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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #336225

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: MicroRNAs associated with muscle growth and fillet quality in rainbow trout

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

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/14/2016
Publication Date: 1/14/2017
Citation: Paneru, B., Al-Tobasei, R., Leeds, T.D., Kenney, B., Salem, M. 2017. MicroRNAs associated with muscle growth and fillet quality in rainbow trout [abstract]. Plant and Animal Genome Conference. P1006.

Interpretive Summary:

Technical Abstract: Selection for improved muscle growth and quality phenotypes requires understanding of post-transcriptional gene-regulation mechanisms. To investigate role of microRNAs in muscle post-transcriptional gene regulation, RNA-seq was used to identify differential expression in microRNAs and SNPs in microRNA target sites in association with 5 fish/muscle growth and quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, shear force and whiteness. Phenotypic data were collected from ~500 fish representing 98 families (5 fish/family) from a USDA growth-selected line. Muscle microRNAs and protein-coding genes were sequenced from 22 families showing divergent phenotypes (4 high- versus 4 low-ranked families/trait). A total of 91 microRNAs were differentially expressed between high and low ranked families. PCR quantification of microRNA in 90 fish showed that variation in expression of muscle-important microRNAs, mir-1, mir-133, mir-206, mir-19, mir-99, mir-148, mir-20, and mir-181 explained 6.7%-18.8%, 5.6%-16.5%, 6.6%-13.8%, and 6.5%-9% variation in muscle yield, WBW, fat content and shear force, respectively. In addition, 160 SNPs creating or destroying putative microRNA target sites were identified in 128 protein-coding genes. SNPs had allelic imbalances (>2.0 as an amplification and <0.5 as loss of heterozygosity) between the low- and high-ranked families. For example, SNPs with allelic imbalances creating target sites in myf2C (myocyte-specific enhancer factor 2c) gene for a novel microRNA were associated with high muscle yield, shear and fat content. These findings suggest an essential role of microRNA in regulating muscle growth and fillet quality in rainbow trout. Additionally, genetic variation at microRNA targets will help develop genetic markers for selection.