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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 #415733
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: The farm animal genotype-tissue expression (FarmGTEx) project

Author
item FANG, LINGZHAO - Aarhus University
item TENG, JINYAN - South China Agricultural University
item LIN, QING - Aarhus University
item BAI, ZHONGHAO - Aarhus University
item LIU, SHULI - Westlake University
item GUAN, DAILU - University Of California, Davis
item LI, BINGJIE - Sruc-Scotland'S Rural College
item GAO, YAHUI - South China Agricultural Univerisity
item HOU, YALI - Chinese Academy Of Sciences
item GONG, MIAN - Chinese Academy Of Agricultural Sciences
item PAN, ZHANGYUAN - Chinese Academy Of Agricultural Sciences
item YU, YING - China Agricultural University
item CLARK, EMILY - University Of Edinburgh
item SMITH, JACQUELINE - University Of Edinburgh
item RAWLIK, KONRAD - University Of Edinburgh
item XIANG, RUIDONG - Agriculture Victoria
item CHAMBERLAIN, AMANDA - Agriculture Victoria
item GODDARD, MICHAEL - Agriculture Victoria
item LITTLEJOHN, MATHEW - Collaborator
item LARSON, GREGER - University Of Oxford
item MACHUGH, DAVID - University College Cork
item O’GRADY, JOHN - University College Dublin
item SORENSEN, PETER - Aarhus University
item SAHANA, GOUTAM - Aarhus University
item LUND, MOGENS SANDO - Aarhus University
item JIANG, ZHIHUA - Washington State University
item PAN, XIANGCHUN - South China Agricultural Univerisity
item GONG, WENTAO - South China Agricultural Univerisity
item ZHANG, HAIHAN - Hunan Agricultural University
item HE, XI - Hunan Agricultural University
item ZHANG, YUEBO - Hunan Agricultural University
item GAO, NING - Hunan Agricultural University
item HE, JUN - Hunan Agricultural University
item YI, GUOQIANG - Chinese Academy Of Agricultural Sciences
item LIU, YUWEN - Chinese Academy Of Agricultural Sciences
item ZHAO, PENGJU - Zhejian University
item ZHOU, YANG - Huazhong Agricultural University
item WANG, XIAO - Shandong Academy Of Agricultural Sciences
item YOUNG, ROBERT - University Of Edinburgh
item XIA, CHARLEY - University Of Edinburgh
item CHENG, HAO - University Of California, Davis
item MA, LI - University Of Maryland
item COLE, JOHN - Council On Dairy Cattle Breeding
item Baldwin, Ransom
item Li, Congjun
item Van Tassell, Curtis
item Lunney, Joan
item LIU, WANSHENG - Pennsylvania State University
item GUAN, LELUO - University Of Alberta
item ZHAO, XIN - McGill University - Canada
item IBEAGHA-AWEMU, EVELINE - Agriculture And Agri-Food Canada
item LUO, ONGLUN - Aarhus University
item LIN, LIN - Aarhus University
item CANELA-XANDRI, ORIOL - University Of Edinburgh
item DERKS, MARTIJN - Wageningen University And Research Center
item CROOIJMANS, RICHARD - Wageningen University And Research Center
item GODIA, MARTA - Wageningen University And Research Center
item MADSEN, OLE - Wageningen University And Research Center
item GROENEN, MARTIEN - Wageningen University And Research Center
item KOLTES, JAMES - Iowa State University
item TUGGLE, CHRISTOPHER - Iowa State University
item MCCARTHY, FIONA - University Of Arizona
item ROCHA, DOMINIQUE - Inrae
item AMILLS, MARCEL - Autonomous University Of Barcelona
item CLOP, ALEX - Autonomous University Of Barcelona
item BALLESTER, MARIA - Institute De Recerca I Tecnologia Agroalimentaries (IRTA)
item TOSSER-KLOPP, GWENOLA - Inrae
item LI, JING - Aarhus University
item FANG, CHAO - Collaborator
item FANG, MING - Jimei University
item WANG, QISHAN - Zhejiang University
item HOU, ZHUOCHENG - China Agricultural University
item WANG, QIN - China Agricultural University
item ZHAO, FUPING - Chinese Academy Of Agricultural Sciences
item JIANG, LIN - Chinese Academy Of Agricultural Sciences
item ZHAO, GUIPING - Chinese Academy Of Agricultural Sciences
item ZHOU, ZHENGKUI - Chinese Academy Of Agricultural Sciences
item ZHOU, RONG - Chinese Academy Of Agricultural Sciences
item LIU, HEHE - Sichuan Agricultural University
item LI, MINGZHOU - Sichuan Agricultural University
item MO, DELIN - Sun Yat-Sen University
item LIU, XIAOHONG - Sun Yat-Sen University
item CHEN, YAOSHENG - Sun Yat-Sen University
item YUAN, XIAOLONG - South China Agricultural Univerisity
item LI, JIAQI - South China Agricultural Univerisity
item ZHAO, SHUHONG - Huazhong Agricultural University
item DING, XIANGDONG - China Agricultural University
item SUN, DONGXIAO - China Agricultural University
item SUN, HUIZENG - Zhejiang University
item LI, CONG - Northwest A&f University
item JIANG, YU - Northwest A&f University
item WU, DONGDONG - Chinese Academy Of Sciences
item WANG, WENWEN - Shandong Agricultural University
item FAN, XINZHONG - Shandong Agricultural University
item ZHANG, QIN - Shandong Agricultural University
item LI, KUI - Chinese Academy Of Sciences
item YANG, NING - China Agricultural University
item HU, XIAOXIANG - China Agricultural University
item Liu, Ge

