ArticleNature genetics2025
A multi-tissue single-cell expression atlas in cattle.
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Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Article
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- A High-Resolution Stereo-Seq Spatial Transcriptomic Resource for Adult Holstein Cattle Liver.International journal of molecular sciences · 2026Article
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Resolving Cattle GWAS Loci: Current Progress, Persistent Challenges and Future Directions.Current issues in molecular biology · 2026Review
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- Integrating bulk and single-cell RNA sequencing with GWAS reveals regulatory networks underpinning complex traits in beef cattle.Journal of animal science and biotechnology · 2026Article
- Single-nucleus transcriptomic atlas of postnatal camel liver development identifies candidate adaptive features.BMC genomics · 2026Article
- Pan-tissue transcriptomic profiling of dairy cattle.Journal of animal science and biotechnology · 2026Article
- Multi-omics atlas of the bovine coronavirus-infected calf jejunum: reduction of Phocaeicola coprophilus and deoxycholic acid linked to Th17/Treg imbalance.NPJ biofilms and microbiomes · 2026Article
- Tick saliva reprograms macrophages into immunosuppressive hubs that regulate T-cell immunity in Rhipicephalus microplus infestation.Communications biology · 2026Article
- Single-Cell Transcriptomic Atlases of Camels and Cattle Unravel Molecular Evolution of Digestive and Metabolic Systems.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comparative Single-Cell Transcriptomic Atlas Reveals the Genetic Regulation of Reproductive Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Advances in Single-Cell Transcriptomics for Livestock Health.Veterinary sciences · 2026Review
- De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots.Biomolecules · 2026Article
- Single cell and single nucleus RNA sequencing in liver tissues: applications and prospects in model and non-model organisms.Frontiers in genetics · 2026Review
- Complementary structure of statistical significance and predictive relevance in explainable machine learning-based transcriptomic tissue classification of Hanwoo cattle.Frontiers in genetics · 2026Article
- Trophoblast differentiation in the bovine placenta.The Journal of reproduction and development · 2026Review
- Nuclei isolation from rat and cow white adipose tissues for single-nucleus RNA sequencing; rat WAT remains a challenge.Frontiers in physiology · 2026Article
- The High-Altitude Adaptation Characteristics of Microbiota-Host Cross-Talk in Yak Gastrointestinal Track.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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Authors and funding
38 authors.
Bo Han *State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.ORCID http://orcid.org/0000-0002-7541-1037
Houcheng Li *Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Weijie Zheng *State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Qi Zhang *State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Ao Chen *State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Senlin Zhu *Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Tao Shi *College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Fei Wang *Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
Dong ZouBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.ORCID http://orcid.org/0000-0002-7169-4965
Yu SongState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Wen YeState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Aixia DuState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Yihan FuState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Minghui JiaKey Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Zhonghao BaiCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Zhixiang YuanBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
Wansheng LiuDepartment of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, USA.ORCID http://orcid.org/0000-0003-1788-7093
Wenbin TuoAnimal Parasitic Diseases Laboratory, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD, USA.
Jayne C HopeThe Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, UK.
David E MacHughUCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.ORCID http://orcid.org/0000-0002-8112-4704
John F O'GradyUCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
Ole MadsenAnimal Breeding and Genomics, Wageningen University and Research, Wageningen, the Netherlands.
Goutam SahanaCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0001-7608-7577
Yonglun LuoDepartment of Biomedicine, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-0007-7759
Lin LinDepartment of Biomedicine, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-7546-4948
Congjun LiAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.ORCID http://orcid.org/0000-0003-1389-9820
Zexi CaiCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-9579-3415
Bingjie LiDepartment of Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Edinburgh, UK.ORCID http://orcid.org/0000-0002-8528-1889
Jinming HuangInstitute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.ORCID http://orcid.org/0000-0001-9621-5652
Lin LiuBeijing Dairy Cattle Center, Beijing, China.
Zhang ZhangBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.ORCID http://orcid.org/0000-0001-6603-5060
Zhu MaBeijing Dairy Cattle Center, Beijing, China.
Yali HouState Key Laboratory of Animal Biotech Breeding, National Germplasm Center of Domestic Animal Resources, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. houyali1210@gmail.com.ORCID http://orcid.org/0000-0002-7421-2431
George E LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA. george.liu@usda.gov.ORCID http://orcid.org/0000-0003-0192-6705
Yu JiangCollege of Animal Science and Technology, Northwest A&F University, Yangling, China. yu.jiang@nwafu.edu.cn.ORCID http://orcid.org/0000-0003-4821-3585
Hui-Zeng SunKey Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China. huizeng@zju.edu.cn.ORCID http://orcid.org/0000-0001-5380-6030
Lingzhao FangCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.ORCID http://orcid.org/0000-0003-1103-3679
Dongxiao SunState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China. sundx@cau.edu.cn.ORCID http://orcid.org/0000-0002-7512-5946
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Single-Cell AnalysisAnimalsCattleFemaleGene Expression ProfilingGene Expression RegulationHumansMaleOrgan SpecificityPhenotypeTranscriptome
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