The bold and the shy: individual differences in rainbow trout

Boldness and shyness were investigated as 'personality' traits in hatchery-reared rainbow trout Oncorhynchus mykiss . Bold fish spent more time in an open area and were more active than shy fish and these behaviours could be used as indicators of boldness and shyness. These differences were related to learning ability in a simple conditioning task. Bold fish learned the task more quickly than shy fish.     

Asymmetry in sexual development of gonads in intersex rainbow trout

Large‐scale sampling of spontaneous rainbow trout Oncorhynchus mykiss intersexes indicated a strong asymmetry of gonad differentiation in XX females; the right gonad was more sensitive to the mutation‐induced masculinization than the left one.     

Adaptation genomics: next generation sequencing reveals a shared haplotype for rapid early development in geographically and genetically distant populations of rainbow trout

Local adaptation occurs when a population evolves a phenotype that confers a selective advantage in its local environment, but which may not be advantageous in other habitats. Restricted gene flow and strong selection pressures are prerequisites for local adaptation. Fishes in the family Salmonidae are predicted to provide numerous examples of local adaptation because of the high fidelity of returning to spawn in their natal streams, which results in highly structured populations, and the wide diversity of environments that salmonids have colonized. These conditions are ideally suited for producing a set of specialist phenotypes, whose fitness is maximized for one specific habitat, rather than a generalist phenotype similarly viable in several environments. Understanding patterns and processes leading to local adaptations has long been a goal of evolutionary biology, but it is only recently that identifying the molecular basis for local adaptation has become feasible because of advances in genomic technologies. The study of shared adaptive phenotypes in populations that are both geographically distant and genetically distinct should reveal some of the fundamental molecular mechanisms associated with local adaptation. In this issue of Molecular Ecology, Miller et al. (2012) make a significant contribution to the development of adaptation genomics. This study suggests that salmonids use standing genetic variation to select beneficial alleles for local adaptations rather than de novo mutations in the same gene or alternative physiological pathways. Identifying the genetic basis for local adaptation has major implications for the management, conservation and potential restoration of salmonid populations.     

The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout

In this study, we describe the development and characterization of the first high‐density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor (Affymetrix). The SNP genotyping quality was high, and validation rate was close to 90%. This is comparable to other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. High quality and integrity of the genotypes are evident from sample reproducibility and from nearly 100% agreement in genotyping results from other methods. The array is very useful for rainbow trout aquaculture populations with more than 40 900 polymorphic markers per population. For wild populations that were confounded by a smaller sample size, the number of polymorphic markers was between 10 577 and 24 330. Comparison between genotypes from individual populations suggests good potential for identifying candidate markers for populations' traceability. Linkage analysis and mapping of the SNPs to the reference genome assembly provide strong evidence for a wide distribution throughout the genome with good representation in all 29 chromosomes. A total of 68% of the genome scaffolds and contigs were anchored through linkage analysis using the SNP array genotypes, including ~20% of the genome assembly that has not been previously anchored to chromosomes.     

Development of a 37 k high-density oligonucleotide microarray: a new tool for functional genome research in rainbow trout

A rainbow trout high-density oligonucleotide microarray was constructed using all tentative consensus (TC) sequences that are publicly available from all international rainbow trout Oncorhynchus mykiss genomic research projects through the Rainbow Trout Gene Index database. The new array contains 60-mer oligonucleotide probes representing 37 394 unique TC sequences and 1417 control spots. The array (4 × 44 format) was manufactured according to the design by Agilent Technologies using the inkjet-based SurePrint technology (design number 016320). The performance of the new microarray platform was evaluated by analysing gene expression associated with rainbow trout, vitellogenesis-induced muscle atrophy. This microarray will open new avenues of research that will aid in the development of novel strategies for genetic improvement for economically important traits benefiting the salmonid aquaculture industries.     

