Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European–Chinese Hybrid Pigs

Understanding how hybrids integrate lineage-specific regulatory variants at the haplotype level is crucial for elucidating the genetic basis of heterosis in livestock. In this study, we established three crossbred pig families derived from distant genetic lineages and systematically identified variants from different lineages, including single nucleotide polymorphisms (SNPs) and structural variations (SVs). At the phase level, we quantitatively analyzed gene expression, four histone modifications (H3K4me3, H3K27ac, H3K4me1, and H3K27me3), and the binding strength of transcription factor (CTCF) in backfat (BF) and longissimus dorsi (LD) muscle. By colocalization analysis of phased genetic variants with phased gene expression levels and with phased epigenetic modifications, we identified 18,670 expression quantitative trait loci (eQTL) (FDR < 0.05) and 8,652 epigenetic modification quantitative trait loci (epiQTL) (FDR < 0.05). The integration of eQTL and epiQTL allowed us to explore the potential regulatory mechanisms by which lineage-specific genetic variants simultaneously influence gene expression and epigenetic modifications. For example, we identified a Large White lineage-specific duplication (DUP) encompassing the <i>KIT</i> gene that was significantly associated with its promoter activity (FDR = 7.83 × 10⁻⁴) and expression levels (FDR = 9.03 × 10⁻⁴). Additionally, we found that a Duroc lineage-specific SNP located upstream of <i>AMIGO2</i> was significantly associated with a Duroc-specific H3K27ac peak (FDR = 0.035) and also showed a significant association with <i>AMIGO2</i> expression levels (FDR = 5.12 × 10⁻⁴). These findings underscore the importance of phased regulatory variants in shaping lineage-specific transcriptional programs and highlight how the haplotype-resolved integration of eQTL and epigenetic signals can reveal the mechanistic underpinnings of hybrid regulatory architecture. Our results offer insights for molecular marker development in precision pig breeding.