Assessment of genetic correlation between bacterial cold water disease resistance and spleen index in a domesticated population of rainbow trout: identification of QTL on chromosome Omy19

Immersion challenge of three salmonid species (family Salmonidae) with three multilocus sequence typing variants of Flavobacterium psychrophilum provides evidence of differential host specificity

Bacterial coldwater disease (BCWD), caused by Flavobacterium psychrophilum, results in significant losses among multiple salmonid (family Salmonidae) species. Molecular epidemiology and serotyping studies have suggested that some variants are host specific; however, these associations have not been evaluated by cross-challenging fish species with putatively host-associated F. psychrophilum isolates via more natural (i.e. immersion) exposure routes. To this end, F. psychrophilum isolates US19-COS, US62-ATS and US87-RBT, each originally recovered from diseased coho salmon (Oncorhynchus kisutch), Atlantic salmon (Salmo salar) or rainbow trout (O. mykiss), and belonging to a host-associated multilocus sequence typing clonal complex (e.g. CC-ST9, CC-ST232 or CC-ST10), were PCR-serotyped, evaluated for proteolytic activity, and used to challenge adipose fin-clipped 4-month old Atlantic salmon, coho salmon and rainbow trout via immersion. Findings showed US87-RBT caused disease and mortality only in rainbow trout (e.g. 56.7% survival probability). US19-COS and US62-ATS caused more mortality in coho salmon and Atlantic salmon but also caused disease in both other host species, albeit to a lesser extent. Observed survival differences may be due to variant antigenic/virulence determinants as differences in serotype and proteolytic activity were discovered. Collectively, results highlight the intricacies of F. psychrophilum-host interactions and provide further in vivo evidence that some F. psychrophilum MLST variants are host specific, which may have implications for the development of BCWD prevention and control strategies.

Plasma proteomic profiling of bacterial cold water disease-resistant and -susceptible rainbow trout lines and biomarker discovery

Genetic variation for disease resistance is present in salmonid fish; however, the molecular basis is poorly understood, and biomarkers of disease susceptibility/resistance are unavailable. Previously, we selected a line of rainbow trout for high survival following standardized challenge with Flavobacterium psychrophilum (Fp), the causative agent of bacterial cold water disease. The resistant line (ARS-Fp-R) exhibits over 60 percentage points higher survival compared to a reference susceptible line (ARS-Fp-S). To gain insight into the differential host response between genetic lines, we compared the plasma proteomes from day 6 after intramuscular challenge. Pooled plasma from unhandled, PBS-injected, and Fp-injected groups were simultaneously analyzed using a TMT 6-plex label, and the relative abundance of 513 proteins was determined. Data are available via ProteomeXchange, with identifier PXD041308, and the relative protein abundance values were compared to mRNA measured from a prior, whole-body RNA-seq dataset. Our results identified a subset of differentially abundant intracellular proteins was identified, including troponin and myosin, which were not transcriptionally regulated, suggesting that these proteins were released into plasma following pathogen-induced tissue damage. A separate subset of high-abundance, secreted proteins were transcriptionally regulated in infected fish. The highest differentially expressed protein was a C1q family member (designated complement C1q-like protein 3; C1q-LP3) that was upregulated over 20-fold in the infected susceptible line while only modestly upregulated, 1.8-fold, in the infected resistant line. Validation of biomarkers was performed using immunoassays and C1q-LP3, skeletal muscle troponin C, cathelcidin 2, haptoglobin, leptin, and growth and differentiation factor 15 exhibited elevated concentration in susceptible line plasma. Complement factor H-like 1 exhibited higher abundance in the resistant line compared to the susceptible line in both control and challenged fish and thus was a baseline differentiator between lines. C1q-LP3 and STNC were elevated in Atlantic salmon plasma following experimental challenge with Fp. In summary, these findings further the understanding of the differential host response to Fp and identifies salmonid biomarkers that may have use for genetic line evaluation and on-farm health monitoring.

Interplay between a bacterial pathogen and its host in rainbow trout isogenic lines with contrasted susceptibility to cold water disease

Infectious diseases are a major constraint on aquaculture. Genetic lines with different susceptibilities to diseases are useful models to identify resistance mechanisms to pathogens and to improve prophylaxis. Bacterial cold-water disease (BCWD) caused by Flavobacterium psychrophilum represents a major threat for freshwater salmonid farming worldwide. A collection of rainbow trout (Oncorhynchus mykiss) isogenic lines was previously produced from a French domestic population. Here, we compared BCWD resistance phenotypes using a subset of isogenic lines chosen for their contrasted susceptibilities to F. psychrophilum. We applied individual monitoring to document the infection process, including time-course quantification of bacteremia and innate immune response. Strikingly, BCWD resistance was correlated with a lower bacterial growth rate in blood. Several immune genes were expressed at higher levels in resistant fish regardless of infection: the Type II arginase (arg2), a marker for M2 macrophages involved in anti-inflammatory responses and tissue repair, and two Toll-like receptors (tlr2/tlr7), responsible for pathogen detection and inflammatory responses. This study highlights the importance of innate and intrinsic defense mechanisms in determining the outcome of F. psychrophilum infections, and illustrates that non-lethal time-course blood sampling for individual monitoring of bacteremia is a powerful tool to resolve within-host pathogen behavior in bacterial fish diseases.

Validation of a QTL associated with resistance to Vibrio anguillarum in rainbow trout (Oncorhynchus mykiss)

Vibriosis is a bacterial disease in fish caused by the Gram negative bacterium Vibrio anguillarum with severe impact on rainbow trout (Oncorhynchus mykiss) farming. Sustainable control methods should be developed and we here show that marker assisted selective breeding of fish naturally resistant to the disease is feasible. We have validated the use of a single nucleotide polymorphism (SNP) marker SNP AX-89,945,921 (QTL on chromosome 21). The QTL was previously found associated with resistance to vibriosis and described following a genome wide association analysis (GWAS) of trout exposed to the bacterium. For this validation spawners were genotyped by use of the 57 K Axiom®Trout Microarray (Affymetrix) and homozygous male fish carrying the allele with the SNP AX-89,945,921 were then selected and used to fertilize eggs from outbred female trout resulting in fish all carrying the SNP (QTL-fish). Control fish (non-QTL fish) were produced by fertilizing the same batch of eggs by use of male parents negative for the SNP. The fish were exposed in freshwater to V. anguillarum (water bath infection) at 19 C°. A total of 900 fish were challenged in a common garden set-up in triplicate. A bacterial solution of V. anguillarum (serotype O1) was added to each of three freshwater fish tanks, each with 150 QTL and 150 non-QTL fish. Fish were tagged by tail fin cut (upper/lower) to discern the two groups, whereafter fish were monitored around the clock to detect disease signs and remove moribund fish. Clinical vibriosis developed within two days in non-QTL-fish (overall morbidity of 70%). QTL fish developed clinical signs later and the morbidity was significantly lower and did not reach 50%. Rainbow trout farming may benefit from using the QTL associated with higher resistance towards vibriosis. The effect may be optimized in the future by use of both male and female parents homozygous for the marker allele.

