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Background  Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been clear. In this study, a systematic identification of differentially expressed genes (DEGs) and molecular regulatory mechanism related to IMF metabolism between Beijing-you chicken breast and thigh at 42 and 90 days of age was performed.    Results  IMF contents, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, The results showed that both IMF contents in breast at 42 and 90 d were significantly lower ( P  < 0.05 or  P  < 0.01) than those in thigh. By microarray, 515 common known DEGs and 36 DEGs related to IMF metabolism were identified between the breast and thigh at 42 and 90 d. Compared to thigh, the expression levels of  PPARG  had significantly down-regulated ( P  < 0.01) in breast, but the expression levels of  RXRA  and  CEBPB  had significantly up-regulated ( P  < 0.01). However, the expression levels of  LPL ,  FABP4 ,  THRSP ,  RBP7 ,  LDLR ,  FABP3 ,  CPT2  and  PPARGC1A  had significantly down-regulated in breast ( P  < 0.01), supporting that  PPARG  and its down-stream genes had the important regulatory function to IMF deposition. In addition, based on of DEGs, KEGG analysis revealed that PPAR signaling pathway and cell junction-related pathways (focal adhesion and ECM-receptor interaction, which play a prominent role in maintaining the integrity of tissues), might contribute to the IMF metabolism in chicken.    Conclusions  Our data had screened the potential candidate genes associated with chicken IMF metabolism, and imply that IMF metabolism in chicken is regulated and mediated not only by related functional genes and PPAR pathway, but also by others involved in cell junctions. These findings establish the groundwork and provide new clues for deciphering the molecular mechanisms underlying IMF deposition in poultry. Further studies at the translational and posttranslational level are now required to validate the genes and pathways identified here.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4292-3) contains supplementary material, which is available to authorized users.

Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens