Integrated analysis of IncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits

Authors: ALI, ALI - 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: 8/4/2018
Publication Date: 8/14/2018
Citation: Ali, A., Al-Tobasei, R., Kenney, B., Leeds, T.D., Salem, M. 2018. Integrated analysis of IncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits. Scientific Reports. 8:12111. https://doi.org/10.1038/s41598-018-30655-8.
DOI: https://doi.org/10.1038/s41598-018-30655-8

Interpretive Summary: Fillet yield, the proportion of the whole fish that is edible fillet, and fillet quality are economically-important traits in rainbow trout aquaculture. Little is known about the genetic control of these traits, and improvement through selective breeding is limited because the traits cannot be measured directly on breeding candidates. In collaboration with scientists from Middle Tennessee State University and West Virginia University, RNA-Seq was used to sequence protein-coding genes and non-coding RNA to identify single nucleotide polymorphisms - genetic variants - and evaluate associations of these polymorphisms with variation in fillet yield and quality traits in the USDA-ARS-NCCCWA rainbow trout population. Unlike coding genes that are transcribed and translated into a specific protein, transcribed non-coding RNA is known in human and terrestrial animal genetics to regulate gene expression and cellular processes. Scientists identified more than 100 polymorphisms in protein-coding genes, and more than 200 non-coding RNAs, that were associated with variation in fillet yield and quality traits. This study furthers our understanding of genetic control of fillet yield and quality traits and will enable rainbow trout breeders to develop more effective, genomic-based selective breeding strategies to accelerate the genetic improvement of these economically-important traits.

Technical Abstract: Muscle yield and quality traits are important for the aquaculture industry and consumers. Genetic selection for these traits is difficult because they are polygenic and result from multifactorial interactions. To study the genetic architecture of these traits, phenotypic characterization of WBW, muscle yield, fat content, shear force and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. We have identified 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, in fish families exhibiting contrasting phenotypes. A total of 102 SNP markers within DE genes were associated with variations in phenotypes. Expression of many DE lncRNAs (n = 229) was positively correlated with overlapping, neighboring or distantly located protein-coding genes (n = 1,030), resulting in 3,392 interactions. Three DE antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. Forty-four DE lncRNAs had potential sponge functions to miRNAs that affect muscle quality traits. This study 1) defines muscle quality associated protein-coding and noncoding genes and 2) provides insight into non-coding RNAs involvement in regulating growth and fillet quality traits in rainbow trout.