Machine Learning-Based Analysis of Differentially Expressed Genes in the Muscle Transcriptome Between Beef Cattle and Dairy Cattle

• Published in: International journal of molecular sciences Vol. 26; no. 11; p. 5046
• Main Authors: Li, Shuai, Guo, Yaqiang, Huo, Chenxi, Zhu, Lin, Shi, Caixia, Gu, Mingjuan, Zhang, Wenguang
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 23.05.2025; MDPI
• Subjects: Accuracy; Adipocytes; Animals; Apolipoproteins; Artificial intelligence; Beef cattle; Biosynthesis; Biotechnology; Cattle - genetics; Dairy cattle; Datasets; Efficiency; Fatty acids; Feeds; Gene Expression Profiling; Gene Expression Regulation; Gene Regulatory Networks; Genes; Genomics; Kinases; Lipid Metabolism - genetics; Lipids; Lipoproteins; Livestock; Machine Learning; Metabolism; Muscle, Skeletal - metabolism; Ontology; Proteins; Red Meat; Support vector machines; Transcriptome - genetics; SHAP; machine learning; transcriptome; muscle
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms26115046

Muscle is a crucial component of cattle, playing a vital role in determining the final quality of beef. This study aimed to identify candidate genes associated with muscle growth and lipid metabolism in beef and dairy cattle by utilizing the public database of the National Center for Biotechnology Information (NCBI) to download bovine muscle transcriptome data. Through differential expression analysis, weighted gene co-expression network analysis (WGCNA), and SHapley Additive exPlanation (SHAP) explains machine learning models, we integrated and screened for relevant genes. The results showed a total of 2588 differentially expressed genes (DEGs), with 933 upregulated and 1655 downregulated in beef cattle compared to dairy cattle. In the WGCNA, the purple, black, green, red, brown, and blue modules were identified as significant modules. Based on the results of five different machine learning models, the Adaptive Boosting (AdaBoost) model demonstrated superior classification performance (accuracy = 0.84) compared to the other four models and was therefore selected as the optimal model. SHAP analysis was then employed to interpret the results, yielding the top 500 SHAP genes. In combination with DEGs and WGCNA, a total of 117 genes were identified. Subsequent functional enrichment analysis of these 117 genes revealed significant enrichment in pathways such as lipoprotein metabolic process, muscle contraction, and cytoskeleton in muscle cells, followed by interaction network analysis of genes and pathways. Ultimately, the APOA1, ACTB, S1PR1, PKLR, and SLC27A6 genes were identified as potential key regulators of lipid metabolism and muscle growth in beef and dairy cattle. In summary, this study provides a feasible method for handling large-scale transcriptome data and lays a foundation for future research on meat quality and improving the economic benefits of Holstein cattle.