Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle
2025
Siwei Wang | Tingting Liu | Peng Peng | Yurong Fu | Shaoqing Shi | Shuang Liang | Xi Chen | Kun Wang | Rongyan Zhou
Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mechanisms governing IMF regulation in these crossbreeds remain poorly understood. To elucidate the mechanism of IMF deposition in these crossbred cattle, we conducted a comparative transcriptomic analysis of <i>longissimus dorsi</i> muscles and livers from cattle with divergent IMF content. RNA-seq revealed 940 and 429 differentially expressed genes (DEGs) in the liver and muscle, respectively, with 60 genes co-differentially expressed (co-DEGs) in both tissues. Functional enrichment highlighted lipid metabolism pathways including fatty acid β-oxidation, PPAR signaling, and glycerolipid metabolism. A total of eleven genes including <i>ACAA2</i>, <i>ACADL</i>, <i>ACOX2</i>, <i>CPT1B</i>, <i>CPT2</i>, <i>LPL</i>, <i>SLC27A1</i>, <i>ACAT1</i>, <i>GK</i>, <i>ACOX3</i>, and <i>ACSM5</i>, were screened as key candidate genes for IMF deposition. A “liver–muscle” regulatory network of IMF deposition was built to illustrate the tissues’ interaction. The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). Our findings provide novel molecular markers for increasing the IMF content and accelerating the genetic improvement of beef quality traits in crossbred cattle.
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