Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle

The dynamics of chromatin patterns underlie the developmental programmes of body tissues. Deciphering how these dynamics modulate the effect of regulatory variants on agronomically important traits across developmental stages remains largely unexplored in farmed animals.

In this work, we focused on the skeletal muscle. We integrated chromatin accessibility, molecular QTL and GWAS data to identify developmental stage–specific regulatory elements and to highlight putative causal regulatory variants underlying complex traits.

To define stage-differential open chromatin regions in the skeletal muscle, we aggregated 202 publicly available ATAC-seq libraries, from four different studies, spanning fetal and postnatal (piglet) stages, processed them through the nf-core ATAC-seq pipeline, obtained the consensus peaks, and performed differential accessibility analysis. We aggregated 202 publicly available ATAC-seq libraries, from four different studies, spanning fetal and postnatal (piglet) stages, processed them through the nf-core ATAC-seq pipeline, obtained the consensus peaks, and performed differential accessibility analysis. These peaks were systematically intersected with five classes of cis-acting molecular QTLs (molQTLs) from the PigGTEx resource, followed by functional enrichment analysis, promoter-focused functional annotation, and integration with gene–trait pairs. Finally, we intersected the eGenes (i.e., genes whose expression is regulated by at least one cis-eQTL) to link variants previously associated with QTLs for production traits.

We identified 132,275 differentially accessible peaks (DAPs) separating fetal from piglet muscle. Fetal DAPs were enriched in promoter and intergenic regions, whereas piglet DAPs were enriched in intronic regions, plausibly reflecting a shift from transcriptional priming to postnatal regulatory refinement. Across all molQTL classes, overlaps with accessible regions were highly significant (p < 0.001). The top 25% strongest effect variants were enriched within DAPs, exhibiting promoter–TSS enrichment in fetuses and intronic enrichment in piglets, with the top 1% of eQTLs predominating in the fetal stage (14 fetal vs. 4 piglet). Gene Ontology analysis of promoter-accessible eGenes revealed prenatal enrichment for RNA metabolism and chromatin organization, contrasting with the postnatal enrichment for muscle contraction and lipid metabolism. Finally, the intersection of promoter eGenes with previously colocalized growth, muscle, and reproductive traits identified 107 fetal-stage and 30 piglet-stage associated regulatory elements, with only three eGenes shared between stages.

Together, these findings demonstrate that combining stage-differential chromatin accessibility and regulatory variants provides pertinent information for prioritizing putative causal variants to refine precision breeding strategies for complex traits in pigs.