Paternal genetic background orchestrates fetal development through tissue-specific cis-regulatory divergence

Paternal influences on offspring development extend beyond Mendelian inheritance, but how sire genetics shape fetal transcription and cis-regulatory landscapes across tissues is unclear. Using a reciprocal backcross in pigs (F₁×German Landrace vs. F₁×Piétrain) and a haplotype-agnostic RNA-seq pipeline, we profiled six fetal tissues to test sire-breed effects. We identified paternal breed-driven transcriptional divergence, with 1,176 genes differentially expressed. Transcriptional divergence was most pronounced in metabolic tissues, revealing a tissue-specific trade-off: F₁ × GL conceptuses prioritized metabolic and energy pathways, whereas F₁ × Pi conceptuses upregulated developmental and cell cycle processes. Allele-specific expression analysis revealed extensive, tissue-dependent cis-regulatory divergence, and differential ASE highlighted candidate mediators, including SLC5A12 and IVD (kidney), BRD3 (brain), and CES1 (liver). These results indicate that paternal genetics programs fetal tissues via cis-regulatory variation, informing strategies to improve livestock traits. Notably, many loci overlapped known QTLs, suggesting that regulatory variants connect sire background to performance-related phenotypes and fetal programming.