open access publication

Article, Early Access, 2024

A compendium of genetic regulatory effects across pig tissues

NATURE GENETICS, ISSN 1061-4036, 1061-4036, Volume 56, 1, 10.1038/s41588-023-01585-7

Contributors

Teng, Jinyan 0000-0002-3046-1452 [1] Gao, Yahui 0000-0003-4044-2295 [1] [2] [3] [4] [5] [6] [7] Yin, Hongwei [5] [6] [7] [8] Bai, Zhonghao [8] [9] Liu, Shuli 0000-0002-8988-8899 [10] Zeng, Haonan Bai, Lijing [5] [6] [7] Cai, Zexi 0000-0002-9579-3415 Zhao, Bingru [11] Li, Xiujin [12] Xu, Zhiting 0000-0001-8830-3580 [1] Lin, Qing [1] Pan, Zhangyuan 0000-0001-5394-3203 [5] [13] [14] [15] Yang, Wenjing 0000-0002-1101-8893 [11] [14] [15] Yu, Xiaoshan [9] Guan, Dailu [14] [15] Hou, Yali 0000-0002-7421-2431 [16] [17] [18] Keel, Brittney N. [4] Rohrer, Gary A. [4] Lindholm-Perry, Amanda K. [4] Oliver, William T. [4] Ballester, Maria 0000-0002-5413-4640 [19] Crespo-Piazuelo, Daniel 0000-0001-7896-2507 [19] Quintanilla, Raquel [19] Canela-Xandri, Oriol 0000-0003-4601-6289 Rawlik, K. [9] Xia, Charley [9] Yao, Yuelin [9] Zhao, Qianyi 0000-0002-4113-3155 Yao, Wenye [20] Yang, Liu [5] [6] [7] Li, Houcheng Zhang, Huicong 0000-0003-0392-7541 Liao, Wang Chen, Tianshuo Karlskov-Mortensen, Peter [21] Fredholm, Merete [21] Amills, Marcel [19] [22] [23] [24] [25] Clop, Alex [19] [22] [23] [24] [25] Giuffra, Elisabetta [26] [27] [28] Wu, Jun Cai, Xiaodian Diao, Shuqi 0000-0002-7017-7595 [1] Pan, Xiangchun [1] Wei, Chen 0000-0001-7615-4215 [1] Li, Jinghui 0000-0002-5074-8346 Cheng, Hao Wang, Sheng [18] [29] Su, Guosheng Sahana, Goutam Lund, Mogens Sando Dekkers, Jack C. [30] Kramer, Luke [30] Tuggle, Christopher K. 0000-0002-4229-5316 [30] Corbett, Ryan [30] Groenen, Martien A. M. Madsen, O. Godia, Marta [25] Rocha, Dominique [18] [26] [27] [28] [29] Charles, Mathieu [26] [27] [28] Li, Cong-jun [4] Pausch, Hubert 0000-0002-0501-6760 [31] [32] Hu, Xiaoxiang 0000-0001-7045-0283 [11] Frantz, Laurent [33] [34] [35] Luo, Yonglun [8] [36] Lin, Lin [8] Zhou, Zhongyin Zhang, Zhe [1] [37] Chen, Zitao 0000-0001-7862-6343 [37] Cui, Leilei 0000-0002-2745-6863 [35] [38] [39] [40] Xiang, Ruidong [41] [42] Shen, Xia [9] [43] Li, Pinghua [44] Huang, Ruihua 0000-0002-4722-2271 [44] Tang, Guoqing [45] Li, Mingzhou [45] Zhao, Yunxiang 0009-0008-8349-0936 [46] Yi, Guoqiang 0000-0001-8248-9126 [5] [6] [7] Tang, Zhonglin 0000-0002-4538-4349 [5] [6] [7] Jiang, Jicai [47] Zhao, Fuping 0000-0001-9582-5993 Yuan, Xiaolong [48] Liu, Xiaohong [48] Chen, Yaosheng Xu, Xuewen 0000-0001-6925-3346 Zhao, Shuhong 0000-0002-3997-2320 [49] Zhao, Pengju 0000-0001-6990-1147 [37] [49] Haley, C. S. 0000-0002-9811-0210 [9] [50] [51] [52] Zhou, Huaijun 0000-0001-6023-9521 Wang, Qishan 0000-0003-3886-3883 Pan, Yuchun 0000-0002-1163-5963 Ding, Xiangdong [11] Ma, Li Li, Jiaqi 0000-0002-6674-098X Navarro, Pau 0000-0001-5576-8584 [9] Zhang, Qin [53] Li, Bingjie 0000-0002-6540-5557 Tenesa, Albert (Corresponding author) [9] [50] [51] [52] [54] Li, Kui 0000-0001-5280-6098 (Corresponding author) [5] [6] [7] Liu, George E. (Corresponding author) [4] Zhang, Zhe (Corresponding author) [1] Fang, Lingzhao (Corresponding author) [9] PigGTEx Consortium

Affiliations

  1. [1] South China Agr Univ SCAU, Coll Anim Sci, Guangdong Prov Key Lab Agro Anim Genom & Mol Bree, Natl Engn Res Ctr Breeding Swine Ind,State Key La, Guangzhou, Peoples R China
    2. [NORA names: China; Asia, East];
  2. [2] Univ Maryland, Dept Anim & Avian Sci, College Pk, MD USA
    3. [NORA names: United States; America, North; OECD];
  3. [3] Univ Maryland, Dept Anim & Avian Sci, College Pk, MD USA
    4. [NORA names: United States; America, North; OECD];
  4. [4] ARS, Anim Genom & Improvement Lab, Henry A Wallace Beltsville Agr Res Ctr, USDA, Beltsville, MD 20705 USA
    5. [NORA names: United States; America, North; OECD];
  5. [5] Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr,Shenzhen Branch, Key Lab Livestock & Poultry Multi Omics MARA, Shenzhen, Peoples R China
    6. [NORA names: China; Asia, East];

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.

Data Provider: Clarivate

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