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

## TL;DR

This study explores how genetic and epigenetic differences from European and Chinese pig lineages influence gene expression in hybrid offspring, offering insights for pig breeding.

## Contribution

The study identifies lineage-specific genetic variants and their regulatory impact on gene expression and epigenetic modifications in hybrid pigs.

## Key findings

- Lineage-specific genetic variants are significantly associated with gene expression and histone modification patterns.
- Integration of eQTL and epiQTL revealed regulatory mechanisms influenced by lineage-specific variants.
- A duplication in the KIT gene and a SNP upstream of AMIGO2 were found to influence gene expression and epigenetic modifications.

## Abstract

Crossbreeding pigs from different breeds can produce offspring with economic traits comparable to or even better than those of their parents. However, the genetic and epigenetic mechanisms underlying these advantages and their impact on gene expression remain to be fully elucidated. Therefore, we selected hybrids pigs born from crosses between European and Chinese lineages and conducted phasing analysis to trace the parental origin of genetic variants—including single nucleotide polymorphisms (SNPs) and structural variations (SVs)—as well as gene expression and epigenetic modifications. Notably, we found that genetic variants inherited from different lineages were significantly associated with phased gene expression and histone modification patterns. By integrating these association results, we inferred potential regulatory mechanisms by the lineage-specific genetic variants and that epigenetic modifications influence lineage-specific gene expression. These findings were also further supported by results from larger population studies. This work elucidated the profound impact of inherited genetic variation on gene regulatory mechanisms in hybrid pigs, offering a theoretical foundation and practical guidance for advancing pig breeding through molecular selection.

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 KIT 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 AMIGO2 was significantly associated with a Duroc-specific H3K27ac peak (FDR = 0.035) and also showed a significant association with AMIGO2 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.