RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout

Authors: PANERU, BAM - Middle Tennessee State University; AL-TOBASEI, RAFET - Middle Tennessee State University; KENNEY, BRETT - West Virginia University; Leeds, Timothy - Tim; SALEM, MOHAMED - Middle Tennessee State University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2017
Publication Date: 8/22/2017
Citation: Paneru, B.D., Al-Tobasei, R., Kenney, B., Leeds, T.D., Salem, M. 2017. RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout [serial online]. Scientific Reports. 7:9078. https://doi.org/10.1038/s41598-017-09515-4.
DOI: https://doi.org/10.1038/s41598-017-09515-4

Interpretive Summary: MicroRNAs are small molecules in animals and plants that play an important role in posttranscriptional gene expression. In fish species important to aquaculture, such as rainbow trout, there is an incomplete understanding of expression and genetic variant profiles of microRNAs and how they affect variation in economically-important production traits. Scientists at the NCCCWA (Leetown, WV) developed a selectively-bred line of rainbow trout that exhibits improved growth performance, and have extensively characterized families within the line for fillet yield and quality traits for several generations. In collaboration with scientists at Middle Tennessee State University (Murfreesboro), we identified and characterized the expression of microRNAs from muscle tissue, and further identified genetic polymorphisms in microRNA binding sites of target genes. This study identified 90 microRNAs with expression profiles that associate with variation in growth, fillet yield, and fillet quality traits including color, texture, and fat content. This study provides important insights into the underlying biological basis for variation in growth, fillet yield, and fillet quality traits that may inform future efforts to improve these traits in rainbow trout, and further develops our genomics resources as a means to do so.

Technical Abstract: The role of microRNA expression and genetic variation in microRNA-binding sites of target genes on growth and muscle quality traits is poorly characterized. We used RNA-Seq approach to investigate their importance on 5 growth and muscle quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, muscle shear force and whiteness. Phenotypic data were collected from 471 fish, representing 98 families (~5 fish/family) from a growth-selected line. Muscle microRNAs and mRNAs were sequenced from 22 families showing divergent phenotypes. Ninety microRNAs showed differential expression between families with divergent phenotypes, and their expression was strongly associated with variation in phenotypes. A total of 204 single nucleotide polymorphisms (SNPs) present in 3’ UTR of target genes either destroyed or created novel illegitimate microRNA target sites; of them, 78 SNPs explained significant variation in the aforementioned 5 muscle traits. Majority of the phenotype-associated SNPs were present in microRNA-binding sites of genes involved in energy metabolism and muscle structure. These findings suggest that variation in microRNA expression and/or sequence variation in microRNA binding sites in target genes play an important role in mediating differences in fish growth and muscle quality phenotypes.