Cattle Cell Atlas: a multi-tissue single cell expression repository for advanced bovine genomics and comparative biology

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 bovine 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 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.