A compendium of genetic regulatory effects across pig tissues

Jinyan Teng; Yahui Gao; Hongwei Yin; Zhonghao Bai; Shuli Liu; Haonan Zeng; Lijing Bai; Zexi Cai; Bingru Zhao; Xiujin Li; Zhiting Xu; Qing Lin; Zhangyuan Pan; Wenjing Yang; Xiaoshan Yu; Dailu Guan; Yali Hou; Brittney N Keel; Gary A Rohrer; Amanda K Lindholm-Perry; William T Oliver; Maria Ballester; Daniel Crespo-Piazuelo; Raquel Quintanilla; Oriol Canela-Xandri; Konrad Rawlik; Charley Xia; Yuelin Yao; Qianyi Zhao; Wenye Yao; Liu Yang; Houcheng Li; Huicong Zhang; Wang Liao; Tianshuo Chen; Peter Karlskov-Mortensen; Merete Fredholm; Marcel Amills; Alex Clop; Elisabetta Giuffra; Jun Wu; Xiaodian Cai; Shuqi Diao; Xiangchun Pan; Chen Wei; Jinghui Li; Hao Cheng; Sheng Wang; Guosheng Su; Goutam Sahana; Mogens Sandø Lund; Jack C M Dekkers; Luke Kramer; Christopher K Tuggle; Ryan Corbett; Martien A M Groenen; Ole Madsen; Marta Gòdia; Dominique Rocha; Mathieu Charles; Cong-Jun Li; Hubert Pausch; Xiaoxiang Hu; Laurent Frantz; Yonglun Luo; Lin Lin; Zhongyin Zhou; Zhe Zhang; Zitao Chen; Leilei Cui; Ruidong Xiang; Xia Shen; Pinghua Li; Ruihua Huang; Guoqing Tang; Mingzhou Li; Yunxiang Zhao; Guoqiang Yi; Zhonglin Tang; Bingjie Li; PigGTEx Consortium

doi:10.1038/s41588-023-01585-7

A compendium of genetic regulatory effects across pig tissues

Jinyan Teng, Yahui Gao, Hongwei Yin, Zhonghao Bai, Shuli Liu, Haonan Zeng, Lijing Bai, Zexi Cai, Bingru Zhao, Xiujin Li, Zhiting Xu, Qing Lin, Zhangyuan Pan, Wenjing Yang, Xiaoshan Yu, Dailu Guan, Yali Hou, Brittney N Keel, Gary A Rohrer, Amanda K Lindholm-PerryWilliam T Oliver, Maria Ballester, Daniel Crespo-Piazuelo, Raquel Quintanilla, Oriol Canela-Xandri, Konrad Rawlik, Charley Xia, Yuelin Yao, Qianyi Zhao, Wenye Yao, Liu Yang, Houcheng Li, Huicong Zhang, Wang Liao, Tianshuo Chen, Peter Karlskov-Mortensen, Merete Fredholm, Marcel Amills, Alex Clop, Elisabetta Giuffra, Jun Wu, Xiaodian Cai, Shuqi Diao, Xiangchun Pan, Chen Wei, Jinghui Li, Hao Cheng, Sheng Wang, Guosheng Su, Goutam Sahana, Mogens Sandø Lund, Jack C M Dekkers, Luke Kramer, Christopher K Tuggle, Ryan Corbett, Martien A M Groenen, Ole Madsen, Marta Gòdia, Dominique Rocha, Mathieu Charles, Cong-Jun Li, Hubert Pausch, Xiaoxiang Hu, Laurent Frantz, Yonglun Luo, Lin Lin, Zhongyin Zhou, Zhe Zhang, Zitao Chen, Leilei Cui, Ruidong Xiang, Xia Shen, Pinghua Li, Ruihua Huang, Guoqing Tang, Mingzhou Li, Yunxiang Zhao, Guoqiang Yi, Zhonglin Tang, Bingjie Li, PigGTEx Consortium

Integrative Animal Sciences

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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. 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.

Original language	English
Pages (from-to)	112-123
Number of pages	12
Journal	Nature Genetics
Volume	56
Issue number	1
Early online date	4 Jan 2024
DOIs	https://doi.org/10.1038/s41588-023-01585-7
Publication status	First published - 4 Jan 2024

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s41588-023-01585-7Final published version, 19.2 MBLicence: CC BY

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Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., Bai, L., Cai, Z., Zhao, B., Li, X., Xu, Z., Lin, Q., Pan, Z., Yang, W., Yu, X., Guan, D., Hou, Y., Keel, B. N., Rohrer, G. A., ... PigGTEx Consortium (2024). A compendium of genetic regulatory effects across pig tissues. Nature Genetics, 56(1), 112-123. Advance online publication. https://doi.org/10.1038/s41588-023-01585-7

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title = "A compendium of genetic regulatory effects across pig tissues",

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. 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.",

