Genome-wide identification of long non-coding RNAs in pigs and their roles in muscle development

Objective: Long non-coding RNAs (lncRNAs) are important regulators of complex traits in pigs and the systematic annotation and functional roles of these genes remain poorly understood.This study aimed to construct a comprehensive porcine lncRNA atlas and explore the regulatory role of lncRNAs in muscle development. Methods:We integrated 8,871 strand-specific RNA-seq datasets to identify porcine lncRNAs.Their transcriptional features, tissue specificity, evolutionary conservation, and eQTLsupported regulatory relationships were characterized.Single-cell RNA-seq, Hi-C, H3K27acChIP-seq, and population differentiation analyses were further incorporated to investigate candidate lncRNAs involved in muscle development. Results:We identified 50,203 porcine lncRNA genes with stronger tissue specificity and lower expression abundance than protein-coding genes.A subset of lncRNAs showed sequence conservation across mammals.Integration with pigGTEx data identified extensive eQTLsupported lncRNA-mRNA candidate regulatory pairs enriched in active promoter and enhancer chromatin states.Single-cell and multi-omics analyses highlighted PRANCR as a candidate regulator of postnatal muscle growth in Laiwu pigs.A highly differentiated enhancer variant (chr5:g.34155013T>C;Sscrofa11.1)may alter SOX8 binding and regulate PRANCR expression in satellite stem cells. Conclusion:This study provides the most comprehensive porcine lncRNA resource currently available and proposes a potential enhancer-lncRNA regulatory mechanism that contributes to muscle development in pigs.