Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages
The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. The...
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MDPI AG
2020-07-01
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| author | Guofang Wu Lin Ma Lei Wang Jiping Zhou Yuhong Ma Chen Yang |
| author_facet | Guofang Wu Lin Ma Lei Wang Jiping Zhou Yuhong Ma Chen Yang |
| author_sort | Guofang Wu |
| collection | DOAJ |
| description | The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding. |
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| last_indexed | 2024-03-10T18:28:15Z |
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| spelling | doaj.art-019060b25eef4a658e07641ac32b68082023-11-20T06:48:06ZengMDPI AGAnimals2076-26152020-07-01107119810.3390/ani10071198Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental StagesGuofang Wu0Lin Ma1Lei Wang2Jiping Zhou3Yuhong Ma4Chen Yang5Stake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, ChinaStake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, ChinaStake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, ChinaStake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, ChinaStake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, ChinaStake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, ChinaThe growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.https://www.mdpi.com/2076-2615/10/7/1198Bamei pigtranscriptomedifferentially expressed (DE) genesmiRNA<i>longissimus dorsi</i> muscle |
| spellingShingle | Guofang Wu Lin Ma Lei Wang Jiping Zhou Yuhong Ma Chen Yang Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages Animals Bamei pig transcriptome differentially expressed (DE) genes miRNA <i>longissimus dorsi</i> muscle |
| title | Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages |
| title_full | Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages |
| title_fullStr | Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages |
| title_full_unstemmed | Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages |
| title_short | Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages |
| title_sort | analysis of transcriptome and mirnaome in the muscle of bamei pigs at different developmental stages |
| topic | Bamei pig transcriptome differentially expressed (DE) genes miRNA <i>longissimus dorsi</i> muscle |
| url | https://www.mdpi.com/2076-2615/10/7/1198 |
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