Pig genetics study finds parent-of-origin effects beyond imprinting

Parent-of-origin effects (POEs), in which the effect of an allele depends on whether it was inherited from the mother or father, were found to influence growth traits in an F2 Eurasian pig population. A study combining genome-wide POE mapping with haplotype-resolved transcriptomes and epigenomes from reciprocal crosses found widespread effects, many outside canonical imprinted regions, indicating that imprinting explains only a subset of parent-of-origin-dependent variation in pigs.

The researchers used genome-wide mapping to identify parental-origin effects affecting pig growth traits, then examined molecular variation using haplotype-resolved transcriptomes and epigenomes from reciprocal crosses. This approach distinguished parental alleles and allowed the investigators to compare their expression, epigenetic features and chromatin organization. The analysis also recapitulated established imprinting effects at loci such as IGF2 and KCNQ1, supporting the view that the method captured known genomic imprinting signals.

One group of signals involved rib length. The researchers linked distal POE loci for this trait with IGF2 through long-range chromatin interactions, indicating that physical contacts between distant genomic regions may contribute to the regulation of rib length. This is a genomic and chromatin association, not evidence that changing the interaction would necessarily alter the trait. The study therefore supports chromatin interactions as a possible contributor to parent-of-origin effects without establishing them as a proven causal mechanism.

The results further indicated that some POEs emerged from parent-specific three-dimensional chromatin architecture independently of allele-specific expression or histone marks. In these cases, parental differences appeared in the spatial organization of DNA even though the analyzed gene-expression and histone-based signals did not account for the effect. The authors identified chromatin topology as a plausible candidate mechanism of parental-origin regulation, while cross-species comparisons nominated additional candidate imprinted genes that require further validation. Together, the findings portray POEs as common and mechanistically diverse features of complex-trait inheritance in pigs.

Subject of Research: Genome-wide and haplotype-resolved analysis of parent-of-origin effects on growth traits in pigs

Article Title: Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin effects in pigs

Article References: Tao, L., Wang, L.-G., Li, J.-B., Zhang, S.-R., Zhang, L.-C., Deng, J.-K., Lin, J.-W., Hu, M., Adeola, A. C., Feng, X.-Y., Cen, D.-J., Huang, Z.-Q., Li, Q.-L., Liao, C.-Y., Yan, S.-S., Wang, L.-X., Xie, H.-B., & Zhang, Y.-P. (2026). Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin effects in pigs. BMC Genomics. https://doi.org/10.1186/s12864-026-13396-1

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13396-1

Keywords: parent-of-origin effects, pigs, genomic imprinting, growth traits, epigenomics, chromatin interactions, three-dimensional chromatin, IGF2, KCNQ1, complex trait inheritance, Integrating, genome-wide