Mitochondrial DNA variation in rainbow trout (Oncorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation

North-western North America has been repeatedly glaciated over most of the past two million years, with the most recent glaciation occurring between 60 000 and 10 000 years ago. Intraspecific genetic variation in many species has been shaped by where they survived glaciation and what postglacial recolonization routes were used. In this study, molecular techniques were used to investigate biogeographical, taxonomic and conservation issues in rainbow trout, Oncorhynchus mykiss. Mitochondrial DNA (mtDNA) variation was assessed using a restriction fragment length polymorphism (RFLP) analysis, focusing mainly on the previously understudied northern extent of the species' range. Two phylogenetically distinct mitochondrial lineages were found that differed from each other by up to 1.8% in sequence. Although the geographical distributions of the two clades overlap extensively, diversity and distributional analyses strongly suggest that trout survived glaciation in both coastal and inland refugia followed by postglacial gene flow and secondary contact. Postglacial dispersal into British Columbia most likely occurred from the Queen Charlotte Islands and the Columbia River. Although trout most likely also survived glaciation along the coast of Washington, Oregon and California, as well as near the Bering Strait, evidence suggests that dispersal into British Columbia from these areas was limited. Sequence analysis of mitochondrial haplotypes revealed higher diversity in California than in the northern part of the species' range, indicating an ancient presence of the species in the south. Phylogeographic divergence probably predates adaptive variation in the species as suggested by evidence for parallel evolution of life history types across the range of O. mykiss.     

Dinucleotide-repeat polymorphism in DNA of rainbow trout and its application in fisheries science

Dinucleotide–repeat DNA polymorphisms for rainbow trout, Oncorhynchus mykiss , are described. The potential applications of these markers in fisheries science are discussed.     

Allelic differences in initial expression of paternal alleles at an isocitrate dehydrogenase locus in rainbow trout (Salmo gairdneri)

We examined a temporal series of embryos from 14 full-sib families of rainbow trout with starch gel electrophoresis to determine the time of initial detection of enzyme produced by ldh-3. Maternal enzyme was detected in unfertilized eggs, whereas paternal alleles showed evidence of initial expression after gastrulation and epiboly. Two alleles, 40 and 71, were expressed synchronously several days before the 114 allele. Measurement of enzyme activity by spectrophotometric analysis and serial dilution supported these observations. The degree of delay of expression of the 114 allele between families was coupled with other estimates of developmental rate. These data suggest the existence of allelic variation at a cis-acting genetic element controlling the pattern of ontogenetic expression of structural alleles at Idh-3.     

Mapping rainbow trout immune genes involved in inflammation reveals conserved blocks of immune genes in teleosts

We report the genetic map location of 14 genes involved in the inflammatory response to salmonid bacterial and viral pathogens, which brings the total number of immune genes mapped in rainbow trout (RT, Oncorhynchus mykiss) to 61. These genes were mapped as candidate genes that may be involved in resistance to bacterial kidney disease, as well as candidates for known QTL for resistance to infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus and Ceratomyxa shasta. These QTL map to one or more of the linkage groups containing immune genes. The combined analysis of these linkage results and those of previously mapped immune genes in RT shows that many immune genes are found in syntenic blocks of genes that have been retained in teleosts despite species divergence and genome duplication events.     

Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication

A 10X rainbow trout bacterial artificial chromosome (BAC) library was constructed to aid in the physical and genetic mapping efforts of the rainbow trout genome. The library was derived from the Swanson clonal line (YY male) and consists of 184,704 clones with an average insert size of 137,500 bp (PFGE) or 118,700 bp (DNA fingerprinting). The clones were gridded onto 10 large nylon membranes to produce high-density arrays for screening the library by hybridization. The library was probed with 11 cDNAs from the NCCCWA EST project chosen because of interest in their homology to known gene sequences, seven known genes, and a Y-specific sex marker. Putative positive clones identified by hybridization were re-arrayed and gridded for secondary confirmation. FPC analysis of HindIII and EcoRV DNA fingerprinting was used to estimate the level of redundancy in the library, to construct BAC contigs and to detect duplicated loci in the semi-duplicated rainbow trout genome. A good correlation (R2 = 0.7) was found between the number of hits per probe and the number of contigs that were assembled from the positive BACs. The average number of BACs per contig was 9.6, which is in good agreement with 10X genome coverage of the library. Two-thirds of the loci screened were predicted to be duplicated as the positive BACs for those genes were assembled into two or three different contigs, which suggests that most of the rainbow trout genome is duplicated.     

