Supplementary material

This study combines transcriptomic and metabolomic analyses of dairy cows across lactation stages to identify key molecular regulators of milk composition. By correlating mammary gene expression with metabolite fluctuations, we identified 21 functional genes (e.g., AOX1, CXCL8, PLA2G1B, FOS, PDE4C, FABP2, CD36, APOA4, and CREB3L3) and 22 metabolic biomarkers (including Oleic acid, Palmitic acid, Stearic acid, Methyl hexadecanoic acid, Heptadecanoic acid, Caprylic acid) associated with milk production. To our knowledge, this is the first study to integrate transcriptomic and metabolomic data across the entire lactation cycle in dairy cattle, providing valuable insights for genomic selection. These findings offer potential targets for genetic selection and nutritional strategies to improve milk quality in dairy herds.