Clonal Lines Of Rainbow Trout Research Articles

Complex relationships among rearing temperature, growth, and sprint speed in clonal lines of rainbow trout

Cold-water dependent rainbow trout (Oncorhynchus mykiss) inhabit a considerably diverse geographic range extending from Alaska to southern California, where adjustments in growth and swim performance in response to temperature may be present. Here we measured four clonal lines of rainbow trout for growth and sprint speed, at two different constant temperatures (10 or 18 °C), across 12 weeks. The objective was to characterize temperature responses among different genotypes originating from Alaska, Oregon, and two hatchery populations; we expected that the lines would respond in a way that implicated their diversity in geographic origin and domestication history. We observed all fish achieve the greatest growth and body size and fastest sprint speed at 18 °C, regardless of origin; substantial variation in growth and swim performance among and within line and temperature was also observed. Surprisingly, the Swanson line from Alaska exhibited very rapid growth at the warmer temperature, which may support the countergradient variation in growth hypothesis. The diversity of responses reported here illustrates the complex nature of the relationship among temperature, growth, and performance and provide groundwork for future genetic analyses utilizing clonal lines of rainbow trout.

Aggressive behavior, brain size and domestication in clonal rainbow trout lines.

Domestication causes behavior and brain size changes in many species. We addressed three questions using clonal rainbow trout lines: What are the mirror-elicited aggressive tendencies in lines with varying degrees of domestication? How does brain size relate to genotype and domestication level? Finally, is there a relationship between aggressive behavior and brain size? Clonal lines, although sampling a limited subset of the species variation, provide us with a reproducible experimental system with which we can develop hypotheses for further research. We performed principal component analyses on 12 continuous behavior and brain/body size variables and one discrete behavioral variable ("yawn") and detected several aggression syndromes. Two behaviors, "freeze" and "escape", associated with high domestication; "display" and "yawn" behavior associated with wild lines and "swim against the mirror" behavior associated with semi-wild and domestic lines. Two brain size traits, total brain and olfactory volume, were significantly related to domestication level when taking total body size into account, with domesticated lines having larger total brain volume and olfactory regions. The aggression syndromes identified indicate that future QTL mapping studies on domestication-related traits would likely be fruitful.

Antipredator behavior QTL: differences in rainbow trout clonal lines derived from wild and hatchery populations.

Variation in antipredator behavior may partially explain the survival differences seen between wild and hatchery trout and salmon. Antipredator behavior is thought to change during the domestication process, along with other traits. Investigations of antipredator behavior could benefit conservation efforts and supplementation programs. Our goal was to characterize the antipredator behavior in clonal rainbow trout lines derived from either wild or hatchery populations and identify genetic loci associated with variation between lines. We identified several behaviors that varied between clonal lines and QTL for several behavioral and size traits. Characterizing genetic variation underlying these behaviors may prove valuable in future conservation efforts by enabling monitoring of allele frequencies of loci affecting predation in wild populations.

Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication.

BackgroundThe common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention complicates efforts to detect allelic variation in salmonid fishes. Specifically, single nucleotide polymorphism (SNP) detection is problematic because nucleotide variation can be found between the duplicate copies (paralogs) of a gene as well as between alleles.ResultsWe present a method of differentiating between allelic and paralogous (gene copy) sequence variants, allowing identification of SNPs in organisms with multiple copies of a gene or set of genes. The basic strategy is to: 1) identify windows of unique cDNA sequences with homology to each other, 2) compare these unique cDNAs if they are not shared between individuals (i.e. the cDNA is homozygous in one individual and homozygous for another cDNA in the other individual), and 3) give a “SNP score” value between zero and one to each candidate sequence variant based on six criteria. Using this strategy we were able to detect about seven thousand potential SNPs from the transcriptomes of several clonal lines of rainbow trout. When directly compared to a pre-validated set of SNPs in polyploid wheat, we were also able to estimate the false-positive rate of this strategy as 0 to 28% depending on parameters used.ConclusionsThis strategy has an advantage over traditional techniques of SNP identification because another dimension of sequencing information is utilized. This method is especially well suited for identifying SNPs in polyploids, both outbred and inbred, but would tend to be conservative for diploid organisms.

Domestication is associated with reduced burst swimming performance and increased body size in clonal rainbow trout lines

Domestication selection combined with inadvertent selection for high growth rate and large body size are common in hatchery salmonids. However, evolutionary trade-offs of various fitness components with body size and domestication are likely. This study explores potential trade-offs between growth and sprint swim performance among five clonal lines of rainbow trout (Oncorhynchus mykiss), varying in the number of generations under domestication. We hypothesized that clonal lines of trout derived from highly domesticated populations would have higher growth rates but slower sprint swimming performance relative to clonal lines derived from less-domesticated populations. Individuals from each of the five lines were repeatedly measured for body size and sprint swimming performance over 10–15weeks. Our findings indicate significant differences in body size and sprint swimming performances between the less-domesticated and the more-domesticated lines, with more-domesticated lines being larger but poorer swimmers. Implications for the survival and reproduction of hatchery salmonids released into the wild are explored.

