Single-nucleus transcriptomics dissects beef quality variation: coordinated reprogramming of myofiber metabolism, FAPs Fate, and ECM–vascular signaling

Beef quality traits significantly varies among cattle breeds. These differences cannot be fully explained using traditional omics techniques as they lack cell-level detail. To address this gap, we integrated phenotypic data, histological analyses, and single-nucleus RNA sequencing (snRNA-seq) of the longissimus dorsi muscle to uncover the cellular and molecular mechanisms underlying breed-specific variation.

Histology and molecular markers indicated that Wagyu (WY) had the highest intramuscular fat(IMF) and the lowest shear force followed by Angus (AN) with the intermediate while Qinchuan cattle (QC) showed the lowest levels. SnRNA-seq resolved 12 cell types, revealing breed-specific cellular compositions. Pseudotime analysis revealed myoblast differentiation through hybrid states to type IIX (IIX), type IIA (IIA), and type I (I) myofibers, with lineage-specific remodeling of glycolysis, oxidative phosphorylation, and Ca²⁺ handling directing QC toward IIX fibers and WY toward Type I fibers. Reclustering of PDGFRα⁺ fibro-adipogenic progenitors (FAPs) revealed a bifurcation between adipogenic and fibrogenic fates, with WY favoring lipid-metabolism and adipogenesis-enriched FAPs alongside stronger FGF/ANGPTL–integrin signaling, while QC showed extracellular matrix (ECM)–integrin and TGF-β/TNFα–NF-κB pathways. Ligand–receptor analysis indicated that, in contrast to QC’s adhesion-centric ECM axis, WY-specific laminin/collagen–integrin and IGF/ANGPT inputs enhance metabolic–mechanical coupling. These results suggested that breed-dependent phenotypes arise from coordinated shifts in FAP fate, myofiber metabolism, and ECM–vascular signaling.

Beef-quality variation reflects coordinated reprogramming along three axes: myofiber metabolic programs, FAP fate specification, and basement-membrane/integrin–vascular coupling, forming a phenotypic gradient from WY, which is pro-adipogenic and anti-fibrotic, through AN, which is intermediate, to QC, which is pro-fibrotic with high stiffness.