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

Chenyu Li, Mei Ge, Keren Long, Ziyin Han, Jing Li, Mingzhou Li, Zhiyan Zhang

Abstract read

In one paragraph

Article in Animals : an open access journal from MDPI, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

7 authors.

Chenyu LiNational Key Laboratory for Swine Genetic Improvement and Germplasm innovation Technology, Jiangxi Agricultural University, Nanchang 330045, China.

Mei GeNational Key Laboratory for Swine Genetic Improvement and Germplasm innovation Technology, Jiangxi Agricultural University, Nanchang 330045, China.

Keren LongState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.

Ziyin HanState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.

Jing LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.

Mingzhou LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.ORCID 0000-0001-8681-7684

Zhiyan ZhangNational Key Laboratory for Swine Genetic Improvement and Germplasm innovation Technology, Jiangxi Agricultural University, Nanchang 330045, China.

Funding

Major science and technology research and development projects of Jiangxi Provincial Depart-ment of science and technology 20232ACF01002The National Key R & D Program of China 2020YFA0509500

6 · The paper itself

Abstract

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

Indexed as

hybrid pigslineage-specific genetic variantsphased epigenetic regulationphased gene expression

Identifiers

PMID40427370

DOI10.3390/ani15101494

PMCPMC12108307

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.