GENOME ANNOTATION AND ROLE OF NON-CODING RNAS IN DISEASE RESISTANCE, GROWTH AND MUSCLE QUALITY TRAITS IN RAINBOW TROUT

Abstract

In Rainbow trout, effort to annotate the genome reference is ongoing. While recently published trout genome has discovered large number of protein coding genes, many protein coding genes appear to be missing. In addition, non-coding RNAs, which occupy vast majority of the transcribed portion of genome, are not investigated. In the present study, we have sequenced and assembled the transcriptomes of lncRNA (long non-coding RNA) and mRNA to facilitate gene discovery, and have investigated the role of non-coding RNAs in disease resistance, muscle atrophy, growth and muscle quality traits.

By sequencing RNA from 13 vital tissues, we identified 44,990 protein-coding and 54,503 lncRNA genes in trout. While lncRNAs were discovered for the first time, 11,843 mRNA genes reported by us were missing in the previously assembled genome reference. A total of 556 lncRNAs were differentially expressed during F. psychrophilum infection. There was strong correlation between lncRNA expression and infection susceptibility of different Rainbow trout genetic lines. These lncRNAs showed correlated expression with immunity related protein-coding genes. In addition, 1,198 lncRNAs showed altered expression during sexual maturation associated muscle atrophy and their expression level correlated with the extent of skeletal muscle atrophy.

We also investigated association of microRNAs with growth parameters and muscle quality traits in Rainbow trout. Twenty-eight microRNAs showed significantly altered expression during sexual maturation associated muscle atrophy. Similarly, 90 microRNAs were differentially expressed between fish families with different phenotypes for 5 fish/muscle growth and quality traits: muscle mass, muscle fat content, muscle shear force (tenderness), muscle whiteness and whole body weight (WBW). Expression of 12 DE microRNAs chosen for ‘genotype-phenotype’ association correlated significantly with the phenotypes. In addition to microRNA expression, at least 72 single nucleotide polymorphisms (SNPs) either destroying or creating novel illegitimate microRNA target sites in protein coding genes explained significant variation in growth and muscle quality phenotypes.

The present study explores role of non-coding RNAs in regulation of important aquaculture traits in Rainbow trout and suggests that non-coding RNA mediated gene regulation plays a critical role in determining these phenotypes.