Effects of some metal ions on rainbow trout erythrocytes glutathione S-transferase enzyme: an in vitro study

Glutathione S-transferase enzyme (GST) (EC 2.5.1.18) was purified from rainbow trout erythrocytes, and some characteristics of the enzyme and effects of some metal ions on enzyme activity were investigated. For this purpose, erythrocyte glutathione S-transferase enzyme which has 16.54 EU/mg protein specific activities was purified 11,026-fold by glutathione-agarose affinity chromatography with a yield of 59%. Temperature was kept under control (+4°C) during purification. Enzyme purification was checked by performing SDS-PAGE. Optimal pH, stable pH, optimal temperature, and K_M and V_max values for GSH and 1-chloro-2, 4-dinitrobenzene (CDNB) were also determined for the enzyme. In addition, IC₅₀ values, K_i constants and the type of inhibition were determined by means of Line-Weaver-Burk graphs obtained for such inhibitors as Ag⁺; Cd²⁺, Cr²⁺ and Mg²⁺.     

Assessment of cardiac output as a predictor of metabolic rate in rainbow trout

When water temperature was increased from 12 to 27°C at a rate of 2°C h⁻¹, oxygen consumption of rainbow trout Oncorhynchus mykiss was correlated strongly with both heart rate and blood oxygen extraction but the relationship with cardiac output was variable and weak. On the other hand, when water temperature was decreased from 21 to 12°C at a rate of 0·5°C h⁻¹, oxygen consumption was correlated with both heart rate and cardiac output but not with blood oxygen extraction. When fish were forced to swim increasingly faster, heart rate, cardiac output and blood oxygen extraction all correlated positively with oxygen consumption. For both cardiac output and heart rate, the slope of the regression line with oxygen consumption was elevated significantly more when the fish were forced to swim at increasingly higher swimming speeds than when water temperature was increased or decreased. The variation of the regression lines between cardiac output and oxygen consumption indicated that cardiac output presents few advantages over heart rate as a predictor of metabolic rate.     

The amount of food ingested in a single meal by rainbow trout offered chopped herring, dry and wet diets

Two-year-old 1·5-kg rainbow trout were held in cages and conditioned by feeding either on low-fat chopped herring (H trout) or dry pellets (P trout) for 15 weeks. Their satiation amounts were then determined under standard conditions. On a wet weight basis H trout ate 2·5-3·5 times more food than P trout; this was sufficient to compensate for the high water content of herring and thereby maintain the dry matter intake. When P trout were offered herring (PH trout) they consumed more food than when offered dry pellets but not as much as H trout. Stomach capacity restricted the intake and their dry matter intake was reduced by c. 40%. When H trout were offered dry pellets (HP trout) they adjusted their intake immediately close to the level of P trout although their larger stomachs could have accommodated more than twice this volume of dry food. The return of appetite after a satiation meal was almost linear with time. Appetite increased at c. 556 mg g^-1 body weight h^-1 for H trout and at 142 mg g^-1 bw h^-1 for P trout. The return of appetite in PH trout was significantly slower (c. 370 mg g^-1 bw h^-1) than in H trout; the previous dietary history of the PH trout limited their capacity to process larger volumes of wet food in a single meal. Fish offered dry diet (P and HP trout) had similar rates of appetite return despite their previous feeding history suggesting that the property of the dry feed itself might limit meal size. The total gastric emptying time of diets of similar dry matter content (with and without large amounts of water) was similar, but the delay time before gastric emptying starts tended to be longer for dry diets. Dry pellets appear to impose a demand for water that prolongs the gastric delay. This water demand is met partly by drinking since the trout fed on dry pellets drank significantly more (436 ± 189 mg kg^-1 h^-1) than unfed and herring-fed trout which drank little or not at all (65 ± 113 and 70 ± 66 mg kg^-1 h^-1 respectively). Dietary water facilitated food processing and increased daily dry matter intake of trout when fed four times a day. When only one satiation meal per day was allowed, dietary water had no effect. It is concluded from this work that, in addition to gastric volume, a short-term limitation on the size of satiation meals in the rainbow trout is the availability of water to moisturize the food and thus to promote gastric digestion and emptying.     

