Fig. 2: Heterogeneity of mammary epithelial cells and the relationship with lactation in dairy cows.

a, UMAP plot displaying the subtypes of mammary epithelial cells. b, Expression heatmap for the top 120 DEGs in eight mammary epithelial subtypes, with cell count (top), selected marker genes (left) and significantly enriched Gene Ontology (GO) terms for the clustered module (right). c, Heatmap showing the odds ratios (ORs) of mammary epithelial cell subtypes in each anatomical structure of the mammary gland. d, Box plot showing the lactation gene signature scores for the epithelial cell subtypes in the mammary gland (n = 4). The y axis represents the module score derived from genes associated with lactation-related processes; the x axis represents cell subtypes. The central band in the box plot represents the median, the box boundaries represent the 25% to 75% percentiles, and the whiskers extend 1.5 times the interquartile range (IQR). The red dashed line indicates the baseline lactation score (0). e, Expression levels of immune genes in different mammary epithelial cell subtypes. Dot size represents the expressed percentage; the color represents the average expression of genes in each subtype. f, Heatmap showing the mammary epithelial cell subtypes significantly associated with MY, FY and PY. *FDR < 0.05, **FDR < 0.01. g, Outgoing signaling pathways in mammary epithelial cell subtypes. Dot size represents the percentage contribution. h, Specific outgoing communication signaling patterns in ME6. Dot size represents the percentage contribution. i, Specific ligand–receptor pairs in ME6-specific outgoing communication pathways. Dot size represents the P significance level; dot color represents the maximum communication probability. j, Expression levels of genes in the oxytocin signaling pathway in different mammary epithelial cell subtypes. Dot size represents the expressed percentage; dot color represents the average expression of genes in each subtype.