Is genetic variability so important? Non-native salmonids in South America

Three salmonid species introduced in Patagonian national parks in Argentine have experienced different degrees of expansion. Atlantic salmon Salmo salar is restricted to a few river-lake systems and its populations have been declining over recent years. Both rainbow Oncorhynchus mykiss and brown trout Salmo trutta populations have expanded from their introduction sites and now occupy a wide range of freshwater ecosystems. Genetic variation at the same neutral markers (microsatellite loci) was examined for different populations of the three species acclimatized to the same areas, and compared with that of native populations. Founder effects denoted as reduced variability and great differentiation with respect to the native populations were detected. Significant reduction in variability has not been an obstacle for successful adaptation of rainbow and brown trout, indicating that genetic variability per se cannot be claimed as the reason for their different outcomes in the new habitats.     

The genetic basis of smoltification-related traits in Oncorhynchus mykiss

The timing and propensity for migration between fresh- and seawater is a key theme in the diversity of life histories within the salmonid fishes. Across salmonid species, life-history strategies range from wholly freshwater-resident populations, to migratory and nonmigratory variation within populations, to populations and species that are primarily migratory. Despite the central theme of migration to the evolution of these fishes, the genetic architecture of migration-related processes is poorly understood. Using a genetic cross of clonal lines derived from migratory and nonmigratory life-history types of Onchorhynchus mykiss (steelhead and rainbow trout, respectively), we have dissected the genetic architecture of the complex physiological and morphological transformation that occurs immediately prior to seaward migration (termed smoltification). Quantitative trait loci (QTL) analyses were used to identify the number, effects, and genomic location of loci associated with smoltification-related traits, including growth and condition factor, body coloration, morphology, and osmoregulatory enzymes during the smoltification period. Genetic analyses revealed numerous QTL, but one locus in particular is associated with multiple traits in single and joint analyses. Dissecting the genetic architecture of this highly complex trait has profound implications for understanding the genetic and evolutionary basis of life-history diversity within and among migratory fishes.     

Who are the missing parents? Grandparentage analysis identifies multiple sources of gene flow into a wild population

In order to increase the size of declining salmonid populations, supplementation programmes intentionally release fish raised in hatcheries into the wild. Because hatchery-born fish often have lower fitness than wild-born fish, estimating rates of gene flow from hatcheries into wild populations is essential for predicting the fitness cost to wild populations. Steelhead trout (Oncorhynchus mykiss) have both freshwater resident and anadromous (ocean-going) life history forms, known as rainbow trout and steelhead, respectively. Juvenile hatchery steelhead that 'residualize' (become residents rather than go to sea as intended) provide a previously unmeasured route for gene flow from hatchery into wild populations. We apply a combination of parentage and grandparentage methods to a three-generation pedigree of steelhead from the Hood River, Oregon, to identify the missing parents of anadromous fish. For fish with only one anadromous parent, 83% were identified as having a resident father while 17% were identified as having a resident mother. Additionally, we documented that resident hatchery males produced more offspring with wild anadromous females than with hatchery anadromous females. One explanation is the high fitness cost associated with matings between two hatchery fish. After accounting for all of the possible matings involving steelhead, we find that only 1% of steelhead genes come from residualized hatchery fish, while 20% of steelhead genes come from wild residents. A further 23% of anadromous steelhead genes come from matings between two resident parents. If these matings mirror the proportion of matings between residualized hatchery fish and anadromous partners, then closer to 40% of all steelhead genes come from wild trout each generation. These results suggest that wild resident fish contribute substantially to endangered steelhead 'populations' and highlight the need for conservation and management efforts to fully account for interconnected Oncorhynchus mykiss life histories.     

Isolation of 15 single nucleotide polymorphisms from coastal steelhead, Oncorhynchus mykiss (Salmonidae)

We describe 15 single nucleotide polymorphisms (SNPs) isolated in coastal California populations of steelhead (Oncorhynchus mykiss). SNP loci were developed using a 'gene-targeted' approach, which involved the development of primers from functional genes in O. mykiss that were deposited in GenBank or in the published literature. These markers show a wide range of variability in three coastal steelhead populations, and will be useful in population genetic studies and in pedigree reconstruction. Potential applications include evaluation of population structure, introgression between native and hatchery trout, and evaluating reproductive success.     

Assembling a dual purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis

We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154 previously developed markers to the TaqMan platform. At the beginning of this study, 59 SNPs with TaqMan assays were available to the scientific community. By adding 176 additional TaqMan assays to this number, we greatly expand the biological applications of TaqMan genotyping within both population genetics and quantitative genetics.     