Astragalus polysaccharide improves the growth, meat quality, antioxidant capacity and bacterial resistance of Furong crucian carp (Furong carp♀ × red crucian carp♂)

To evaluate the functional effects of APS (Astragalus polysaccharide) on Furong crucian carp, APS-supplemented diets (0.00 %, 0.05 %, 0.10 % and 0.15 %) were prepared and utilized in feeding experiment. The results showed that the 0.05 % APS group has the highest weight gain rate and specific growth rate, and the lowest feed coefficient rate. In addition, 0.05 % APS supplement could improve muscle elasticity, adhesiveness and chewiness. Moreover, the 0.15 % APS group had the highest spleen-somatic index and the 0.05 % group had the maximum intestinal villus length. 0.05 % and 0.10 % APS addition significantly increased T-AOC and CAT activities while MDA contents decreased in all APS groups. The plasma TNF-α levels in all APS groups significantly increased (P<0.05), and the 0.05 % group showed the highest TNF-α level in spleen. In APS addition groups, the tlr8, lgp2 and mda5 gene expressions were significantly elevated, while xbp1, caspase-2 and caspase-9 expressions decreased in uninfected and A. hydrophila-infected fish. Finally, higher survival rate and slower disease outbreak rate were observed in APS-supplemented groups after being infected by A. hydrophila. In conclusion, Furong crucian carp fed by APS-supplemented diets possesses elevated weight gain rate and specific growth rate, and improved meat quality, immunity and disease resistance.

Control of parasitic diseases in aquaculture

Finfish aquaculture in freshwater and marine environments is continuously expanding globally, and the potential for a substantial further increase is well documented. The industry is supplying fish products for human consumption to the same extent as capture fisheries, and new fish species for domestication are still being selected by the industry. The challenge faced by all aquacultured species, classical and novel, is the range of pathogens associated with each new fish type. A fish host in its natural environment carries a series of more or less specific parasites (specialists and generalists). Some of these show a marked ability to propagate in aquaculture settings. They may then elicit disease when infection intensities in the confined aquaculture environment reach high levels. In addition, the risk of transmission of parasites from aquaculture enterprises to wild fish stocks adds to the parasitic challenge. Control programmes of various kinds are needed and these may include chemotherapeutants and medicines as the farmer's first and convenient choice, but mechanical, biological, immunological and genetic control methods are available solutions. New methods are still to be developed by scrutinizing the life cycle of each particular parasite species and pin-pointing the vulnerable stage to be targeted. As parasites exhibit a huge potential for adaptation to environmental changes, one must realize that only one approach rarely is sufficient. The present work therefore elaborates on and advocates for implementation of integrated control strategies for diseases caused by protozoan and metazoan parasites.

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.

Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing

Bacterial cold water disease (BCWD) is an important disease in rainbow trout aquaculture. Previously, we have identified and validated two major QTL (quantitative trait loci) for BCWD resistance, located on chromosomes Omy08 and Omy25, in the odd-year Troutlodge May spawning population. We also demonstrated that marker-assisted selection (MAS) for BCWD resistance using the favorable haplotypes associated with the two major QTL is feasible. However, each favorable haplotype spans a large genomic region of 1.3–1.6 Mb. Recombination events within the haplotype regions will result in new haplotypes associated with BCWD resistance, which will reduce the accuracy of MAS for BCWD resistance over time. The objectives of this study were 1) to identify additional SNPs (single nucleotide polymorphisms) associated with BCWD resistance using whole-genome sequencing (WGS); 2) to validate the SNPs associated with BCWD resistance using family-based association mapping; 3) to refine the haplotypes associated with BCWD resistance; and 4) to evaluate MAS for BCWD resistance using the refined QTL haplotypes. Four consecutive generations of the Troutlodge May spawning population were evaluated for BCWD resistance. Parents and offspring were sequenced as individuals and in pools based on their BCWD phenotypes. Over 12 million SNPs were identified by mapping the sequences from the individuals and pools to the reference genome. SNPs with significantly different allele frequencies between the two BCWD phenotype groups were selected to develop SNP assays for family-based association mapping in three consecutive generations of the Troutlodge May spawning population. Among the 78 SNPs derived from WGS, 77 SNPs were associated with BCWD resistance in at least one of the three consecutive generations. The additional SNPs associated with BCWD resistance allowed us to reduce the physical sizes of haplotypes associated with BCWD resistance to less than 0.5 Mb. We also demonstrated that the refined QTL haplotypes can be used for MAS in the Troutlodge May spawning population. Therefore, the SNPs and haplotypes reported in this study provide additional resources for improvement of BCWD resistance in rainbow trout.

Genome-Wide Association Analysis Reveals the Genetic Architecture of Parasite (Cryptocaryon irritans) Resistance in Large Yellow Croaker (Larimichthys crocea)

Large yellow croaker is an important marine culture species in China. Recently, the large yellow croaker industry is threatened by various disease problems, especially for the white spot disease, which is caused by parasite Cryptocaryon irritans. In the current study, we conducted a genome-wide association study (GWAS) for C. irritans resistance in two large yellow croaker populations (n = 264 and n = 480, respectively). We identified 15 QTL with explained genetic variance ranging from 1 to 8% in the two populations. One QTL on chromosome 23 was shared by the two populations, and three QTL had been reported in the previous study. We identified a lot of biological pathways associated with C. irritans resistance, such as hormone transport, response to bacterium, apoptotic process, acute inflammatory response to antigenic stimulus, and NF-kappa B signaling pathway. The genes casp8 and traf6 involved in regulatory network for apoptosis and inflammation were identified to be candidate genes for C. irritans resistance. Our results showed the complex polygenic architecture of resistance of large yellow croaker against C. irritans. These results would be helpful for the researches of the molecular mechanism of C. irritans resistance and genome-assisted breeding of large yellow croaker.

