Antisense Long Non-Coding RNAs in Rainbow Trout: Discovery and Potential Role in Muscle Growth and Quality Traits

Endogenous mRNA-antisense transcripts are involved in regulation of a wide range of biological processes, including muscle development and quality traits of terrestrial food animal species. 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 tissues were used. Applying a computational pipeline that we previously described (Al-Tobasei et al 2016), a total of 30,907 lncRNAs was identified; of these lncRNAs, 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) of 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. This study highlights the role of AS-lncRNAs in post-transcriptional gene regulation governing muscle growth and quality traits in salmonids.