RNA-Seq Reveals Differentially Expressed Genes and Pathways Affecting Intramuscular Fat Metabolism in Huangshan Black Chicken Population

Intramuscular fat (IMF) plays an important role in meat quality due to its positive correlation with juiciness, tenderness, and flavor. However, for chickens, the molecular mechanisms underlying IMF deposition in thigh muscle have not yet been determined. Here, to identify candidate genes and signaling pathways related to IMF deposition, we deeply explored the chicken transcriptome from thigh muscles of Huangshan Black Chickens with extremely high and low phenotypic values for intramuscular fat content. A total of 128 genes differentially expressed genes (DEGs) were detected, of which 94 were up-regulated and 34 were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed these DEGs (including FABP4, G0S2, PLIN1, SCD1, LFABP, SLC1A6, SLC45A3, ACSBG1, LY86, ST8SIA5, SNAI2, HPGD, EDN2, and THRSP) were significantly enriched in lipid biosynthetic process, steroid biosynthetic and metabolic process, fatty acid metabolic process, and regulation of unsaturated fatty acid metabolic pathways. Additionally, we concluded an interaction network related to lipid metabolism, which might be contributed to the IMF deposition in chicken. Overall, we proposed some new candidate genes and interaction networks that can be associated with IMF deposition and used as biomarkers in meat quality improvement.