, Oriol</au><au>Rawlik, Konrad</au><au>Xia, Charley</au><au>Yao, Yuelin</au><au>Zhao, Qianyi</au><au>Yao, Wenye</au><au>Yang, Liu</au><au>Li, Houcheng</au><au>Zhang, Huicong</au><au>Liao, Wang</au><au>Chen, Tianshuo</au><au>Karlskov-Mortensen, Peter</au><au>Fredholm, Merete</au><au>Amills, Marcel</au><au>Clop, Alex</au><au>Giuffra, Elisabetta</au><au>Wu, Jun</au><au>Cai, Xiaodian</au><au>Diao, Shuqi</au><au>Pan, Xiangchun</au><au>Wei, Chen</au><au>Li, Jinghui</au><au>Cheng, Hao</au><au>Wang, Sheng</au><au>Su, Guosheng</au><au>Sahana, Goutam</au><au>Lund, Mogens Sandø</au><au>Dekkers, Jack</au><au>Kramer, Luke</au><au>Tuggle, Christopher</au><au>Corbett, Ryan</au><au>Groenen, Martien</au><au>Madsen, Ole</au><au>Gòdia, Marta</au><au>Rocha, Dominique</au><au>Charles, Mathieu</au><au>Li, Cong-Jun</au><au>Pausch, Hubert</au><au>Hu, Xiaoxiang</au><au>Frantz, Laurent</au><au>Luo, Yonglun</au><au>Lin, Lin</au><au>Zhou, Zhongyin</au><au>Zhang, Zhe</au><au>Chen, Zitao</au><au>Cui, Leilei</au><au>Xiang, Ruidong</au><au>Shen, Xia</au><au>Li, Pinghua</au><au>Huang, Ruihua</au><au>Tang, Guoqing</au><au>Li, Mingzhou</au><au>Zhao, Yunxiang</au><au>Yi, Guoqiang</au><au>Tang, Zhonglin</au><au>Jiang, Jicai</au><au>Zhao, Fuping</au><au>Yuan, Xiaolong</au><au>Liu, Xiaohong</au><au>Chen, Yaosheng</au><au>Xu, Xuewen</au><au>Zhao, Shuhong</au><au>Zhao, Pengju</au><au>Haley, Chris</au><au>Zhou, Huaijun</au><au>Wang, Qishan</au><au>Pan, Yuchun</au><au>Ding, Xiangdong</au><au>Ma, Li</au><au>Li, Jiaqi</au><au>Navarro, Pau</au><au>Zhang, Qin</au><au>Li, Bingjie</au><au>Tenesa, Albert</au><au>Li, Kui</au><au>Liu, George</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A compendium of genetic regulatory effects across pig tissues</atitle><jtitle>Nature genetics</jtitle><date>2024-01-04</date><risdate>2024</risdate><volume>56</volume><issue>1</issue><spage>112</spage><epage>123</epage><pages>112-123</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><abstract>The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. 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| fulltext | fulltext |
| identifier | ISSN: 1061-4036 |
| ispartof | Nature genetics, 2024-01, Vol.56 (1), p.112-123 |
| issn | 1061-4036 1546-1718 |
| language | eng |
| recordid | cdi_hal_primary_oai_HAL_hal_04712071v1 |
| source | Nature; Alma/SFX Local Collection |
| subjects | Computer Science Life Sciences |
| title | A compendium of genetic regulatory effects across pig tissues |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-17T22%3A24%3A37IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-hal&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=A%20compendium%20of%20genetic%20regulatory%20effects%20across%20pig%20tissues&rft.jtitle=Nature%20genetics&rft.au=Teng,%20Jinyan&rft.date=2024-01-04&rft.volume=56&rft.issue=1&rft.spage=112&rft.epage=123&rft.pages=112-123&rft.issn=1061-4036&rft.eissn=1546-1718&rft_id=info:doi/10.1038/s41588-023-01585-7&rft_dat=%3Chal%3Eoai_HAL_hal_04712071v1%3C/hal%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/38177344&rfr_iscdi=true |