Oxidative stress among SOD-1 genotypes in rainbow trout (Oncorhynchus mykiss)

Natural variation in the antioxidant-enzyme SOD-1 (superoxide dismutase) is known to alter the impacts of oxidative damage at both the cellular and organismal levels. Using three homozygous clonal lines of rainbow trout [Hot Creek (n=30), Arlee (n=21), and Swanson (n=10)], which differ for single nucleotide polymorphisms (SNPs) and amino acid substitutions at the SOD-1 locus, we investigated the functional effects of this variation on SOD-1 activity during ozone stress and subsequent levels of oxidative damage to DNA and cell membranes. Fish from each line were subjected to either control conditions or 24h of ozone stress, after which tissues were analyzed for antioxidant status and oxidative damage. Liver SOD-1 activity was lower in ozonated vs. control fish in the Hot Creek line, and among ozonated fish, Hot Creek was lower than Arlee. Total erythrocyte SOD activity was not significantly impacted by ozonation; however significant differences in total erythrocyte SOD activity were measured among clonal lines, driven primarily by lower activity in the Hot Creek line. Ozone had a significant treatment effect in all oxidative damage parameters assessed: it increased DNA lesions in erythrocytes and levels of lipid peroxidation in gill tissue and plasma. Among lines, Swanson showed higher lipid peroxidation levels in gill tissue after ozonation than Arlee or Hot Creek. Conversely, Swanson control and treatment fish had significantly lower plasma lipid peroxidation levels than did fish from the other lines. Overall, the among-line differences in SOD and SOD-1 activity and oxidative damage provide evidence that SOD-1 genotypes differ functionally under both oxidative stress and control conditions; however, other genetic differences among lines should be investigated in order to further explain the phenotypic differences in SOD enzyme activity and oxidative damage described here.

Lack of correlation between the resistances to two rhabdovirus infections in rainbow trout

The Viral Hemorrhagic Septicemia Virus (VHSV) and the Infectious Hematopoietic Necrosis Virus (IHNV) are two rhabdoviruses responsible for serious outbreaks in salmonid farms. To date, little is known about the variability of host response to these viruses. Using gynogenetic clonal lines of rainbow trout exhibiting a wide range of resistance to viral infections, we showed that there was no correlation between the resistance to VHSV and IHNV. We also confirmed the importance of fish weight for its susceptibility to IHNV infection. Finally, using a chimeric recombinant IHNV expressing the VHSV glycoprotein, we showed that the glycoprotein plays a key role in the virulence and in the level of resistance observed in different genetic backgrounds. Taken together, our results provide new prospects for a better understanding of host responses to rhabdovirus infections in salmonids.

Heat shock protein (HSP70) RNA expression differs among rainbow trout (Oncorhynchus mykiss) clonal lines

Heat shock protein 70 (HSP70, 70 kDa) is the most commonly expressed protein in response to thermal stress. The extent of its expression is associated with differences in environmental temperatures. We investigated the heat shock response in red blood cells collected from one-year-old rainbow trout (Oncorhynchus mykiss). Three different clonal lines of rainbow trout (Arlee, OSU and Whale Rock) were utilized, originating from habitats that likely experienced different thermal profile. The relative expression of HSP70 from blood cells treated at 13 °C, 16 °C, 18 °C, 20 °C, 22 °C, and 24 °C was quantified using real-time PCR. The use of red blood cells allows for the control and replication of HSP70 expression patterns.Relative expression of HSP70 differed significantly among the three clonal lines. The Arlee line had the lowest HSP70 response of the three clonal lines at any temperature; indicating a heritable difference. Maximum expression of HSP70 occurred at 22 °C in the OSU line and at 24 °C in the Whale Rock line. The discovery of variation in HSP70 expression among the clonal lines indicates that future studies to map the genetic control of HSP70 expression differences are possible.

