Comprehensive SHAP Values and Single-Cell Sequencing Technology Reveal Key Cell Clusters in Bovine Skeletal Muscle.

Area of Science:

• Animal Science
• Genomics
• Cell Biology

Background:

• Bovine skeletal muscle is vital for cattle, yet its cellular composition and functional hierarchy remain incompletely understood.
• Identifying the most important cell populations and their regulatory genes is crucial for advancing muscle biology and livestock productivity.

Purpose of the Study:

• To construct a high-resolution single-cell atlas of bovine skeletal muscle.
• To identify and rank the importance of different cell types within bovine skeletal muscle.
• To elucidate the key genes and regulatory mechanisms governing muscle development and function across species.

Main Methods:

• Trained and selected optimal machine learning models for bovine skeletal muscle analysis.
• Utilized SHAP (Shapley Additive exPlanations) analysis to identify and quantify gene importance.
• Reconstructed a 476-gene SHAP value matrix to map the single-cell atlas.
• Employed protein language models for cross-species comparisons between cattle and pigs.

Main Results:

• Successfully mapped the single-cell atlas of bovine skeletal muscle based on gene interactions.
• Identified myofiber cells as the most representative cell type, followed by neutrophils.
• Determined key genes for myofiber cells, revealing their critical roles in muscle growth and development.
• Established cross-species conservation of Myofiber cell functions and regulatory mechanisms between cattle and pigs.

Conclusions:

• Myofiber cells are the predominant and functionally critical cell type in bovine skeletal muscle.
• SHAP analysis effectively identifies key genes and cell types, enabling single-cell atlas construction.
• Understanding cross-species muscle development mechanisms offers insights into evolutionary biology and potential agricultural applications.