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Comparative Study
. 2017 Dec 22;19(1):21.
doi: 10.3390/ijms19010021.

Transcriptomics Analysis on Excellent Meat Quality Traits of Skeletal Muscles of the Chinese Indigenous Min Pig Compared with the Large White Breed

Yingzi Liu  1 , Xiuqin Yang  2 , Xiaoyan Jing  3 , Xinmiao He  4 , Liang Wang  5 , Yang Liu  6 , Di Liu  7   8
Affiliations
Comparative Study

Transcriptomics Analysis on Excellent Meat Quality Traits of Skeletal Muscles of the Chinese Indigenous Min Pig Compared with the Large White Breed

Yingzi Liu et al. Int J Mol Sci. .

Abstract

The Min pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. Additionally, different cuts of pig also show some different traits of meat quality. To explore the underlying mechanism responsible for the differences of meat quality between different breeds or cuts, the longissimus dorsi muscle (LM) and the biceps femoris muscle (BF) from Min and Large White pigs were investigated using transcriptome analysis. The gene expression profiling identified 1371 differentially expressed genes (DEGs) between LM muscles from Min and Large White pigs, and 114 DEGs between LM and BF muscles from the same Min pigs. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the IRS1/Akt/FoxO1 signaling pathway, adenosine 5'-monophosphate-activated protein kinase (AMPK) cascade effects, lipid metabolism and amino acid metabolism pathway. Such pathways contributed to fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in Min pig. These results give an insight into the mechanisms underlying the formation of skeletal muscle and provide candidate genes for improving meat quality. It will contribute to improving meat quality of pigs through molecular breeding.

Keywords: Min pig; biceps femoris; longissimus dorsi; meat quality; transcriptomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(a) The density plot of genes’ log10 (FPKM) distribution visualized by CummeRbund. The X-axis represents the log10 (FPKM) of all the genes. The Y-axis represents the genes’ distribution density. The nine groups were shown by different colors; (b) The histogram of gene expression. The X-axis represents individual sample. The Y-axis represents the number of expressed genes. The color depth represents the expression level of genes.
Figure 2
Figure 2
Volcano plot for differentially expressed genes (DEGs). The X-axis represents the log2 (FPKM) of all the genes. The Y-axis represents –log10 (p value). Red represents up-regulate DEGs. Blue represents down-regulate DEGs. Grey represents no-DEGs. (a) DEGs of Group LM; (b) DEGs of Group Min.
Figure 3
Figure 3
Pheatmaps for DEGs. The X-axis represents samples. The Y-axis represents DEGs. The color depth represents –log10 (FPKM). Red represents up-regulate DEGs. Blue represents down-regulate DEGs. (a) DEGs of Group LM; (b) DEGs of Group Min.
Figure 4
Figure 4
Real-time PCR validation of the DEGs analyzed by RNA-seq. (a) 13 genes that were identified as DEGs in Group LM; (b) 8 genes that were identified as DEGs in Group Min. The Y-axis shows the relative expression levels.
Figure 5
Figure 5
The column diagrams for Gene Ontology (GO) analysis of DEGs. The X-axis represents the functions of GO analysis. The Y-axis represents the numbers of DEGs. Red represents up-regulate DEGs. Blue represents down-regulate DEGs. (a) DEGs of Group LM; (b) DEGs of Group Min.
Figure 5
Figure 5
The column diagrams for Gene Ontology (GO) analysis of DEGs. The X-axis represents the functions of GO analysis. The Y-axis represents the numbers of DEGs. Red represents up-regulate DEGs. Blue represents down-regulate DEGs. (a) DEGs of Group LM; (b) DEGs of Group Min.
Figure 6
Figure 6
The column diagrams for Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs. The X-axis represents the numbers of DEGs. The Y-axis represents the functions of pathways. Each color represents the appropriate biological process. (a) DEGs of Group LM; (b) DEGs of Group Min.
Figure 6
Figure 6
The column diagrams for Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs. The X-axis represents the numbers of DEGs. The Y-axis represents the functions of pathways. Each color represents the appropriate biological process. (a) DEGs of Group LM; (b) DEGs of Group Min.
Figure 7
Figure 7
The diagrams for the enrichment degree of pathways. The X-axis represents the value of rich factors (the ratio of annotated DEGs to all genes of enriched pathway). The Y-axis represents the names of pathways. The color depth of each point represents q value. The size of each point represents the number of DEGs. (a) Enrichment degree of Group LM; (b) Enrichment degree of Group Min.
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