Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs

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.

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

“…The efficiency of translation affects protein synthesis rate, which in turn is directly impacted by the number of ribosomes providing a possible mechanism for this effect [70,71]. Furthermore, both in pigs and cattle, The muscle has also been investigated in the context of FE, particularly at the molecular level [16,17,20,[65][66][67]. It is common for beef producers to simultaneously target improved FE, increased muscling and higher marbling in their animals [68].…”

“…The muscle has also been investigated in the context of FE, particularly at the molecular level [ 16 , 17 , 20 , 65 , 66 , 67 ]. It is common for beef producers to simultaneously target improved FE, increased muscling and higher marbling in their animals [ 68 ].…”

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

“…ETV1 is one of the strongest candidate genes for marbling score in Korean cattle ( Ryu and Lee, 2016 ). Likewise, in a previous study analyzing the muscle transcriptome in pigs, ETV1 was found among the top 20 differentially expressed genes between Duroc and Landrace breeds in a feed efficiency context ( Carmelo and Kadarmideen, 2020 ).…”

“…Indeed, meat quality of beef is likely to be impacted by breed differences in postmortem mitochondrial respiratory activity within the muscle tissue ( Ramos et al, 2020 ). Furthermore, previous studies have suggested a link between muscle mitochondrial function and feed efficiency in several species, such as chickens ( Ojano-Dirain et al, 2005 ), beef cattle ( Fernandez et al, 2020 ), and pigs ( Carmelo and Kadarmideen, 2020 ). Overall, several of our candidate genes affect multiple, apparently unrelated, phenotypes (pleiotropic effect), which represents one of the difficulties in identifying phenotypic targets of selection.…”

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

“…Indeed, TCONS_00061987 is the lncRNA with the highest degree of connectivity in the overall liver network and has high similarity with a lncRNA thought to be associated with FE in taurine cattle. The muscle has also been investigated in the context of FE, particularly at the molecular level [16,17,20,[65][66][67]. It is common for beef producers to simultaneously target improved FE, increased muscling and higher marbling in their animals [68].…”