Screening of Differentially Expressed Genes Related to Growth, Development and Meat Quality Traits of Huanghuai Sheep Based on RNA-Seq Technology

Huanghuai sheep, a newly developed meat-specialized breed in China, are valued for their rapid growth and high meat quality, but the optimal slaughter age and the molecular basis of these traits remain poorly understood. Gaining insight into these mechanisms is vital for improving production efficiency and guiding molecular breeding in this economically important breed. Although previous studies have described the phenotypic characteristics of Huanghuai sheep, the genetic regulatory networks controlling muscle growth and meat quality at different developmental stages remain unclear. No thorough analysis of growth traits and transcriptomic variations across key age points has been conducted. Therefore, in this study, we aimed to evaluate how growth stage influences muscle development, carcass characteristics, and meat quality in Huanghuai sheep by integrating phenotypic characterization with transcriptomic profiling to identify key genes and molecular pathways underlying these economically important traits throughout development. Sixty Huanghuai sheep were assigned to three groups (twenty per group) representing key developmental stages (3, 9, and 18 months of age). Carcass traits and meat quality were evaluated. RNA sequencing of the longissimus dorsi muscle was performed to identify differentially expressed genes (DEGs), followed by bioinformatics analysis and experimental validation. The results indicated that the 9-month-old sheep presented a favorable balance of dressing percentage and intramuscular unsaturated fatty acid content, while those aged 18 months old exhibited the highest dressing percentage (61.23%). Transcriptome analysis identified 1395 DEGs (p < 0.05 and |log2FC| > 1) and enrichment analysis revealed key pathways involved in thyroid hormone synthesis, skeletal muscle satellite cell proliferation, and skeletal muscle tissue growth. Several candidate genes for muscle development (e.g., ACTC1, SIX2, HK2) and meat quality (e.g., TLR2, CHI3L1, ACOT7) were identified and validated. Their expression patterns showed significant correlations between critical growth performance and fatty acid composition metrics. These findings provide novel insights into the molecular networks regulating economically important traits in Huanghuai sheep, offering valuable targets for future molecular breeding programs aimed at enhancing productivity and meat quality.