To investigate molecular regulation involved in lactation during pregnancy, this study focused on the transcriptomic profiles of mammary tissue from lactating and non-lactating Mongolian mares at the second month of gestation. A total of 4197 differentially expressed genes were identified by comparing mammary tissues from pregnant mares at two different states, including 1974 differentially expressed genes such as the milk protein-related genes a-s1-casein (CSN1S1), k-casein (CSN3), lactalbumin (LALBA), and lactoferrin (LTF), which were highly expressed in the lactating mares group, and overall, these differentially expressed genes were mainly associated with biological processes such as endoplasmic reticulum protein processing, the Toll-like receptor signaling pathway, steroid biosynthesis, cytokine–cytokine receptor interactions, and amino sugar and nucleotide glycolysis. These findings serve as a foundation for investigating the molecular underpinnings of lactation in pregnant equids.
