MicroRNAs Associated with Muscle Growth and Fillet Quality in Rainbow Trout

Selection for improved muscle growth and quality phenotypes requires an understanding of post-transcriptional, gene-regulation mechanisms. To investigate the 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 associated 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 90 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.