Integrated lncRNA and mRNA Transcriptome Analysis Reveals Candidate Regulatory Networks Associated with Postnatal Longissimus Dorsi Muscle Development in Hanper Sheep

Skeletal muscle development is a key determinant of meat production and meat-quality traits in sheep, but the coordinated long non-coding RNA (lncRNA) and messenger RNA (mRNA) co-expression landscape underlying postnatal muscle development in Hanper sheep remains unclear. In this study, RNA sequencing was performed on Longissimus Dorsi muscle samples from Hanper sheep at 1 month (M1), 7 months (M7), and 13 months (M13) of age to characterize lncRNA and mRNA expression profiles during postnatal growth. A total of 13,940 candidate lncRNAs were identified, and these lncRNAs exhibited typical structural features, including shorter transcript lengths, fewer exons, and shorter open reading frames than mRNAs. Differential expression analysis identified 39, 11, and 174 differentially expressed lncRNAs in M7_vs_M1, M13_vs_M7, and M13_vs_M1, respectively, while 357, 160, and 446 differentially expressed mRNAs were detected in the corresponding comparisons. Functional enrichment analyses showed that differentially expressed mRNAs and co-expressed mRNAs associated with differentially expressed lncRNAs were mainly involved in RNA metabolism, translation, ribosome biogenesis, amino acid biosynthesis, energy and lipid metabolism, extracellular matrix remodeling, and cell adhesion. Several muscle-development-related signaling pathways, including AMPK, insulin, PI3K-Akt, PPAR, mTOR, FoxO, ECM–receptor interaction, and focal adhesion pathways, were also enriched. Integrated lncRNA–mRNA analysis further identified candidate lncRNA-associated differentially expressed genes, including IGF2, FOS, ACTC1, ADIPOQ, SPP1, PECAM1, and SLC16A7. These findings provide a comprehensive lncRNA and mRNA transcriptomic resource and reveal candidate regulatory molecules potentially involved in postnatal Longissimus Dorsi muscle development in Hanper sheep.