Submitted to: Nature Genetics
Publication Type: Review Article
Publication Acceptance Date: 2/6/2025
Publication Date: 3/17/2025
Citation: Fang, L., Teng, J., Lin, Q., Bai, Z., Liu, S., Guan, D., Li, B., Gao, Y., Hou, Y., Gong, M., Pan, Z., Yu, Y., Clark, E., Smith, J., Rawlik, K., Xiang, R., Chamberlain, A.J., Goddard, M.E., Littlejohn, M., Larson, G., Machugh, D.E., O’Grady, J.F., Sorensen, P., Sahana, G., Lund, M., Jiang, Z., Pan, X., Gong, W., Zhang, H., He, X., Zhang, Y., Gao, N., He, J., Yi, G., Liu, Y., Zhao, P., Zhou, Y., Wang, X., Young, R.S., Xia, C., Cheng, H., Ma, L., Cole, J.B., Baldwin, R.L., Li, C., Van Tassell, C.P., Lunney, J.K., Liu, W., Guan, L., Zhao, X., Ibeagha-Awemu, E., Luo, O., Lin, L., Canela-Xandri, O., Derks, M., Crooijmans, R., Godia, M., Madsen, O., Groenen, M., Koltes, J.E., Tuggle, C.K., Mccarthy, F.M., Rocha, D., Amills, M., Clop, A., Ballester, M., Tosser-Klopp, G., Li, J., Fang, C., Fang, M., Wang, Q., Hou, Z., Wang, Q., Zhao, F., Jiang, L., Zhao, G., Zhou, Z., Zhou, R., Liu, H., Li, M., Mo, D., Liu, X., Chen, Y., Yuan, X., Li, J., Zhao, S., Ding, X., Sun, D., Sun, H., Li, C., Jiang, Y., Wu, D., Wang, W., Fan, X., Zhang, Q., Li, K., Yang, N., Hu, X., Liu, G. 2025. The farm animal genotype-tissue expression (FarmGTEx) project. Nature Genetics. https://doi.org/10.1038/s41588-025-02121-5.
DOI: https://doi.org/10.1038/s41588-025-02121-5

Interpretive Summary: The Farm animal Genotype-Tissue Expression (FarmGTEx) Project studies the genetic and evolutionary factors affecting gene expression in domestic species. This review covers the FarmGTEx Pilot and future phases, study design, research opportunities, and the importance of data sharing. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Genetic mutation and drift, coupled with natural and human-meditated selection, have created a wide variety of genotypes and phenotypes in farmed animals. Here, we describe the Farm animal Genotype-Tissue Expression (FarmGTEx) Project that aims to elucidate the genetic and evolutionary determinants of gene expression variation in terrestrial and aquatic domestic species across diverse biological and environmental contexts. We provide an overview of the FarmGTEx Pilot and its future phases, outline its study design, highlight key research opportunities and future priorities, as well as advocate for coordinated data analytic strategies and resource-sharing initiatives. By leveraging the advantages of studying farmed animals, such as pan-tissue sampling in large, diverse, and outbred populations, FarmGTEx will contribute to a sustainable agriculture-based food system, deepen our understanding of molecular and evolutionary mechanisms underlying phenotypic diversity within and between species, and provide a platform for fundamental discoveries in genetics, biology, evolution, and human biomedicine.