Abstract
Improvement of feed efficiency (FE) is key for Sustainability and cost reduction in pig production. Our aim was to characterize the muscle transcriptomic profiles in Danbred Duroc (Duroc; n = 13) and Danbred Landrace (Landrace; n = 28), in relation to FE for identifying potential biomarkers. RNA-seq data on the 41 pigs was analyzed employing differential gene expression methods, gene-gene interaction and network analysis, including pathway and functional analysis. We also compared the results with genome regulation in human exercise data, hypothesizing that increased FE mimics processes triggered in exercised muscle. In the differential expression analysis, 13 genes were differentially expressed, including: MRPS11, MTRF1, TRIM63, MGAT4A, KLH30. Based on a novel gene selection method, the divergent count, we performed pathway enrichment analysis. We found five significantly enriched pathways related to feed conversion ratio (FCR). These pathways were mainly related to mitochondria, and summarized in the mitochondrial translation elongation (MTR) pathway. In the gene interaction analysis, the most interesting genes included the mitochondrial genes: PPIF, MRPL35, NDUFS4 and the fat metabolism and obesity genes: AACS, SMPDL3B, CTNNBL1, NDUFS4, and LIMD2. In the network analysis, we identified two modules significantly correlated with FCR. Pathway enrichment of module genes identified MTR, electron transport chain and DNA repair as enriched pathways. The network analysis revealed the mitochondrial gene group NDUF as key network hub genes, showing their potential as biomarkers. Results show that genes related to human exercise were enriched in identified FCR related genes. We conclude that mitochondrial activity is a key driver for FCR in muscle tissue, and mitochondrial genes could be potential biomarkers for FCR in pigs.
Highlights
In commercial pig production, the cost of feed is the highest individual economic factor (Jing et al, 2015; Gilbert et al, 2017)
As lower components will explain less of the overall variation, the majority of the variation cannot be explained by breed alone. This does not mean individual genes do not have different expression due to breed, as we see in the differential expression analysis (DEA)
Using multiple types of transcriptomic analysis based on novel biostatistical/bioinformatics methods, we have reinforced the knowledge that mitochondrial activity is important for feed efficiency (FE)
Summary
The cost of feed is the highest individual economic factor (Jing et al, 2015; Gilbert et al, 2017). Reduction in feed consumption per unit growth is beneficial for the environment, which is a key factor in being able to maintain sustainable and resource efficient production. In this context, there have been continuous efforts to increase feed utilization. For the majority of Danish production pigs, breeding boars are selected at a core central facility where potential breeding boars are tested for FCR through accurate individual measurements of feed intake and growth. The Durocs are well known for being heavily selected for growth and efficiency, while the two other breeds have been heavily selected for litter size and piglet survival related traits
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