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. 2024 Jan 5:10:1296208.
doi: 10.3389/fvets.2023.1296208. eCollection 2023.

Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq

Qiuyan Li  1 , Meilin Hao  2 , Junhong Zhu  1 , Lanlan Yi  1 , Wenjie Cheng  1 , Yuxiao Xie  1   2 , Sumei Zhao  1
Affiliations

Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq

Qiuyan Li et al. Front Vet Sci. .

Abstract

Introduction: Pig growth is an important economic trait that involves the co-regulation of multiple genes and related signaling pathways. High-throughput sequencing has become a powerful technology for establishing the transcriptome profiles and can be used to screen genome-wide differentially expressed genes (DEGs). In order to elucidate the molecular mechanism underlying muscle growth, this study adopted RNA sequencing (RNA-seq) to identify and compare DEGs at the genetic level in the longissimus dorsi muscle (LDM) between two indigenous Chinese pig breeds (Diannan small ears [DSE] pig and Wujin pig [WJ]) and one introduced pig breed (Landrace pig [LP]).

Methods: Animals under study were from two Chinese indigenous pig breeds (DSE pig, n = 3; WJ pig, n = 3) and one introduced pig breed (LP, n = 3) were used for RNA sequencing (RNA-seq) to identify and compare the expression levels of DEGs in the LDM. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs.

Results: The results revealed that for the DSE, WJ, and LP libraries, more than 66, 65, and 71 million clean reads were generated by transcriptome sequencing, respectively. A total of 11,213 genes were identified in the LDM tissue of these pig breeds, of which 7,127 were co-expressed in the muscle tissue of the three samples. In total, 441 and 339 DEGs were identified between DSE vs. WJ and LP vs. DSE in the study, with 254, 193 up-regulated genes and 187, 193 down-regulated genes in DSE compared to WJ and LP. GO analysis and KEGG signaling pathway analysis showed that DEGs are significantly related to contractile fiber, sarcolemma, and dystrophin-associated glycoprotein complex, myofibril, sarcolemma, and myosin II complex, Glycolysis/Gluconeogenesis, Propanoate metabolism, and Pyruvate metabolism, etc. In combination with functional annotation of DEGs, key genes such as ENO3 and JUN were identified by PPI network analysis.

Discussion: In conclusion, the present study revealed key genes including DES, FLNC, PSMD1, PSMD6, PSME4, PSMB4, RPL11, RPL13A, ROS23, RPS29, MYH1, MYL9, MYL12B, TPM1, TPM4, ENO3, PGK1, PKM2, GPI, and the unannotated new gene ENSSSCG00000020769 and related signaling pathways that influence the difference in muscle growth and could provide a theoretical basis for improving pig muscle growth traits in the future.

Keywords: Diannan small ears pig; Wujin pig; differentially expressed genes; landrace pig; longissimus dorsi muscle; transcriptome sequencing (RNA-seq).

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Venn diagrams of the number of genes expressed in each group. DSE, Diannan small ears pig; LP, Landrace pig; WJ, Wujin pig.
Figure 2
Figure 2
Venn diagrams of differentially expressed genes in the comparisons of LP vs. DSE, DSE vs. WJ, and WJ vs. LP. DSE, Diannan small ears pig; LP, Landrace pig; WJ, Wujin pig.
Figure 3
Figure 3
Significantly enriched GO for differentially expressed genes. (A) DSE vs. WJ, (B) LP vs. DSE. DSE, Diannan small ears pig; LP, Landrace pig; WJ, Wujin pig.
Figure 4
Figure 4
Significantly enriched KEGG for differentially expressed genes. (A) DSE vs. WJ, (B) LP vs. DSE. DSE, Diannan small ears pig; LP, Landrace pig; WJ, Wujin pig.
Figure 5
Figure 5
Significantly enriched PPI for differentially expressed genes. (A) DSE vs. WJ, (B) LP vs. DSE. DSE, Diannan small ears pig; LP, Landrace pig; WJ, Wujin pig.
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