Integrated analysis of phenotypes and whole-transcriptome data for the preliminary exploration of molecular...

Guyuan cattle are a unique indigenous genetic resource in Northwest China, characterized by favorable roughage utilization efficiency and meat production potential. However, the molecular mechanisms governing their meat quality traits remain poorly elucidated. In this exploratory study, we characterized meat quality phenotypes and transcriptomic profiles in Guyuan cattle and Wagyu cattle, which differ significantly in intramuscular fat (IMF) content. Phenotypic comparisons (n = 6) revealed significant interbreed divergences in slaughter performance, IMF content, drip loss, moisture content, shear force, fatty acid composition, amino acid profile, and muscle fiber type. Through integrated whole-transcriptome sequencing (n = 3) and phenotypic analysis, and based on differential expression analysis coupled with phenotype correlation screening, we preliminarily identified 37 differentially genes associated with fat deposition (16), shear force (11), and muscle development (10). Based on seed region complementarity, phenotypic correlation, and signaling pathway enrichment analysis, we predicted potential target genes and constructed 16 co-expression networks. It should be noted that this study is limited by a small sample size, and the multi-omics data are associative in nature, which does not allow for causal inference. Therefore, the above genes and networks are predictive and have not undergone independent functional validation. These findings offer preliminary, exploratory insights into the potential molecular mechanisms associated with key meat quality traits in Guyuan cattle, and serve as a reference for future functional gene validation, genetic improvement of indigenous yellow cattle, and related industrial applications.