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.
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Acknowledgements
L. Fang is supported by Agriculture and Food Research Initiative Competitive grant 2022-67015-36215 from the USDA National Institute of Food and Agriculture, and seed funding from CellFood Hub (Aarhus University Foundation). Y. Luo is supported by the Innovative Health Initiative Joint Undertaking under grant agreement 101165643. Z. Zhang is supported by funding from the China Agriculture Research System (CARS-35). We thank all the researchers who have contributed to the generation and analyses of both publicly available and newly generated data used in the pilot phase of FarmGTEx. We thank I. Kaplow at the Department of Biological Sciences and the Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University for valuable comments on the manuscript.
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L. Fang took the lead in writing the manuscript with input from all authors. J.J.L., A.A.P., L. Frantz, H. Zhou, Z. Zhang and G.E.L. made critical revisions to the manuscript and made major contributions to the pilot phase of FarmGTEx. L. Fang, J.T., Q.L., Z.B., Y.H., X.P. and W.G. contributed to figure generation. S.L., D.G., B.L., Y.G., Y.H., M. Gong, Z.P., Y.Y., E.L.C., J. Smith., K.R., R.X., A.J.C., M.E.G., M. Littlejohn, G.L., D.E.M., J.F.O’G., P.S., G.S., M.S.L., Z.J., X.P., W.G., Haihan Zhang, X. He, Yuebo Zhang, N.G., J.H., G.Y., Y. Liu, Z.T., P.Z., Y. Zhou, L. Fu, X.W., D.H., L. Liu, S.C., R.S.Y., X.S., C.X., H.C., L.M., J.B.C., R.L.B., C.j.L., C.P.V.T., B.D.R., N.B., J. Lunney., W. Liu., L.G., X. Zhao., E.M.I.-A., Y. Luo, L. Lin, O.C.-X., M.F.L.D., R.P.M.A.C., M. Gòdia, O.M., M.A.M.G., J.E.K., C.K.T., F.M.M., D.R., E.G., M.A., A.C., M.B., G.T.-K., Jing Li, C.F., M.F., Qishan Wang, Z.H., Qin Wang, F.Z., L. Jiang, G.Z., Z. Zhou, R.Z., H.L., J.D., L. Jin, M. Li, D.M., Xiaohong Liu, Y.C., X. Yuan, Jiaqi Li, S.Z., Yi Zhang, X.D., D.S., H.-Z.S., C.L., Y. Wang, Y.J., D.W., W. Wang, X.F., Q.Z., K.L., Hao Zhang, N.Y., X. Hu, W.H., J. Song., Y. Wu, J.Y., W. Wu, C.K., Xinfeng Liu, X. Yu., L.C., X. Zhou, S.K., W. Li, H.K.I., E.S.B., B.R. and M.C.S. have provided valuable comments and edits to the manuscript. All authors provided critical feedback and helped shape the manuscript.
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Fang, L., Teng, J., Lin, Q. et al. The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project. Nat Genet 57, 786–796 (2025). https://doi.org/10.1038/s41588-025-02121-5
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DOI: https://doi.org/10.1038/s41588-025-02121-5
