Integrated Analysis of lncRNA and mRNA Expression in Rainbow Trout Families Showing Variation in Muscle Growth and Fillet Quality Traits

Muscle yield and quality are important traits for industry and consumers. Genetic selection for these traits is difficult because they result from the interaction of multiple factors.  Additionally, quality may signify one or a combination of attributes such as texture, color and composition. Importantly, these traits are polygenic or controlled by many genes. To study the genetic architecture of these traits at the transcription level, phenotypic characterization of total body weight, muscle yield, muscle fat content, shear force and whiteness were measured in 500 fish representing 98 families (5 fish/family) from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families showing divergent phenotypes (high versus low ranked families) for each trait. Seventy-five differentially expressed protein-coding genes and 162 lncRNAs were identified between fish families with contrasting phenotypes. Remarkably, the expression of some differentially expressed protein-coding genes was correlated with that of differentially expressed lncRNAs. Transcripts encoding stanniocalcin, connective tissue growth factor-like isoform X1, large neutral amino acids small subunit 2-like transporter, and Response gene to complement-32 protein (RGC-32) were positively correlated with the following lncRNAs, respectively: Omy100092090 (R²=0.91), Omy100115680 (R²=0.81), Omy400009923 (R²=0.93) & Omy200090267 (R²=0.88), and Omy200080884 (R²=0.84). Interestingly, Omy200080884 was antisense (exonic) with RGC-32.  This study 1) defines muscle quality associated protein-coding and lncRNA genes and 2) provides the first evidence of lncRNA involvement in regulating growth and fillet quality traits in fish. This information enhances our understanding of molecular mechanisms regulating economically important phenotypic traits in aquaculture species.