single-cell RNA-seq of Asian water buffalo

Characterizing the cell type-specific transcriptome is crucial for understanding the cellular and molecular regulatory mechanisms underlying adaptive evolution and complex phenotypes. Here, we used single-cell/nucleus RNA sequencing to construct a cell transcriptomic atlas of 397,011 cells, representing 56 cell types, from 12 tissues in river and swamp buffalo, which exhibit significant divergence in milk production. Differential expression analyses identified metabolic and neuronal tissues (i.e., mammary gland, liver, and pituitary) and cell types (e.g., luminal cells, cholangiocytes, somatotropes, and lactotropes) that mediate the divergence of milk production. Lactotrope-specific downregulation of TRHDE in the thyroid hormone signaling pathway promoted milk production. Enrichment analyses revealed key cell types (e.g., luminal cells and cholangiocytes) and genes (e.g., RPL13 and LALBA) associated with milk production. Ultimately, our buffalo cell atlas (http://bovomicshub.com) will serve as a valuable resource for buffalo genetics and genomics research and provide further insights into the regulation of milk synthesis and secretion.