Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

A MicroRNA Repertoire For Functional Genome Research In Rainbow Trout (Oncorhynchus mykiss)

Mohamed Salem¹ , Caide Xiao¹ , Jonah Womack¹ , Caird E. Rexroad III² , Jianbo Yao¹

¹  Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108

²  National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430

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 microRNA prediction for this important aquaculture and biomedical research species. To identify microRNAs from rainbow trout, we constructed a microRNA library from a pool of nine tissues. Analysis of the library identified 280 unique 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 and single nucleotide polymorphisms (SNPs) were identified in the microRNAs and their target sites in the rainbow trout transcripts. The rainbow trout microRNAs identified and characterized in this study provide 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.