Background Meat quality characteristics, including juiciness, flavor, and tenderness, can be mostly attributed to the total muscle fat content, intramuscular fat (IMF), and the composition of its fatty acids (FAs), which are regulated by the balance between lipid uptake, transport, synthesis, and subsequent metabolism, involving many genes and pathways. However, the detailed molecular mechanisms remain unclear. Results The present study reports the RNA-sequencing (RNA-seq) analysis of chest

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... le and leg muscle tissue of the Zhuanghe dagu chicken (ZD chicken) and the Arbor Acres Broiler chicken (AA chicken). We identified certain differentially expressed genes that affect IMF deposition , such as EHHADH , TECRL , NDUFAB1 , PCCB , and HIBCH , which were upregulated in ZD chickens, and GCDH , TPI1 , ABHD13 , PSMC1 , MYST2 , and FBXO11 , which were upregulated in AA chickens. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes indicated that the extracellular matrix (ECM)–­receptor interaction pathway is co-enriched in both tissues, and forms a sub-pathway of other enriched pathways. Intriguingly, the ECM–receptor interaction pathway genes are regulated differently in different gene pools. Collagens, which are main ECM constituents, and laminin and integrinβ1 transmembrane receptors were significantly downregulated in both tissues of the AA chicken. Conclusions RNA-seq analysis of two tissues from two breeds of chicken hinted that interactions between transmembrane receptors and ECM components of fat cells affect breed-specific adipogenesis, which would affect quality and flavor of chicken meat. These findings will contribute to improving the quality attributes of chicken meat.