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Heritability Patterns of Protein-Coding Genes Expression: Insights From the Pig Genotype-Tissue Expression Project
Chao Su1, Wenjing Zhang1, Wenzhe Ning1
1State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.
Animal Genetics
|June 15, 2026
Summary
Pigs show high global and distal genetic control over protein-coding gene expression, unlike local control. This reveals insights into genetic regulation in pigs, valuable for human biology research.
Area of Science:
- Genomics
- Molecular Biology
- Animal Genetics
Background:
- Gene expression underpins complex traits, with protein-coding genes (PCGs) directly impacting protein function.
- Understanding cis- and trans-regulatory mechanisms is key, but pig PCG expression heritability is understudied.
- Pigs serve as valuable models for human biology research.
Purpose of the Study:
- To comprehensively analyze the heritability patterns of protein-coding gene expression across multiple pig tissues.
- To estimate cis-, trans-, and global-heritability of PCG expression using genomic and transcriptomic data.
- To compare the genetic regulation of housekeeping genes (HKGs) and tissue-specific genes (TSGs).
Main Methods:
- Utilized genomic and transcriptomic data from 4760 pigs (PigGTEx project) across 13 tissues.
- Applied linear mixed models (LMMs) to estimate cis-, trans-, and global-heritability of PCG expression.
- Analyzed the relationship between heritability, expression levels, and cis-expression quantitative trait loci (cis-eQTLs).
Main Results:
- Average cis-heritability was 0.13, significantly lower than trans- (0.64) and global-heritability (0.67).
- Cis-regulatory variants explained minor expression variance; single strong variants were near transcription start sites (TSS).
- Housekeeping genes (HKGs) showed genome-wide genetic influence, while tissue-specific genes (TSGs) were primarily affected by cis-region variants.
Conclusions:
- Gene expression heritability in pigs is predominantly controlled by distal and global genetic factors, not just local cis-elements.
- This study provides a detailed map of genetic regulation for PCG expression in pigs.
- Findings enhance understanding of genetic architecture in pigs, relevant for comparative genomics and human biology.
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