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.
Highlights
To date, based on genome-wide association analysis (GWAS) of pigs, some SNPs and candidate genes that might affect Feed efficiency (FE) have been identified
We investigated the liver transcriptome of 6 extremely high feed efficiency pigs (HE- group) and 6 extremely low feed efficiency pigs (LE- group)
gene ontology (GO) and pathway enrichment analyses revealed that the differentially expressed genes (DEGs) were mainly enriched in glycolysis and lipid synthesis
Summary
To date, based on genome-wide association analysis (GWAS) of pigs, some SNPs and candidate genes that might affect FE have been identified. A growing number of transcriptome analysis has focused on the liver tissue of pigs to identify candidate genes and pathways associated with FE14–16. Many transcriptome studies focused on purebred pigs (including Yorkshire and Duroc) and crossbred pigs, such as Large White × (Landrace × Pietrain) and Maxgro × (Landrace × Large White) pigs, have made some progress in identifying candidate genes and pathways linked with FE14,20–22. In this study, we used RNA-seq technology to profile the liver transcriptome of 6 extremely high-FE DLY pigs (HE- group) and 6 extremely low-FE DLY pigs (LE- group) to identify candidate genes and pathways that significantly correlated with the FE of DLY pigs. The identified genes and pathways that affect FE can provide theoretical support for pig selection, to improve the feed efficiency and economic benefits in commercial pig production in the future
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