Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development
The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−S...
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MDPI AG
2021-08-01
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| author | Hao Ding Yueyue Lin Tao Zhang Lan Chen Genxi Zhang Jinyu Wang Kaizhou Xie Guojun Dai |
| author_facet | Hao Ding Yueyue Lin Tao Zhang Lan Chen Genxi Zhang Jinyu Wang Kaizhou Xie Guojun Dai |
| author_sort | Hao Ding |
| collection | DOAJ |
| description | The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle. |
| first_indexed | 2024-03-10T09:03:55Z |
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| id | doaj.art-02ad57b3aa6f435a9e37891bcbebf4c8 |
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| language | English |
| last_indexed | 2024-03-10T09:03:55Z |
| publishDate | 2021-08-01 |
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| series | Animals |
| spelling | doaj.art-02ad57b3aa6f435a9e37891bcbebf4c82023-11-22T06:30:17ZengMDPI AGAnimals2076-26152021-08-01118231110.3390/ani11082311Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle DevelopmentHao Ding0Yueyue Lin1Tao Zhang2Lan Chen3Genxi Zhang4Jinyu Wang5Kaizhou Xie6Guojun Dai7College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225000, ChinaThe mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.https://www.mdpi.com/2076-2615/11/8/2311pigeonskeletal muscledevelopment and growthWGCNAtranscriptomics |
| spellingShingle | Hao Ding Yueyue Lin Tao Zhang Lan Chen Genxi Zhang Jinyu Wang Kaizhou Xie Guojun Dai Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development Animals pigeon skeletal muscle development and growth WGCNA transcriptomics |
| title | Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development |
| title_full | Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development |
| title_fullStr | Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development |
| title_full_unstemmed | Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development |
| title_short | Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development |
| title_sort | transcriptome analysis of differentially expressed mrna related to pigeon muscle development |
| topic | pigeon skeletal muscle development and growth WGCNA transcriptomics |
| url | https://www.mdpi.com/2076-2615/11/8/2311 |
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