A BCWD-Resistant line of rainbow trout is less sensitive to cortisol implant-induced changes in IgM response as compared to a susceptible (control) line

In salmonids, stress responses increase cortisol levels and disease susceptibility, including to Flavobacterium psychrophilum (Fp), the causative agent of BCWD. A BCWD-resistant line (R-line) of rainbow trout was used here to investigate potential differences in immunoglobulin response after a combined treatment of cortisol and Fp, as compared to a susceptible (S-line) control line. Expression of membrane and secreted immunoglobulin heavy chains mu and tau were determined by RT-qPCR in spleen and anterior kidney. Cortisol treatment did not affect B cell development in the anterior kidney, but delayed IgM responses at the early stage of infection in the spleen of both lines. An earlier IgM response was a determining factor in differential disease progression between resistant- and susceptible fish after Fp-challenge. S-line fish had a delayed and exacerbated IgM response after cortisol implant indicative of a detrimental cycle of sustained IgM responses and high pathogen loads. In contrast, R-line fish had delayed but milder, and protective IgM responses and cleared pathogen successfully. Fp challenge after cortisol implant increased serum cortisol levels on days 3 and 5 compared to mock treatments in S-line fish, but only on day 3 in R-line. Hence, combined cortisol treatment and Fp challenge differentially modulated B cell activation and Fp loads in BCWD-resistant and susceptible lines of rainbow trout. We propose that under conditions of increased stress, BCWD-resistant fish may remain immunologically better equipped to respond to infections compared to BCWD susceptible fish.

A Major QTL for Resistance to Vibrio anguillarum in Rainbow Trout

Genetic selection of disease resistant fish is a major strategy to improve health, welfare and sustainability in aquaculture. Mapping of single nucleotide polymorphisms (SNP) in the fish genome may be a fruitful tool to define relevant quantitative trait loci (QTL) and we here show its use for characterization of Vibrio anguillarum resistant rainbow trout (Oncorhynchus mykiss). Fingerlings were exposed to the pathogen V. anguillarum serotype O1 in a solution of 1.5 × 10⁷ cfu/ml and observed for 14 days. Disease signs appeared 3 days post exposure (dpe) whereafter mortality progressed exponentially until 6 dpe reaching a total mortality of 55% within 11 days. DNA was sampled from all fish – including survivors – and analyzed on a 57 k Affymetrix SNP platform whereby it was shown that disease resistance was associated with a major QTL on chromosome 21 (Omy 21). Gene expression analyses showed that diseased fish activated genes associated with innate and adaptive immune responses. The possible genes associated with resistance are discussed.

Quantitative trait loci (QTL) associated with resistance of rainbow trout Oncorhynchus mykiss against the parasitic ciliate Ichthyophthirius multifiliis

The parasitic ciliate Ichthyophthirius multifiliis has a low host specificity eliciting white spot disease (WSD) in a wide range of freshwater fishes worldwide. The parasite multiplies rapidly whereby the infection may reach problematic levels in a host population within a few days. The parasite targets both wild and cultured fish but the huge economic impact of the protozoan is associated with mortality, morbidity and treatment in aquacultural enterprises. We have investigated the potential for genetic selection of WSD-resistant strains of rainbow trout. Applying the DNA typing system Affymetrix® and characterizing the genome of the individual fish by use of 57,501 single nucleotide polymorphisms (SNP) and their location on the rainbow trout chromosomes, we have genetically characterized rainbow trout with different levels of natural resistance towards WSD. Quantitative trait loci (QTL) used for the selection of breeders with specific markers for resistance are reported. We found a significant association between resistance towards I. multifiliis infection and SNP markers located on the two specific rainbow trout chromosomes Omy 16 and Omy 17. Comparing the expression of immune-related genes in fish-with and without clinical signs-we recorded no significant difference. However, trout surviving the infection showed high expression levels of genes encoding IgT, T-cell receptor TCRβ, C3, cathelicidins 1 and 2 and SAA, suggesting these genes to be associated with protection.

Immune gene expression and genome-wide association analysis in rainbow trout with different resistance to Yersinia ruckeri infection

Selective breeding programmes involving marker assisted selection of innately pathogen resistant strains of rainbow trout rely on reliable controlled infection studies, extensive DNA typing of individual fish and recording of expression of relevant genes. We exposed juvenile rainbow trout (6 h bath to 2.6 × 10⁵ CFU mL^-1) to the fish pathogen Yersinia ruckeri serotype O1, biotype 2, eliciting Enteric Red Mouth Disease ERM, and followed the disease progression over 21 days. Cumulative mortality reached 42% at 12 days post challenge (dpc) after which no disease signs were recorded. All fish were sampled for DNA-typing (50 k SNP chip, Affymetrix®) throughout the course of infection when they showed clinical signs of disease (susceptible fish) or at day 21 when fish showed no clinical signs of disease (survivors - resistant fish). Genome-wide association analyses of 1027 trout applying single nucleotide polymorphisms (SNPs) as markers revealed an association between traits (susceptible/resistant) and certain regions of the trout genome. It was indicated that multiple genes are involved in rainbow trout resistance towards ERM whereby it is considered a polygenic trait. A corresponding trout group was kept as non-exposed controls and a comparative expression analysis of central innate and adaptive immune genes in gills, spleen and liver was performed for three fish groups: 1) moribund trout exhibiting clinical signs 7 dpc (CS), 2) exposed fish without clinical signs at the same sampling point (NCS) and 3) surviving fish at 21 dpc (survivors). Immune genes encoding inflammatory cytokines (IL-1β, IL-2A, IL-6A, IL-8, IL-10A, IL-12, IL-17A/F2A, IL-17C1, IL-17C2, IL-22, IFNγ, TNFα), acute phase reactants (SAA, C3, cathelicidins, lysozyme) were expressed differently in CS and NCS fish. Correlation (negative or positive) between expression of genes and bacterial load suggested involvement of immune genes in protection. Down-regulation of adaptive immune genes including IgDm, IgDs, IgT and TCR-β was seen primarily in CS and NCS fish whereas survivors showed up-regulation of effector molecule genes such as cathelicidins, complement and lysozyme suggesting their role in clearing the infection. In conclusion, SNP analyses indicated that ERM resistance in rainbow trout is a multi-locus trait. The gene expression in surviving fish suggested that several immune genes are associated with the trait conferring resistance.

Salmonid Antibacterial Immunity: An Aquaculture Perspective

The aquaculture industry is continuously threatened by infectious diseases, including those of bacterial origin. Regardless of the disease burden, aquaculture is already the main method for producing fish protein, having displaced capture fisheries. One attractive sector within this industry is the culture of salmonids, which are (a) uniquely under pressure due to overfishing and (b) the most valuable finfish per unit of weight. There are still knowledge gaps in the understanding of fish immunity, leading to vaccines that are not as effective as in terrestrial species, thus a common method to combat bacterial disease outbreaks is the use of antibiotics. Though effective, this method increases both the prevalence and risk of generating antibiotic-resistant bacteria. To facilitate vaccine design and/or alternative treatment efforts, a deeper understanding of the teleost immune system is essential. This review highlights the current state of teleost antibacterial immunity in the context of salmonid aquaculture. Additionally, the success of current techniques/methods used to combat bacterial diseases in salmonid aquaculture will be addressed. Filling the immunology knowledge gaps highlighted here will assist in reducing aquaculture losses in the future.

