A multi-tissue single-cell expression atlas in cattle

Bo Han; Houcheng Li; Weijie Zheng; Qi Zhang; Ao Chen; Senlin Zhu; Tao Shi; Fei Wang; Dong Zou; Yu Song; Wen Ye; Aixia Du; Yihan Fu; Minghui Jia; Zhonghao Bai; Zhixiang Yuan; Wansheng Liu; Wenbin Tuo; Jayne C. Hope; David E. MacHugh; John F. O’Grady; Ole Madsen; Goutam Sahana; Yonglun Luo; Lin Lin; Congjun Li; Zexi Cai; Bingjie Li; Jinming Huang; Lin Liu; Zhang Zhang; Zhu Ma; Yali Hou; George E. Liu; Yu Jiang; Hui-zeng Sun; Lingzhao Fang; Dongxiao Sun

doi:10.1038/s41588-025-02329-5

A multi-tissue single-cell expression atlas in cattle

Bo Han, Houcheng Li, Weijie Zheng, Qi Zhang, Ao Chen, Senlin Zhu, Tao Shi, Fei Wang, Dong Zou, Yu Song, Wen Ye, Aixia Du, Yihan Fu, Minghui Jia, Zhonghao Bai, Zhixiang Yuan, Wansheng Liu, Wenbin Tuo, Jayne C. Hope, David E. MacHughJohn F. O’Grady, Ole Madsen, Goutam Sahana, Yonglun Luo, Lin Lin, Congjun Li, Zexi Cai, Bingjie Li, Jinming Huang, Lin Liu, Zhang Zhang, Zhu Ma, Yali Hou^*, George E. Liu^*, Yu Jiang^*, Hui-zeng Sun^*, Lingzhao Fang^*, Dongxiao Sun^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding the cellular and genetic mechanisms underlying economically and ecologically important physiological traits. Here, as part of the Farm Animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map including 1,793,854 cells from 59 bovine tissues in calves and adult cattle, spanning both sexes, which reveals intra-tissue and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation and intercellular communication. Integrative analysis with genetic variants that underpin bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes, responsible for sperm motility and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans, allowing for the detection of relevant cell types to study human complex phenotypes. This Cattle Cell Atlas will serve as a key resource for cattle genetics and genomics, selective breeding and comparative biology.

Original language	English
Pages (from-to)	2546-2561
Number of pages	16
Journal	Nature Genetics
Volume	57
Issue number	10
Early online date	5 Sept 2025
DOIs	https://doi.org/10.1038/s41588-025-02329-5
Publication status	Print publication - 1 Oct 2025

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@article{54cdbdb7a3984a4a872dfc7b293da914,

title = "A multi-tissue single-cell expression atlas in cattle",

abstract = "Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding the cellular and genetic mechanisms underlying economically and ecologically important physiological traits. Here, as part of the Farm Animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map including 1,793,854 cells from 59 bovine tissues in calves and adult cattle, spanning both sexes, which reveals intra-tissue and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation and intercellular communication. Integrative analysis with genetic variants that underpin bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes, responsible for sperm motility and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans, allowing for the detection of relevant cell types to study human complex phenotypes. This Cattle Cell Atlas will serve as a key resource for cattle genetics and genomics, selective breeding and comparative biology.",

author = "Bo Han and Houcheng Li and Weijie Zheng and Qi Zhang and Ao Chen and Senlin Zhu and Tao Shi and Fei Wang and Dong Zou and Yu Song and Wen Ye and Aixia Du and Yihan Fu and Minghui Jia and Zhonghao Bai and Zhixiang Yuan and Wansheng Liu and Wenbin Tuo and Hope, \{Jayne C.\} and MacHugh, \{David E.\} and O{\textquoteright}Grady, \{John F.\} and Ole Madsen and Goutam Sahana and Yonglun Luo and Lin Lin and Congjun Li and Zexi Cai and Bingjie Li and Jinming Huang and Lin Liu and Zhang Zhang and Zhu Ma and Yali Hou and Liu, \{George E.\} and Yu Jiang and Hui-zeng Sun and Lingzhao Fang and Dongxiao Sun",

year = "2025",

month = oct,

day = "1",

doi = "10.1038/s41588-025-02329-5",

language = "English",

volume = "57",

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journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

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}

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, JC, MacHugh, DE, O’Grady, JF, 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, GE, Jiang, Y, Sun, H, Fang, L & Sun, D 2025, 'A multi-tissue single-cell expression atlas in cattle', Nature Genetics, vol. 57, no. 10, pp. 2546-2561. https://doi.org/10.1038/s41588-025-02329-5

TY - JOUR

T1 - A multi-tissue single-cell expression atlas in cattle

AU - Han, Bo

AU - Li, Houcheng

AU - Zheng, Weijie

AU - Zhang, Qi

AU - Chen, Ao

AU - Zhu, Senlin

AU - Shi, Tao

AU - Wang, Fei

AU - Zou, Dong

AU - Song, Yu

AU - Ye, Wen

AU - Du, Aixia

AU - Fu, Yihan

AU - Jia, Minghui

AU - Bai, Zhonghao

AU - Yuan, Zhixiang

AU - Liu, Wansheng

AU - Tuo, Wenbin

AU - Hope, Jayne C.

AU - MacHugh, David E.

AU - O’Grady, John F.

AU - Madsen, Ole

AU - Sahana, Goutam

AU - Luo, Yonglun

AU - Lin, Lin

AU - Li, Congjun

AU - Cai, Zexi

AU - Li, Bingjie

AU - Huang, Jinming

AU - Liu, Lin

AU - Zhang, Zhang

AU - Ma, Zhu

AU - Hou, Yali

AU - Liu, George E.

AU - Jiang, Yu

AU - Sun, Hui-zeng

AU - Fang, Lingzhao

AU - Sun, Dongxiao

PY - 2025/10/1

Y1 - 2025/10/1

N2 - Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding the cellular and genetic mechanisms underlying economically and ecologically important physiological traits. Here, as part of the Farm Animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map including 1,793,854 cells from 59 bovine tissues in calves and adult cattle, spanning both sexes, which reveals intra-tissue and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation and intercellular communication. Integrative analysis with genetic variants that underpin bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes, responsible for sperm motility and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans, allowing for the detection of relevant cell types to study human complex phenotypes. This Cattle Cell Atlas will serve as a key resource for cattle genetics and genomics, selective breeding and comparative biology.

AB - Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding the cellular and genetic mechanisms underlying economically and ecologically important physiological traits. Here, as part of the Farm Animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map including 1,793,854 cells from 59 bovine tissues in calves and adult cattle, spanning both sexes, which reveals intra-tissue and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation and intercellular communication. Integrative analysis with genetic variants that underpin bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes, responsible for sperm motility and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans, allowing for the detection of relevant cell types to study human complex phenotypes. This Cattle Cell Atlas will serve as a key resource for cattle genetics and genomics, selective breeding and comparative biology.

U2 - 10.1038/s41588-025-02329-5

DO - 10.1038/s41588-025-02329-5

M3 - Article

C2 - 40913183

SN - 1061-4036

VL - 57

SP - 2546

EP - 2561

JO - Nature Genetics

JF - Nature Genetics

IS - 10

ER -

A multi-tissue single-cell expression atlas in cattle

Abstract

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