Antisense long non-coding RNAs in rainbow trout: Discovery and potential role in muscle growth and quality traits

Authors: ALI, ALI - Middle Tennessee State University; AL-TOBASEI, RAFET - Middle Tennessee State University; Leeds, Timothy - Tim; KENNEY, BRETT - West Virginia University; 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: Ali, A., Al-Tobasei, R., Leeds, T.D., Kenney, B., Salem, M. 2017. Antisense long non-coding RNAs in rainbow trout: Discovery and potential role in muscle growth and quality traits [abstract]. Plant and Animal Genome Conference. P1008.

Interpretive Summary:

Technical Abstract: Endogenous mRNA-antisense transcripts are involved in regulation of a wide range of biological processes including muscle development and quality traits of farm animals. Standard RNA-Seq can be used to identify sense-antisense transcripts. However, strand-specific RNA-Seq is required to resolve ambiguity in overlapping genes. To precisely identify antisense lncRNAs (AS-lncRNAs) in rainbow trout, two stranded RNA-Seq data sets from muscle and gill were used. Applying a computational pipeline that we previously described (Al-Tobasei et al 2016), a total of 30,907 lncRNAs have been identified, of them, 862 (2.79%) were transcribed from the opposite strands of protein-coding genes in the rainbow trout genome. RNA-Seq was used to identify differential and co-expression of AS-lncRNA-protein coding genes in association with 5 important growth and muscle 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 AS-lncRNAs and protein-coding genes were sequenced from 26 families showing divergent phenotypes (4 high- versus 4 low-ranked families/trait). AS-lncRNA and their sense genes coding for lipoprotein lipase and adipocyte plasma membrane-associated protein, were upregulated in families showing higher WBW, fat content, muscle yield, and whiteness. Conversely, AS-lncRNA and its sense gene coding for response gene to complement 32 protein were downregulated in families showing increased WBW. Current study will help understanding role of AS-lncRNAs in post-transcriptional gene regulation involved in muscle growth and quality traits in salmonids.