The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project

The FarmGTEx Consortium; Zhuocheng  Hou; Qin  Wang; Fuping  Zhao; Lin  Jiang; Guiping  Zhao; Zhengkui  Zhou; Rong  Zhou; Hehe  Liu; Juan  Deng; Long  Jin; Mingzhou  Li; Delin  Mo; Xiaohong  Liu; Yaosheng  Chen; Xiaolong  Yuan; Jiaqi  Li; Shuhong  Zhao; Yi  Zhang; Xiangdong  Ding; Dongxiao  Sun; Hui-Zeng  Sun; Cong  Li; Yu  Wang; Yu  Jiang; Dongdong  Wu; Wenwen  Wang; Xinzhong  Fan; Qin  Zhang; Kui  Li; Hao  Zhang; Ning  Yang; Xiaoxiang  Hu; Wen  Huang; Jiuzhou  Song; Yang  Wu; Jian  Yang; Weiwei  Wu; Claudia  Kasper; Xinfeng  Liu; Xiaofei  Yu; Leilei  Cui; Xiang  Zhou; Seyoung  Kim; Wei  Li; Hae Kyung  Im; Edward S.  Buckler; Bing  Ren; Michael C.  Schatz; Jingyi Jessica  Li; Abraham A.  Palmer; Laurent  Frantz; Huaijun  Zhou; Zhe  Zhang; George E.  Liu

doi:10.1038/s41588-025-02121-5

The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project

The FarmGTEx Consortium, Zhuocheng Hou, Qin Wang, Fuping Zhao, Lin Jiang, Guiping Zhao, Zhengkui Zhou, Rong Zhou, Hehe Liu, Juan Deng, Long Jin, Mingzhou Li, Delin Mo, Xiaohong Liu, Yaosheng Chen, Xiaolong Yuan, Jiaqi Li, Shuhong Zhao, Yi Zhang, Xiangdong DingDongxiao Sun, Hui-Zeng Sun, Cong Li, Yu Wang, Yu Jiang, Dongdong Wu, Wenwen Wang, Xinzhong Fan, Qin Zhang, Kui Li, Hao Zhang, Ning Yang, Xiaoxiang Hu, Wen Huang, Jiuzhou Song, Yang Wu, Jian Yang, Weiwei Wu, Claudia Kasper, Xinfeng Liu, Xiaofei Yu, Leilei Cui, Xiang Zhou, Seyoung Kim, Wei Li, Hae Kyung Im, Edward S. Buckler, Bing Ren, Michael C. Schatz, Jingyi Jessica Li, Abraham A. Palmer, Laurent Frantz, Huaijun Zhou, Zhe Zhang, George E. Liu

Research output: Contribution to journal › Review article › peer-review

4 Citations (Scopus)

Abstract

Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.

Original language	English
Article number	604
Pages (from-to)	786-796
Number of pages	11
Journal	Nature Genetics
Volume	57
Issue number	4
Early online date	17 Mar 2025
DOIs	https://doi.org/10.1038/s41588-025-02121-5
Publication status	Print publication - Apr 2025

Bibliographical note

Publisher Copyright:
© Springer Nature America, Inc. 2025.

Keywords

Animals
Animals, Domestic
Genomics
Genotype
Humans
Phenotype
Transcriptome
Animals, Domestic/genetics
Genomics/methods

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41588-025-02121-5

Cite this

The FarmGTEx Consortium, Hou, Z., Wang, Q., Zhao, F., Jiang, L., Zhao, G., Zhou, Z., Zhou, R., Liu, H., Deng, J., Jin, L., Li, M., Mo, D., Liu, X., Chen, Y., Yuan, X., Li, J., Zhao, S., Zhang, Y., ... Liu, G. E. (2025). The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project. Nature Genetics, 57(4), 786-796. Article 604. https://doi.org/10.1038/s41588-025-02121-5

@article{57be1c90f2af40c08756dd9828cb33c8,

title = "The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project",

abstract = "Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.",

keywords = "Animals, Animals, Domestic, Genomics, Genotype, Humans, Phenotype, Transcriptome, Animals, Domestic/genetics, Genomics/methods",

