Identification of SNPs with Allelic Imbalances in Rainbow Trout Genetic Lines Showing Different Susceptibility to Infection with Flavobacterium psychrophilum

RNA-Seq was used to identify coding/functional SNPs in fish from two genetic lines showing significant difference in susceptibility to Flavobacterium psychrophilum (Fp); the causative pathogen of the salmonid’s bacterial cold water disease (BCWD).

Whole-body fish fry representing resistant and susceptible genetic lines were collected at day-1 and day-5 post-challenge with Fp- versus PBS-injection. 16 RNA-Seq libraries (representing genetic-line X infection status X day of infection) were mapped to the rainbow trout genome. SNPs were predicted using GATK pipeline. A total of 246,506 SNPs were identified in all fish groups. About 57% of the SNPs were distributed in 18,679 genes and the rest of the SNPs were intergenic. Pairwise comparison between the genetic lines and different infection statuses was used to identify SNPs with allelic imbalances at cut-off values of >2.0 as an amplification and <0.5 as loss of heterozygosity.

In resistance verse susceptible lines (regardless of the infection status/day), there were 4,737 SNPs. In the PBS-injected resistance verse susceptible fish, there were 6,463 SNPs. In the Fp-infected resistance verse susceptible fish, there were 5,230 SNPs. In the day-1 versus day-5 Fp-infected fish, there were 2,747 SNPs. In the Fp- verse PBS-injected fish, there were 2,535 SNPs.

Genome distribution of the SNPs with allelic imbalances exhibited high density in several chromosomes, especially chromosome 9 and 28. The SNPs identified in this study were included in a new SNP-chip for genomic and genetic analyses in rainbow trout. The SNP-chip will be used to verify genetic markers predictive of resistance to BCWD.