A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs

Abstract

Feed efficiency (FE) is an important trait in the porcine industry. Therefore, understanding the molecular mechanisms of FE is vital for the improvement of this trait. In this study, 6 extreme high-FE and 6 low-FE pigs were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) in the liver tissues of the 12 individuals, and 507 DEGs were identified between high-FE pigs (HE- group) and low-FE pigs (LE- group). A gene ontology (GO) enrichment and pathway enrichment analysis were performed and revealed that glycolytic metabolism and lipid synthesis-related pathways were significantly enriched within DEGs; all of these DEGs were downregulated in the HE- group. Moreover, Weighted gene co-expression analysis (WGCNA) revealed that oxidative phosphorylation, thermogenesis, and energy metabolism-related pathways were negatively related to HE- group, which might result in lower energy consumption in higher efficiency pigs. These results implied that the higher FE in the HE- group may be attributed to a lower glycolytic, energy consumption and lipid synthesizing potential in the liver. Furthermore, our findings suggested that the inhibition of lipid synthesis and glucose metabolic activity in the liver may be strategies for improving the FE of DLY pigs.

Figure 1

Feed efficiency (FE) phenotypic parameters in Duroc × (Landrace × Yorkshire) (DLY) pigs from high-FE pigs (HE- group) and low-FE pigs (LE- group). (A) Boxplot of the feed conversion ratio (FCR) and residual feed intake (RFI) in the two groups. (B) The correlation coefficient between FCR and RFI in the two groups.

Figure 2

Differentially expressed genes (DEGs) between the HE- and LE- groups. A plot of DEGs with |log₂(Foldchange)| > 1 and q-value < 0.001. Red dots represent significantly upregulated genes, and green dots represent significantly downregulated genes. The genes marked in the figure are the 5 most significantly upregulated and 5 most downregulated named genes. The x-axis and y-axis represent the −log₁₀(qvalue) and log₂(Foldchange), respectively.

Figure 3

The key network of DEGs in the liver from HE- compared with LE- group. The network diagram centers on the ACACB gene, which has the largest degree of change, and the DEGs are directly or indirectly related to ACACB. Node shape represents the change in gene expression. The node fill color represents the functional classification of the gene.

Figure 4

Weighted gene co-expression analysis (WGCNA). (A) Correlations between hepatic genes co-expression modules and feed efficiency traits of DLY pig. Modules represent the network of co-expressed genes and are named by different colors. Correlations are presented in the rectangles and the value in parentheses represent the p-value. (B) The number and percentage of genes in various modules.

Figure 5

Correlation analysis of RNA-seq and quantitative polymerase chain reaction (qPCR) of 6 randomly selected DEGs. Six randomly selected DEGs were analyzed by real-time qPCR. The x-axis represents the fragments per kilobase of transcript per million mapped reads (FPKM) of each gene calculated by RNA-seq analysis, and the y-axis represents the relative expression of each gene calculated by qPCR. The correlation coefficient was calculated between the two measures.