Compensatory growth performance testing of clonal rainbow trout lines

Compensatory growth performance testing of clonal rainbow trout lines

Transcriptome profiles of livers and kidneys from three rainbow trout ( Oncorhynchus mykiss) clonal lines distinguish stocks from three allopatric populations

Transcriptome profiling is a powerful means of simultaneously identifying large numbers of genes that respond transcriptionally to stimuli of any sort. Whereas individuality at the level of genomic sequence is readily revealed and can be expected to influence transcriptional responses, knowledge of the global transcriptomic consequences of genomic individuality is in its infancy. Appreciation of the inherent variability of biological systems gives us confidence in predicting that no two individuals in any outbred population will respond identically to a stimulus. More critical for comparative studies, even unstimulated transcriptomes will be distinctive for each individual. To assess the confidence with which inferences may be drawn from transcriptome profiling when genetically identical samples can be assured, we examined the unprovoked transcriptomes of hepatic and pronephric (head kidney) tissues in three clonal lines of Rainbow trout ( Oncorhynchus mykiss). Clonal individuals derived from three allopatric populations presented transcriptional profiles for both liver and pronephros that were not statistically significantly different within each clonal line; however each clonal line was distinguished by a subset of genes with constitutively different transcript abundance. Among these, immunologically-relevant genes were over-represented, possibly reflecting evolutionarily recent, pathogen-driven genetic sweeps.

Use of androgenesis for estimating maternal and mitochondrial genome effects on development and oxygen consumption in rainbow trout, Oncorhynchus mykiss

Chromosome set manipulation was used to produce rainbow trout, Oncorhynchus mykiss, with identical nuclear backgrounds, but different maternal backgrounds to determine mitochondrial effects on development rate and oxygen consumption. Significant differences in development rate and oxygen consumption were observed between groups from different females. Development rates ranged from a mean of 317.97 degree days (°d) to 335.25 °d in progeny from different females. Mean oxygen consumption rates ranged from 3.31 μmol O 2 g − 1 wet mass h − 1 to 9.66 μmol O 2 g − 1 wet mass h − 1 . Oxygen consumption and development rate analysis revealed the two slowest developing groups had the highest oxygen consumption rates. Development rate differences between second generation clonal females indicate that mitochondrial genomes play a significant role on early development and are comparable to development rate differences between clonal lines of rainbow trout. These results indicate that selection for mitochondrial genomes could increase growth rates and possibly food conversion ratios in aquaculture species.

Rainbow Trout (Oncorhynchus mykiss) of Idaho and Alaskan Origin (2n = 58) Share a Chromosome Fusion Relative to Trout of California Origin (2n = 60)

Fluorescence in situ hybridization (FISH) was used to identify which chromosome pairs are involved in the difference in karyotypes of three clonal lines of Rainbow Trout (Oncorhynchus mykiss): OSU with 2n = 60, Clearwater with 2n = 58, and Swanson with 2n = 58. These lines appear to have karyotypes typical of strains from the regions from which they were derived (California, Idaho, and Alaska, respectively). Bacterial artificial chromosome clones containing mapped markers specific for different acrocentric pairs in the OSU strain were hybridized to chromosomes of hybrid fish. The OSU × Clearwater and OSU × Swanson hybrids have 2n = 59 with a chromosome pair consisting of one metacentric (fusion) chromosome and two acrocentrics. Both strains have the same chromosome fusion involving acrocentric chromosomes 25 and 29 of the OSU strain although they are from widely separate geographic regions. These results suggest that all of the 2n = 58 Rainbow Trout may have the same karyotype and a common origin.

An AFLP-based approach for the identification of sex-linked markers in rainbow trout ( Oncorhynchus mykiss)

A DNA AFLP-fingerprinting approach has been used in this study for the identification of sex-linked markers in rainbow trout. Using a sex-typed pool strategy we analyzed a total of 486 different primer combinations of which 19 gave sex-associated amplification across the pooled DNA samples. Segregation analysis showed that 18 out of 19 AFLPs (95%) were informative for individual sexing and genetic mapping. Fifteen AFLPs that showed sex-associated amplification in the pooled segregant analysis were converted into single locus markers (SCARs). One out of 15, the SCAR Omy-163, was Y chromosome-linked and mapped near the sex locus in all of four genetically diverse male clonal lines of rainbow trout examined. Three microsatellites, Ots517NWFSC, OmyFGT19TUF and Omm1026, which were previously mapped on the sex linkage group in rainbow trout, were also analyzed. The SCAR Omy-163, Ots517NWFC and OmyFGT19TUF showed low levels of intraspecific allelic polymorphism. Y chromosome-linked AFLP markers were relatively strain-specific suggesting an intraspecific genetic polymorphism of the rainbow trout Y-chromosome. Estimation of the level of polymorphism for AFLPs using one of our strains revealed that approximately 34,506 putative loci were tested in our study of which about 4374 were polymorphic. Considering 11 Y-linked polymorphic loci in this strain, we estimated that 0.25% of polymorphic loci (11/4374) were confined to a single sex. Assuming that the length of the rainbow trout genome is estimated to be 2627.5 cM (2.4×10 6 kb), the male-determining region detected using our screen may span 6.6 cM (6100 kb). The AFLP technique provides an efficient marker system for revealing polymorphic loci and for linkage map construction. An AFLP approach in combination with a sex-type pool strategy resulted in a quick analysis for identifying sex-linked loci in rainbow trout. Similar approaches may be useful for molecular mapping of markers linked to genes of interest in other species.

