Integrated targeted metabolomics and transcriptomics analysis reveals heterogeneity of subcutaneous and pericardial adipose tissues in Yili horses

Fat deposition is a key economic trait in livestock, yet distinct adipose depots often display marked functional heterogeneity. The molecular basis underlying this divergence in Yili horses, however, remains poorly understood. Therefore, we hypothesized that the heterogeneity in fatty acid composition between subcutaneous (SAT) and pericardial adipose tissues (PCAT) in Yili horses is associated with distinct transcriptional programs, which can be explored using an integrated multi-omics approach. Using targeted metabolomics, we found that PCAT contained significantly higher levels of total, saturated, and polyunsaturated fatty acids, but lower monounsaturated fatty acids (MUFAs) compared with SAT. Transcriptomic profiling identified 1513 differentially expressed genes (DEGs), which were primarily enriched in metabolic, endocrine, and signal transduction pathways. Integrative analysis further highlighted <i>IGF1</i>, <i>LEP</i>, <i>BMP2</i>, <i>SOX9</i>, <i>COL1A2</i>, and <i>FGF9</i> as key regulators associated with depot-specific fatty acid differences. Collectively, these findings demonstrate the molecular heterogeneity between SAT and PCAT in Yili horses, support our original hypothesis, and provide a molecular basis for understanding adipose depot-specific lipid metabolism, with potential implications for improving fat deposition traits in Yili horses.