author = "Lingzhao Fang and Jinyan Teng and Qing Lin and Zhonghao Bai and Shuli Liu and Dailu Guan and Bingjie Li and Yahui Gao and Yali Hou and Mian Gong and Zhangyuan Pan and Ying Yu and Clark, \{Emily L.\} and Jacqueline Smith and Konrad Rawlik and Ruidong Xiang and Chamberlain, \{Amanda J.\} and Goddard, \{Michael E.\} and Mathew Littlejohn and Greger Larson and MacHugh, \{David E.\} and O{\textquoteright}Grady, \{John F.\} and Peter S{\o}rensen and Goutam Sahana and Lund, \{Mogens Sand{\o}\} and Zhihua Jiang and Xiangchun Pan and Wentao Gong and Haihan Zhang and Xi He and Yuebo Zhang and Ning Gao and Jun He and Guoqiang Yi and Yuwen Liu and Zhonglin Tang and Pengju Zhao and Yang Zhou and Liangliang Fu and Xiao Wang and Dan Hao and Lei Liu and Siqian Chen and Young, \{Robert S.\} and Xia Shen and Charley Xia and Hao Cheng and Li Ma and Cole, \{John B.\} and Baldwin, \{Ransom L.\} and Li, \{Cong Jun\} and \{Van Tassell\}, \{Curtis P.\} and Rosen, \{Benjamin D.\} and Nayan Bhowmik and Joan Lunney and Wansheng Liu and Leluo Guan and Xin Zhao and Ibeagha-Awemu, \{Eveline M.\} and Yonglun Luo and Lin Lin and Oriol Canela-Xandri and Derks, \{Martijn F.L.\} and Crooijmans, \{Richard P.M.A.\} and Marta G{\`o}dia and Ole Madsen and Groenen, \{Martien A.M.\} and Koltes, \{James E.\} and Tuggle, \{Christopher K.\} and McCarthy, \{Fiona M.\} and Dominique Rocha and Elisabetta Giuffra and Marcel Amills and Alex Clop and Maria Ballester and Gwenola Tosser-Klopp and Jing Li and Chao Fang and Ming Fang and Qishan Wang and \{The FarmGTEx Consortium\} and Zhuocheng Hou and Qin Wang and Fuping Zhao and Lin Jiang and Guiping Zhao and Zhengkui Zhou and Rong Zhou and Hehe Liu and Juan Deng and Long Jin and Mingzhou Li and Delin Mo and Xiaohong Liu and Yaosheng Chen and Xiaolong Yuan and Jiaqi Li and Shuhong Zhao and Yi Zhang and Xiangdong Ding and Dongxiao Sun and Hui-Zeng Sun and Cong Li and Yu Wang and Yu Jiang and Dongdong Wu and Wenwen Wang and Xinzhong Fan and Qin Zhang and Kui Li and Hao Zhang and Ning Yang and Xiaoxiang Hu and Wen Huang and Jiuzhou Song and Yang Wu and Jian Yang and Weiwei Wu and Claudia Kasper and Xinfeng Liu and Xiaofei Yu and Leilei Cui and Xiang Zhou and Seyoung Kim and Wei Li and Im, \{Hae Kyung\} and Buckler, \{Edward S.\} and Bing Ren and Schatz, \{Michael C.\} and Li, \{Jingyi Jessica\} and Palmer, \{Abraham A.\} and Laurent Frantz and Huaijun Zhou and Zhe Zhang and Liu, \{George E.\}",

note = "Publisher Copyright: {\textcopyright} Springer Nature America, Inc. 2025. ",

year = "2025",

month = apr,

doi = "10.1038/s41588-025-02121-5",

language = "English",

volume = "57",

pages = "786--796",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

number = "4",

}

The FarmGTEx Consortium, Hou, Z, Wang, Q, Zhao, F, Jiang, L, Zhao, G, Zhou, Z, Zhou, R, Liu, H, Deng, J, Jin, L, Li, M, Mo, D, Liu, X, Chen, Y, Yuan, X, Li, J, Zhao, S, Zhang, Y, Ding, X, Sun, D, Sun, H-Z, Li, C, Wang, Y, Jiang, Y, Wu, D, Wang, W, Fan, X, Zhang, Q, Li, K, Zhang, H, Yang, N, Hu, X, Huang, W, Song, J, Wu, Y, Yang, J, Wu, W, Kasper, C, Liu, X, Yu, X, Cui, L, Zhou, X, Kim, S, Li, W, Im, HK, Buckler, ES, Ren, B, Schatz, MC, Li, JJ, Palmer, AA, Frantz, L, Zhou, H, Zhang, Z & Liu, GE 2025, 'The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project', Nature Genetics, vol. 57, no. 4, 604, pp. 786-796. https://doi.org/10.1038/s41588-025-02121-5

TY - JOUR

T1 - The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project

AU - Fang, Lingzhao

AU - Teng, Jinyan

AU - Lin, Qing

AU - Bai, Zhonghao

AU - Liu, Shuli

AU - Guan, Dailu

AU - Li, Bingjie

AU - Gao, Yahui

AU - Hou, Yali

AU - Gong, Mian

AU - Pan, Zhangyuan

AU - Yu, Ying

AU - Clark, Emily L.