Combining Multiple Approaches and Models to Dissect the Genetic Architecture of Resistance to Infections in Fish

Infectious diseases represent a major threat for the sustainable development of fish farming. Efficient vaccines are not available against all diseases, and growing antibiotics resistance limits the use of antimicrobial drugs in aquaculture. It is therefore important to understand the basis of fish natural resistance to infections to help genetic selection and to develop new approaches against infectious diseases. However, the identification of the main mechanisms determining the resistance or susceptibility of a host to a pathogenic microbe is challenging, integrating the complexity of the variation of host genetics, the variability of pathogens, and their capacity of fast evolution and adaptation. Multiple approaches have been used for this purpose: (i) genetic approaches, QTL (quantitative trait loci) mapping or GWAS (genome-wide association study) analysis, to dissect the genetic architecture of disease resistance, and (ii) transcriptomics and functional assays to link the genetic constitution of a fish to the molecular mechanisms involved in its interactions with pathogens. To date, many studies in a wide range of fish species have investigated the genetic determinism of resistance to many diseases using QTL mapping or GWAS analyses. A few of these studies pointed mainly toward adaptive mechanisms of resistance/susceptibility to infections; others pointed toward innate or intrinsic mechanisms. However, in the majority of studies, underlying mechanisms remain unknown. By comparing gene expression profiles between resistant and susceptible genetic backgrounds, transcriptomics studies have contributed to build a framework of gene pathways determining fish responsiveness to a number of pathogens. Adding functional assays to expression and genetic approaches has led to a better understanding of resistance mechanisms in some cases. The development of knock-out approaches will complement these analyses and help to validate putative candidate genes critical for resistance to infections. In this review, we highlight fish isogenic lines as a unique biological material to unravel the complexity of host response to different pathogens. In the future, combining multiple approaches will lead to a better understanding of the dynamics of interaction between the pathogen and the host immune response, and contribute to the identification of potential targets of selection for improved resistance.

Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations

Background

Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population.

Methods

Two aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fish from NCCCWA and TLUM, respectively. SNP effects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fivefold cross-validation scheme and using a linear regression method.

Results

Validation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations.

Conclusions

Our results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufficiently informative for selection decisions across populations.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0484-4) contains supplementary material, which is available to authorized users.

Variance and covariance estimates for resistance to bacterial cold water disease and columnaris disease in two rainbow trout breeding populations1

Family-based selective breeding can be an effective strategy for controlling diseases in aquaculture. This study aimed to estimate (co)variance components for resistance to bacterial cold water disease (BCWD) and columnaris disease (CD) in two unrelated rainbow trout nucleus breeding populations: the USDA, ARS, National Center for Cool and Cold Water Aquaculture odd-year line (ARS-Fp-R), which has been subjected to five generations of selection for improved resistance to BCWD, and the Troutlodge, Inc., May-spawning odd-year line (TLUM), which has been selected for improved growth performance but not for disease resistance. A total of 46,805 and 27,821 pedigree records were available from both populations, respectively. Between 44 and 138 families per generation and population were evaluated under controlled BCWD and CD challenges, providing 32,311 and 17,861 phenotypic records for BCWD resistance, and 13,603 and 9,413 for CD resistance, in the ARS-Fp-R and TLUM populations, respectively. A two-trait animal threshold model assuming an underlying normal distribution for the binary survival phenotypes was used to estimate (co)variance components separately for each population. Resistance to BCWD (h2 = 0.27 ± 0.04 and 0.43 ± 0.08) and CD (h2 = 0.23 ± 0.07 and 0.34 ± 0.09) was moderately heritable in the ARS-Fp-R and TLUM populations, respectively. The genetic correlation between the resistance to BCWD and CD was favorably positive in the ARS-Fp-R (0.40 ± 0.17) and TLUM (0.39 ± 0.18) populations. These findings suggest that both disease resistance traits can be improved simultaneously even if genetic selection pressure is applied to only one of the two traits.

Major Histocompatibility Complex (MHC) Genes and Disease Resistance in Fish

Fascinating about classical major histocompatibility complex (MHC) molecules is their polymorphism. The present study is a review and discussion of the fish MHC situation. The basic pattern of MHC variation in fish is similar to mammals, with MHC class I versus class II, and polymorphic classical versus nonpolymorphic nonclassical. However, in many or all teleost fishes, important differences with mammalian or human MHC were observed: (1) The allelic/haplotype diversification levels of classical MHC class I tend to be much higher than in mammals and involve structural positions within but also outside the peptide binding groove; (2) Teleost fish classical MHC class I and class II loci are not linked. The present article summarizes previous studies that performed quantitative trait loci (QTL) analysis for mapping differences in teleost fish disease resistance, and discusses them from MHC point of view. Overall, those QTL studies suggest the possible importance of genomic regions including classical MHC class II and nonclassical MHC class I genes, whereas similar observations were not made for the genomic regions with the highly diversified classical MHC class I alleles. It must be concluded that despite decades of knowing MHC polymorphism in jawed vertebrate species including fish, firm conclusions (as opposed to appealing hypotheses) on the reasons for MHC polymorphism cannot be made, and that the types of polymorphism observed in fish may not be explained by disease-resistance models alone.

Aluminum adjuvant potentiates gilthead seabream immune responses but induces toxicity in splenic melanomacrophage centers

A key goal of a successful vaccine formulation is the strong induction of persistent protective immune responses without producing side-effects. Adjuvants have been proved to be successful in several species at inducing increased immune responses against poorly immunogenic antigens. Fish are not the exception and promising results of adjuvanted vaccine formulations in many species are needed. In this study, over a period of 300 days, we characterized the apparent damage and immune response in gilthead seabream immunized by intraperitoneal injection with the model antigen keyhole limpet hemocyanin (KLH) alone or formulated with Montanide ISA water-in-oil (761 or 763), or Imject™ aluminum hydroxide (aluminium), as adjuvants. Throughout the trial, external tissue damage was examined visually, but no change was observed. Internally, severe adhesions, increased fat tissue, and hepatomegaly were recorded, but, without impairing animal health. At 120 days post priming (dpp), histopathological evaluations of head-kidney, spleen and liver revealed the presence of altered melanomacrophage centers (MMC) in HK and spleen, but not in liver. Surprisingly, in all aluminium treated fish, classical stains unmasked a toxic effect on splenic-MMC, unequivocally characterized by a strong cell depletion. Furthermore, at 170 dpp transmission electron microscopy confirmed this data. Paradoxically, at the same time powerful immune responses were recorded in most vaccinated groups, including the aluminium treatment. Whatever the case, despite the observed adhesions and MMC depletion, fish physiology was not affected, and most side-effects were resolved after 300 dpp. Therefore, our data support adjuvant inclusion, but strongly suggest that use of aluminium must be further explored in detail before it might benefit the rational design of new vaccination strategies in aquaculture.

