Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts

Ten primer pairs were screened to develop single nucleotide polymorphism (SNP) TaqMan assays that will distinguish California golden trout and some rainbow trouts (Oncorhynchus mykiss sspp., O. m. aguabonita) from the Paiute and Lahontan cutthroat trouts (Oncorhynchus clarkii seleniris, O. c. henshawi). From these 10 primer pairs, one mitochondrial and five nuclear fixed SNP differences were discovered and developed into TaqMan assays. These six assays will be useful for characterizing and monitoring hybridization between these groups. Additional Oncorhynchus clarkii sspp. and Oncorhynchus mykiss sspp. were assayed to determine if these assays are useful in closely related species.     

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.     

Characterization of 19 single nucleotide polymorphism markers for coho salmon

We report 39 single nucleotide polymorphisms (SNPs) observed in 23 nuclear DNA sequences in coho salmon Oncorhynchus kisutch. High‐throughput genotyping assays based on the 5′‐nuclease reaction were developed for 17 of these nuclear SNPs and for two previously published mitochondrial DNA SNPs. Minor allele frequency differences (Δq) among collections were between 5.2% and 51.2%, resulting in per locus F_ST estimates of 0.00–0.24 with an average of 0.09.     

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.     

A genetic analysis of the London strain of rainbow trout

The London strain of rainbow trout (Oncorhynchus mykiss) was created by interbreeding three other strains of rainbow trout and therefore was expected to have higher levels of genetic variation than other strains of rainbow trout. We examined 129 London strain rainbow trout from Indiana by allozyme electrophoresis to assess levels of genetic variation and to examine the relationship between the London strain and other hatchery strains. When using the same loci to compare with other hatchery strains the London strain showed levels of genetic variation within the range of other hatchery strains: mean heterozygosity of 0.053 (0.031-0.099), 1.27 (1.20-1.60) alleles per locus and 20.0% (20.0-40.0%) of the loci were polymorphic. The London strain is somewhat distinct from other hatchery strains (D=0.009-0.072), in part because of the high frequency of the sIDHP*40 allele.     

Relationship between stress, feeding and plasma ghrelin levels in rainbow trout, Oncorhynchus mykiss

Sexually immature rainbow trout were acclimated to small-volume (1 m³) holding tanks and then exposed to short-term stress to examine the relationship between feeding, stress, plasma ghrelin levels and other plasma stress parameters. Plasma ghrelin levels showed an increase 24 h after a single feed, plasma lactate and glucose levels decreased over the same period and plasma cortisol levels were low and constant. One hour of confinement stress resulted in elevations of plasma cortisol, glucose and lactate and depression of plasma ghrelin levels. In a separate experiment, 2 h of confinement stress also depressed feeding immediately after stress, concomitant with increases in plasma cortisol, lactate and glucose; however, in this case there was no change in plasma ghrelin concentrations. A repeat of the 2-h confinement experiment using fish that had not been acclimated to small-volume holding tanks produced a more marked elevation in plasma cortisol and a stronger suppression of feeding post-stress but in this case also, there was no change in plasma ghrelin levels. The results of this study confirm that feeding in rainbow trout is suppressed by confinement stress although the effect is transitory in this domesticated stock. Similar to that in other fishes, plasma ghrelin levels appear to be modulated by feeding status and may be influenced by stress, suggesting an orexigenic role for ghrelin in rainbow trout.     

Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Oncorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (Oncorhynchus mykiss)

We describe 12 diagnostic single nucleotide polymorphism (SNP) assays for use in species identification among rainbow and cutthroat trout: five of these loci have alleles unique to rainbow trout (Oncorhynchus mykiss), three unique to westslope cutthroat trout (O. clarkii lewisi) and four unique to Yellowstone cutthroat trout (O. clarkii bouvieri). These diagnostic assays were identified using a total of 489 individuals from 26 populations and five fish hatchery strains.     

Characterization of tetranucleotide microsatellites for Rio Grande cutthroat trout and rainbow trout,and their cross‐amplification in other cutthroat trout subspecies

We describe the isolation and characterization of 12 tetranucleotide microsatellites for Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis) and rainbow trout (Oncorhynchus mykiss), and subsequently investigate their performance in Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus), greenback cutthroat trout (Oncorhynchus clarkii stomias) and Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri). All 12 loci are polymorphic in all subspecies of O. clarkii examined.     

Thirty‐two single nucleotide polymorphism markers for high‐throughput genotyping of sockeye salmon

We characterize 32 single nucleotide polymorphism genotyping assays for resolving genotypic variation in sockeye salmon Oncorhynchus nerka in the Pacific Rim. These assays are based on the 5′‐nuclease reaction and thus facilitate high‐throughput genotyping with minimal optimization time. Minor allele frequency differences (Δq) among collections were between 4.7% and 97.9%, resulting in per locus F_ST estimates of 0.02–0.71 with an average of 0.22.     

