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RNA-seq transcriptome analysis of extensor digitorum longus and soleus muscles in large white pigs

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Abstract

Skeletal muscle fibers are mainly categorized into red and white fiber types, and the ratio of red/white fibers within muscle mass plays a crucial role in meat quality such as tenderness and flavor. To better understand the molecular difference between the two muscle fibers, this study takes advantage of RNA-seq to compare differences in the transcriptome between extensor digitorum longus (EDL; white fiber) and soleus (Sol; red fiber) muscles of large white pigs. In total, 89,658,562 and 46,723,568 raw reads from EDL and Sol were generated, respectively. Comparison between the two transcriptomes revealed 561 differentially expressed genes, with 408 displaying higher and 153 lower levels of expression in Sol. Quantitative real-time polymerase chain reaction validated the differential expression of nine genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis discovered several differentially enriched biological functions and processes of the two muscles. Moreover, transcriptome comparison between EDL and Sol identified many muscle-related genes (CSRP3, ACTN2, MYL1, and MYH6) and pathways related to myofiber formation, such as focal adhesion, tight junction formation, extracellular matrix (ECM)–receptor pathway, calcium signaling, and Wnt signaling. In addition, 58,362 and 58,359 single nucleotide polymorphisms were identified in EDL and Sol, respectively, and the sequence of 9069 genes was refined at the 5′, 3′ or both ends. Numerous novel transcripts and alternatively spliced RNAs were also identified. Our transcriptome analysis constitutes valuable sequence resource for uncovering important genes and pathways involved in muscle fiber type determination, and might help further our understanding of the molecular mechanisms in different types of muscle.

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Abbreviations

EDL:

Extensor digitorum longus

Sol:

Soleus

DEGs:

Differentially expressed genes

GO:

Gene ontology

SNPs:

Single nucleotide polymorphisms

CPC:

Coding potential calculator

FDR:

False discovery rate

AS:

Alternative splicing

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Acknowledgments

We thank the Beijing Genomics Institute (BGI)-Shenzhen for helping us with technical assistance in DGE and Edanz for providing language editing service.

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    Authors and Affiliations

    1. Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwestern A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi Province, People’s Republic of China

      Jiayu Zhu, Xin’e Shi, Hongzhao Lu, Bo Xia, Yuefeng Li, Xiao Li, Qiangling Zhang & Gongshe Yang

    2. School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, Shaanxi Province, People’s Republic of China

      Hongzhao Lu

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    1. Jiayu Zhu
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    2. Xin’e Shi
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    3. Hongzhao Lu
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    Correspondence to Gongshe Yang.

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    None of the authors declare any conflict of interest.

    Ethical approval

    The large white pigs were supplied by the Northwest A&F University Experiment Station (Yangling, China). Experiments were handled in accordance with the guidelines of the Administration of Affairs Concerning Experimental Animals and authorized by the Institutional Animal Care and Use Committee of the College of Animal Science and Technology, Northwest A&F University, Shaanxi, China. All applicable international, national, and institutional guidelines for the care and use of animals were followed.

    Funding

    This study was supported by the National Basic Research Program of China (Grant No. 2015CB943102), the National Natural Science Foundation of China (Grant No. 31272410), and the Scientific and Technological Innovation Project for Youths of Northwest A&F University (Grant No. ZD2012007). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

    Additional information

    Communicated by S. Hohmann.

    Jiayu Zhu and Xin’e Shi contributed equally to this work.

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    Zhu, J., Shi, X., Lu, H. et al. RNA-seq transcriptome analysis of extensor digitorum longus and soleus muscles in large white pigs. Mol Genet Genomics 291, 687–701 (2016). https://doi.org/10.1007/s00438-015-1138-z

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    • DOI: https://doi.org/10.1007/s00438-015-1138-z

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