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. 2025 Oct 9;26(1):899.
doi: 10.1186/s12864-025-12029-3.

The genetic influence of sex on gene expression for blood in pigs

Qing Lin  1 , Junxiong Huang  1 , Tianru Zhou  1 , Teddy Tinashe Chitotombe  1 , Jinyan Teng  1 , Jiaqi Li  2
Affiliations

The genetic influence of sex on gene expression for blood in pigs

Qing Lin et al. BMC Genomics. .

Abstract

Background: Pigs are one of the most important farm animals in the agrifood industry. Many complex traits and patterns of gene expression exhibit sexual dimorphisms in pigs. However, the impact of sex on gene expression remains poorly understood.

Results: In this study, we utilized the gene expression data of blood tissue derived from PigGTEx project to explore the genetic influence of sex on gene expression in pigs. Differential gene expression analysis identified 116 male-biased and 248 female-biased genes. Sex-combined and sex-stratified cis-heritability (cis-h2) were highly positively correlated, while the low correlation were observed between male-stratified and female-stratified cis-h2. Sex-interaction expression quantitative trait locus (eQTL) mapping identified 16 genes with at least one sex-biased eQTL (sb-eGenes) in blood, including 7 female-specific eGenes and 4 male-specific eGenes. Notable examples included the immunology-associated male-specific eGene SLC4A1 and the female-specific eGene PRR14, illustrating sex-specific regulation of gene expression in blood. We further found that sb-eGenes were associated with various complex traits through distinct genetic regulation mechanisms. For example, the male-specific gene SLC4A1 was associated with average daily gain with the identical effect, while the female-specific gene MFGE8 exhibited opposite effect.

Conclusions: This study revealed sex-biased gene expression patterns and sex-dependent regulatory effect of gene expression of blood tissues in pigs. Additionally, this study found the sexually dimorphic regulation of gene expression underlying complex traits. These findings provided a comprehensive insight and resource and advance our understanding of sexual dimorphism in genetic mechanism underlying complex traits in blood.

Keywords: Blood; Expression quantitative trait locus; Gene expression; Pig; Sex-biased gene.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: Not appliable. Consent for publication: Not appliable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The differentially expressed gene analysis and clustering of sex-biased genes. The volcano plot of differentially expressed gene analysis on autosomes (a) and X chromosome (b). The t-SNE of sex-biased genes on autosomes (c) and X chromosome (d)
Fig. 2
Fig. 2
The Manhattan plot of sex-interaction cis-eQTL mapping across all genes in blood. Blue points indicate SNPs surpassing the sb-eQTL significance threshold. Red points mark the top cis-eQTL for each sb-eGene
Fig. 3
Fig. 3
The example of sb-eQTL/eGenes. a The locus zoom of SLC4A1 gene and PRR14 gene (b). The locus zoom indicated sex-combined, sex-interaction, male-stratified and female-specific cis-eQTL mapping from the top to the bottom, respectively. The color of points represents the degree of linkage disequilibrium labeled in the figures
Fig. 4
Fig. 4
The Phenome-wide association studies (PheWAS) between sb-eGenes and GWAS of complex traits in pig. The color of text in y-axis indicated the male-specific (blue), female-specific eGene (red), both (black) and neither (grey). The size of points indicated the -log10(P) of GWAS meta-analysis corresponding the top cis-eQTL of sb-eGenes in sex-interaction cis-eQTL mapping. The direction indicated the direction of effect size between top cis-eQTL and GWAS meta-analysis. The text in x-axis indicated the abbreviation of complex traits. The full name of complex traits could be found in Table S2 and PigBiobank [30]
See this image and copyright information in PMC

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