James E. Parsons

Association between DNA polymorphisms tightly linked to MHC class II genes and IHN virus resistance in backcrosses of rainbow and cutthroat trout

Abstract Infectious hematopoietic necrosis (IHN) is a rhabdoviral disease of salmonid species. Single strand conformation polymorphism (SSCP) was used to identify association between DNA polymorphism of the major histocompatibility complex (MHC) class II beta-chain intron and IHN virus (IHNV) resistance in backcrosses of rainbow trout ( Oncorhynchus mykiss ) and cutthroat trout ( O. clarki ). Association was significant ( P =0.024) in four half-sib families from one sire (number 2), but not among half-sibs from another sire (number 1). DNA sequencing analysis revealed that the polymorphism originating from sire 1 is the result of a single base substitution. Sire 2 polymorphism was caused by three different base substitutions. The source of the susceptible allele appears to be from cutthroat trout and not from the rainbow trout population used to produce the hybrids. The results suggest that MHC polymorphism can contribute to linkage and association studies of immunity to infectious diseases in rainbow trout.

Single pair mating indicates maternal effects on embryo survival in rainbow trout, Oncorhynchus mykiss

Abstract The maternal and paternal influences on early embryo survival in rainbow trout are not established. The purpose of this study was to determine whether variability in the survival of rainbow trout embryos could be attributed to either the female or male parent. Gametes from individual female and male rainbow trout were used in single pair matings to produce families whose survival was followed from fertilization to the time of swim-up (i.e., ∼7 weeks post-fertilization). Survival was assessed at 0.5, 9, 19, 33, and 48 days post-fertilization, corresponding to second cleavage, embryonic keel formation, retinal pigmentation, hatch, and swim-up, respectively. The variability of survival at all times was significantly ( P P >0.05). Therefore, in rainbow trout embryo survival can be equated with the quality of the egg. To predict survival at swim-up (i.e., after 48 days) it was found that embryonic keel formation, measured 9 days after fertilization, was the earliest time at which a highly significant positive correlation ( r =0.889, P

Identification of candidate DNA markers associated with IHN virus resistance in backcrosses of rainbow (Oncorhynchus mykiss) and cutthroat trout (O. clarki)

Abstract Infectious hematopoietic necrosis (IHN) is a rhabdoviral disease of salmonid species. Initial observations suggested that cutthroat trout ( Oncorhynchus clarki ) and hybrids of rainbow trout ( Oncorhynchus mykiss ) and cutthroat trout are significantly less susceptible to IHN virus (IHNV) than rainbow trout. Sixteen full-sib families of backcross progeny (female rainbow×male hybrid) were produced and three replicates per family were challenged with IHNV. DNA fingerprints of mixtures from first mortalities and survivors of the IHNV challenges were compared using two restriction enzymes and 10 multilocus probes. An estimated 98–102 polymorphic loci were screened by the bulked segregant analysis (BSA) of the DNA mixtures. Thirty-three multilocus RFLP markers differing between first mortalities and survivors were detected. Of 17 tested a significantly higher frequency of two markers was detected among individuals first to die in one family (C2), and another marker was significantly associated with IHNV resistance in family A4.

Residual paternal inheritance in gynogenetic rainbow trout: implications for gene transfer.

SummaryPollen irradiation has recently been widely investigated as a method for differential gene transfer in plants. Using an albino color marker in rainbow trout (Salmo gairdneri), we have investigated whether irradiated sperm might be used in an analogous manner for gene transfer in fish. Our results indicate that paternal chromosome fragments are genetically active in gynogenetic offspring, but that these fragments may be lost during mitotic cell division, producing mosaic fish.

Increased resistance of triploid rainbow trout × coho salmon hybrids to infectious hematopoietic necrosis virus

Abstract Diploid and heat-induced triploid treatment groups of rainbow trout ( Salmo gairdneri ), coho salmon ( Oncorhynchus kisutch ), and reciprocal hybrid crosses were produced and monitored for survival and growth through early life stages. Survival to the fry stage showed a significant increase in the triploid rainbow trout female × coho salmon male hybrids relative to the diploid hybrid group. At a mean weight of 0.65 g all groups were administered a standardized static bath challenge with Leong Type 2 virulent IHN virus. The triploid rainbow trout female × coho salmon male hybrids showed a significant increase in IHN resistance when compared to pure-species rainbow trout groups. Early growth results suggest a poorer growth rate for the triploid hybrid. Triploid hybridization improved viability of the hybrid cross, increased relative resistance to IHN virus challenge, and may provide a useful method for the interspecific transfer of desired characters into commercial fish stocks.

