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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #399702
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: A compendium of genetic regulatory effects across pig tissues

Author
item TENG, JINYAN - South China Agricultural University
item GAO, YAHUI - University Of Maryland
item YIN, HONGWEI - Chinese Academy Of Agricultural Sciences
item BAI, ZHONGHAO - Aarhus University
item LIU, SHULI - Westlake University
item ZENG, HAONAN - South China Agricultural University
item CONSORTIUM, T - Collaborator
item BAI, LIJING - Chinese Academy Of Agricultural Sciences
item CAI, ZEXI - Aarhus University
item ZHAO, BINGRU - China Agricultural University
item LI, XIUJIN - Zhongkai University
item XU, ZHITING - South China Agricultural University
item LIN, QING - South China Agricultural University
item PAN, ZHANGYUAN - University Of California, Davis
item YANG, WENJING - China Agricultural University
item YU, XIAOSHAN - University Of Edinburgh
item GUAN, DAILU - University Of California, Davis
item HOU, YALI - Chinese Academy Of Sciences
item Keel, Brittney
item Rohrer, Gary
item Lindholm-Perry, Amanda
item Oliver, William
item BALLESTER, MARIA - Collaborator
item CRESPO, DANIEL - Collaborator
item QUINTANILLA, RAQUEL - Collaborator
item CANELA-XANDRI, ORIOL - University Of Edinburgh
item RAWLIK, KONRAD - University Of Edinburgh
item XIA, CHARLEY - University Of Edinburgh
item YAO, YUELIN - University Of Edinburgh
item ZHAO, QIANYI - Chinese Academy Of Agricultural Sciences
item YAO, WENYE - Chinese Academy Of Agricultural Sciences
item YANG, LIU - Chinese Academy Of Agricultural Sciences
item LI, HOUCHENG - Aarhus University
item ZHANG, HUICONG - Aarhuis University
item LIAO, WANG - University Of Edinburgh
item CHEN, TIANSHUO - University Of Edinburgh
item KARLSKOV-MORTENSEN, PETER - University Of Copenhagen
item FREDHOLM, MERETE - University Of Copenhagen
item AMILLS ERAS, MARCEL - Collaborator
item CLOP, ALEX - Collaborator
item GIUFFRA, ELISABETTA - Inrae
item WU, JUN - South China Agricultural University
item CAI, XIAODIAN - South China Agricultural Univerisity
item DIAO, SHUQI - South China Agricultural Univerisity
item PAN, XIANGCHUN - South China Agricultural Univerisity
item WEI, CHEN - South China Agricultural University
item LI, JINGHUI - University Of California, Davis
item CHENG, HAO - University Of California, Davis
item WANG, SHENG - Chinese Academy Of Sciences
item SU, GUOSHENG - Aarhus University
item SAHANA, GOUTAM - Aarhus University
item LUND, MOGENS SANDO - Aarhus University
item DEKKERS, JACK - Iowa State University
item KRAMER, LUKE - Iowa State University
item TUGGLE, CHRISTOPHER - Iowa State University
item CORBETT, RYAN - Iowa State University
item GROENEN, MARTIEN - Iowa State University
item MADSEN, OLE - Wageningen University And Research Center
item GODIA, MARTA - Wageningen University And Research Center
item ROCHA, DOMINIQUE - Inrae
item Li, Congjun - Cj
item PAUSCH, HUBERT - Eth Zurich
item HU, XIAOXIANG - China Agricultural University
item FRANTZ, LAURENT - Ludwig-Maximilians University
item LUO, YONGLUN - Aarhus University
item LIN, LIN - Aarhus University
item ZHOU, ZHONGYIN - Chinese Academy Of Sciences
item ZHANG, ZHE - Zhejiang University
item CHEN, ZITAO - Zhejiang University
item CUI, LEILEI - University College London
item XIANG, RUIDONG - University Of Melbourne
item SHEN, XIA - Fudan University
item LI, PINGHUA - Nanjing Agricultural University
item HUANG, RUIHUA - Nanjing Agricultural University
item TANG, GUOQING - Sichuan Agricultural University
item LI, MINGZHOU - Sichuan Agricultural University
item ZHAO, YUNXIANG - Foshan University
item YI, GUOQIANG - Chinese Academy Of Agricultural Sciences
item TANG, ZHONGLIN - Chinese Academy Of Agricultural Sciences
item JIANG, JICAI - North Carolina State University
item ZHAO, FUPING - Chinese Academy Of Agricultural Sciences
item YUAN, XIAOLONG - South China Agricultural University
item LIU, XIAOHONG - Sun Yat-Sen University
item CHEN, YAOSHENG - Sun Yat-Sen University
item XU, XUEWEN - Huazhong Agricultural University
item ZHAO, SHUHONG - Huazhong Agricultural University
item ZHAO, PENGJU - Zhejiang University
item HALEY, CHRIS - University Of Edinburgh
item ZHOU, HUAIJUN - University Of California, Davis
item WANG, QISHAN - Zhejiang University
item PAN, YUCHUN - Zhejiang University
item DING, XIANGDONG - China Agricultural University
item MA, LI - University Of Maryland
item LI, JIAQI - South China Agricultural University
item NAVARRO, PAU - University Of Edinburgh
item ZHANG, QIN - Shandong Agricultural University
item LI, BINGJIE - Sruc-Scotland'S Rural College
item TENESA, ALBERT - University Of Edinburgh
item Liu, Ge - George

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2023
Publication Date: 1/4/2024
Citation: Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., Consortium, T., Bai, L., Cai, Z., Zhao, B., Li, X., Xu, Z., Lin, Q., Pan, Z., Yang, W., Yu, X., Guan, D., Hou, Y., Keel-Mercer, B.N., Rohrer, G.A., Lindholm-Perry, A.K., Oliver, W.T., Ballester, M., Crespo, 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 Eras, 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, M., Dekkers, J., Kramer, L., Tuggle, C.K., Corbett, R., Groenen, M.A., Madsen, O., Godia, M., Rocha, D., Li, C., 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., Jiang, J., Zhao, F., Yuan, X., Liu, X., Chen, Y., Xu, X., Zhao, S., Zhao, P., Haley, C., Zhou, H., Wang, Q., Pan, Y., Ding, X., Ma, L., Li, J., Navarro, P., Zhang, Q., Li, B., Tenesa, A., Liu, G. 2024. A compendium of genetic regulatory effects across pig tissues. Nature Genetics. 56:112-123. https://doi.org/10.1038/s41588-023-01585-7.
DOI: https://doi.org/10.1038/s41588-023-01585-7

Interpretive Summary: Comprehensive analyses of genetic regulatory variants will benefit our understanding of genetic bases for complex traits. We provided the first pig Genotype-Tissue Expression atlas. These results fill our knowledge gaps and provide the foundation for incorporating new transcriptome insights into the future animal breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: The Farm animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in animal breeding and human biomedicine. Here we present results from the pilot phase of PigGTEx, where we processed 9,530 RNA-sequencing and 1,602 whole-genome sequencing samples from pigs. We build a pig genotype imputation panel, characterize the transcriptional landscape across over 100 tissues, and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We study interactions between genotype and breed/cell type, evaluate tissue specificity of regulatory effects, and elucidate the molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying about 80% of the genetic associations for 207 pig complex phenotypes, and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, corroborating the importance of pigs as a human biomedical model.