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Research article
Lingbing Liu
Southwest University
Corresponding Author
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Background: Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21.
Results: Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P<0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,251 (E12vsE16), 4,324 (E12vsE19), and 5,224 (E12vsE21), 1,274 (E16vsE19), 2,735 (E16vsE21) and 857 (E19vsE21) differentially expressed mRNAs were identified. It is worth noting that 6,726 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The downward trend was the most important and was enriched in 3,963 DEGs. GO enrichment analysis provided three significantly enriched categories of the down-trending genes, including 91 cellular components, 53 molecular functions, and 248 biological processes. Through KEGG analysis, we explored the pathway of downtrend genes. A total of 183 KEGG pathways were enriched, including 17 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P<0.05), MAPK signalingpathway, TGF-beta signaling pathway, and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3.
Conclusion: Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.
Keywords
Chengkou Mountain Chicken, Embryo muscle development, Transcriptome analysis
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This is a list of supplementary files associated with this preprint. Click to download.
- supplementarymetirals.docx
Supplementary information Supplementary information accompanies this paper as follow: Additional file 1: Table S1. Sequencing data quality control Additional file 2: Table S2. Statistics of clean reads at 4 different time points of chicken muscle embryo Additional file 3: Table S3. Comparison of reference area statistics Additional file 4: Table S4. Reference genome alignment Additional file 4: Table S5. Primer sequencing in this study Additional file 5: Figure S1.Gene coverage of different samples Additional file 6: Figure S2. Sample randomness distribution Additional file 6: Figure S3. Volcano plot of differentially expressed genes
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CURRENT STATUS: Under Review
Version 1
Posted 21 Dec, 2020
No community comments so far
Editorial decision: Major revision
On 07 Mar, 2021
Review #2 received
Received 04 Mar, 2021
Reviewer #2 agreed
On 15 Feb, 2021
Review #1 received
Received 25 Jan, 2021
Editor assigned
On 21 Dec, 2020
Reviewers invited
Invitations sent on 21 Dec, 2020
Reviewer #1 agreed
On 21 Dec, 2020
Submission checks complete
On 17 Dec, 2020
Editor invited
On 14 Dec, 2020
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Lingbing Liu
Southwest University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 21 Dec, 2020
No community comments so far
Editorial decision: Major revision
On 07 Mar, 2021
Review #2 received
Received 04 Mar, 2021
Reviewer #2 agreed
On 15 Feb, 2021
Review #1 received
Received 25 Jan, 2021
Editor assigned
On 21 Dec, 2020
Reviewers invited
Invitations sent on 21 Dec, 2020
Reviewer #1 agreed
On 21 Dec, 2020
Submission checks complete
On 17 Dec, 2020
Editor invited
On 14 Dec, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21.
Results: Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P<0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,251 (E12vsE16), 4,324 (E12vsE19), and 5,224 (E12vsE21), 1,274 (E16vsE19), 2,735 (E16vsE21) and 857 (E19vsE21) differentially expressed mRNAs were identified. It is worth noting that 6,726 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The downward trend was the most important and was enriched in 3,963 DEGs. GO enrichment analysis provided three significantly enriched categories of the down-trending genes, including 91 cellular components, 53 molecular functions, and 248 biological processes. Through KEGG analysis, we explored the pathway of downtrend genes. A total of 183 KEGG pathways were enriched, including 17 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P<0.05), MAPK signalingpathway, TGF-beta signaling pathway, and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3.
Conclusion: Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- supplementarymetirals.docx
Supplementary information Supplementary information accompanies this paper as follow: Additional file 1: Table S1. Sequencing data quality control Additional file 2: Table S2. Statistics of clean reads at 4 different time points of chicken muscle embryo Additional file 3: Table S3. Comparison of reference area statistics Additional file 4: Table S4. Reference genome alignment Additional file 4: Table S5. Primer sequencing in this study Additional file 5: Figure S1.Gene coverage of different samples Additional file 6: Figure S2. Sample randomness distribution Additional file 6: Figure S3. Volcano plot of differentially expressed genes
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