Thirty‐eight single nucleotide polymorphism markers for high‐throughput genotyping of chum salmon

We characterize 38 single nucleotide polymorphism genotyping assays for chum salmon (Oncorhynchus keta), an important species for both commercial and subsistence fisheries in western Alaska. These assays are based on the 5′‐nuclease reaction and thus facilitate high‐throughput genotyping with minimal optimization time. Minor allele frequency differences (Δq) among collections were between 0.01 and 0.50 resulting in per locus F_ST estimates of 0.00–0.08 with an average of 0.03.     

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.     

Primary and secondary indices of stress in the progeny of rainbow trout (Oncorhynchus mykiss) selected for high and low responsiveness to stress

A series of pooled gamete matings was carried out employing eggs and milt from mature male and female rainbow trout selected for a consistently high- or low-responsiveness to stress, as indicated by post-stress plasma cortisol elevation. Development of the progeny was closely monitored and the responsiveness to stress of the progeny of high-responding parents and the progeny of low-responding parents was assessed by two methods. For a period of 14 months, at approximately monthly intervals, the plasma cortisol elevation evoked by a standardized confinement stress was determined in fish from each group, and secondly, on one occasion, the time-course of the plasma cortisol response to a 24-h period of confinement was monitored. Progeny of high-responding parents snowed a significantly greater cortisol response to stress than the progeny of low-responding parents during both testing procedures. However, when the effect of a 14-day confinement stress was examined, high-responding progeny showed a more rapid recovery of plasma cortisol levels, while levels in the low-responding progeny, although initially lower, showed a more sustained elevation. To assess the possible functional implications of these observations, circulating lymphocyte numbers, an immunologically important cortisol-sensitive component of the blood cell complement, were determined. The duration of the lymphocytopenia observed following the onset of confinement was found to be related to the initial, not the sustained, cortisol response. These data suggest that manipulation of the sensitivity to stress of fish is feasible by selective breeding, but that careful.choice of the indices employed to identify traits considered desirable is necessary.     

In vitro differentiation of myoblasts from skeletal muscle of rainbow trout

Substrata, plating densities and tissue culture media were compared for their effects on the proliferation and differentiation of myoblasts from skeletal muscle of rainbow trout. Mononuclear cells were isolated from the lateralis muscle of 4–11-month-old trout and plated on to glass coverslips coated with fibronectin, laminin or Matrigel. Cell proliferation was estimated by determining the density of nuclei on successive days in culture, and myoblast differentiation was detected by immunostaining cultures with the myosin-specific monoclonal antibody MF20. Mononuclear cell proliferation was highest for cells cultured on fibronectin or laminin and lowest for cells cultured on Matrigel, but the total number of nuclei in myosin-positive cells did not differ between substrata. The percentage of nuclei in myosin-positive myocytes and myotubes was significantly higher for cells cultured on Matrigel. The proportion of cells adhering to Matrigel and undergoing differentiation increased with plating density. Of three media tested, Dulbecco's Modified Eagle Medium (DMEM), RPMI 1640 (RPMI), Leibovitz's L-15 (L-15) supplemented with 1 or 10% fetal bovine serum (FBS), a significantly greater proportion of the myoblasts differentiated when cells were cultured in L-15+ 10% FBS. These results suggest that culturing trout muscle-derived cells on a substratum of Matrigel at a high density and maintaining cells in L-15+ 10% FBS provide the conditions that maximize the proportion of cells that actively synthesize muscle myosin and facilitate trout myoblast differentiation in vitro .     

Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

DNA sequence data were collected and screened for single nucleotide polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki lewisi) and also for substitutions that could be used to genetically discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as several cutthroat trout subspecies. In total, 260 expressed sequence tag‐derived loci were sequenced and allelic discrimination genotyping assays developed from 217 of the variable sites. Another 50 putative SNPs in westslope cutthroat trout were identified by restriction‐site‐associated DNA sequencing, and seven of these were developed into assays. Twelve O. mykiss SNP assays that were variable within westslope cutthroat trout and 12 previously published SNP assays were also included in downstream testing. A total of 241 assays were tested on six westslope cutthroat trout populations (N = 32 per population), as well as collections of four other cutthroat trout subspecies and a population of rainbow trout. All assays were evaluated for reliability and deviation from Hardy–Weinberg and linkage equilibria. Poorly performing and duplicate assays were removed from the data set, and the remaining 200 assays were used in tests of population differentiation. The remaining markers easily distinguished the various subspecies tested, as evidenced by mean G_ST of 0.74. A smaller subset of the markers (N = 86; average G_ST = 0.40) was useful for distinguishing the six populations of westslope cutthroat trout. This study increases by an order of magnitude the number of genetic markers available for the study of westslope cutthroat trout and closely related taxa and includes many markers in genes (developed from ESTs).     

