A multi-tissue single-cell expression atlas in cattle

IF 29 1区生物学 Q1 GENETICS & HEREDITY

Nature genetics Pub Date : 2025-09-05 DOI:10.1038/s41588-025-02329-5

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

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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.

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牛多组织单细胞表达图谱

系统表征家畜组织中细胞的分子状态对于理解经济和生态重要生理性状背后的细胞和遗传机制至关重要。在这里，作为农场动物基因型-组织表达（FarmGTEx）项目的一部分，我们描述了一个综合的参考图谱，包括来自小牛和成年牛的59个组织的1,793,854个细胞，跨越两性，揭示了组织内和组织间细胞在基因表达、转录因子调控和细胞间通讯方面的异质性。对支撑牛单基因和复杂性状的遗传变异进行综合分析，揭示了相关的细胞类型，如负责精子运动的精细胞和负责乳脂产量的兴奋性神经元。比较分析揭示了牛和人之间基因表达的相似性，允许检测相关细胞类型来研究人类复杂表型。这个牛细胞图谱将作为牛遗传学和基因组学、选择育种和比较生物学的关键资源。

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来源期刊

Nature genetics 生物-遗传学

CiteScore

43.00

自引率

2.60%

发文量

241

审稿时长

3 months

期刊介绍： Nature Genetics publishes the very highest quality research in genetics. It encompasses genetic and functional genomic studies on human and plant traits and on other model organisms. Current emphasis is on the genetic basis for common and complex diseases and on the functional mechanism, architecture and evolution of gene networks, studied by experimental perturbation. Integrative genetic topics comprise, but are not limited to: -Genes in the pathology of human disease -Molecular analysis of simple and complex genetic traits -Cancer genetics -Agricultural genomics -Developmental genetics -Regulatory variation in gene expression -Strategies and technologies for extracting function from genomic data -Pharmacological genomics -Genome evolution