Cattle, being ruminants, have a pivotal role in converting fibrous feed, which is not directly consumable by humans, into beef and milk that are abundant in nutrients, thus making a positive contribution to maintaining food balance. Nevertheless, the cultivation of cattle presents significant environmental challenges on a global scale, particularly regarding greenhouse gas emissions. Enhancing production efficiency emerges as an opportunity to ensure the sustainability of milk and meat production, mitigate emissions, and enhance economic viability. This necessitates a comprehensive understanding of cattle genetics and genomics.

The Cattle Genotype-Tissue Expression project (CattleGTEx), which is a part of the Farm animal GTEx (FarmGTEx) initiative, aims to characterize the genetic effects of regulatory variations on pan-transcriptome and complex traits. This endeavor aims to unravel the molecular and cellular mechanisms underlying cattle variations. The CattleGTEx provides valuable resources and insights for cattle genomics, breeding, adaptive evolution, veterinary medicine, and comparative genomics, serving as a primary reference in various fields related to cattle.

The Cattle Cell Atlas (CattleCA), as an important part of the CattleGTEx project, provides a comprehensive single-cell/nucleus transcriptomic resource for cattle, which has yet to be explored. The CattleCA was built by analyzing an extensive dataset of 1,793,854 single-cell/nucleus RNA sequencing (sc/snRNA-seq), comprising 1,715,753 newly generated and 78,101 pre-existing profiles. These profiles were derived from cells spanning 59 tissues across 11 organ systems of 15 dairy cattle, representing both genders and 3 distinct developmental stages (fetus, calves, and adults). Harmony was employed to efficiently integrate datasets across different technologies and platforms.

The atlas provides the gene expression profiles for a total of 130 distinct cell types and 1,175 cell clusters across 59 tissues, representing canonical immune (n = 679,021), endothelial (n = 308,878), epithelial (n = 268,626), stromal (n = 240,771), nerve (n = 181,863), muscle (n = 81,438), and germline (n= 4,404) cells. CattleCA will be an invaluable resource for advancing fundamental biology, understanding evolution, studying mammalian genetics, enhancing precision breeding efforts, and exploring the emerging field of cell-based food systems.

https://github.com/FarmGTEx/CattleCA-Pipeline-v0

The web portal was developed by NGDC: Zou dong (zoud@big.ac.cn); Yali Hou (houyali@caas.cn); Zhang Zhang (zhangzhang@big.ac.cn); Yuan Zhixiang (yuanzhixiang@big.ac.cn) .