author = "Jinyan Teng and Yahui Gao and Hongwei Yin and Zhonghao Bai and Shuli Liu and Haonan Zeng and Lijing Bai and Zexi Cai and Bingru Zhao and Xiujin Li and Zhiting Xu and Qing Lin and Zhangyuan Pan and Wenjing Yang and Xiaoshan Yu and Dailu Guan and Yali Hou and Keel, {Brittney N} and Rohrer, {Gary A} and Lindholm-Perry, {Amanda K} and Oliver, {William T} and Maria Ballester and Daniel Crespo-Piazuelo and Raquel Quintanilla and Oriol Canela-Xandri and Konrad Rawlik and Charley Xia and Yuelin Yao and Qianyi Zhao and Wenye Yao and Liu Yang and Houcheng Li and Huicong Zhang and Wang Liao and Tianshuo Chen and Peter Karlskov-Mortensen and Merete Fredholm and Marcel Amills and Alex Clop and Elisabetta Giuffra and Jun Wu and Xiaodian Cai and Shuqi Diao and Xiangchun Pan and Chen Wei and Jinghui Li and Hao Cheng and Sheng Wang and Guosheng Su and Goutam Sahana and Lund, {Mogens Sand{\o}} and Dekkers, {Jack C M} and Luke Kramer and Tuggle, {Christopher K} and Ryan Corbett and Groenen, {Martien A M} and Ole Madsen and Marta G{\`o}dia and Dominique Rocha and Mathieu Charles and Cong-Jun Li and Hubert Pausch and Xiaoxiang Hu and Laurent Frantz and Yonglun Luo and Lin Lin and Zhongyin Zhou and Zhe Zhang and Zitao Chen and Leilei Cui and Ruidong Xiang and Xia Shen and Pinghua Li and Ruihua Huang and Guoqing Tang and Mingzhou Li and Yunxiang Zhao and Guoqiang Yi and Zhonglin Tang and Bingjie Li and {PigGTEx Consortium}",

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doi = "10.1038/s41588-023-01585-7",

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Teng, J, Gao, Y, Yin, H, Bai, Z, Liu, S, Zeng, H, Bai, L, Cai, Z, Zhao, B, Li, X, Xu, Z, Lin, Q, Pan, Z, Yang, W, Yu, X, Guan, D, Hou, Y, Keel, BN, Rohrer, GA, Lindholm-Perry, AK, Oliver, WT, Ballester, M, Crespo-Piazuelo, D, Quintanilla, R, Canela-Xandri, O, Rawlik, K, Xia, C, Yao, Y, Zhao, Q, Yao, W, Yang, L, Li, H, Zhang, H, Liao, W, Chen, T, Karlskov-Mortensen, P, Fredholm, M, Amills, M, Clop, A, Giuffra, E, Wu, J, Cai, X, Diao, S, Pan, X, Wei, C, Li, J, Cheng, H, Wang, S, Su, G, Sahana, G, Lund, MS, Dekkers, JCM, Kramer, L, Tuggle, CK, Corbett, R, Groenen, MAM, Madsen, O, Gòdia, M, Rocha, D, Charles, M, Li, C-J, Pausch, H, Hu, X, Frantz, L, Luo, Y, Lin, L, Zhou, Z, Zhang, Z, Chen, Z, Cui, L, Xiang, R, Shen, X, Li, P, Huang, R, Tang, G, Li, M, Zhao, Y, Yi, G, Tang, Z, Li, B & PigGTEx Consortium 2024, 'A compendium of genetic regulatory effects across pig tissues', Nature Genetics, vol. 56, no. 1, pp. 112-123. https://doi.org/10.1038/s41588-023-01585-7

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T1 - A compendium of genetic regulatory effects across pig tissues

AU - Teng, Jinyan

AU - Gao, Yahui

AU - Yin, Hongwei

AU - Bai, Zhonghao

AU - Liu, Shuli

AU - Zeng, Haonan

AU - Bai, Lijing

AU - Cai, Zexi

AU - Zhao, Bingru

AU - Li, Xiujin

AU - Xu, Zhiting

AU - Lin, Qing

AU - Pan, Zhangyuan

AU - Yang, Wenjing

AU - Yu, Xiaoshan

AU - Guan, Dailu

AU - Hou, Yali

AU - Keel, Brittney N

AU - Rohrer, Gary A

AU - Lindholm-Perry, Amanda K

AU - Oliver, William T

AU - Ballester, Maria

AU - Crespo-Piazuelo, Daniel

AU - Quintanilla, Raquel

AU - Canela-Xandri, Oriol

AU - Rawlik, Konrad

AU - Xia, Charley

AU - Yao, Yuelin

AU - Zhao, Qianyi

AU - Yao, Wenye

AU - Yang, Liu

AU - Li, Houcheng

AU - Zhang, Huicong

AU - Liao, Wang

AU - Chen, Tianshuo

AU - Karlskov-Mortensen, Peter

AU - Fredholm, Merete

AU - Amills, Marcel

AU - Clop, Alex

AU - Giuffra, Elisabetta

AU - Wu, Jun

AU - Cai, Xiaodian

AU - Diao, Shuqi

AU - Pan, Xiangchun

AU - Wei, Chen

AU - Li, Jinghui

AU - Cheng, Hao

AU - Wang, Sheng

AU - Su, Guosheng

AU - Sahana, Goutam

AU - Lund, Mogens Sandø

AU - Dekkers, Jack C M

AU - Kramer, Luke

AU - Tuggle, Christopher K

AU - Corbett, Ryan

AU - Groenen, Martien A M

AU - Madsen, Ole

AU - Gòdia, Marta

AU - Rocha, Dominique

AU - Charles, Mathieu

AU - Li, Cong-Jun

AU - Pausch, Hubert

AU - Hu, Xiaoxiang

AU - Frantz, Laurent

AU - Luo, Yonglun

AU - Lin, Lin

AU - Zhou, Zhongyin

AU - Zhang, Zhe

AU - Chen, Zitao

AU - Cui, Leilei

AU - Xiang, Ruidong

AU - Shen, Xia

AU - Li, Pinghua

AU - Huang, Ruihua

AU - Tang, Guoqing

AU - Li, Mingzhou

AU - Zhao, Yunxiang

AU - Yi, Guoqiang

AU - Tang, Zhonglin

AU - Li, Bingjie

AU - PigGTEx Consortium

PY - 2024/1/4

Y1 - 2024/1/4

N2 - 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.

AB - 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.

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VL - 56

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JO - Nature Genetics

JF - Nature Genetics

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ER -

A compendium of genetic regulatory effects across pig tissues

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