Comparison of liver transcriptome from high- and low-intramuscular fat Chaohu ducks provided additional candidate genes for lipid selection.

The meat quality of ducks is closely related to the intramuscular fat (IMF) content. This study explored the candidate regulatory genes of IMF formation and lipid deposition in Chaohu ducks. The IMF of breast muscle in 100 ducks was determined and statistically analysed by normal distribution test. Duck liver samples with high IMF (CH, n = 3) and low IMF (CL, n = 3) were selected for transcriptome analysis by RNA sequencing (RNA-Seq). The IMF was in accordance with normal distribution (T = 0.001, P = 0.999). The IMF from two tails of the normal distribution was significantly different with 2.9983% ± 0.3296% in the CH group and 1.1960% ± 0.1481% in the CL group (P < 0.0001). RNA-Seq revealed 147 differentially expressed genes, including 78 up-regulated and 69 down-regulated genes in both groups. Validation by qRT-PCR was in agreement with RNA-Seq (R 2 = 0.838). Gene ontology analysis revealed that organophosphate catabolism, oxidation-reduction process, cellular lipid catabolism, lipid transport, lipid localisation, lipid biosynthesis and cellular lipid catabolism were involved in lipid metabolism. Meanwhile, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that steroid hormone biosynthesis, ovarian steroidogenesis, alpha-linolenic acid metabolism, glycosylphosphatidylinositol anchor biosynthesis and linoleic acid metabolism were involved in lipid deposition, wherein the genes COMT, NT5E, PDE4D, PLA2G4F, A-FABP, ADRA2A, HSD17B2, PPP1R3C, PPP1R3B and NR0B2 were involved in lipid deposition. This study provided insights into the molecular mechanism for regulating lipid metabolism and identified candidate genes for selecting markers to control IMF formation in Chaohu ducks.