Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq
ABSTRACT: Duck is an economically important poultry, and there is currently a major focus on improving its meat quality through breeding. There are wide variations in the growth regulation mechanisms of different duck breeds, that fundamental research on skeletal muscle growth is essential for under...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579123006417 |
| _version_ | 1797401807438217216 |
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| author | Chang Cao Yingjie Cai Yuxiao Li Tao Li Jiqiao Zhang Zhigang Hu Jianqin Zhang |
| author_facet | Chang Cao Yingjie Cai Yuxiao Li Tao Li Jiqiao Zhang Zhigang Hu Jianqin Zhang |
| author_sort | Chang Cao |
| collection | DOAJ |
| description | ABSTRACT: Duck is an economically important poultry, and there is currently a major focus on improving its meat quality through breeding. There are wide variations in the growth regulation mechanisms of different duck breeds, that fundamental research on skeletal muscle growth is essential for understanding the regulation of unknown genes. The study aimed to broaden the understanding the duck skeletal muscle development and thereby to improve the performance of domestic ducks. In this study, RNA-seq data from skeletal muscles (breast muscle and leg muscle) of Pekin duck and Hanzhong Ma duck sampled at d 17, 21, and 27 of embryo (E17d, E21d, and E27d), as well as at 6-mo-old following birth (M6), to investigate and compare the mRNA temporal expression profiles and associated pathways that regulate skeletal myogenesis of different duck breeds. There were 331 to 1,440 annotated differentially expressed genes (DEGs) in breast muscle and 380 to 1,790 annotated DEGs in leg muscle from different databases between 2 duck breeds. Gene ontology (GO) enrichment in skeletal muscles indicated that these DEGs were mainly involved in biosynthetic process, developmental process, regulation of protein metabolic process and regulation of gene expression. KEGG analysis in skeletal muscles showed that a total of 41 DEGs were mapped to 7 KEGG pathways, including ECM-receptor interaction, focal adhesion, carbon metabolism, regulation of actin cytoskeleton, calcium signaling pathway, biosynthesis of amino acids and PPAR signaling pathway. The differential expression of 8 selected DEGs was verified by qRT-PCR, and the results were consistent with RNA-seq data. The identified DEGs, such as SDC, SPP1, PAK1, MYL9, PGK1, NOS1, PHGDH, TNNT2, FN1, and AQP4, were specially highlighted, indicating their associations with muscle development in the Pekin duck and Hanzhong Ma duck. This study provides a basis for revealing the differences in skeletal muscle development between Pekin duck and Hanzhong Ma duck. |
| first_indexed | 2024-03-09T02:15:36Z |
| format | Article |
| id | doaj.art-2e81462438494074985c7062218b24f9 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-03-09T02:15:36Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-2e81462438494074985c7062218b24f92023-12-07T05:27:17ZengElsevierPoultry Science0032-57912023-12-0110212103122Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seqChang Cao0Yingjie Cai1Yuxiao Li2Tao Li3Jiqiao Zhang4Zhigang Hu5Jianqin Zhang6College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaCollege of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaCollege of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaCollege of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaCollege of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaCollege of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaCorresponding author:; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR ChinaABSTRACT: Duck is an economically important poultry, and there is currently a major focus on improving its meat quality through breeding. There are wide variations in the growth regulation mechanisms of different duck breeds, that fundamental research on skeletal muscle growth is essential for understanding the regulation of unknown genes. The study aimed to broaden the understanding the duck skeletal muscle development and thereby to improve the performance of domestic ducks. In this study, RNA-seq data from skeletal muscles (breast muscle and leg muscle) of Pekin duck and Hanzhong Ma duck sampled at d 17, 21, and 27 of embryo (E17d, E21d, and E27d), as well as at 6-mo-old following birth (M6), to investigate and compare the mRNA temporal expression profiles and associated pathways that regulate skeletal myogenesis of different duck breeds. There were 331 to 1,440 annotated differentially expressed genes (DEGs) in breast muscle and 380 to 1,790 annotated DEGs in leg muscle from different databases between 2 duck breeds. Gene ontology (GO) enrichment in skeletal muscles indicated that these DEGs were mainly involved in biosynthetic process, developmental process, regulation of protein metabolic process and regulation of gene expression. KEGG analysis in skeletal muscles showed that a total of 41 DEGs were mapped to 7 KEGG pathways, including ECM-receptor interaction, focal adhesion, carbon metabolism, regulation of actin cytoskeleton, calcium signaling pathway, biosynthesis of amino acids and PPAR signaling pathway. The differential expression of 8 selected DEGs was verified by qRT-PCR, and the results were consistent with RNA-seq data. The identified DEGs, such as SDC, SPP1, PAK1, MYL9, PGK1, NOS1, PHGDH, TNNT2, FN1, and AQP4, were specially highlighted, indicating their associations with muscle development in the Pekin duck and Hanzhong Ma duck. This study provides a basis for revealing the differences in skeletal muscle development between Pekin duck and Hanzhong Ma duck.http://www.sciencedirect.com/science/article/pii/S0032579123006417duckskeletal muscletranscriptomeDEGpathway |
| spellingShingle | Chang Cao Yingjie Cai Yuxiao Li Tao Li Jiqiao Zhang Zhigang Hu Jianqin Zhang Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq Poultry Science duck skeletal muscle transcriptome DEG pathway |
| title | Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq |
| title_full | Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq |
| title_fullStr | Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq |
| title_full_unstemmed | Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq |
| title_short | Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq |
| title_sort | characterization and comparative transcriptomic analysis of skeletal muscle in female pekin duck and hanzhong ma duck during different growth stages using rna seq |
| topic | duck skeletal muscle transcriptome DEG pathway |
| url | http://www.sciencedirect.com/science/article/pii/S0032579123006417 |
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