open access publication

Article, 2024

A compendium of genetic regulatory effects across pig tissues

Nature Genetics, ISSN 1061-4036, 1546-1718, Volume 56, 1, Pages 112-123, 10.1038/s41588-023-01585-7

Contributors

Teng, Jin-Yan 0000-0002-3046-1452 [1] Gao, Yahui [1] [2] [3] Yin, Hongwei [4] Bai, Zhonghao [5] [6] Liu, Shuli [2] [7] Zeng, Haonan [1] Bai, Li-Jing [4] Cai, Ze-Xi 0000-0002-9579-3415 [6] Zhao, Bingru [8] Li, Xiujin [9] Xu, Zhiting 0000-0001-8830-3580 [1] Lin, Qing 0000-0002-8416-9748 [1] Pan, Zhang-Yuan 0000-0001-5394-3203 [10] [11] Yang, Wenjing [8] [10] Yu, Xiaoshan [5] Guan, Dai-Lu 0000-0001-8800-3158 [10] Hou, Yali 0000-0002-7421-2431 [12] Keel, Brittney N [13] Rohrer, Gary Alan 0000-0002-8252-9308 [13] Lindholm-Perry, Amanda K 0000-0002-5555-118X [13] Oliver, William T [13] Ballester, Maria 0000-0002-5413-4640 [14] Crespo-Piazuelo, Daniel 0000-0001-7896-2507 [14] Quintanilla, Raquel 0000-0003-3274-3434 [14] Canela-Xandri, Oriol 0000-0003-4601-6289 [5] Rawlik, Konrad 0000-0002-0010-370X [5] Xia, Charley [5] Yao, Yuelin 0000-0001-9868-2801 [5] Zhao, Qianyi [4] Yao, Wenye [4] [15] Yang, Liu 0000-0002-4179-8587 [4] Li, Houcheng [6] Zhang, Huicong [6] Liao, Wang [5] Chen, Tianshuo [5] Karlskov-Mortensen, Peter 0000-0002-2491-2763 [16] Fredholm, Merete 0000-0002-3563-7648 [16] Amills, Marcel 0000-0002-8999-0770 [17] Clop, Alex 0000-0001-9238-2728 [17] [18] Giuffra, Elisabetta [19] Wu, Jun [1] Cai, Xiaodian 0000-0001-9924-8580 [1] Diao, Shu-Qi 0000-0002-7017-7595 [1] Pan, Xiangchun 0000-0002-3737-0414 [1] Wei, Chen [1] Li, Jinghui [10] Cheng, Hao [10] Wang, Sheng 0000-0003-2611-3559 [20] Su, Guosheng [6] Sahana, Goutam 0000-0001-7608-7577 [6] Lund, Mogens Sandø [6] Dekkers, Jack C M 0000-0003-1557-7577 [21] Kramer, Luke [21] Tuggle, Christopher Keith 0000-0002-4229-5316 [21] Corbett, Ryan [21] Groenen, Martien A M 0000-0003-0484-4545 [15] Madsen, Ole 0000-0001-8082-7881 [15] Gòdia, Marta 0000-0002-0439-4014 [15] [17] Rocha, Dominique [19] Charles, Mathieu [22] Li, Cong-Jun 0000-0003-1389-9820 [2] Pausch, Hubert 0000-0002-0501-6760 [23] Hu, Xiao-Xiang 0000-0001-7045-0283 [8] Frantz, Laurent Alain François 0000-0001-8030-3885 [24] [25] Luo, Yonglun 0000-0002-0007-7759 [6] [26] [27] Lin, Lin [6] [27] Zhou, Zhongyin 0000-0002-9715-9821 [20] Zhang, Zhe [28] Chen, Zitao [28] Cui, Leilei [29] [30] Xiang, Ruidong 0000-0002-1584-7605 [31] [32] Shen, Xia 0000-0003-4390-1979 [5] [33] Li, Pinghua [34] Huang, Ruihua [34] Tang, Guo-Qing [35] Li, Ming-Zhou 0000-0001-8681-7684 [35] Zhao, Yunxiang [36] Yi, Guo-Qiang 0000-0001-8248-9126 [4] Tang, Zhong-Lin 0000-0002-4538-4349 [4] Jiang, Jicai 0000-0001-6890-7539 [37] Zhao, Fu-Ping 0000-0001-9582-5993 [11] Yuan, Xiao-Long 0000-0002-3743-0130 [1] Liu, Xiaohong [38] Chen, Yaosheng 0000-0002-3871-7651 [38] Xu, Xuewen [39] Zhao, Shuhong [39] Zhao, Pengju [28] Haley, Chris Simon 0000-0002-9811-0210 [5] [40] Zhou, Huai-Jun 0000-0001-6023-9521 [10] Wang, Qishan [28] Pan, Yuchun [28] Ding, Xiangdong [8] Ma, Li 0000-0003-1038-1081 [3] Li, Jiaqi [1] Navarro, Pau 0000-0001-5576-8584 [5] [40] Zhang, Qin [41] Li, Bingjie 0000-0002-8528-1889 [42] Tenesa, Albert 0000-0003-4884-4475 (Corresponding author) [5] [40] Li, Kui (Corresponding author) [4] Liu, George E 0000-0003-0192-6705 (Corresponding author) [2] Zhang, Zhe 0000-0001-7338-7718 (Corresponding author) [1] Fang, Ling-Zhao (Corresponding author) [5] [6]

Affiliations

  1. [1] South China Agricultural University
  2. [NORA names: China; Asia, East];
  3. [2] Agricultural Research Service - Northeast Area
  4. [NORA names: United States; America, North; OECD];
  5. [3] University of Maryland, College Park
  6. [NORA names: United States; America, North; OECD];
  7. [4] Agricultural Genomics Institute at Shenzhen
  8. [NORA names: China; Asia, East];
  9. [5] University of Edinburgh
  10. [NORA names: United Kingdom; Europe, Non-EU; OECD];

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.

Keywords

Genotype-Tissue Expression, RNA sequencing, action, animal breeding, biological discovery, biomedical model, biomedicine, breeding, complex phenotypes, control, data, discovery, effect, exploitation, expression, farms, gene expression, genes, genetic regulation, genetic regulatory effects, genetic regulatory variants, genetic variants, human biomedical model, human biomedicine, humans, imputation panel, livestock, mechanism, model, molecular mechanisms, multi-omics data, panel, phenotype, pig tissues, pig-to-human, pigs, pilot, pilot phase, project, public resources, regulation, regulatory effects, regulatory mechanisms, regulatory variants, resources, results, samples, sequenced samples, similarity, tissue, transcriptomic phenotypes, variants, variation, whole-genome sequencing samples

Funders

  • National Natural Science Foundation of China
  • National Institute of Food and Agriculture
  • Biotechnology and Biological Sciences Research Council
  • Agricultural Research Service
  • United States Department of Agriculture
  • Ministry of Science and Technology of the People's Republic of China
  • Australian Research Council
  • Medical Research Council
  • European Commission

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