How to cite the FarmGTEx project?

The pilot phase of CattleGTEx:

• A multi-tissue atlas of regulatory variants in cattle

Shuli Liu†, Yahui Gao†, Oriol Canela-Xandri†, Sheng Wang†, Ying Yu†, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda J. Chamberlain, Erola Pairo-Castineira, Kenton D’Mellow, Konrad Rawlik, Charley Xia, Yuelin Yao, Pau Navarro, Dominique Rocha, Xiujin Li, Ze Yan, Congjun Li, Benjamin D. Rosen, Curtis P. Van Tassell, Paul M. Vanraden, Shengli Zhang, Li Ma, John B. Cole, George E. Liu*, Albert Tenesa*, Lingzhao Fang*

Nature Genetics, 2022, 54(9), 1438-1447, DOI: 10.1038/s41588-022-01153-5

The pilot phase of PigGTEx:

• A compendium of genetic regulatory effects across pig tissues

Jinyan Teng†, Yahui Gao†, Hongwei Yin†, Zhonghao Bai†, Shuli Liu†, Haonan Zeng†, The PigGTEx Consortium, 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, Jicai Jiang, Fuping Zhao, Xiaolong Yuan, Xiaohong Liu, Yaosheng Chen, Xuewen Xu, Shuhong Zhao, Pengju Zhao, Chris Haley, Huaijun Zhou, Qishan Wang, Yuchun Pan, Xiangdong Ding, Li Ma, Jiaqi Li, Pau Navarro, Qin Zhang, Bingjie Li, Albert Tenesa*, Kui Li*, George E. Liu*, Zhe Zhang*, Lingzhao Fang*

Nature Genetics, 2024, 56, 112–123, DOI: 10.1038/s41588-023-01585-7

The pilot phase of ChickenGTEx:

• The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues [bioRxiv]

Dailu Guan†, Zhonghao Bai†, Xiaoning Zhu†, Conghao Zhong†, Yali Hou†, The ChickenGTEx Consortium, Fangren Lan, Shuqi Diao, Yuelin Yao, Bingru Zhao, Di Zhu, Xiaochang Li, Zhangyuan Pan, Yahui Gao, Yuzhe Wang, Dong Zou, Ruizhen Wang, Tianyi Xu, Congjiao Sun, Hongwei Yin, Jinyan Teng, Zhiting Xu, Qing Lin, Shourong Shi, Dan Shao, Fabien Degalez, Sandrine Lagarrigue, Ying Wang, Mingshan Wang, Minsheng Peng, Dominique Rocha, Mathieu Charles, Jacqueline Smith, Kellie Watson, Albert Johannes Buitenhuis, Goutam Sahana, Mogens Sando Lund, Wesley Warren, Laurent Frantz, Greger Larson, Susan J. Lamont, Wei Si, Xin Zhao, Bingjie Li, Haihan Zhang, Chenglong Luo, Dingming Shu, Hao Qu, Wei Luo, Zhenhui Li, Qinghua Nie, Xiquan Zhang, Zhe Zhang, Zhang Zhang, George E. Liu, Hans Cheng, Ning Yang*, Xiaoxiang Hu*, Huaijun Zhou*, Lingzhao Fang*

bioRxiv, 2023, DOI: 10.1101/2023.06.27.546670

• Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs

Lijuan Chen†, Houcheng Li†, Jinyan Teng†, Zhen Wang, Xiaolu Qu, Zhe Chen, Xiaodian Cai, Haonan Zeng, Zhonghao Bai, Jinghui Li, Xiangchun Pan, Leyan Yan, Fei Wang, Lin Lin, Yonglun Luo, Goutam Sahana, Mogens Sandø Lund, Maria Ballester, Daniel Crespo-Piazuelo, Peter Karlskov-Mortensen, Merete Fredholm, Alex Clop, Marcel Amills, Crystal Loving, Christopher K. Tuggle, Ole Madsen, Jiaqi Li, Zhe Zhang, George E. Liu, Jicai Jiang, Lingzhao Fang*, Guoqiang Yi*

bioRxiv, 2023, DOI: 10.1101/2023.06.12.544530

• FarmGTEx TWAS-server: an interactive web server for customized TWAS analysis in both human and farm animals

Zhenyang Zhang, Zitao Chen, Jinyan Teng, Shuli Liu, Qing Lin, Yahui Gao, Zhonghao Bai, The FarmGTEx Consortium, Bingjie Li, George Liu, Zhe Zhang, Yuchun Pan*, Zhe Zhang*, Lingzhao Fang*, Qishan Wang*

bioRxiv, 2023, DOI: 10.1101/2023.02.03.527092

• Genetic score omics regression and multi-trait meta-analysis detect widespread cis-regulatory effects shaping bovine complex traits

