Identification of lncRNAs expression and their regulatory networks associated with development and growth of skeletal muscle in sheep using RNA-Seq

Abstract

Importance of the work: Sheep are a major source of mutton production. Therefore, recognizing the genes that influence muscle growth rates in sheep is useful in breeding programs.
Objectives: To identify the genes regulated by long non-coding RNAs (lncRNAs) that are effective in sheep skeletal muscle growth and development.
Materials & Methods: In total, 141,079,400 short reads for 12 muscle tissue (longissimus dorsal) samples of 6 young animals and 6 adults from domestic sheep were used as input for the FastQC and Trimmomatic software packages. Expression analysis was investigated using Cuffdiff. The ClueGO plug-in in Cytoscape was used for gene ontology. Novel lncRNAs were distinguished using Cuffcompare.
Results: Of the 82 lncRNA genes, 15 genes were up-regulated and 67 genes were down-regulated in adults compared with young animals and there was a higher expression of the lncRNA genes in the young than in the adult individuals based on cluster analysis. There were 26 genes of Gene Ontology classified as Biological Processes that significantly enriched the regulation of muscle development and differentiation. The findings showed that lncRNAs regulated both miRNAs and mRNAs that chiefly participate in the muscle growth and development in Texel sheep. Novel lncRNA transcripts were identified, such as TCONS_00063730, TCONS_00063387, TCONS_00063388 and TCONS_00033181, that had a strong correlation with mRNAs, while other novel lncRNA transcripts, such as TCONS_00040327, TCONS_00061518, TCONS_00064968 and TCONS_00033645, had greater correlation with miRNAs.
Main finding: New candidate regulator genes were identified for future molecular and genetic studies on sheep muscle growth and development. This might be helpful in selection programs to improve mutton production.