Defining desired genetic gains for rainbow trout breeding objective using analytic hierarchy process

Distributing animals from a single breeding program to a global market may not satisfy all producers, as they may differ in market objectives and farming environments. Analytic hierarchy process (AHP) is used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The aim of this study was to use an AHP-WGP based approach to derive desired genetic gains for rainbow trout breeding and to study whether breeding trait preferences vary depending on commercial products and farming environments. Two questionnaires were sent out. Questionnaire-A (Q-A) was distributed to 178 farmers from 5 continents and used to collect information on commercial products and farming environments. In this questionnaire, farmers were asked to rank the 6 most important traits for genetic improvement from a list of 13 traits. Questionnaire B (Q-B) was sent to all farmers who responded to Q-A (53 in total). For Q-B, preferences of the 6 traits were obtained using pairwise comparison. Preference intensity was given to quantify (in % of a trait mean; G%) the degree to which 1 trait is preferred over the other. Individual preferences, social preferences, and consensus preferences (Con-P) were estimated using AHP and WGP. Desired gains were constructed by multiplying Con-P by G%. The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Ranking of traits based on average Con-P values were Surv (0.271), FCR (0.246), TGC (0.246), LMat (0.090), FIL% (0.081), and CF (0.067). Corresponding desired genetic gains (in % of trait mean) were 1.63, 1.87, 1.67, 1.29, 0.06, and 0.33%, respectively. The results from Con-P values show that trait preferences may vary for different types of commercial production or farming environments. This study demonstrated that combination of AHP and WGP can be used to derive desired gains for a breeding program and to quantify differences due to variations market demand or production environment.

Genotype-by-environment interaction of growth traits in rainbow trout (Oncorhynchus mykiss): a continental scale study.

Rainbow trout is a globally important fish species for aquaculture. However, fish for most farms worldwide are produced by only a few breeding companies. Selection based solely on fish performance recorded at a nucleus may lead to lower-than-expected genetic gains in other production environments when genotype-by-environment (G × E) interaction exists. The aim was to quantify the magnitude of G × E interaction of growth traits (tagging weight; BWT, harvest weight; BWH, and growth rate; TGC) measured across 4 environments, located in 3 different continents, by estimating genetic correlations between environments. A total of 100 families, of at least 25 in size, were produced from the mating 58 sires and 100 dams. In total, 13,806 offspring were reared at the nucleus (selection environment) in Washington State (NUC) and in 3 other environments: a recirculating aquaculture system in Freshwater Institute (FI), West Virginia; a high-altitude farm in Peru (PE), and a cold-water farm in Germany (GER). To account for selection bias due to selective mortality, a multitrait multienvironment animal mixed model was applied to analyze the performance data in different environments as different traits. Genetic correlation (rg) of a trait measured in different environments and rg of different traits measured in different environments were estimated. The results show that heterogeneity of additive genetic variances was mainly found for BWH measured in FI and PE. Additive genetic coefficient of variation for BWH in NUC, FI, PE, and GER were 7.63, 8.36, 8.64, and 9.75, respectively. Genetic correlations between the same trait in different environments were low, indicating strong reranking (BWT: rg = 0.15 to 0.37, BWH: rg = 0.19 to 0.48, TGC: rg = 0.31 to 0.36) across environments. The rg between BWT in NUC and BWH in both FI (0.31) and GER (0.36) were positive, which was also found between BWT in NUC and TGC in both FI (0.10) and GER (0.20). However, rg were negative between BWT in NUC and both BWH (-0.06) and TGC (-0.20) in PE. Correction for selection bias resulted in higher additive genetic variances. In conclusion, strong G × E interaction was found for BWT, BWH, and TGC. Accounting for G × E interaction in the breeding program, either by using sib information from testing stations or environment-specific breeding programs, would increase genetic gains for environments that differ significantly from NUC.

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.

Early onset of embryonic mortality in sub-fertile families of rainbow trout (Oncorhynchus mykiss)

Survival during early embryonic development is highly variable in oviparous fishes and appears to be related to events associated with the female at the time of ovulation and spawning. The goal of this study was to identify critical periods of mortality associated with early embryonic development in egg batches from female rainbow trout (Oncorhynchus mykiss) that were checked for ovulation every 5-7 days. The experiment was designed to specifically remove post-ovulatory ageing and reduce paternal variability. Embryo viability in 269 single-pair-mated families was systematically tracked at the following five stages: second cleavage (0.5 days post fertilisation (dpf)), elevated blastula (2.5 dpf), embryonic shield (6 dpf), embryonic keel (9 dpf), and retinal pigmentation (19 dpf). At each of the five stages families with embryo viability assessments of <80% were classed as sub-fertile, whereas those with >80% embryo viability were classed as fertile. Embryo viability in sub-fertile families was distinctly reduced at 0.5 dpf, in contrast to fertile families, but remained constant from that point through to 19 dpf. These results suggest that the critical period of early embryonic mortality in sub-fertile families of rainbow trout parallels events that occur at or shortly after fertilisation and is independent of post-ovulatory aging.

Microarray analysis of differential utilization of plant-based diets by rainbow trout

Microarray analysis was conducted using liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals fed a fishmeal or plant protein-based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 expressed sequence tags (ESTs). Eight of the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes, we were able to map gene pathways and process interactions. From this information, we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed in immune response gene expression that ingestion of this plant-based diet upregulated the expression of genes involved in immunoregulatory processes.