In current study, crucial pathways closely associated with mitochondrial function and/or immune response were identified to play essential regulatory roles in the development of fatty liver disease in dairy cows (Fig. 8), such as metabolic pathways, cyclochrome P450 related metabolism, amino acid metabolism and/or biosynthesis, retinol metabolism and PPAR signaling pathway (Figs. 2D and E and 4A). This evidence concerns the gene PPARA and fatty liver disease.