Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

• Published in: Functional & integrative genomics 2023-03, Vol.23 (1), p.63-63, Article 63
• Main Authors: Shen, Jiyuan, Luo, Yuzhu, Wang, Jiqing, Hu, Jiang, Liu, Xiu, Li, Shaobin, Hao, Zhiyun, Li, Mingna, Zhao, Zhidong, Zhang, Yuting, Yang, Shutong, Wang, Longbin, Gu, Yuanhua
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Animals; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Cell Biology; Cell differentiation; Gene Expression Profiling; Gene Regulatory Networks; Goats - genetics; Life Sciences; Meat; Meat quality; Microbial Genetics and Genomics; MicroRNAs; MicroRNAs - genetics; miRNA; Muscle contraction; Muscle, Skeletal - metabolism; Musculoskeletal system; Non-coding RNA; Original Article; p53 Protein; Plant Genetics and Genomics; RNA, Long Noncoding - genetics; RNA, Messenger - genetics; Signal transduction; Skeletal muscle; Transcriptome; Transcriptomes
• ISSN: 1438-793X; 1438-7948
• DOI: 10.1007/s10142-023-00987-4

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.