Composite interval mapping reveals three QTL associated with pyloric caeca number in rainbow trout, Oncorhynchus mykiss

The pyloric caeca of fishes are a major site for nutrient digestion and absorption. Some studies have reported an association between increased caeca number, improved feed efficiency and faster overall growth in rainbow trout. However, little is known concerning the genetic basis underlying pyloric caeca development in any fish species. We have identified two clonal rainbow trout lines that differ in pyloric caeca number. Doubled haploid progeny produced from an F 1 hybrid of these lines were used to evaluate the possibility of joint segregation of pyloric caeca phenotype with 330 amplified fragment length polymorphic (AFLP) markers and 39 microsatellites genotyped in 54 individuals. A genetic map has been constructed based on these genotypes and composite interval mapping revealed three major quantitative trait loci (QTL) associated with pyloric caeca number. These QTL respectively explain 19.2%, 18.6% and 13.5% of the variation in pyloric caeca number observed within the doubled haploid progeny. Because these QTL span 3 separate linkage groups, our results demonstrate the phenotype of pyloric caeca number is a polygenic trait in rainbow trout.

Behavioral differences among rainbow trout clonal lines.

Salmonid fish show considerable geographical variation in morphology, physiology, and behavior. Understanding the genetic mechanisms underlying this variation could be useful for enhancing aquaculture stocks, identifying unique populations for conservation, and determining the genetic factors underlying natural adaptation and domestication. As a first step toward the genetic dissection of salmonid behavioral diversity, we examined variation in behavior patterns among four clonal lines of rainbow trout ( Oncorhynchus mykiss ) derived from geographically diverse source populations with different domestication histories. Clonal lines were crossed with two outbred (i.e., not homozygous) females, and the resulting progenies were reared and tested under identical conditions. Clonal line had significant genetic effects on mean swim level, hiding, foraging, startle response, and aggression level. Multiple comparisons suggest that domestication history of the source populations had a strong influence on these behavior patterns. Progeny of two clonal lines derived from populations reared in captivity for over 100 years exhibited reductions in predator avoidance behavior patterns and increases in aggression compared to progeny of two clonal lines from more recently domesticated populations. These results will facilitate future investigation of the genetic factors underlying population variation in these behavior patterns influenced by domestication.

Variation in development rate among clonal lines of rainbow trout ( Oncorhynchus mykiss)

The genetic basis of development rate was examined using clonal lines of rainbow trout produced by androgenesis. We examined development rate, as indicated by physiological time to hatch (°days), of four clonal lines of rainbow trout crossed to outbred females in three separate experiments. In the first experiment, the Swanson line, derived from an Alaskan population, displayed a significantly earlier physiological time to hatch than the Arlee line, derived from a domesticated rainbow trout ( P<0.001). In the second experiment, this trend was maintained across three temperatures (approximately 8, 10, and 14°C) and two females, although the experiment lacked the statistical power to detect a difference ( P=0.052). In the third experiment, the Swanson line had a significantly earlier physiological time to hatch than three other clonal lines ( P<0.01) when tested across three temperatures (8, 10, and 16°C) and two females. There was no evidence of genotype by environment interaction in any of the experiments. These data indicate that development rate has a strong genetic component, and that the clonal lines of rainbow trout available should be highly suitable for QTL analysis of development rate in rainbow trout.

DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines.

Homozygous and hybrid clonal lines of rainbow trout (Oncorhynchus mykiss) were confirmed to be isogenic using multilocus DNA fingerprinting. Homozygous clones were produced by androgenesis and gynogenesis using gametes from androgenetic male and female rainbow trout, respectively. Isogenic F1 hybrid lines were produced by crossing homozygous fish from different strains. One line of hybrid clones showed segregation for maternally inherited DNA fingerprint markers. The female from this cross, the only presumptive homozygous gynogenetic individual used in this study, was thought to have been produced by gynogenesis followed by blockage of the first cleavage division, but based on the DNA fingerprint analysis, apparently was derived by spontaneous polar body retention that maintained heterozygosity at some loci. Mutations at DNA fingerprint loci were not observed, indicating relative stability of fingerprint loci in the clonal lines. DNA fingerprinting appears to be a useful tool for identifying and genetically monitoring clonal lines of rainbow trout. Isogenic lines of rainbow trout will facilitate the production of saturated genetic maps for rainbow trout and enhance such endeavors as quantitative trait locus (QTL) analysis and loss of heterozygosity (LOH) studies in tumors.