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

Abstract

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.

Keywords: Breast and thigh; Chicken; Differentially expressed gene; Intramuscular fat; Microarray; Regulatory mechanism.

Fig. 1

IMF contents in breast and thigh tissues at 42 and 90 d. The IMF contents in thigh were significantly higher (P < 0.05, P < 0.01, respectively) compared with those in breast at 42 and 90 d. Data are the means ± SD, n = 12

Fig. 2

Detection of RNA quality. The total RNAs were separate, their qualities were identified. The results of gel electrophoresis, the ratios of A260/A280 and 2100 RIN showed that the obtained total RNA had the higher acceptance for microarray

Fig. 3

Validation of data in the microarray. a the normal distribution test. In each microarray, data was in accordance with normal distribution; b cluster analysis of all microarrays. The results showed that the data in the microarrays of chickens at 42 d and 90 d within the same tissue were closely related

Fig. 4

The expression levels of DEGs related to IMF metabolism by q-PCR between breast and thigh tissues at 42d and 90 d. a and c. Some representative genes involved in accelerating lipid deposition (PPARG, PPARGC1A, LPL, FABP4, THRSP, RBP7 and LDLR) were significantly (P <0.01) down-regulated in breast compared with that in thigh at 42 d and 90 d; b Other representative genes involved in regulating PPARG (RXRA and CEBPB) were significantly (P < 0.01) up-regulated, and fatty acid metabolism (CPT2, FABP3 and KLF2) were significantly (P < 0.01) down-regulated in breast compared with that in thigh at 42 d and 90 d. Data are the means ± SD, n = 6

Fig. 5

Technical validation of microarray results using q-PCR correlation. a and b. The r = 0.9861 (42 d, P < 0.01) (a) and r = 0.9534 (90 d, P < 0.01) (b) indicate that the Spearman Rank Correlation between breast and thigh were positive. This indicated that the q-PCR fold changes were in complete correspondence with the microarray data in two days of age. Data are the means ± SD, n = 12

Fig. 6

The potentially regulatory network of IMF metabolism according to DEGs the enriched KEGG pathways. This network is involved in IMF metabolism including PPAR signaling pathway and cell junction (focal adhesion, ECM-receptor interaction)