Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing
| Autor: | Chao-Long Zhang, Xin Li, Rui-Min Wang, Su-Xian Zeng, Jin Yan, Cui-Cui Sun, Shang-Qiao Song, Zong-Qiang Li, Wei-wei Ma |
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| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
0301 basic medicine Swine Paraspinal Muscles Biophysics Breeding Biology Muscle Development 01 natural sciences Biochemistry Genome Gene dosage Transcriptome 03 medical and health sciences Agricultural & Industrial Bioscience Gene expression Animals Debao pig Protein Interaction Maps RNA-Seq KEGG Landrace pig Muscle Skeletal Molecular Biology Gene Research Articles GO analysis Genetics Gene Expression Profiling qRT-PCR KEGG pathway enrichment Cell Biology Gene Ontology 030104 developmental biology Gene Expression Regulation 010606 plant biology & botany Reference genome |
| Zdroj: | Bioscience Reports |
| ISSN: | 1573-4935 0144-8463 |
| Popis: | RNA-seq analysis was used to identify differentially expressed genes (DEGs) at the genetic level in the longissimus dorsi muscle from two pigs to investigate the genetic mechanisms underlying the difference in meat quality between Debao pigs and Landrace pigs. Then, these DEGs underwent functional annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein–protein interaction (PPI) analyses. Finally, the expression levels of specific DEGs were assessed using qRT-PCR. The reference genome showed gene dosage detection of all samples which showed that the total reference genome comprised 22342 coding genes, including 14743 known and 190 unknown genes. For detection of the Debao pig genome, we obtained 14168 genes, including 13994 known and 174 unknown genes. For detection of the Landrace pig genome, we obtained 14404 genes, including 14223 known and 181 unknown genes. GO analysis and KEGG signaling pathway analysis show that DEGs are significantly related to metabolic regulation, amino acid metabolism, muscular tissue, muscle structure development etc. We identified key genes in these processes, such as FOS, EGR2, and IL6, by PPI network analysis. qRT-PCR confirmed the differential expression of six selected DEGs in both pig breeds. In conclusion, the present study revealed key genes and related signaling pathways that influence the difference in pork quality between these breeds and could provide a theoretical basis for improving pork quality in future genetic thremmatology. |
| Databáze: | OpenAIRE |
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