Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum

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.

Differential expression of long non-coding RNAs in three genetic lines of rainbow trout in response to infection with Flavobacterium psychrophilum

“…GPB1 gene transcript also shows correlated expression with lncRNA in human26. Previous reports suggested that gbp1 is one of the differentially regulated immune response genes against microbial pathogens in salmon and trout927.…”

“…Previously, we analyzed mRNA expression in three genetic lines of fish sampled at 1 and 5 days post- Fp challenge9. In our prior analyses, slightly more than half (51.77%) of the RNA-Seq reads aligned to the 46,585 predicted coding mRNAs and thus considerable sequence information remained unaligned and thus enigmatic.…”

“…Of these, 556 were unique lncRNA showing differential expression in at least one comparison (Supplementary Dataset 2 tab “ALL DEF, non-redundant”). In our previous study using the same genetic lines, ~2,600 DE immune-related and other protein-coding genes were identified in response to Fp infection9. We quantified the number of DE lncRNAs between different genetic lines and infection statuses (total 24 comparisons) and compared the number with that of DE protein-coding genes.…”

“…This line has improved disease resistance against Fp infection in both laboratory and field settings compared to a susceptible (ARS-Fp-S) and randomly bred control (ARS-Fp-C) lines8. Previously, we performed global expression analysis of protein-coding genes in these genetic lines upon Fp challenge9. The study identified a large number of DE protein-coding genes among genetic lines, a significant proportion of which were genes with described roles in the immune response, especially the innate immune system.…”

Genomics in Aquaculture to Better Understand Species Biology and Accelerate Genetic Progress

“…These resources will provide powerful tools for the research community and will aid in the determination of the genetic factors involved in the regulation of complex traits. For example, high-throughput RNA sequencing can give a holistic view of the host response to infectious diseases, and help identify the important genes and pathways defining genetic resistance, as demonstrated in this issue for rainbow trout (Ali et al, 2014;Marancik et al, 2014) and panaeid shrimp (Santos et al, 2014). Sequencing technology has also facilitated the development of abundant genetic markers that have multi-faceted applications for selective breeding of aquatic species, including parentage assignment in mixedfamily environments, providing greater control over family representation and inbreeding (Vandeputte and Haffray, 2014).…”