Innate immune cell signatures in a BCWD-Resistant line of rainbow trout before and after in vivo challenge with Flavobacterium psychrophilum

Phenotypes of myeloid-lineage cells remain poorly understood in the rainbow trout, and were the focus of this study, including effects of in vivo challenge to Flavobacterium psychrophilum (Fp), the cause of Bacterial Cold Water Disease (BCWD). A genetic line was used that is highly resistant to BCWD (R-line) as well as a susceptible control line (S-line). Using flow cytometry, we describe two Pax5-negative, myeloid-lineage populations: Population 1 consisted of small cells with high SSC and strong staining for Q4E, MPO, Pu1, EBF, and IL- 1β, which we named "neutrophil-like" cell. Population 2 had high Q4E, but weaker MPO, Pu1, EBF, and IL-1β staining. Five days after Fp-challenge, both genetic lines had a reduced abundance of neutrophil-like cells in anterior kidney, PBL, and spleen. Pop. 2 abundance was reduced in anterior kidney, and increased in spleen. S-line fish responded more strongly to Fp-challenge compared to R-line fish. Challenged fish with a higher abundance of neutrophil-like cells had significantly lower Fp-loads after challenge, suggesting that these cells aid in the resistance to BCWD.

Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions

Background

Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledge of the genetic basis of resistance to F. psychrophilum would help to implement this trait in selection schemes and to investigate the immune mechanisms associated with resistance. Various studies have revealed that skin and mucus may contribute to response to infection. However, previous quantitative trait loci (QTL) studies were conducted by using injection as the route of infection. Immersion challenge, which is assumed to mimic natural infection by F. psychrophilum more closely, may reveal different defence mechanisms.

Results

Two isogenic lines of rainbow trout with contrasting susceptibilities to F. psychrophilum were crossed to produce doubled haploid F2 progeny. Fish were infected with F. psychrophilum either by intramuscular injection (115 individuals) or by immersion (195 individuals), and genotyped for 9654 markers using RAD-sequencing. Fifteen QTL associated with resistance traits were detected and only three QTL were common between the injection and immersion. Using a model that accounted for epistatic interactions between QTL, two main types of interactions were revealed. A “compensation-like” effect was detected between several pairs of QTL for the two modes of infection. An “enhancing-like” interaction effect was detected between four pairs of QTL. Integration of the QTL results with results of a previous transcriptomic analysis of response to F. psychrophilum infection resulted in a list of potential candidate immune genes that belong to four relevant functional categories (bacterial sensors, effectors of antibacterial immunity, inflammatory factors and interferon-stimulated genes).

Conclusions

These results provide new insights into the genetic determinism of rainbow trout resistance to F. psychrophilum and confirm that some QTL with large effects are involved in this trait. For the first time, the role of epistatic interactions between resistance-associated QTL was evidenced. We found that the infection protocol used had an effect on the modulation of defence mechanisms and also identified relevant immune functional candidate genes.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0431-9) contains supplementary material, which is available to authorized users.

Retrospective Evaluation of Marker-Assisted Selection for Resistance to Bacterial Cold Water Disease in Three Generations of a Commercial Rainbow Trout Breeding Population

Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is an endemic and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. Previously, we have identified SNPs (single nucleotide polymorphisms) associated with BCWD resistance in rainbow trout. The objectives of this study were (1) to validate the SNPs associated with BCWD resistance in a commercial breeding population; and (2) to evaluate retrospectively the accuracy of MAS (marker-assisted selection) for BCWD resistance in this commercial breeding program. Three consecutive generations of the Troutlodge May breeding population were evaluated for BCWD resistance. Based on our previous studies, a panel of 96 SNPs was selected and used to genotype the parents and ten offspring from each of the 138 full-sib families of the 2015 generation, and 37 SNPs associated with BCWD resistance were validated. Thirty-six of the validated SNPs were clustered on chromosomes Omy3, Omy8 and Omy25. Thus, at least three QTL (quantitative trait loci) for BCWD resistance were validated in the 2015 generation. Three SNPs from each QTL region were used for haplotype association analysis. Three haplotypes, Omy3TGG, Omy8GCG and Omy25CGG, were found to be associated with BCWD resistance in the 2015 generation. Retrospective analyses were then performed to evaluate the accuracy of MAS for BCWD resistance using these three favorable haplotypes. The accuracy of MAS was estimated with the Pearson correlation coefficient between the total number of favorable haplotypes in the two parents and the family BCWD survival rates. The Omy8 and Omy25 haplotypes were positively correlated with the family BCWD survival rates across all three generations. The accuracies of MAS using these two haplotypes together were consistently around 0.5, which was equal or greater than the accuracy of the conventional family-based selection in the same generation. In conclusion, we have demonstrated that MAS for BCWD resistance is feasible in this commercial rainbow trout breeding population.

Teleosts Genomics: Progress and Prospects in Disease Prevention and Control

Genome wide studies based on conventional molecular tools and upcoming omics technologies are beginning to gain functional applications in the control and prevention of diseases in teleosts fish. Herein, we provide insights into current progress and prospects in the use genomics studies for the control and prevention of fish diseases. Metagenomics has emerged to be an important tool used to identify emerging infectious diseases for the timely design of rational disease control strategies, determining microbial compositions in different aquatic environments used for fish farming and the use of host microbiota to monitor the health status of fish. Expounding the use of antimicrobial peptides (AMPs) as therapeutic agents against different pathogens as well as elucidating their role in tissue regeneration is another vital aspect of genomics studies that had taken precedent in recent years. In vaccine development, prospects made include the identification of highly immunogenic proteins for use in recombinant vaccine designs as well as identifying gene signatures that correlate with protective immunity for use as benchmarks in optimizing vaccine efficacy. Progress in quantitative trait loci (QTL) mapping is beginning to yield considerable success in identifying resistant traits against some of the highly infectious diseases that have previously ravaged the aquaculture industry. Altogether, the synopsis put forth shows that genomics studies are beginning to yield positive contribution in the prevention and control of fish diseases in aquaculture.

Similar Genetic Architecture with Shared and Unique Quantitative Trait Loci for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations

Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57 K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57 K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered.