Ruidong Xiang*, Lingzhao Fang, Shuli Liu, George E. Liu, Albert Tenesa, Yahui Gao, CattleGTEx Consortium, Brett A Mason, Amanda J. Chamberlain, Michael E. Goddard

bioRxiv, 2022, DOI: 10.1101/2022.07.13.499886

2024

• A compendium of genetic regulatory effects across pig tissues

Jinyan Teng†, Yahui Gao†, Hongwei Yin†, Zhonghao Bai†, Shuli Liu†, Haonan Zeng†, The PigGTEx Consortium, 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, Jicai Jiang, Fuping Zhao, Xiaolong Yuan, Xiaohong Liu, Yaosheng Chen, Xuewen Xu, Shuhong Zhao, Pengju Zhao, Chris Haley, Huaijun Zhou, Qishan Wang, Yuchun Pan, Xiangdong Ding, Li Ma, Jiaqi Li, Pau Navarro, Qin Zhang, Bingjie Li, Albert Tenesa*, Kui Li*, George E. Liu*, Zhe Zhang*, Lingzhao Fang*

Nature Genetics, 2024, DOI: 10.1038/s41588-023-01585-7

• PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Haonan Zeng†, Wenjing Zhang†, Qing Lin†, Yahui Gao†, Jinyan Teng, Zhiting Xu, Xiaodian Cai, Zhanming Zhong, Jun Wu, Yuqiang Liu, Shuqi Diao, Chen Wei, Wentao Gong, Xiangchun Pan, Zedong Li, Xiaoyu Huang, Xifan Chen, Jinshi Du, The PigGTEx Consortium, Fuping Zhao, Yunxiang Zhao, Maria Ballester, Daniel Crespo-Piazuelo, Marcel Amills,, Alex Clop,, Peter Karlskov-Mortensen, Merete Fredholm, Pinghua Li, Ruihua Huang,Guoqing Tang, Mingzhou Li, Xiaohong Liu, Yaosheng Chen, Qin Zhang, Jiaqi Li, Xiaolong Yuan, Xiangdong Ding*, Lingzhao Fang*, Zhe Zhang*

Nucleic Acids Research, 2024, 52(D1), DOI: 10.1093/nar/gkad1080

2023

• Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits

Pengju Zhao, Lihong Gu, Yahui Gao, Zhangyuan Pan, Lei Liu, Xingzheng Li, Huaijun Zhou, Dongyou Yu, Xinyan Han, Lichun Qian, George E. Liu*, Lingzhao Fang* & Zhengguang Wang*

Communications Biology, 6, 894 (2023), DOI: 10.1038/s42003-023-05234-x

• Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits

Jinghui Li, Tianjing Zhao, Dailu Guan, Zhangyuan Pan, Zhonghao Bai, Jinyan Teng, Zhe Zhang, Zhili Zheng, Jian Zeng, Huaijun Zhou, Lingzhao Fang* and Hao Cheng*

Cell Genomics, 3, 100390 (2023), DOI: 10.1016/j.xgen.2023.100390

• Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle

Ruidong Xiang*, Lingzhao Fang, Shuli Liu, Iona M. Macleod, Zhiqian Liu, Edmond J. Breen, Yahui Gao, George E. Liu, Albert Tenesa, CattleGTEx Consortium, Brett A Mason, Amanda J. Chamberlain, Naomi R. Wray, Michael E. Goddard

Cell Genomics, 3, 100385 (2023), DOI: 10.1016/j.xgen.2023.100385

2022

• Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits

Siqian Chen, Shuli Liu, Shaolei Shi, Yifan Jiang, Mingyue Cao, Yongjie Tang, Wenlong Li, Jianfeng Liu, Lingzhao Fang, Ying Yu & Shengli Zhang

BMC Biology, 20, 273 (2022), DOI: 10.1186/s12915-022-01459-0

• Comparative immune-relevant transcriptome reveals the evolutionary basis of complex traits

Wenjing Yang, Jian Yu, Yuelin Yao, Siqian Chen, Bingru Zhao, Shuli Liu, LeiZhou, Lingzhao Fang & Jianfeng Liu

iScience, 25(12), 105572 (2022), DOI: 10.1016/j.isci.2022.105572

• The CattleGTEx atlas reveals regulatory mechanisms underlying complex traits

Lingzhao Fang

Nature Genetics, 54, 1273-1274 (2022), DOI: 10.1038/s41588-022-01155-3

• A multi-tissue atlas of regulatory variants in cattle

Shuli Liu†, Yahui Gao†, Oriol Canela-Xandri†, Sheng Wang†, Ying Yu†, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda J. Chamberlain, Erola Pairo-Castineira, Kenton D’Mellow, Konrad Rawlik, Charley Xia, Yuelin Yao, Pau Navarro, Dominique Rocha, Xiujin Li, Ze Yan, Congjun Li, Benjamin D. Rosen, Curtis P. Van Tassell, Paul M. Vanraden, Shengli Zhang, Li Ma, John B. Cole, George E. Liu*, Albert Tenesa*, Lingzhao Fang*

