Identification of Candidate Genes and eQTLs Related to Porcine Reproductive Function

Abstract

Expression quantitative trait locus (eQTL) mapping is an effective tool for identifying genetic variations that regulate gene expression. An increasing number of studies suggested that SNPs associated with complex traits in farm animals are considered as expression quantitative trait loci. Identifying eQTLs associated with gene expression levels in the endometrium helps to unravel the regulatory mechanisms of genes related to reproductive functions in this tissue and provides molecular markers for the genetic improvement of high-fertility sow breeding. In this study, 218 RNA-seq data from pig endometrial tissue were used for eQTL analysis to identify genetic variants regulating gene expression. Additionally, weighted gene co-expression network analysis (WGCNA) was performed to identify hub genes involved in reproductive functions. The eQTL analysis identified 34,876 significant cis-eQTLs regulating the expression of 5632 genes (FDR ≤ 0.05), and 90 hub genes were identified by WGCNA analysis. By integrating eQTL and WGCNA results, 14 candidate genes and 16 fine-mapped cis-eQTLs were identified, including FRK, ARMC3, SLC35F3, TMEM72, FFAR4, SOWAHA, PSPH, FMO5, HPN, FUT2, RAP1GAP, C6orf52, SEL1L3, and CLGN, which were involved in the physiological processes of reproduction in sows through hormone regulation, cell adhesion, and amino acid and lipid metabolism. These eQTLs regulate the high expression of candidate genes in the endometrium, thereby affecting reproductive-related physiological functions. These findings enhance our understanding of the genetic basis of reproductive traits and provide valuable genetic markers for marker-assisted selection (MAS), which can be applied to improve sow fecundity and optimize breeding strategies for high reproductive performance.

Keywords: WGCNA; eQTL; endometrium; pigs; reproductive function.

Figure 1

The distribution of significant cis-eQTLs. (A) The CMplot of significant cis-eQTLs; chromosomes are shown in different colors; (B) number of significant cis-eQTLs on each autosomal chromosome.

Figure 2

Effect sizes of significant cis-eQTLs and functions of eGenes. (A) Percentage of significant cis-eQTLs with different aFC sizes; (B) the KEGG pathways of significant eGenes.

Figure 3

WGCNA in 341 samples. (A) Sample clustering by hierarchical clustering: red represents endometrium, green represents ovaries, and blue represents placenta. (B) Sample clustering by principal component analysis. (C) Gene dendrogram and modules; branches of the same color were divided into the same gene modules. (D) Pearson correlation analysis of gene modules and three tissues.

Figure 4

(A) GO enrichment analysis for genes in the green and blue modules. (B) KEGG enrichment analysis for genes in the green and blue modules. (C) Scatterplot of gene significance (GS) for endometrium and module membership (MM) in the green module. (D) Scatterplot of GS for endometrium and MM in the blue module.

Figure 5

Integration of data from eQTL analysis and WGCNA results. (A) Venn map of eGenes associated with fine-mapped eQTLs and hub genes in WGCNA results. (B) Heatmap of expression of 14 candidate genes in 341 samples.