Poststress levels of lysozyme and cortisol in adult rainbow trout: heritabilities and genetic correlations

Lysozyme response in stressed rainbow trout was compared with measurements of poststress cortisol activity. Estimates of heritability of lysozyme and cortisol were both moderate-to-high and both traits displayed positive genetic correlations in pair-wise comparisons of stress exposures. Genetic correlations between lysozyme and cortisol in stressed rainbow trout tended to be negative, although insignificant. Neither lysozyme, nor cortisol exhibited significant correlations with serum haemolytic activity. It is concluded that the data do not confirm earlier suggestions that lysozyme should be superior to cortisol in consistency of stress response in rainbow trout.     

Linkage arrangement of Na,K-ATPase genes in the tetraploid-derived genome of the rainbow trout (Oncorhynchus mykiss)

As part of our efforts to characterize Na,K-ATPase isoforms in salmonid fish, we investigated the linkage arrangement of genes coding for the alpha and beta-subunits of the enzyme complex in the tetraploid-derived genome of the rainbow trout (Oncorhynchus mykiss). Genetic markers were developed from four of five previously characterized alpha-subunit isoforms (alpha1b, alpha1c, alpha2 and alpha3) and four expressed sequence tags derived from yet undescribed beta-subunit isoforms (beta1a, beta1b, beta3a and beta3b). Sex-specific linkage analysis of polymorphic loci in a reference meiotic panel revealed that Na,K-ATPase genes are generally dispersed throughout the rainbow trout genome. A notable exception was the colocalization of two alpha-subunit genes and one beta-subunit gene on linkage group RT-12, which may thus share a conserved orthologous segment with linkage group 1 in zebrafish (Danio rerio). Consistent with previously reported homeologous relationships among the chromosomes of the rainbow trout, primers designed from the alpha3-isoform detected a pair of duplicated genes on linkage groups RT-27 and RT-31. Similarly, the evolutionary conservation of homeologous regions on linkage groups RT-12 and RT-16 was further supported by the map localization of gene duplicates for the beta1b isoform. The detection of homeologs within each gene family also raises the possibility that novel isoforms may be discovered as functional duplicates.     

Characterization and expression of embryonic globin in the rainbow trout, Oncorhynchus mykiss: Intra-embryonic initiation of erythropoiesis

When fractionated by reverse-phase high performance liquid chromatography (HPLC), the embryonic hemoglobin of the rainbow trout, Oncorhynchus mykiss, consisted of eight globins different from adult globins in terms of retention time. Amino acid sequences of the N-terminal regions of some globins were determined. In addition, four cDNA clones for embryonic globins from 10-day embryos were isolated (at 15 degrees C), sequenced and the amino acid sequences predicted. In comparison with the sequences of previously characterized globins, they corresponded to two alpha-type and two beta-type globins and therefore were named em.alpha-1, em.alpha-2, em.beta-1 and em.beta-2. The N-terminal 36 amino acids of one (E2) of the embryonic globins isolated by HPLC were identical to those of the sequence deduced from a cDNA, em.beta-2. The phylogenetic relationship between the embryonic globins and other globins previously reported was discussed. The present study is the first demonstration of amino acid sequences of embryonic globins in a teleost. To understand the initiation of erythropoiesis in the early development of the rainbow trout, histochemistry using o-dianisidine/hydrogen peroxide, immunohistochemistry using an antibody against embryonic hemoglobin, and northern blotting and whole embryo in situ hybridization using antisense RNA probe for em.beta-2 were performed. Embryonic globin mRNA, globin and hemoglobin appeared first in the anterior part of the intermediate cell mass (ICM) located in the median line beneath the notochord of embryos 6-7 days after fertilization at 15 degrees C (Vernier's stages 16-20). Shortly after that, the expression signal extended to the posterior part of the ICM and spread out laterally to blood islands on the posterior yolk sac. Thus, the initiation of erythropoiesis in the early embryo of rainbow trout is intraembryonic.     

