Integrative transcriptomic and metabolomic analyses identify lipid-related genes and metabolites associated with intramuscular fat deposition between two cattle breeds

Intramuscular fat (IMF) deposition serves as a critical determinant of beef quality, the underlying molecular and metabolic characteristics remain incompletely elucidated. Here, we integrated transcriptomic sequencing with untargeted profiling to investigate molecular features associated with IMF deposition in two cattle breeds. Transcriptomic analysis identified multiple differentially expressed genes (DEGs) involved in lipid metabolism, including SCD, FASN, and ELOVL6. Untargeted metabolomic profiling revealed a series of differentially accumulated metabolites (DEMs) predominantly associated with fatty acid and coenzyme metabolism, such as arachidonyl-CoA, trans-oct-2-enoyl-CoA, oleoylethanolamide. Integrated analysis demonstrated significant correlations between subsets of differentially expressed genes and metabolites within lipid metabolism-related pathways, indicating coordinated molecular and metabolic alterations during IMF deposition. Based on these findings, representative genes exhibiting strong correlations with differential metabolites were further validated at the cellular level, providing experimental support for the integrated multi-omics findings. This study delineates transcriptomic and metabolomic signatures of bovine IMF, providing a valuable data resource for understanding its metabolic basis.