Abstract
Genetic improvement for enhanced disease resistance in fish is an increasingly utilized approach to mitigate endemic infectious disease in aquaculture. In domesticated salmonid populations, large phenotypic variation in disease resistance has been identified but the genetic basis for altered responsiveness remains unclear. We previously reported three generations of selection and phenotypic validation of a bacterial cold water disease (BCWD) resistant line of rainbow trout, designated ARS-Fp-R. This line has higher survival after infection by either standardized laboratory challenge or natural challenge as compared to two reference lines, designated ARS-Fp-C (control) and ARS-Fp-S (susceptible). In this study, we utilized 1.1 g fry from the three genetic lines and performed RNA-seq to measure transcript abundance from the whole body of naive and Flavobacterium psychrophilum infected fish at day 1 (early time-point) and at day 5 post-challenge (onset of mortality). Sequences from 24 libraries were mapped onto the rainbow trout genome reference transcriptome of 46,585 predicted protein coding mRNAs that included 2633 putative immune-relevant gene transcripts. A total of 1884 genes (4.0% genome) exhibited differential transcript abundance between infected and mock-challenged fish (FDR < 0.05) that included chemokines, complement components, tnf receptor superfamily members, interleukins, nod-like receptor family members, and genes involved in metabolism and wound healing. The largest number of differentially expressed genes occurred on day 5 post-infection between naive and challenged ARS-Fp-S line fish correlating with high bacterial load. After excluding the effect of infection, we identified 21 differentially expressed genes between the three genetic lines. In summary, these data indicate global transcriptome differences between genetic lines of naive animals as well as differentially regulated transcriptional responses to infection.
Highlights
Selective breeding programs contribute to increased aquaculture production through the generation of animals with improved resistance/tolerance toward infectious disease causing microorganisms (Gjedrem, 1983, 2005; Van Muiswinkel et al, 1999; Cock et al, 2009; Gjedrem et al, 2012)
Differences in bacterial load cannot account for transcriptional differences observed on day 1, as bacterial loads were similar between genetic lines
In this study we did not analyze long non-coding RNA, microRNA and splice variants. We suggest that this data set represents an important future resource for exploration of candidate genes identified from Quantitative trait loci (QTL) analyses being conducted in parallel with this study
Summary
Selective breeding programs contribute to increased aquaculture production through the generation of animals with improved resistance/tolerance toward infectious disease causing microorganisms (Gjedrem, 1983, 2005; Van Muiswinkel et al, 1999; Cock et al, 2009; Gjedrem et al, 2012). In 2005, a family-based selective breeding program was initiated at the National Center for Cool and Cold Water Aquaculture (NCCCWA) to improve rainbow trout (Oncorhynchus mykiss) survival following exposure to Flavobacterium psychrophilum (Silverstein et al, 2009). This pathogen is the etiologic agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS), and causes considerable losses to the rainbow trout aquaculture industry within the U.S and to trout and salmon populations worldwide (Nematollahi et al, 2003; Barnes and Brown, 2011). Disease prevention is difficult as the pathogen is geographically wide spread, limited chemotherapeutants are available for treatment, and there is currently no commercial vaccine available in the U.S, killed, subunit, and live-attenuated vaccines are all active areas of research (Gómez et al, 2014; Sundell et al, 2014)
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