ARS | Publication request: MicroRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss)

Submitted to: Meeting Abstract
Publication Type: Abstract
Publication Acceptance Date: November 3, 2008
Publication Date: January 10, 2009
Citation: Salem, M., Xiao, C., Jonah, T., Rexroad III, C.E., Yao, J. 2009. MicroRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss). Meeting Abstract.

Technical Abstract: MicroRNAs are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. MicroRNAs are most often identified through computational prediction from genome sequences. The rainbow trout genome sequence is not available yet, which does not allow microRNAs prediction for this important aquaculture and biomedical research species. To identify microRNAs from rainbow trout tissues, we constructed a microRNA library from a pool of nine tissues. Analysis of the library identified unique 280 sequences representing 57 distinct microRNAs; 48 with conserved sequences matching previously identified microRNAs and 9 novel microRNAs. In addition, 18 microRNAs were computationally predicted from the rainbow trout transcriptome. Real-time PCR was used to measure microRNA expression patterns in adult somatic tissues and unfertilized eggs. The majority of the microRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. Potential microRNA-target interactions were computationally predicted in the rainbow trout transcriptome. In addition, single nucleotide polymorphisms (SNPs) were identified in microRNAs and their target sites in the rainbow trout transcripts. This study describes a large-scale cloning, identification and characterization of microRNAs and their target prediction. The microRNA repertoire is a new tool for functional genome research in salmonids. Tissue-specific microRNAs may be evaluated to serve as molecular markers predictive of specific functional and diagnostic implications. Identification of the genetic polymorphism in the microRNA -target interactions is a novel source of genetic polymorphism which may be useful for rainbow trout breeding programs.