Differential expression patterns of growth-related microRNAs in the skeletal muscle of Nile tilapia (Oreochromis niloticus)1

Abstract

MicroRNA (miRNA) are a class of small, single-stranded, non-coding RNA that regulate mRNA expression at the post-transcriptional level and play important roles in many fundamental biological processes. There is emerging evidence that miRNA are critical regulators of widespread cellular functions, such as differentiation, proliferation, and migration. At present, little is known about miRNA expression profiles related to skeletal muscle growth in aquatic organisms. This study aimed to investigate the phenotypic variation in the body growth of the Nile tilapia (Oreochromis niloticus) and to identify and quantify the differential expression levels of selected growth-related transcriptomic miRNA in the skeletal muscle of this fish. To this end, we performed next-generation sequencing to define the full miRNA transcriptome in muscle tissue from Nile tilapia and to detect differentially expressed miRNA between 2 strains of Nile tilapia. These tilapia strains exhibited significant (P < 0.05) phenotypic variation with respect to growth-related traits (body length and BW), mitochondrial DNA (mtDNA) haplotype diversity, and the differential expression of selected growth-related genes. The results obtained from the transcriptome analysis and real-time quantitative reverse transcription PCR (qRT-PCR) revealed significant differences in miRNA expression between fast-growing and control strains of tilapia. Digital gene expression (DGE) profiling was performed based on the obtained read abundance, and we identified down-regulated miRNA, including let-7j, miR-140, miR-192, miR-204, miR-218a, miR-218b, miR-301c, and miR-460, and up-regulated miRNA, including let-7b, let-7c, miR-133, miR-152, miR-15a, miR-193a, miR-30b, and miR-34, associated with body growth in tilapia. These results were further validated using real-time qRT-PCR and microarray profiling. In summary, the up- and down-regulation of miRNA involved in the GH/IGF-1 axis signaling pathway suggests that the differential expression levels of growth-related miRNA may serve as molecular markers that are predictive of specific functional and diagnostic implications. The obtained data on genetic polymorphisms in miRNA-target interactions are particularly useful for Nile tilapia breeding programs.

Identification of conserved microRNAs and their target genes in Nile tilapia (Oreochromis niloticus) by bioinformatic analysis

“…mir-1 expression in the muscle modulates cardiac and skeletal muscle proliferation and differentiation in zebrafish (Mishima et al, 2009) and humans (Koutsoulidou et al, 2011). Moreover, Nile tilapia mir-1 expression has been observed in skeletal muscle (Huang et al, 2012). This suggests that mir-1 plays important roles in modulating muscle contraction in tilapia.…”

“…With its fast growth rate and ability to adapt to a wide range of culture conditions, tilapia is one of the most widely farmed fish in the world. Because miRNA is involved in growth and resistance to environmental stresses, several studies have attempted to identify miRNAs related to muscle growth, regulation of osmotic stress, and salt tolerance (Huang et al, 2012;Yan et al, 2013a). The full-miRNA transcriptome in muscle tissue revealed significant differences in miRNA expression between fast-growing and control strains of tilapia (Huang et al, 2012).…”

“…Because miRNA is involved in growth and resistance to environmental stresses, several studies have attempted to identify miRNAs related to muscle growth, regulation of osmotic stress, and salt tolerance (Huang et al, 2012;Yan et al, 2013a). The full-miRNA transcriptome in muscle tissue revealed significant differences in miRNA expression between fast-growing and control strains of tilapia (Huang et al, 2012). miR-206, a muscle-specific miRNA, regulates the growth of teleost tilapia (O. niloticus) by regulating insulin-like growth factor 1 gene expression (Yan et al, 2013a).…”

Current Advances in Functional Genomics in Aquaculture

“…These traits inluence the commercial value of farmed aquatic organisms. Traits for body weight and length have been identiied in several ish species such as Atlantic salmon [149], rainbow trout [150], Big heard carp (H. nobilis) [151], common carp [152,153] and tilapia (Oreochromis niloticus) [154], nine spined stickleback (Pungitius pungitius) [155] and Arctic char (Salvelinus alpinus) [156]. In shrimps and prawns, body weight and length traits have been identiied in kruma shrimp [157,158], Chinese shrimp [159], Giant fresh water prawn [160], Ridge white prawn [161] and Oriental river prawns [162].…”

“…Hence, the selection of males for aquaculture increases production in tilapia while the females increase production in carp. Important traits related to improving meat quality include muscle quality [154], muscle ibre [165], texture [165], colour [166,167], fat percentage [166] and dressed weight percentage [166]. Body appearance traits identiied include the red body colour excluding normal black pigmentation in tilapia [168], silvery skin with few spots in rainbow trout [169], albinism in rainbow trout [170] and melanization in threespine sticklebacks (Gasterosteus aculeatus) [171].…”