What does this research mean for the field?

The full-length transcriptome atlas of porcine skeletal muscle reveals that isoform regulation significantly influences muscle growth and body weight determination in pigs. Novelty: ClaimNovelty.NOVEL_FINDING. Consensus alignment: ConsensusAlignment.ESTABLISHES_NEW_DIRECTION.

What question did this study set out to answer?

To explore the genetic regulatory mechanisms governing skeletal muscle growth at the isoform level in pigs.

March 5, 2026BMC Genomics0 citationsOpen Access

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

JHJianchao HuJiangxi Agricultural University ZDZifeng DingJiangxi Agricultural University TYTianxiong YaoJiangxi Agricultural University

Key Points

To explore the genetic regulatory mechanisms governing skeletal muscle growth at the isoform level in pigs.
Generated high-quality long-read RNA-seq datasets from a chimeric breed and its ancestral breeds.
Annotated over 13,900 genes and 54,000 isoforms, identifying novel isoforms.
Conducted multi-level QTL analyses to identify isoform expression QTLs in a large sample.
Integrated iso-eQTL data with GWAS to associate isoforms with body weight.
Annotated 13,926 genes and identified 54,599 isoforms, with 65% being novel.
Detected 500 unique isoform expression QTLs that were not present in gene-eQTLs or sQTLs.
Found 306 isoforms associated with body weight, including the genes UBXN2B and LYN.
Identified 16 isoforms with specific iso-eQTLs that were undetected at the gene level.

Abstract

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.

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