A BCWD-resistant line of rainbow trout exhibits higher abundance of IgT+ B cells and heavy chain tau transcripts compared to a susceptible line following challenge with Flavobacterium psychrophilum

Bacterial Cold Water Disease (BCWD) is a common, chronic disease in rainbow trout, and is caused by the gram-negative bacterium Flavobacterium psychrophilum (Fp). Through selective breeding, the National Center for Cool and Cold Water Aquaculture has generated a genetic line that is highly resistant to Fp challenge, designated ARS-Fp-R (or R-line), as well as a susceptible "control" line, ARS-Fp-S (S-line). In previous studies, resistance to Fp had been shown to correlate with naive animal spleen size, and further, naïve R-line trout had been shown to have a lower abundance of IgM+ and IgM++ cells compared to S-line fish. Here we wished to first determine whether the abundance of IgT+ and/or IgT++ cells differed between the two lines in naïve fish, and if so, how these patterns differed after in vivo challenge with Fp. Fp challenge was by intramuscular injection of live Fp and tissue collections were on days 5, 6, and/or 28 post-challenge, in two independent challenge experiments. Flow cytometric and gene expression analyses revealed that naïve R-line fish had a higher abundance of IgT+ B cells in their anterior kidney, spleen, and blood, compared to S line fish. Further, that after Fp challenge, this difference was maintained between the two lines. Lastly, abundance of IgT+ B cells and expression of secHCtau correlated with lower Fp pathogen loads in challenged fish. In the anterior kidney, IgM+ B cell abundance correlated with increased Fp loads. Together, these results suggest that IgT+ B lineage cells may have a protective function in the immune response to Fp.

Antitumor activity of yulangsan polysacchrides in mice bearing S180 sarcoma tumors

Sarcoma is one of the most prevalent pediatric tumors and the therapeutic role of chemotherapy has yet to be elucidated. It has been reported that extracts of Longyanshen (Yulangsan) may enhance the sensitivity of drug-resistant cancer cell lines, and improve the immune dysfunction induced by cyclophosphamide (CTX) in mice. The present in vivo study investigated the antitumor effects of Yulangsan polysaccharides (YLSPS) and their interaction with CTX in murine sarcoma 180 (S180)-bearing mice. Immunohistochemistry was used to detect the expression of apoptosis-related proteins. The ultrastructure of sarcoma cells was examined by transmission electron microscopy and the tumor growth rate was determined by measuring the tumor weight. A dose-dependent inhibition of sarcoma growth was observed in S180-bearing mice following administration of YLSPS. In combination with CTX, an additive antitumor effect was obtained, which was accompanied by amelioration of immune function. YLSPS also potentiated the tumor suppression effect of CTX while avoiding cytotoxicity against immune cells. YLSPS inhibited sarcoma growth in S180-bearing mice through the induction of apoptosis in S180 sarcoma cells. YLSPS also attenuated CTX-induced cytotoxicity to the immune system while potentiating the tumor suppression effect. These results provide additional information regarding combination therapy with YLSPS and chemotherapy for the treatment of sarcoma.

Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes

Background

Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown.

Results

To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A⁺, candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A⁺, F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as “chemokine signaling pathway”, “Toll-like receptor signaling pathway” and others, were remarkably much more than those from clone A⁺ and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A⁺. In contrast to strong immune defense in resistant clone H, susceptible clone A⁺ showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A⁺ failed to resist virus offensive and evidently induced apoptosis or death.

Conclusions

Our study is the first attempt to screen distinct resistances and immune responses of three gynogenetic gibel carp clones to herpesvirus infection by comprehensive transcriptomes. These differential DEUs, immune-related pathways and IFN system genes identified from susceptible and resistant clones will be beneficial to marker-assisted selection (MAS) breeding or molecular module-based resistance breeding in gibel carp.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3945-6) contains supplementary material, which is available to authorized users.

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture

Background

Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation.

Methods

We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model. We also assessed the impact of sampling design on the accuracy of GEBV predictions. For these comparisons, we used BCWD survival phenotypes recorded on 7893 fish from 102 families, of which 1473 fish from 50 families had genotypes [57 K single nucleotide polymorphism (SNP) array]. Naïve siblings of the training fish (n = 930 testing fish) were genotyped to predict their GEBV and mated to produce 138 progeny testing families. In the following generation, 9968 progeny were phenotyped to empirically assess the accuracy of GEBV predictions made on their non-phenotyped parents.

Results

The accuracy of GEBV from all tested GS models were substantially higher than the P-BLUP model EBV. The highest increase in accuracy relative to the P-BLUP model was achieved with BayesB (97.2 to 108.8%), followed by wssGBLUP at iteration 2 (94.4 to 97.1%) and 3 (88.9 to 91.2%) and ssGBLUP (83.3 to 85.3%). Reducing the training sample size to n = ~1000 had no negative impact on the accuracy (0.67 to 0.72), but with n = ~500 the accuracy dropped to 0.53 to 0.61 if the training and testing fish were full-sibs, and even substantially lower, to 0.22 to 0.25, when they were not full-sibs.

Conclusions

Using progeny performance data, we showed that the accuracy of genomic predictions is substantially higher than estimates obtained from the traditional pedigree-based BLUP model for BCWD resistance. Overall, we found that using a much smaller training sample size compared to similar studies in livestock, GS can substantially improve the selection accuracy and genetic gains for this trait in a commercial rainbow trout breeding population.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0293-6) contains supplementary material, which is available to authorized users.

Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

Flavobacterium psychrophilum (Fp) is the causative agent of bacterial cold water disease (BCWD) which causes appreciable economic losses in rainbow trout aquaculture. We previously reported development of a genetic line, designated ARS-Fp-R that exhibits higher survival relative to a susceptible line, designated ARS-Fp-S, following either laboratory or natural on-farm challenge. The objectives of this study were to determine the temporal kinetics of gene expression between experimentally-challenged ARS-Fp-R and ARS-Fp-S fish and the correlation between gene expression and pathogen load. We developed a GeXP multiplex RT-PCR assay to simultaneously examine expression of immune-relevant genes, concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. Spleen tissue was sampled at 6 h, 24 h, 48 h and 144 h post-challenge and pathogen load quantified by qPCR. Transcript abundance of cytokine genes tnfa1, tnfa2, tnfa3, il1b1, il1b2, il11a; acute phase response genes saa and drtp1; and putative cytokine receptors il1r1-like-b, il1r2, tnfrsf1a, tnfrsf9, tnfrsf1a-like-b increased following challenge while the transcript abundance of il1r-like-1 and tnfrsf1a-like-a decreased compared to PBS-injected line-matched control fish. Principal component analysis identified transcript levels of genes il1r-like-1 and tnfrsf1a-like-a as exhibiting differential expression between genetic lines. In summary, Fp i.p. injection challenge elicited a proinflammatory cytokine gene expression response in the spleen, with ARS-Fp-R line fish exhibiting modestly higher basal expression levels of several putative cytokine receptors. This study furthers the understanding of the immune response following Fp challenge and differences in gene expression associated with selective breeding for disease resistance.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations.

Omics approaches to probe markers of disease resistance in animal sciences

Disease pathways can be explained into a list of biomarkers at different scales to develop applications.

Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout

Bacterial cold water disease (BCWD) is one of the frequent causes of elevated mortality in salmonid aquaculture. Previously, we identified and validated microsatellites on chromosome Omy19 associated with QTL (quantitative trait loci) for BCWD resistance and spleen size in rainbow trout. Recently, SNPs (single nucleotide polymorphism) have become the markers of choice for genetic analyses in rainbow trout as they are highly abundant, cost-effective and are amenable for high throughput genotyping. The objective of this study was to identify SNP markers associated with BCWD resistance and spleen size using both genome-wide association studies (GWAS) and linkage-based QTL mapping approaches. A total of 298 offspring from the two half-sib families used in our previous study to validate the significant BCWD QTL on chromosome Omy19 were genotyped with RAD-seq (restriction-site-associated DNA sequencing), and 7,849 informative SNPs were identified. Based on GWAS, 18 SNPs associated with BCWD resistance and 20 SNPs associated with spleen size were identified. Linkage-based QTL mapping revealed three significant QTL for BCWD resistance. In addition to the previously validated dam-derived QTL on chromosome Omy19, two significant BCWD QTL derived from the sires were identified on chromosomes Omy8 and Omy25, respectively. A sire-derived significant QTL for spleen size on chromosome Omy2 was detected. The SNP markers reported in this study will facilitate fine mapping to identify positional candidate genes for BCWD resistance in rainbow trout.

Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellite markers in a genome scan, we previously detected significant and suggestive QTL affecting phenotypic variation in survival following challenge with Flavobacterium psychrophilum, the causative agent of BCWD in rainbow trout. In this study, we performed selective genotyping of SNPs from restriction-site associated DNA (RAD) sequence data from two pedigreed families (2009070 and 2009196) to validate the major QTL from the previous work and to detect new QTL. The use of RAD SNPs in the genome scans increased the number of mapped markers from ~300 to ~5,000 per family. The significant QTL detected in the microsatellites scan on chromosome Omy8 in family 2009070 was validated explaining up to 58% of the phenotypic variance in that family, and in addition, a second QTL was also detected on Omy8. Two novel QTL on Omy11 and 14 were also detected, and the previously suggestive QTL on Omy1, 7 and 25 were also validated in family 2009070. In family 2009196, the microsatellite significant QTL on Omy6 and 12 were validated and a new QTL on Omy8 was detected, but none of the previously detected suggestive QTL were validated. The two Omy8 QTL from family 2009070 and the Omy12 QTL from family 2009196 were found to be co-localized with handling and confinement stress response QTL that our group has previously identified in a separate pedigreed family. With the currently available data we cannot determine if the co-localized QTL are the result of genes with pleiotropic effects or a mere physical proximity on the same chromosome segment. The genetic markers linked to BCWD resistance QTL were used to query the scaffolds of the rainbow trout reference genome assembly and the QTL-positive scaffold sequences were found to include 100 positional candidate genes. Several of the candidate genes located on or near the two Omy8 QTL detected in family 2009070 suggest potential linkages between stress response and the regulation of immune response in rainbow trout.

Reduction of rainbow trout spleen size by splenectomy does not alter resistance against bacterial cold water disease

In lower vertebrates, the contribution of the spleen to anti-bacterial immunity is poorly understood. We have previously reported a phenotypic and genetic correlation between resistance to Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD) and spleen somatic index (spleen weight normalized to body weight, SI). Fish families with larger pre-challenge SI values were found to have greater BCWD survival (resistance) following intraperitoneal injection of a lethal dose of F. psychrophilum. Since the mammalian spleen is known to be crucial for capture and destruction of encapsulated bacteria, we tested the hypothesis that reduction of spleen size, by surgical splenectomy, should reduce the survival advantage of the larger-spleen, disease-resistant fish. Experiments were performed using two separate lines of fish that had previously been selected either based on BCWD survival (resistant and susceptible), or selected based on spleen size (high and low SI). Following 65 to 81 days post-surgical recovery, fish were challenged with F. psychrophilum and mortality monitored for a minimum of 21 days. No significant difference in the relative survival was detected between splenectomized or sham-operated groups, while SI of splenectomized fish was reduced to an average of 8-12% of control animals. A positive correlation was observed between the SI, measured at the time of splenectomy, and time-to-death post-challenge. In summary, these experiments argue that larger spleen size alone is not sufficient for greater BCWD resistance, but rather it is an indirect indicator of immunological status.

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

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.

B cell signatures of BCWD-resistant and susceptible lines of rainbow trout: a shift towards more EBF-expressing progenitors and fewer mature B cells in resistant animals

Bacterial cold water disease (BCWD) is a chronic disease of rainbow trout, and is caused by the Gram-negative bacterium Flavobacterium psychrophilum (Fp), a common aquaculture pathogen. The National Center for Cool and Cold Water Aquaculture has bred two genetic lines of rainbow trout: a line of Fp-resistant trout (ARS-Fp-R or R-line trout) and a line of susceptible trout (ARS-Fp-S, or S-line). Little is known about how phenotypic selection alters immune response parameters or how such changes relate to genetic disease resistance. Herein, we quantify interindividual variation in the distribution and abundance of B cell populations (B cell signatures) and examine differences between genetic lines of naive animals. There are limited trout-specific cell surface markers currently available to resolve B cell subpopulations and thus we developed an alternative approach based on detection of differentially expressed transcription factors and intracellular cytokines. B cell signatures were compared between R-line and S-line trout by flow cytometry using antibodies against transcription factors early B cell factor-1 (EBF1) and paired domain box protein Pax5, the pro-inflammatory cytokine IL-1β, and the immunoglobulin heavy chain mu. R-line trout had higher percentages of EBF(+) B myeloid/ progenitor and pre-B cells in PBL, anterior and posterior kidney tissues compared to S-line trout. The opposite pattern was detected in more mature B cell populations: R-line trout had lower percentages of both IgM(+) mature B cells and IgM-secreting cells in anterior kidney and PBL compared to S-line trout. In vitro LPS-activation studies of PBL and spleen cell cultures revealed no significant induction differences between R-line and S-line trout. Together, our findings suggest that selective resistance to BCWD may be associated with shifts in naive animal developmental lineage commitment that result in decreased B lymphopoiesis and increased myelopoiesis in BCWD resistant trout relative to susceptible trout.

Genetics and genomics of disease resistance in salmonid species

Infectious and parasitic diseases generate large economic losses in salmon farming. A feasible and sustainable alternative to prevent disease outbreaks may be represented by genetic improvement for disease resistance. To include disease resistance into the breeding goal, prior knowledge of the levels of genetic variation for these traits is required. Furthermore, the information from the genetic architecture and molecular factors involved in resistance against diseases may be used to accelerate the genetic progress for these traits. In this regard, marker assisted selection and genomic selection are approaches which incorporate molecular information to increase the accuracy when predicting the genetic merit of selection candidates. In this article we review and discuss key aspects related to disease resistance in salmonid species, from both a genetic and genomic perspective, with emphasis in the applicability of disease resistance traits into breeding programs in salmonids.

