Evidence map›Paper›PMID 41952218›Full record

ArticleJournal of animal science and biotechnology2026

Characterizing breed-shared and breed-specific genetic regulatory effects of gene expression across three pig breeds.

Xiaojing Li, Xiaodian Cai, Jiajian Chen, Xiangchun Pan, Wentao Gong, Zhanming Zhong, Jinyan Teng, Zhe Zhang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of animal science and biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Xiaojing LiState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Xiaodian CaiState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Jiajian ChenState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Xiangchun PanState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Wentao GongState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Zhanming ZhongState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Jinyan TengState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
Zhe ZhangState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. zhezhang@scau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundDifferences across breeds in adaptation to various environments and in performance on complex traits such as growth rate are very common in livestock. These differences have been attributed to various factors, including genetic variation, selection, and environmental influences. Gene expression regulation, serving as a critical intermediary mechanism that bridges genotypes and phenotypes, may play a pivotal role in driving these differences across breeds. Hence, we characterized the breed-shared and breed-specific pattern in genetic regulatory effects on gene expression via expression quantitative trait locus (eQTL) mapping in three pig breeds (Duroc, Landrace, and Yorkshire), aiming to gain a deeper understanding of the molecular basis underlying complex trait differences across breeds.

resultsWe observed breed differentiation at both the single-nucleotide polymorphism (SNP) and gene expression levels. By eQTL mapping, within each tissue, an average of 71.1% of the eGenes identified in each breed were breed-shared, while the remaining 28.9% were breed-specific. We found that some regulatory effects are relevant to either the difference in average gene expression or expression variance among populations. Breed-shared eGenes were more abundant, showed larger effect sizes and lower evolutionary conservation, and vice versa. Enrichment analysis showed that the genome-wide association studies (GWAS) loci were significantly enriched in the cis-eQTLs of eGenes for an average of 12 of 19 complex traits per breed. These loci exhibited higher enrichment for breed-specific eGenes than for breed-shared eGenes. Through colocalization analyses with GWAS loci, we observed 220 colocalization events (PP.H4 > 0.8) with breed-specific eGenes and 758 events with breed-shared eGenes.

conclusionsOur study reveals breed-shared and breed-specific effects and characteristics of genetic regulation on gene expression in three pig breeds. Both breed-shared and breed-specific eGenes contribute to the regulatory variation in complex traits, with breed-specific eGenes capturing additional regulatory signals not explained by breed-shared eGenes. Together, these findings demonstrate that both shared and breed-specific regulatory variation play important roles in shaping gene expression and suggest their potential contribution to complex traits.

Indexed as

Breed-stratified analysisCis-eQTL mappingComplex traitsGene expressionRegulatory architecture

Identifiers

PMID41952218
PMCPMC13063976

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.