The immaturity interval in Tetrahymena: Genetic and environmental sources of variation

The development of sexual maturity has been studied in Tetrahymena hegewischi. Progeny lines do not typically change from immaturity to mating with all different mating types during a single test interval, but about 30% do mature abruptly. Some testers are more likely than others to participate in the earliest mating reactions of progeny lines which do not mature abruptly. Subcaryonidal vegetative pedigrees of 10 pairs from 4 crosses revealed considerable intrapair variation in the time, measured in fissions, of maturity. The average intrapair coefficient of variation was 20%. A nested ANOVA revealed significant genomic effects on the immaturity interval, but no significant cytoplasmic or caryonidal effects; 56% of the total variation was non-genomic. Growth in different environments had highly significant effects on the immaturity interval. Subclones grown at 27°C with alternate day transfers took on the average 2 to 3 times as many fissions to mature as sister subclones grown at 27°C with daily transfers. Subclones grown at 18°C or 34°C and transferred on alternate days had intermediate maturation times. The greatest range in the immaturity interval among lines of the same genotype was from 34 to 143 fissions. The development of maturity in this species involves genetic control of timing, but the genetic differences are obscured by a large amount of intraclonal variation and sensitivity to the environment.     

Effects of capture and recovery on plasma levels of cortisol, lactate and gonadal steroids in a natural population of rainbow trout

Rainbow trout were captured by angling from a run of spawning fish on the Tongariro River in northern New Zealand, to examine the effects of catch and release angling on stress and reproductive parameters. Fish were blood sampled immediately after capture at playing times of <5 or 15 min, or after 1 or 24 h of recovery in stream enclosures. Plasma samples were assayed for cortisol (F), lactate, testosterone (T), 17β-oestradiol (E₂), and 17a,20β-dihydroxy-4-pregnen-3-one (17,20βP). Plasma F levels were similar to those of hatchery stocks of rainbow trout, at capture, and became significantly elevated 1 h after capture. Plasma F was still clevated in some fish 24 h after capture. Plasma lactate levels began to increase 15 min after capture, were further elevated 1 h after capture, and had returned to normal 24 h after capture. We proposed that metabolic recovery had occurred but that some animals were still experiencing some degree of stress, possibly in response to holding conditions in the river. Both plasma T and E₂ were depressed 24 h after capture, whereas there was no change in plasma 17,20βP. This is consistent with other findings showing that acute stress is associated with depression of plasma levels of T and E₂. There was no mortality as a result of capture or any of the handling protocols. We conclude that catch and release angling will result in negligible mortality, but may have an inhibitory effect on some reproductive processes.     

Interindividual variations in feeding and growth in rainbow trout during restricted feeding and in a subsequent period of compensatory growth

Compensatory growth responses of rainbow trout Oncorhynchus mykiss were studied by examining food intake and growth of individual fish held within groups that were switched between regimes that involved full and restricted feeding. Restricted feeding led to marked interindividual variability in food intake, probably as a result of the establishment of feeding hierarchies. This disparity in food acquisition was reflected in highly heterogeneous growth amongst the fish fed low rations. When fish were transferred from restricted to full rations, they became hyperphagic and displayed high rates of growth. Growth compensation was most marked amongst those fish which had shown the poorest growth during the period of feed restriction. These results suggest that the feeding hierarchies established under feed restriction did not persist, but were rapidly broken down when food became increasingly available, enabling the previously suppressed fish to gain access to food and to display rapid growth.