Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq

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 t...

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Autores principales: Cao, Chang, Cai, Yingjie, Li, Yuxiao, Li, Tao, Zhang, Jiqiao, Hu, Zhigang, Zhang, Jianqin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10568565/
https://www.ncbi.nlm.nih.gov/pubmed/37832186
http://dx.doi.org/10.1016/j.psj.2023.103122
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author Cao, Chang
Cai, Yingjie
Li, Yuxiao
Li, Tao
Zhang, Jiqiao
Hu, Zhigang
Zhang, Jianqin
author_facet Cao, Chang
Cai, Yingjie
Li, Yuxiao
Li, Tao
Zhang, Jiqiao
Hu, Zhigang
Zhang, Jianqin
author_sort Cao, Chang
collection PubMed
description 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.
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spelling pubmed-105685652023-10-13 Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq Cao, Chang Cai, Yingjie Li, Yuxiao Li, Tao Zhang, Jiqiao Hu, Zhigang Zhang, Jianqin Poult Sci GENETICS AND MOLECULAR BIOLOGY 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. Elsevier 2023-09-18 /pmc/articles/PMC10568565/ /pubmed/37832186 http://dx.doi.org/10.1016/j.psj.2023.103122 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle GENETICS AND MOLECULAR BIOLOGY
Cao, Chang
Cai, Yingjie
Li, Yuxiao
Li, Tao
Zhang, Jiqiao
Hu, Zhigang
Zhang, Jianqin
Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq
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 GENETICS AND MOLECULAR BIOLOGY
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10568565/
https://www.ncbi.nlm.nih.gov/pubmed/37832186
http://dx.doi.org/10.1016/j.psj.2023.103122
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