| Summary: | There are differences in lipid deposition in fatty-type (FT) and lean-type (LT) ducks. Fatty ducks have a higher rate of sebum and abdominal fat, lower meat yield and hepatic lipid contents than LT ducks. However, the underlying changes in gene expression profiles regarding the lipid deposition between FT and LT ducks have not yet been clarified. To identify the differentially expressed genes in the liver, sebum, and abdominal fat between both ducks, we identified the gene expression profiles in the liver, sebum, and abdominal fat derived from FT and LT ducks by comparing the multistage transcriptomes. Our results showed that there were 622, 1536, and 224 differentially expressed genes (DEGs) in the liver, sebum, and abdominal fat between the FT and LT ducks, respectively. KEGG enrichment showed that the DEGs related to lipid metabolism were enriched in the biosynthesis of unsaturated fatty acid, glycerolipid and fatty acid metabolism in the liver; and were enriched in the fatty acid metabolism, fatty acid biosynthesis, glycerolipid metabolism, linoleic acid metabolism, and the PPAR signaling pathway in the sebum. There was no pathway related to a lipid metabolism enriched in abdominal fat. A gene functional analysis showed that the DEGs involved in adipogenesis were found to be upregulated. In contrast, those involved in lipolysis were downregulated in the liver and serum of FT ducks. The DEGs showed that ATP-binding cassette sub-family G member 8 (<i>ABCG8</i>), fatty acid synthase (<i>FASN</i>), and phospholipid transfer protein (<i>PLTP</i>) were highly expressed in the liver of FT ducks, and acyl-CoA synthetase long-chain family member3 (<i>ACSL3</i>), <i>ACSL5</i>, <i>ACSL6</i>, 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (<i>AGPAT1</i>), <i>AGPAT9</i>, ELOVL fatty acid elongase 6 (<i>ELVOL6</i>), fatty acid desaturase 1 (<i>FADS1</i>), FADS2, monoacylglycerol O-acyltransferase 1 (<i>MOGAT1</i>), serine/threonine kinase 17a (<i>STK17A</i>), and serine/threonine kinase 39 (STK39) were highly expressed in the sebum of FT ducks. A weighted correlation network analysis (WGCNA) of the DEGs showed <i>ABCG8</i>, <i>FADS2</i>, <i>ACSL5</i>, and <i>ELOVL6</i> positively correlated with hepatic fatty acid synthesis, and <i>AGPAT1</i>, <i>STK17A</i>, <i>STK32A</i>, <i>FADS1</i>, and <i>ACSL3</i> positively correlated with lipid deposition in the sebum. In summary, <i>ABCG8</i> might be the key gene for the reduced hepatic lipid deposition in FT Pekin ducks, and <i>FADS2</i>, <i>ACSL5</i>, <i>ELOVL6</i>, <i>AGPAT1</i>, <i>STK17A</i>, <i>STK32A</i>, <i>FADS1</i>, and <i>ACSL3</i> were the key genes for lipid deposition in the sebum of FT Pekin ducks. Our results provide new insights into the transcriptome regulation in lipid deposition of Pekin ducks and will be helpful for duck breeding.
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