Abstract
Long non-coding RNAs (lncRNAs) play important roles in the growth and development of skeletal muscle. However, there is limited information on goats. In this study, expression profiles of lncRNAs in Longissimus dorsi muscle from Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with divergent meat yield and meat quality were compared using RNA-sequencing. Based on our previous microRNA (miRNA) and mRNA profiles obtained from the same tissues, the target genes and binding miRNAs of differentially expressed lncRNAs were obtained. Subsequently, lncRNA-mRNA interaction networks and a ceRNA network of lncRNA-miRNA-mRNA were constructed. A total of 136 differentially expressed lncRNAs were identified between the two breeds. Fifteen cis target genes and 143 trans target genes were found for differentially expressed lncRNAs, and they were enriched in muscle contraction, muscle system process, muscle cell differentiation, and p53 signaling pathway. A total of 69 lncRNA-trans target gene pairs were constructed, with close relationship with muscle development, intramuscular fat deposition, and meat tenderness. A total of 16 lncRNA-miRNA-mRNA ceRNA pairs were identified, of which some reportedly associated with skeletal muscle development and fat deposition were found. The study will provide an improved understanding of the roles of lncRNAs in caprine meat yield and meat quality.
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Data availability
The raw data of RNA-sequencing is available at the NCBI GenBank Sequence Read Archive (SRA), under accession number PRJNA675157. Other data generated or analyzed during this study are included in this article and its supplementary information files.
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Funding
This research was funded by the Fuxi Young Talent Fund of Gansu Agricultural University (Gaufx-02Y02), the Science and Technology project of Lanzhou city (2021-1-162), the Central Guidance on Local Science and Technology Development Fund of Gansu Province, Lanzhou City Overseas Expertise Introduction Base for Molecular Breeding of Mutton Sheep, the Projects of Gansu Agricultural University (GSAU-ZL-2015-033), and Discipline Team Project of Gansu Agricultural University (GAU-XKTD-2022-21).
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Jiyuan Shen and Jiqing Wang conceived and designed the experiments; Jiyuan Shen, Yuzhu Luo, Jiang Hu, Xiu Liu, and Shaobin Li conducted the experiments; Zhiyun Hao, Mingna Li, Zhidong Zhao, Yuting Zhang, Shutong Yang, Longbin Wang, and Yuanhua Gu analyzed the data; Jiyuan Shen and Jiqing Wang drafted and revised the manuscript. All authors read and approved the final manuscript.
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All animal procedures in this study were approved by the Animal Experiment Ethics Committee of Gansu Agricultural University with an approval number of GSAU-ETH-AST-2021-028.
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Shen, J., Luo, Y., Wang, J. et al. Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality. Funct Integr Genomics 23, 63 (2023). https://doi.org/10.1007/s10142-023-00987-4
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DOI: https://doi.org/10.1007/s10142-023-00987-4