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Transcriptome Analysis of the Liver and Muscle Tissues of Black Carp (Mylopharyngodon piceus) of Different Growth Rates

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Abstract

In this study, we used RNA-seq to analyze the muscle and liver tissues of black carps (Mylopharyngodon piceus) of different growth rates from the same batch to evaluate their growth traits. We have two groups; they are the black carp group with fast-growth rate and the slow-growth rate. A total of 23,132 genes were enriched in the Gene Ontology analysis, and 285 related pathways were found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The KEGG pathway analysis showed significant differences in the expression of some genes involved in growth- and development-related metabolic pathways such as the FoxO signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, apoptosis, TGF-β signaling pathway, and insulin signaling pathway. The numbers of differentially expressed genes in muscle and liver are 1913 and 1775. Nine of the differently expressed genes involved in the different growth traits and accuracy of the transcriptome data were validated using quantitative real-time PCR. We found that the expression levels of some growth-related genes were significantly higher in the fast-growth rate black carps than in the slow-growth rate black carps. The large number of transcriptome sequences obtained in this study has enriched the black carp gene resources, and the obtained differentially expressed genes and related pathway analysis provide valuable information for understanding the growth traits of the black carp.

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Acknowledgments

We thank Weili Liu (Shanghai OE Biotech Technology Co. Ltd) for her help in sequencing and data analysis. We thank the native English-speaking scientists of Elixigen Company (Huntington Beach, CA) for editing our manuscript.

Funding

This research was supported by China’s Agricultural Research System (CARS-45-03).

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Authors and Affiliations

  1. Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rual Affairs, Shanghai Ocean University, Shanghai, China

    Jiahua Zhang, Yubang Shen, Xiaoyan Xu, Yafan Dai & Jiale Li

  2. Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China

    Yubang Shen, Xiaoyan Xu & Jiale Li

  3. College of Aquaculture and Life science, Shanghai Ocean University, Shanghai, 201306, China

    Yubang Shen

  4. Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China

    Jiale Li

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  1. Jiahua Zhang
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  3. Xiaoyan Xu
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  4. Yafan Dai
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  5. Jiale Li
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Correspondence to Yubang Shen or Jiale Li.

Ethics declarations

In this study, all experiments with the fish were conducted in accordance with the guidelines on the care and use of animals for scientific purposes set up by the Institutional Animal Care and Use Committee (IACUS) of Shanghai Ocean University, Shanghai, China. The IACUS approved this study within the project “Breeding of Black Carp” (approval number SHOU-16-014). The dissection experiments were performed with 3-aminobenzoic acid ethyl ester methanesulfonate (MS-222; Sigma, USA) anesthesia to minimize the suffering of the fish.

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Zhang, J., Shen, Y., Xu, X. et al. Transcriptome Analysis of the Liver and Muscle Tissues of Black Carp (Mylopharyngodon piceus) of Different Growth Rates. Mar Biotechnol 22, 706–716 (2020). https://doi.org/10.1007/s10126-020-09994-z

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  • DOI: https://doi.org/10.1007/s10126-020-09994-z

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