Comparative Single‐Cell Transcriptomic Landscape Reveals the Regulatory Mechanisms of Lactation during Selective Breeding in Asian Water Buffalo

Abstract Characterizing the cell type‐specific transcriptome is crucial for understanding the cellular and molecular regulatory mechanisms underlying adaptive evolution and complex phenotypes. Here, single‐cell/nucleus RNA sequencing (sc/snRNA‐seq) is used to construct a cell transcriptomic atlas of 397,011 cells, representing 57 cell types, from 12 tissues in river and swamp buffalo, which exhibit significant divergence in milk production. Differential expression analyses identify metabolic and secretory tissues (i.e., liver, mammary gland, and pituitary) and cell types (e.g., hepatocytes, luminal cells, somatotropes, and lactotropes) that mediate the divergence of milk production. Lactotrope‐specific downregulation of TRHDE in river buffalo is associated with high milk production. Integrative analyses of sc/snRNA‐seq data with genomic data in buffalo and cattle reveal key cell types (e.g., luminal cells and excitatory neurons) and genes (e.g., RPL13 and LALBA ) associated with milk production. Ultimately, the Buffalo Cell Atlas (http://bovomicshub.com) will serve as a valuable resource for advancing buffalo genetics and genomics research, enabling cross‐species comparative transcriptome studies and providing deeper insights into the regulation of milk synthesis and secretion.