A suite of twelve single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trout

A suite of 12 subspecies and species-specific single nucleotide polymorphism (species-specific SNP) markers was developed to distinguish rainbow trout (RT) Oncorhynchus mykiss from the four major subspecies of cutthroat trout: westslope cutthroat trout (WCT) Oncorhynchus clarki lewisi, Yellowstone cutthroat trout (YCT) Oncorhynchus clarki bouvieri, coastal cutthroat trout (CCT) Oncorhynchus clarki clarki, Lahontan cutthroat trout (LCT) Oncorhynchus clarki henshawi, and their hybrids. Several of the markers were linked to help strengthen hybrid determinations, and sex-specific species-specific SNP assays were also developed.     

虹鳟对时间和地点的学习记忆(英文)

为确定虹鳟(Oncorhynchus mykiss)是否能将日投放两次食物的不同时间和地点联系起来,在30天内,于09:00-10:00将食饵投放在水族箱一侧,于15:00-16:00将食饵投放在水族箱另一侧.在第21天和28天,不放食饵以确定虹鳟对时间-地点的学习记忆.结果表明,虹鳟将不同时间和地点联系起来以获取食物,并且在水族箱两个投放食饵之处均表现出预取食活动,提示该物种具有控制时间-地点学习任务的内在机制.     

Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia

Bacterial artificial chromosome (BAC) libraries are important tools for genomic research. We have constructed seven genomic BAC libraries from three fish species, rainbow trout (Oncorhynchus mykiss), carp (Cyprinus carpio) and tilapia (Oreochromis niloticus). The two rainbow trout BAC libraries have average insert sizes of 58 and 110 kb. The average size of inserts in the carp BAC library is 160 kb. The average insert sizes of the four tilapia BAC libraries are 65, 105, 145 and 194 kb, respectively. These libraries represent good coverage of each genome (2-64 x coverage). The libraries can be screened by conventional colony hybridization and provide a starting point for the construction of high-density filtres or polymerase chain reaction (PCR) screening approaches. These BAC libraries will facilitate the positional cloning of quantitative trait loci (QTLs) for a variety of economically important traits in these species.     

Differences in plasma cortisol and cortisone dynamics during stress in two strains of rainbow trout (Oncorhynchus mykiss)

Plasma levels of cortisone, a steroid hormone of potential physiological significance in fish, have rarely been measured. This study examines the interrelationship between circulating levels of cortisone and the major teleost corticosteroid, cortisol, in the blood of two strains of rainbow trout subject to confinement stress, a condition know to stimulate corticosteroidogenic activity. In unstressed fish from both strains, mean plasma cortisol levels were within the range 0.4–7.5 ng ml⁻¹. Mean plasma cortisone levels were within the range 7.1–15.9 ng ml⁻¹. Plasma cortisol levels were elevated within 5 min of the onset of strees and reached peak values within 45 min, although there was a marked difference betweed the maxima observed in the two strains (strain 1:70 ng ml⁻¹; strain 2:150 ng ml⁻¹). The rate of increase of plasma cortisone levels during strees was more rapid than that of cortisol, maximum values (strain 1:100ng ml⁻¹; strain 2:160 ng ml⁻¹) being reached within 10 to 20 min of the onset of stress. This rapid stress-induced elevation of plasme cortisone has not previously been reported in fish. We suggest that rapid conversion of cortisol to cortisone during the initial response to stress accounts for the appearance of large amounts of cortisone in the blood, indicating that circulating for the appearance of large amounts of cortisone in the blood, indicating that circulating levels of cortisol alone do not fully reflect the secretory activity of the interregnal during the initial of cortisol alone do not fully the secretory activity of the interregnal during the initial phase of the stress response. The results also indicate that the rate of clearance of cortisone from the circulation may be a major factor in determining stress-stimulated levels of plasma cortisol.     

Subspecies-informative SNP assays for evaluating introgression between native golden trout and introduced rainbow trout

We characterize 20 single nucleotide polymorphism assays for evaluating hybridization between native golden trout subspecies (Oncorhynchus mykiss aguabonita and O. m. whitei) and introduced rainbow trout strains. These assays utilize the 5′‐nuclease reaction, facilitating high‐throughput genotyping of many individuals and making them useful in quantifying and monitoring introgression and potentially applicable to studies of other O. mykiss groups. Minor allele frequency differentials (δq) among native and introduced rainbow groups ranged from 0 to 1, with an average differential of 0.75 for both subspecies aguabonita and whitei relative to the hatchery rainbow trout strain.     

Genetic comparison between sympatric anadromous steelhead and freshwater resident rainbow trout in British Columbia, Canada

Sympatrically occurring steelhead and rainbowtrout (n = 100) were collected from fiveriver systems in British Columbia, Canada, and1300 bp from the mitochondrial genome and 270bp of the nuclear growth hormone 2 gene weresequenced to determine if the two forms aregenetically differentiated. ND3 and D-loopsequence differences produced nine haplotypeswhile two length variants of the GH2 intron Dwere present. In one river system, steelheadand rainbow were genetically divergent based onmtDNA data but overall, no consistent geneticdifference between life history types wasfound. Rather, genetic differences wereassociated with geography, suggesting thatsteelhead and rainbow trout are polyphyleticand the result of parallel evolution ratherthan members of two distinct lineages.