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To provide new ideas for improving meat quality and generating new breeds of cattle, the important candidate genes affecting fat deposition in two kinds of cattle were identified. Eighteen months Shandong black cattle (n = 3) and Luxi cattle (n = 3) were randomly assigned into two environmental. The longissimus dorsi muscles of Shandong Black Cattle and Luxi Cattle were collected and analyzed by fatty acid determination, high-throughput sequencing transcriptomics, qRT-PCR expression profile and western blot. The ratio of unsaturated fatty acids to saturated fatty acids was 1.37:1 and 1.24:1 in the muscle tissues of Shandong black cattle and Luxi cattle, respectively. The results of RNA-Seq analysis revealed 1320 DEGs between the longissimus dorsi of Shandong black cattle and Luxi cattle. A total of 867 genes were upregulated, and the other 453 genes were downregulated. With GO enrichment analysis, it was found that the identified DEGs were significantly enriched in regulation of the Wnt signaling pathway, negative regulation of the Wnt signaling pathway, cAMP metabolic process, fat cell differentiation and among other functions. We found that regulation of lipolysis in adipocytes was the significant enrichment pathway of upregulated genes and downregulated genes, PPAR signaling pathway and AMPK signaling pathway are highly representative pathways of lipid metabolism in Shandong black cattle. Network analysis showed that  PPARGC1A ,  ADCY4 ,  ANKRD6 ,  COL1A1 ,  FABP4 ,  ADIPOQ ,  PLIN1 ,  PLIN2 , and  LIPE  genes were correlated with key loci genes in multiple metabolic pathways. Meanwhile we found that  FABP4  and  ADIPOQ  had 7 common regulatory factors in different genes, which were  PLIN1 ,  PLIN2 ,  PPARGC1A ,  RXRA ,  PCK1 ,  LEPR ,  LEP . These genes were involved in regulation of lipolysis in adipocytes, adipocytokine signaling pathway, PPAR signaling pathway.  FABP4  and  ADIPOQ  were selected as important candidate marker genes for fat deposition based on the results.

Different expression of lipid metabolism-related genes in Shandong black cattle and Luxi cattle based on transcriptome analysis