Biochemical reference intervals and pathophysiological changes in Flavobacterium psychrophilum-resistant and -susceptible rainbow trout lines

Host genetic resistance against disease-causing pathogens can be enhanced through family-based selective breeding. At present, there is an incomplete understanding of how artificial selection of fish alters host physiology and response following pathogen exposure. We previously reported the generation of selectively-bred rainbow trout Oncorhynchus mykiss lines with either increased resistance (ARS-Fp-R) or susceptibility (ARS-Fp-S) to bacterial cold water disease (BCWD). This study (1) determined baseline reference-range intervals for packed cell volume (PCV) and 18 plasma biochemistry analytes, and (2) examined pathophysiological changes following infection between the genetic lines. PCV and biochemistry reference-range intervals did not significantly differ between genetic lines; thus data were pooled into a single reference-range population (n = 85). ARS-Fp-R and ARS-Fp-S line fish were intraperitoneally challenged with Flavobacterium psychrophilum, and plasma was collected on Days 1, 3, 6, and 9 post-challenge. Splenic bacterial load was measured using an F. psychrophilum-specific qPCR assay. In both genetic lines, changes were observed in mean PCV, total protein, albumin, glucose, cholesterol, chloride, and calcium, falling outside the established reference intervals and significantly differing from phosphate-buffered saline challenged fish, on at least 1d post-challenge. Mean PCV, total protein, and calcium significantly differed between ARS-Fp-R and ARS-Fp-S line fish on Day 9 post-infection, with values in the ARS-Fp-S line deviating most from the reference interval. PCV, total protein, cholesterol, and calcium negatively correlated with bacterial load. These findings identify divergent pathophysiological responses between ARS-Fp-R and ARS-Fp-S line fish following laboratory challenge that are likely associated with differential survival.

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

Resistance against diseases affects profitability of rainbow trout. Limited information is available about functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for genomic selection. RNA-Seq sequencing of the rainbow trout spleen yielded 93,532,200 reads (100 bp). High quality reads were assembled into 43,047 contigs. 26,333 (61.17%) of the contigs had hits to the NR protein database and 7024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (51%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related genes. KEGG annotation revealed 2825 sequences belonging to "organismal systems" with the highest number of sequences, 842 (29.81%), assigned to immune system. A number of sequences were identified for the first time in rainbow trout belonging to Toll-like receptor signaling (35), B cell receptor signaling pathway (44), T cell receptor signaling pathway (56), chemokine signaling pathway (73), Fc gamma R-mediated phagocytosis (52), leukocyte transendothelial migration (60) and NK cell mediated cytotoxicity (42). In addition, 51 transcripts were identified as spleen-specific genes. The list includes 277 full-length cDNAs. The presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish are conserved. This study provides deep-sequence data of rainbow trout spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help identify allelic variations suitable for genomic selection and genetic manipulation in aquaculture.

Complete Genome Sequence of Flavobacterium psychrophilum Strain CSF259-93, Used To Select Rainbow Trout for Increased Genetic Resistance against Bacterial Cold Water Disease

The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow trout (Oncorhynchus mykiss), consists of a single circular genome of 2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has been used to select a line of rainbow trout with increased genetic resistance against bacterial cold water disease.

Histopathologic Changes in Disease-Resistant-Line and Disease-Susceptible-Line Juvenile Rainbow Trout Experimentally Infected with Flavobacterium psychrophilum

Abstract A challenge to selectively breeding fish populations for improved disease resistance in aquaculture is an incomplete understanding of how artificial selection affects innate immunity at the host-pathogen level. The objective of this study was to determine whether Rainbow Trout Oncorhynchus mykiss bred for differential susceptibility to bacterial cold-water disease exhibited altered tissue damage and cellular inflammatory response following experimental challenge with Flavobacterium psychrophilum. Fish from disease-resistant (ARS-Fp-R) and disease-susceptible (ARS-Fp-S) lines were experimentally challenged as juveniles, and mortalities, as well as survivors, were sampled for histopathology during the acute phase of the disease. Microscopic lesions were quantified or semiquantified and statistically compared for changes over time and between genetic lines. Significant progression in the degree of perisplenitis, splenic necrosis, splenic inflammatory infiltrates, average splenic ellipsoid area, total splenic ellipsoid area, and peritonitis was present over time in both genetic lines on at least one postinfection time point. No differences were found between renal inflammatory infiltrates and renal hematopoietic cell depletion over time. Perisplenitis was significantly lower in fish from the ARS-Fp-R line on day 9 postinfection than in fish from the ARS-Fp-S line. The ARS-Fp-R line demonstrated a trend towards reduced splenic necrosis compared with the ARS-Fp-S line that approached significance, and fish from the ARS-Fp-S line were 3.6 times more likely than fish from the ARS-Fp-R line to have a higher splenic necrosis lesion score after day 3 postinfection. These findings support the hypothesis that differential survival is a result of divergence in disease magnitude and not altered disease course between genetic lines. Characterization of histopathologic changes between genetic lines and over time helps elucidate mechanisms of disease resistance and contributes to our understanding of disease pathogenesis in fish infected with F. psychrophilum. Received January 7, 2014; accepted March 10, 2014.

Detection of QTL in rainbow trout affecting survival when challenged with Flavobacterium psychrophilum

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation in survival following challenge with Flavobacterium psychrophilum (Fp), the causative agent of BCWD in rainbow trout (Oncorhynchus mykiss). A family-based selection program to improve resistance was initiated in 2005 at the USDA National Center for Cool and Cold Water Aquaculture. Select crosses were made in 2007 and 2009 to evaluate family-based disease survival using Fp injection challenges. From each putative F₂/BC₁ family generated in 2009, 200-260 fish were challenged in 4-7 replicates per family. Whole genome QTL scans of three F₂/BC₁ families were conducted with about 270 informative microsatellite loci per family spaced at an average interval size of 6 cM throughout the rainbow trout genome. Markers on chromosomes containing QTL were further evaluated in three additional F₂/BC₁ families. The additional F₂/BC₁ families were sire or dam half-sibs (HS) of the initially genome scanned families. Overall, we identified nine major QTL on seven chromosomes that were significant or highly significant with moderate to large effects of at least 13 % of the total phenotypic variance. The largest effect QTL for BCWD resistance explaining up to 40 % of the phenotypic variance was detected on chromosome OMY8 in family 2009070 and in the combined dam HS family 2009069-070. The nine major QTL identified in this study are candidates for fine mapping to identify new markers that are tightly linked to disease resistance loci for using in marker assisted selection strategies.