Full-length transcriptome atlas of porcine skeletal muscle reveals isoform-resolved genetic regulatory mechanisms for muscle growth

Skeletal muscle plays a crucial role in maintaining normal physiological function and body weight in pigs. However, the complexity of the skeletal muscle transcriptome at the isoform level and its underlying genetic regulatory mechanisms remains largely unexplored. We generated eight high-quality long-read RNA-seq datasets from a chimeric breed and its ancestral breeds. By integrating these data with publicly available samples, we constructing a comprehensive full-length transcriptome atlas of porcine skeletal muscle. We annotated 13,926 genes and 54,599 isoforms, of which 65% as novel, and characterized alternative splicing and alternative polyadenylation patterns. We further incorporated short-read RNA-seq and whole-genome sequencing data from 579 individuals from the chimeric breed to investigate the genetic regulation of isoform diversity. Notably, multi-level quantitative trait locus analyses identified 500 unique isoform expression QTLs (iso-eQTLs) that were not detected in gene expression QTLs (gene-eQTLs) or splicing QTLs (sQTLs). Integrating iso-eQTL and GWAS data uncovered 306 isoforms associated with body weight, including isoforms of UBXN2B, LYN, and RPS20. Among these, 16 isoforms have specific iso-eQTLs that were not detected at the gene level, including isoforms of transcription factor CEBPD and the mitochondrial function-related genes MRPL15 and MPC2. Overall, this study presents a comprehensive full-length transcriptome of porcine skeletal muscle, highlighting the role of isoform regulation in skeletal muscle development and body weight determination, and providing a valuable resource for future research.