IPGCA: A Comprehensive Single Cell Atlas of 1 074 127 Porcine Intestinal Cells Revealing Cellular Dynamics, Genetic Regulation, and Cross‐Species Conservation

Abstract The porcine intestinal tract is vital for nutrient absorption, immune regulation, and various physiological processes. However, a comprehensive understanding of its cellular composition and gene regulatory landscape remains limited. Here, the Integrated Pig Gut Cell Atlas (IPGCA) is presented, a comprehensive single cell resource comprising 1 074 127 cells spanning five intestinal segments, six developmental stages, and nine breeds. IPGCA enables the discovery of previously overlooked cell types (e.g., Paneth cells) and reveals dynamic B cell remodeling during weaning. Combining with genome‐wide association studies (GWAS), complex traits are linked to potential causal cell types. Furthermore, the utility of IPGCA as a reference for the deconvolution of bulk RNA‐seq data is demonstrated, enabling the identification of cell type interaction expression quantitative trait loci (ieQTLs) and deconvolutional eQTLs (decon‐eQTL). Co‐localization analyses implicate enterocyte BNC2 functions in loin muscle area trait and endothelial cell BAG3 in backfat thickness. Strikingly, comparative analysis with human intestinal atlases reveals a high degree of conservation, reinforcing the pig's value as a model for human gut biology. To empower the community, scGutDB ( http://alphaindex.zju.edu.cn/scgut ) is developed, an interactive platform for data exploration. IPGCA provides a foundational resource for agricultural genomics, precision breeding, and translational studies of intestinal physiology and diseases.