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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 #416525
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: A multi-tissue single-cell expression atlas in cattle

Author
item HAN, BO - China Agricultural University
item LI, HOUCHENG - Aarhus University
item ZHENG, WEIJIE - China Agricultural University
item ZHANG, QI - China Agricultural University
item CHEN, AO - China Agricultural University
item ZHU, SENLIN - Zhejiang University
item SHI, TAO - Northwest A&f University
item WANG, FEI - Xi'An Jiaotong-Liverpool University
item ZOU, DONG - Chinese Academy Of Sciences
item SONG, YU - China Agricultural University
item YE, WEN - China Agricultural University
item DU, AIXIA - China Agricultural University
item FU, YIHAN - China Agricultural University
item JIA, MINGHUI - Zhejiang University
item BAI, ZHONGHAO - Aarhus University
item YUAN, ZHIXIANG - Chinese Academy Of Sciences
item LIU, WANSHENG - Pennsylvania State University
item Tuo, Wenbin
item HOPE, JAYNE - University Of Edinburgh
item MACHUGH, DAVID - University College Dublin
item O’GRADY, JOHN - University College Dublin
item MADSEN, OLE - Wageningen University
item SAHANA, GOUTAM - Aarhus University
item LUO, YONGLUN - Aarhus University
item LIN, LIN - Aarhus University
item Li, Congjun
item CAI, ZEXI - Aarhus University
item LI, BINGJIE - Sruc-Scotland'S Rural College
item HUANG, JINMING - Shandong Academy Of Agricultural Sciences
item LIU, LIN - Collaborator
item ZHANG, ZHANG - Chinese Academy Of Sciences
item MA, ZHU - Collaborator
item HOU, YALI - Chinese Academy Of Agricultural Sciences
item Liu, Ge
item JIANG, YU - Northwest A&f University
item SUN, HUIZENG - Zhejiang University
item FANG, LINGZHAO - Aarhus University
item SUN, DONGXIAO - China Agricultural University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2025
Publication Date: 9/5/2025
Citation: Han, B., Li, H., Zheng, W., Zhang, Q., Chen, A., Zhu, S., Shi, T., Wang, F., Zou, D., Song, Y., Ye, W., Du, A., Fu, Y., Jia, M., Bai, Z., Yuan, Z., Liu, W., Tuo, W., Hope, J.C., MacHugh, D.E., O’Grady, J.F., Madsen, O., Sahana, G., Luo, Y., Lin, L., Li, C., Cai, Z., Li, B., Huang, J., Liu, L., Zhang, Z., Ma, Z., Hou, Y., Liu, G., Jiang, Y., Sun, H., Fang, L., Sun, D. 2025. A multi-tissue single-cell expression atlas in cattle. Nature Genetics. https://doi.org/10.1038/s41588-025-02329-5.
DOI: https://doi.org/10.1038/s41588-025-02329-5

Interpretive Summary: Since cells are the basic units of life, one of the main interests is to study the similarities and differences in cell types between tissues and their shared functions, both within cattle and between cattle and humans. The FarmGTEx project created a detailed map showing gene activity in 1,793,854 cells from 59 different cattle tissues, identifying 131 different cell types. This information helps us understand the genetic mechanisms in cattle, which is important for both farming and human health research. 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: Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms underlying economically and ecologically important physiological traits. This knowledge contributes to the advancement of sustainable and precision agriculture-food systems. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map comprising 1,793,854 cells from 59 cattle tissues, spanning both sexes and multiple developmental stages. This map, generated by single-cell/nucleus RNA sequencing, identifies 131 distinct cell types, revealing intra- and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation, and intercellular communication. Integrative analysis with genetic variants that underpin various bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes responsible for sperm motilities and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans at single-cell resolution, allowing for detection of relevant cell types for studying human complex phenotypes. This cattle cell atlas will serve as a key resource for cattle genetics and genomics, immunology, comparative biology, and ultimately human biomedicine.