A spatiotemporal single-cell atlas of porcine development reveals regulatory dynamics and cellular targets of domestication.

Systematic characterization of cellular gene expression in livestock tissues during development is essential for understanding the regulation of complex traits. Despite the comprehensive profiling of cell atlases in livestock, a dynamic view of tissue development remains lacking. Here, using both single-cell and single-nucleus RNA sequencing, we present a comprehensive single-cell transcriptomic landscape of 252,033 cells/nuclei, mapping 83 distinct cell types across five pig tissues from prenatal to postnatal developmental stages. Our findings highlight the coordinated remodeling of tissue architecture through stem/progenitor cell proliferation, lineage specification, and functional maturation during organogenesis. We identified key transcription factors and regulatory networks that drive lineage-specific and spatiotemporally dynamic transcriptional programs. Developmental trajectory analysis identified a conserved bifurcated transcriptional organization of immune cells, accompanied by dynamic changes in transcription factors associated with immune cell maturation. Integrative analysis utilizing multi-omic, single-cell, and pig population genomics data identified a muscle-specific enhancer of the MYOT gene as a target of artificial selection, underlying meat-quality divergence between Asian and European pig breeds. Moreover, cross-species comparison between pigs and humans revealed conserved cell types, underscoring the evolutionary link. In summary, the comprehensive pig developmental cell atlas serves as a key resource for understanding livestock development, provides insights for precision breeding, and highlights the value of the reference pig cell atlas as a powerful resource for biomedical research.