Identification of Differentially Expressed Genes in Resistant and Susceptible Doubled Haploid Fishes in Response to VHS-Virus Infection By RNA-Seq Analysis

Viral diseases constitute a major threat for aquaculture industry. The Viral Hemorrhagic Septicemia Virus (VHSV) is a rhabdovirus reported to cause economic losses in salmonid farms. We previously produced gynogenetic doubled haploid fishes with a wide range of susceptibility to VHS-V. We selected two clonal lines (one resistant and one susceptible) to investigate the molecular mechanisms of viral resistance.

To this aim, we undertook a whole-genome transcriptome analysis of susceptible and resistant fishes by RNA seq analysis. We investigated the gene expression in control and infected spleens (6 days after infection) and fins (1 day after waterborne infection) of susceptible and resistant fish.

A total of 3.119 billions reads were produced. After quality filtering, these paired end reads were analyzed with Cuffink software. PCA analysis showed concordance among triplicates and clear separation between infected and control samples. Differentially expressed (DE) genes were called via DEseq2 R package.

In spleen, for susceptible fish, we identified 19,324 DE genes whereas for resistant fish, 593 genes were found differentially expressed (padj <0.01 and absolute log2 foldchange = 1). For fin, we identified 47 DE genes in susceptible fish and 28 in resistant fish.

Quantitative PCR will be done in order to validate some of these differentially expressed genes. Pathway analysis and comparison between resistant and susceptible fish will strengthen the understanding of the antiviral response and provide new clues to identify responsible genes for known resistance QTLs.