Expression quantitative trait loci associated with performance traits, blood biochemical parameters, and cytokine profile in pigs

Abstract

Identifying expression Quantitative Trait Loci (eQTL) and functional candidate variants associated with blood biochemical parameters can contribute to the understanding of genetic mechanisms underlying phenotypic variation in complex traits in pigs. We identified eQTLs through gene expression levels in muscle and liver tissues of Large White pigs. The identified eQTL were then tested for association with biochemical parameters, cytokine profiles, and performance traits of pigs. A total of 41,759 SNPs and 15,093 and 15,516 expression gene levels from muscle and liver tissues, respectively, enabled the identification of 1,199 eQTL. The eQTL identified related the SNP rs345667860 as significantly associated with interleukin-6 and interleukin-18 in liver tissue, while the rs695637860 SNP was associated with aspartate aminotransferase and interleukin-6, and rs337362164 was associated with high-density lipoprotein of the blood serum. In conclusion, the identification of three eQTL significantly associated with aspartate aminotransferase and cytokine levels in both serum and liver tissues suggests a potential role for these variants in modulating immune function and overall health in production pigs. Further research is needed to validate these findings and explore their potential for improving pig health and productivity.

Keywords: GWAS; blood serum indicators; cytokine profile; eQTL; gene expression; inflammatory process; pig; swine.

FIGURE 1

Number of cis- and trans-eQTL and the regulated genes for each tissue evaluated (muscle and liver). The SNP dataset includes genotypes from the GGP-50K plus the RNA-Seq SNP calling of the skeletal muscle and liver tissues after linkage disequilibrium pruning.

FIGURE 2

Number of eQTL within 1 Mb window size along the chromosomes, used to test associations with the traits. Each vertical bar represents a genomic window, and the density of eQTLs is indicated by the color scale, ranging from green to red as the eQTL density increases.

FIGURE 3

Expected distribution of -log10(p) values versus the observed distribution for the phenotypes (A) Interleukin-6 (IL6_l, liver tissue, λ = 1.048), and Interleukin-18 (IL18_l, liver tissue, λ = 1.016) (B) Aspartate Aminotransferase (AST_s, blood serum, λ = 0.876), High-Density Lipoprotein (HDL_s, blood serum, λ = 1.252), Interleukin-6 (IL6_s, blood serum, λ = 0.878).

FIGURE 4

Manhattan plot for the (A) Interleukin-6 and (B) Interleukin-18 from pigs. The Manhattan plot displays the genomic positions of eQTLs on the x-axis and the -log10(p) values on the y-axis for the phenotypes IL-6 and IL-18 in pig liver tissue. The highlighted points represent eQTLs with significant associations based on the FDR <0.05. The variant rs345667860 (3′UTR) is indicated with respective effect predicted using the Variant Effect Predictor (VEP) from Ensembl. IL-6 = Interleukin-6 (MFI), IL-18 = Interleukin-18 (MFI).

FIGURE 5

Manhattan plots for the (A) aspartate aminotransferase (B) High-Density Lipoprotein, and (C) Interleukin-6 from pigs. Manhattan shows the distribution of p-values by genomic positions of eQTLs on the x-axis and the -log10(p) values on the y-axis for the phenotype’s aspartate aminotransferase (AST; U/L), high-density lipoprotein (HDL; mg/dL) and interleukin-6 (IL-6; MFI) in pig serum. The highlighted points represent eQTLs with significant associations based on the FDR <0.05 threshold. The variants rs695637860 (Downstream) and rs337362164 (Missense) are indicated with respective effects predicted using the Variant Effect Predictor (VEP) from Ensembl.

FIGURE 6

Top significant traits in Production, Health, Meat, and Carcass enrichment analyses around eQTL associated with AST, HDL, IL-6 in pig serum, and IL-18 and IL-6 in pig liver tissue. The area of the bubbles represents the number of observed QTL for that class, while the color represents the p-value scale (the darker the color, the more significant the p-values). Additionally, the X-axis shows the richness factor for each QTL, representing the ratio of the number of QTL and the expected number of that QTL. AST = Aspartate aminotransferase (U/L), HDL = high-density lipoprotein (mg/dL) and IL-6 = interleukin-6 (MFI) in pig serum, IL-6 = Interleukin-6 (MFI), IL-18 = Interleukin-18 (MFI) in pig liver tissue.

FIGURE 7

Distribution of Gene Ontology (GO) categories identified in enrichment analysis annotated around eQTLs associated with biochemical parameters and cytokine profiles from pig blood serum and liver tissue. The left chart (red) shows the Biological Process (BP) categories. The middle chart (blue) presents Cellular Component (CC) categories. The right chart (green) illustrates the Molecular Function (MF) category.

FIGURE 8

Distribution of Gene Ontology (GO) terms and metabolic pathways terms (MP) based on gene enrichment analysis annotated around eQTLs associated with biochemical parameters from pig blood serum and liver tissue. The x-axis displays the log₂ of the enrichment ratio, indicating the magnitude of enrichment, while the y-axis shows the -log₁₀ of the FDR, representing the statistical significance. Each point on the plot corresponds to a specific GO term or pathway, with points further to the right and higher on the plot indicating terms with both high enrichment and strong significance. The color gradient represents varying levels of enrichment, with darker colors indicating higher enrichment scores.

FIGURE 9

The hierarchical structure of biological processes identified through enrichment analysis for biological processes ontology terms. Highlighted nodes correspond to processes related to “Response to cytokine–GO:0034097”, and the complete directed acyclic graph (DAG) with all GO terms and metabolic pathways is available in Supplementary Figure S1.

FIGURE 10

A network of genes annotated around eQTLs associated with blood biochemical parameters and cytokines from pig blood serum and liver tissue. The line thickness indicates the strength of data support, and the clusters are represented by letters (and colors). The clusters are (A) SYNRG, DDX52, and HNF1B (B) AP2B1, and PEX12 (C) HEATR9, RASL10B, GAS2L2, MMP28, and SLFN11 (D) CCL14, CCL5, CCL4, CCL16, and LOC100516039 (E) CCL3L1, and LOC100515857 (F) CWH43, SPATA18, DCUN1D4, and FRYL (G) LRRC66, and USP46. These results can also be accessed at https://version-12-0.string-db.org/cgi/network?networkId=bE85LK5REtmx.