AU - Smith, Jacqueline

AU - Rawlik, Konrad

AU - Xiang, Ruidong

AU - Chamberlain, Amanda J.

AU - Goddard, Michael E.

AU - Littlejohn, Mathew

AU - Larson, Greger

AU - MacHugh, David E.

AU - O’Grady, John F.

AU - Sørensen, Peter

AU - Sahana, Goutam

AU - Lund, Mogens Sandø

AU - Jiang, Zhihua

AU - Pan, Xiangchun

AU - Gong, Wentao

AU - Zhang, Haihan

AU - He, Xi

AU - Zhang, Yuebo

AU - Gao, Ning

AU - He, Jun

AU - Yi, Guoqiang

AU - Liu, Yuwen

AU - Tang, Zhonglin

AU - Zhao, Pengju

AU - Zhou, Yang

AU - Fu, Liangliang

AU - Wang, Xiao

AU - Hao, Dan

AU - Liu, Lei

AU - Chen, Siqian

AU - Young, Robert S.

AU - Shen, Xia

AU - Xia, Charley

AU - Cheng, Hao

AU - Ma, Li

AU - Cole, John B.

AU - Baldwin, Ransom L.

AU - Li, Cong Jun

AU - Van Tassell, Curtis P.

AU - Rosen, Benjamin D.

AU - Bhowmik, Nayan

AU - Lunney, Joan

AU - Liu, Wansheng

AU - Guan, Leluo

AU - Zhao, Xin

AU - Ibeagha-Awemu, Eveline M.

AU - Luo, Yonglun

AU - Lin, Lin

AU - Canela-Xandri, Oriol

AU - Derks, Martijn F.L.

AU - Crooijmans, Richard P.M.A.

AU - Gòdia, Marta

AU - Madsen, Ole

AU - Groenen, Martien A.M.

AU - Koltes, James E.

AU - Tuggle, Christopher K.

AU - McCarthy, Fiona M.

AU - Rocha, Dominique

AU - Giuffra, Elisabetta

AU - Amills, Marcel

AU - Clop, Alex

AU - Ballester, Maria

AU - Tosser-Klopp, Gwenola

AU - Li, Jing

AU - Fang, Chao

AU - Fang, Ming

AU - Wang, Qishan

AU - The FarmGTEx Consortium

AU - Hou, Zhuocheng

AU - Wang, Qin

AU - Zhao, Fuping

AU - Jiang, Lin

AU - Zhao, Guiping

AU - Zhou, Zhengkui

AU - Zhou, Rong

AU - Liu, Hehe

AU - Deng, Juan

AU - Jin, Long

AU - Li, Mingzhou

AU - Mo, Delin

AU - Liu, Xiaohong

AU - Chen, Yaosheng

AU - Yuan, Xiaolong

AU - Li, Jiaqi

AU - Zhao, Shuhong

AU - Zhang, Yi

AU - Ding, Xiangdong

AU - Sun, Dongxiao

AU - Sun, Hui-Zeng

AU - Li, Cong

AU - Wang, Yu

AU - Jiang, Yu

AU - Wu, Dongdong

AU - Wang, Wenwen

AU - Fan, Xinzhong

AU - Zhang, Qin

AU - Li, Kui

AU - Zhang, Hao

AU - Yang, Ning

AU - Hu, Xiaoxiang

AU - Huang, Wen

AU - Song, Jiuzhou

AU - Wu, Yang

AU - Yang, Jian

AU - Wu, Weiwei

AU - Kasper, Claudia

AU - Liu, Xinfeng

AU - Yu, Xiaofei

AU - Cui, Leilei

AU - Zhou, Xiang

AU - Kim, Seyoung

AU - Li, Wei

AU - Im, Hae Kyung

AU - Buckler, Edward S.

AU - Ren, Bing

AU - Schatz, Michael C.

AU - Li, Jingyi Jessica

AU - Palmer, Abraham A.

AU - Frantz, Laurent

AU - Zhou, Huaijun

AU - Zhang, Zhe

AU - Liu, George E.

PY - 2025/4

Y1 - 2025/4

N2 - Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.

AB - Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.

KW - Animals

KW - Animals, Domestic

KW - Genomics

KW - Genotype

KW - Humans

KW - Phenotype

KW - Transcriptome

KW - Animals, Domestic/genetics

KW - Genomics/methods

UR - https://www.scopus.com/pages/publications/105000826160

U2 - 10.1038/s41588-025-02121-5

DO - 10.1038/s41588-025-02121-5

M3 - Review article

C2 - 40097783

AN - SCOPUS:105000826160

SN - 1061-4036

VL - 57

SP - 786

EP - 796

JO - Nature Genetics

JF - Nature Genetics

IS - 4

M1 - 604

ER -

The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project

Abstract

Bibliographical note

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this