Nature Genetics, 54(9), 1438-1447 (2022), DOI: 10.1038/s41588-022-01153-5

• Comparative transcriptome in large-scale human and cattle populations

Yuelin Yao, Shuli Liu, Charley Xia, Yahui Gao, Zhangyuan Pan, Oriol Canela-Xandri, Ava Khamseh, Konrad Rawlik, Sheng Wang, Bingjie Li, Yi Zhang, Erola Pairo-Castineira, Kenton D’Mellow, Xiujin Li, Ze Yan, Cong-jun Li, Ying Yu, Shengli Zhang, Li Ma, John B. Cole, Pablo J. Ross, Huaijun Zhou, Chris Haley, George E. Liu, Lingzhao Fang & Albert Tenesa

Genome Biology, 23, 176 (2022), DOI: 10.1186/s13059-022-02745-4

• Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide

Yahui Gao, Jianbin Li, Gaozhan Cai, Yujiao Wang, Wenjing Yang, Yanqin Li, Xiuxin Zhao, Rongling Li, Yundong Gao, Wenbin Tuo, Ransom L. Baldwin VI, Cong-jun Li, Lingzhao Fang & George E. Liu

BMC genomics, 23, 338 (2022), DOI: 10.1186/s12864-022-08562-0

• Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning

Yahui Gao, Shuli Liu, Ransom L. Baldwin VI, Erin E. Connor, John B. Cole, Li Ma, Lingzhao Fang, Cong-jun Li, George E. Liu

Genomics, 114(2): 110296 (2022), DOI: 10.1016/j.ygeno.2022.110296

• Single-cell transcriptomic analyses of dairy cattle ruminal epithelial cells during weaning

Yahui Gao, Lingzhao Fang, Ransom L. Baldwin VI, Erin E. Connor, John B. Cole, Curtis P. Van Tassell, Li Ma, Cong-Jun Li, George E. Liu

Genomics, 113(4): 2045-2055 (2021), DOI: 10.1016/j.ygeno.2021.04.039

2021

• Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep

Bingru Zhao, Hanpeng Luo, Junmin He, Xixia Huang, Siqian Chen, Xuefeng Fu, Weidan Zeng, Yuezhen Tian, Shuli Liu, Cong-jun Li, George E. Liu, Lingzhao Fang, Shengli Zhang & Kechuan Tian

BMC Biology, 19, 197 (2021), DOI: 10.1186/s12915-021-01127-9

• Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

Zhangyuan Pan, Yuelin Yao, Hongwei Yin, Zexi Cai, Ying Wang, Lijing Bai, Colin Kern, Michelle Halstead, Ganrea Chanthavixay, Nares Trakooljul, Klaus Wimmers, Goutam Sahana, Guosheng Su, Mogens Sandø Lund, Merete Fredholm, Peter Karlskov-Mortensen, Catherine W. Ernst, Pablo Ross, Christopher K. Tuggle, Lingzhao Fang & Huaijun Zhou

Nature Communications, 12, 5848 (2021), DOI: 10.1038/s41467-021-26153-7

2020

• Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

Lingzhao Fang, Wentao Cai, Shuli Liu, Oriol Canela-Xandri, Yahui Gao, Jicai Jiang, Konrad Rawlik, Bingjie Li, Steven G. Schroeder, Benjamin D. Rosen, Cong-jun Li, Tad S. Sonstegard, Leeson J. Alexander, Curtis P. Van Tassell, Paul M. VanRaden, John B. Cole, Ying Yu, Shengli Zhang, Albert Tenesa, Li Ma and George E. Liu

Genome research, 30(5): 790-801 (2020), DOI: 10.1101/gr.250704.119

• Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

Shuli Liu, Ying Yu, Shengli Zhang, John B. Cole, Albert Tenesa, Ting Wang, Tara G. McDaneld, Li Ma, George E. Liu & Lingzhao Fang 

BMC biology, 18, 80 (2020), DOI: 10.1186/s12915-020-00792-6

• Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle

Ze Yan, Hetian Huang, Ellen Freebern, Daniel J. A. Santos, Dongmei Dai, Jingfang Si, Chong Ma, Jie Cao, Gang Guo, George E. Liu, Li Ma, Lingzhao Fang & Yi Zhang

BMC genomics, 21, 489 (2020), DOI: 10.1186/s12864-020-06909-z

2019

• Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle

Shuli Liu, Lingzhao Fang, Yang Zhou, Daniel J.A. Santos, Ruidong Xiang, Hans D. Daetwyler, Amanda J. Chamberlain, John B. Cole, Cong-jun Li, Ying Yu, Li Ma, Shengli Zhang & George E. Liu 

BMC genomics, 20, 888 (2019), DOI: 10.1186/s12864-019-6228-6