Transcriptome analysis reveals the long intergenic noncoding RNAs contributed to skeletal muscle differences between Yorkshire and Tibetan pig

Abstract

The difference between the skeletal muscle growth rates of Western and domestic breeds is remarkable, but the potential regulatory mechanism involved is still unclear. Numerous studies have pointed out that long intergenic noncoding RNA (lincRNA) plays a key role in skeletal muscle development. This study used published Yorkshire (LW) and Tibetan pig (TP) transcriptome data to explore the possible role of lincRNA in the difference in skeletal muscle development between the two breeds. 138 differentially expressed lincRNAs (DELs) were obtained between the two breeds, and their potential target genes (PTGs) were predicted. The results of GO and KEGG analysis revealed that PTGs are involved in multiple biological processes and pathways related to muscle development. The quantitative trait loci (QTLs) of DELs were predicted, and the results showed that most QTLs are related to muscle development. Finally, we constructed a co-expression network between muscle development related PTGs (MDRPTGs) and their corresponding DELs on the basis of their expression levels. The expression of DELs was significantly correlated with the corresponding MDRPTGs. Also, multiple MDRPTGs are involved in the key regulatory pathway of muscle fiber hypertrophy, which is the IGF-1-AKT-mTOR pathway. In summary, multiple lincRNAs that may cause differences in skeletal muscle development between the two breeds were identified, and their possible regulatory roles were explored. The findings of this study may provide a valuable reference for further research on the role of lincRNA in skeletal muscle development.

Figure 1

LincRNA analysis pipeline, classification and chromosome distribution. (A) LincRNAs identification pipeline. (B) Venn diagram of the proportion of different lincRNAs. (C) LincRNAs chromosome distribution.

Figure 2

Characterization of identified lincRNAs. Characterization of identified lincRNAs. (A) The number of exons of different lincRNAs and protein-coding genes. (B) Probability density graph of the transcription length of different lincRNA and protein coding genes. (C) Probability density graph of the exon length of different lincRNAs and protein-encoding genes.

Figure 3

The results of expression analysis. (A) Expression levels of different lincRNA and protein-encoding genes. (B) Differential expression analysis of differential lincRNAs, the bar code represents the color scale of the log₁₀^(FPKM) .

Figure 4

The results of Gene ontology and pathway analysis. (A) Gene ontology and pathway related to muscle development. (B) Gene expression in Gene ontology and pathway related to muscle development, the bar code represents the color scale of the log₁₀ ^(FC).

Figure 5

QTL analysis results. (A) Percentage of muscle development-related QTLs among all QTLs. (B) Distribution of QTL in each chromosome. (C) The Top 10 of QTLs.

Figure 6

DELs-MDRPTGs co-expression network diagram. Green dots represent MDRPTG, red dots represent DEL; green lines indicate that DEL is negatively correlated with the corresponding MDRPTG, and red indicates that DEL is positively correlated with the corresponding MDRPTG.

Figure 7

Linear regression of lincRNA and PTG expression. The r₀ and p₀ represent the Pearson correlation coefficient and p value of each pair of lincRNA and PTG in 6 samples, respectively; The r and p represent verification in 9 samples. (A) MSTRG.12010 vs IGF-2. (B) MSTRG.2530 vs WDR5. (C) MSTRG.24143 vs SESN3. (D) MSTRG.21771 vs SRF. (E) MSTRG.14875 vs UNKL.

Figure 8

Schematic diagram of lincRNAs involvement in muscle fiber hypertrophy signaling by regulating its target genes. IGF-1, insulin-like growth factor-1; IRS, insulin receptor substrate; PI3K, phosphatidylinositol 3 kinase; mTORC1, mechanistic target of rapamycin in complex 1; IGF-2, Insulin-like growth factor 2; TNNT3, troponin T-3; SRF, Serum response factor; PLD, phospholipase D; PC, phosphatidylcholine; PA, phosphatidic acid; MCU, Mitochondrial calcium unidirectional transporter. Red indicates key genes in the IGF-1-Akt-mTOR signaling pathway; orange indicates lincRNA; and green indicates PTG.