RNA-Seq and WGCNA Identify Key Regulatory Modules and Genes Associated with Water-Holding Capacity and Tenderness in Sheep

Meat quality traits, particularly WHC and tenderness, are pivotal for consumer satisfaction and economic value in the sheep industry. However, their genetic regulatory mechanisms remain unclear. We used RNA-Seq and WGCNA to identify genes regulating WHC and tenderness. Sixty longissimus thoracis samples were classified into high/low WHC (HWHC vs. LWHC) and high/low tenderness (HTN vs. LTN) groups. Comparative transcriptomics identified 270 differentially expressed genes (DEGs) linked to WHC, enriched in pathways like the regulation of the ATP metabolic process and the inhibition of canonical Wnt signaling. Key DEGs (e.g., <i>SORBS1</i>, <i>FOXO1</i>, <i>PDE4B</i>, <i>CDH1</i>) correlated significantly with WHC-associated traits. For tenderness, 165 DEGs were identified, including <i>LEP</i>, <i>FABP4</i>, <i>PLIN1</i>, and <i>GLP1R</i>, enriched in PPAR signaling, fat cell differentiation, and cAMP signaling pathways. WGCNA revealed modules associated with WHC and tenderness, with hub genes (<i>ATP2C1</i>, <i>GSKIP</i>, <i>PATL1</i>, <i>PPARA</i>, <i>CYLD</i>) involved in ATP metabolism, lipid biosynthesis, and myofibril assembly. Tissue-specific gene integration prioritized muscle-enriched candidates (<i>METTL21C</i> and <i>ACTC1</i>) with strong trait correlations. Our findings unveil interconnected gene networks governing WHC and tenderness, highlighting some candidate genes as potential biomarkers for precision breeding. This study provides novel insights into the molecular determinants of meat quality, offering actionable targets to enhance mutton production sustainability and consumer appeal.