A genetically distinct wild redband trout (<Emphasis Type="Italic">Oncorhynchus mykiss gairdneri</Emphasis>) population in Crane Prairie Reservoir,Oregon, persists despite extensive stocking of hatchery rainbow trout (<Emphasis Type="Italic">O. m. irideus</Emphasis>)

Crane Prairie Reservoir in the upper Deschutes River Basin has historically supported a wild population of migratory Deschutes River redband trout. Owing to its status as a premier destination for recreational angling in Oregon, the reservoir has been stocked with domesticated hatchery rainbow trout since 1955. In recent years the wild redband trout population has experienced a substantial decline. Effects on productivity related to genetic interaction with naturally spawning hatchery-origin fish (fitness risks) have not been determined. The species Oncorhynchus mykiss has been characterized with substantial genetic diversity throughout the Deschutes River Basin that further heightens the challenge of identifying specific conservation needs of wild populations. A conservation plan for Crane Prairie wild redband trout requires a better understanding of the natural reproductive success of out-of-basin hatchery trout in the reservoir tributaries, and the similarity between Crane Prairie redband trout with other extant redband trout populations in the basin. Using a suite of 17 microsatellite nuclear DNA markers, we evaluated the genetic structure among Crane Prairie Reservoir redband trout, hatchery rainbow trout, and two adjacent populations of redband trout from within the Upper Deschutes River Basin. We observed significant heterogeneity between the hatchery and wild Crane Prairie populations that may reflect differences in life histories, differential productivity and assortative mating. The genetic distinctions observed among the three redband trout populations suggest restricted gene flow and genetic drift within the upper basin. Temporally stratified sampling and larger numbers of samples will be necessary to confirm these conclusions.     

Analysis of microsatellite variation in the rainbow trout (Parasalmo (Oncorhynchus) mykiss) from Kamchatka

Genetic variation of Kamchatka rainbow trout Parasalmo (O.) mykiss was examined using 10 microsatellite DNA loci, and phylogeographic comparison with other representatives of the species across the distribution range was performed. It was demonstrated that Kamchatka populations differed from other geographic groups of rainbow trout in a number of microsatellite loci. These populations also displayed distinct clustering and were characterized by lower genetic diversity. Analysis of a set of 26 different microsatellite loci (personal and literature data) demonstrated that most of the populations within the Kamchatka region were separated from one another, characterized by marked geographic differentiation, and affiliation to certain river basins. In Kamchatka rainbow trout, with high degree of probability, three geographic clusters (northwestern, southwestern, and eastern) were identified. In general, analysis of microsatellite DNA supported the data on low genetic diversity of the Kamchatka group Parasalmo (O.) mykiss, based on the variation estimates for a number of genes of nuclear and mitochondrial DNA, and allozyme loci.     

Population genetic structure and ancestry of steelhead/rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) at the extreme southern edge of their range in North America

Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwater resident form of the species O. mykiss, is one factor threatening the long-term persistence of native steelhead and other trout populations. To identify where native fish of coastal steelhead lineage remained, we performed a population genetic analysis of microsatellite and SNP genotypes from O. mykiss populations at the extreme southern end of their range in Southern California, USA and Baja California, Mexico. In the northern part of this region, nearly all populations appeared to be primarily descendants of native coastal steelhead. However, in the southern, more urbanized part of this region, the majority of the sampled populations were derived primarily from hatchery trout, indicating either complete replacement of native fish or a strong signal of introgression overlaying native ancestry. Nevertheless, these genetically introgressed populations represent potentially critical genetic resources for the continued persistence of viable networks of O. mykiss populations, given the limited native ancestry uncovered in this region and the importance of genetic variation in adaptation. This study elucidates the geographic distribution of native trout populations in this region, and serves as a baseline for evaluating the impacts of hatchery trout on native O. mykiss populations and the success of steelhead conservation and recovery efforts.     

Efficiency of Portable Antennas for Detecting Passive Integrated Transponder Tags in Stream-Dwelling Salmonids

Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT) tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta), bull trout (Salvelinus confluentus), and redband trout (Oncorhynchus mykiss newberrii) marked with 12-mm PIT tags. We redetected 56% (20/36) of brown trout, 34% (68/202) of bull trout, and 33% (20/61) of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE]) are approximately four times as high as bull trout (0.4 ± 1.6) or redband trout (0.3 ± 1.8) and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species.     

Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous where they are sympatric, either naturally or owing to introductions. The ability to detect hybridization and introgression between the two species would be greatly improved by the development of more diagnostic markers validated across the two species' many phylogenetic lineages. Here, we describe 81 novel genetic markers and associated assays for discriminating the genomes of these sister species. These diagnostic nucleotide polymorphisms were discovered by sequencing of rainbow trout expressed sequence tags (ESTs) in a diverse panel of both cutthroat trout and steelhead/rainbow trout. The resulting markers were validated in a large number of lineages of both species, including all extant subspecies of cutthroat trout and most of the lineages of rainbow trout that are found in natural sympatry with cutthroat trout or used in stocking practices. Most of these markers (79%) distinguish genomic regions for all lineages of the two species, but a small number do not reliably diagnose coastal, westslope and/or other subspecies of cutthroat trout. Surveys of natural populations and hatchery strains of trout and steelhead found rare occurrences of the alternative allele, which may be due to either previous introgression or shared polymorphism. The availability of a large number of genetic markers for distinguishing genomic regions originating in these sister species will allow the detection of both recent and more distant hybridization events, facilitate the study of the evolutionary dynamics of hybridization and provide a powerful set of tools for the conservation and management of both species.     

An experimental analysis of self-thinning in juvenile steelhead trout

Mobile animal populations have been proposed to decline in density according to a slope based on the allometry of metabolic requirements or space requirements. In salmonid fishes, metabolic rate and food consumption scale to body mass by the exponent 0.87 and 0.73, respectively; whereas the territory size of steelhead trout scales to body mass by the exponent 0.86. Experimental cohorts of juvenile steelhead trout ( Oncorhynchus mykiss ) were used to test the hypothesis that mobile animal populations composed of individuals with indeterminate growth decline in density as a result of self-thinning. After controlling for experimentally manipulated levels of food abundance and stocking density, cohorts of steelhead trout declined in density with increasing body size according to a slope closest to the allometry of food consumption. Densities of steelhead trout were inversely related to average mass by the exponent −0.74. Despite the similarity to the food consumption slope, a relatively wide confidence interval also precluded distinguishing the slope either the metabolic rate or territory size slopes. Data from the literature were also examined to determine if there was general support for the idea of self-thinning in natural populations of stream-dwelling salmonid fish. Although not all data suggest that populations of salmonids in streams decline as a result of density-dependent intraspecific competition, at least some appear to fit the idea of self-thinning; especially when density is above a minimum level of habitat saturation.     

Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss)

Infectious pancreatic necrosis (IPN) is a well-known acute viral disease of salmonid species. We have identified quantitative trait loci (QTLs) associated with resistance to this disease in rainbow trout. We searched for linkage among 51 microsatellite markers used to construct a framework linkage map in backcross families of rainbow trout (Oncorhynchus mykiss), produced by crossing IPN-resistant (YN-RT201) and -susceptible (YK-RT101) strains. Two putative QTLs affecting disease resistance were detected on chromosomes A (IPN R S-1) and C (IPN R/S-2), respectively, suggesting that this is a polygenic trait in rainbow trout. These markers have great potential for use in marker-assisted selection (MAS) for IPN resistance and provide the basis for cloning of IPN resistance genes. Clarification of the genetic bases of complex traits has broad implications for fundamental research, but will also be of practical benefit to fish breeding.     

Adaptation of redband trout in desert and montane environments

Natural populations that evolve under extreme climates are likely to diverge because of selection in local environments. To explore whether local adaptation has occurred in redband trout (Oncorhynchus mykiss gairdneri) occupying differing climate regimes, we used a limited genome scan approach to test for candidate markers under selection in populations occurring in desert and montane streams. An environmental approach to identifying outlier loci, spatial analysis method and linear regression of minor allele frequency with environmental variables revealed six candidate markers (P < 0.01). Putatively neutral markers identified high genetic differentiation among desert populations relative to montane sites, likely due to intermittent flows in desert streams. Additionally, populations exhibited a highly significant pattern of isolation by temperature (P< 0.0001) and those adapted to the same environment had similar allele frequencies across candidate markers, indicating selection for differing climates. These results imply that many genes are involved in the adaptation of redband trout to differing environments, and selection acts to reinforce localization. The potential to predict genetic adaptability of individuals and populations to changing environmental conditions may have profound implications for species that face extensive anthropogenic disturbances.     

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

ABSTRACT: BACKGROUND: There is considerable interest in developing high-throughput genotyping with singlenucleotide polymorphisms (SNPs) for the identification of genes affecting importantecological or economical traits. SNPs are evenly distributed throughout the genome and arelikely to be functionally relevant. In rainbow trout, in silico screening of EST databasesrepresents an attractive approach for de novo SNP identification. Nevertheless, ESTsequencing errors and assembly of EST paralogous sequences can lead to the identification offalse positive SNPs which renders the reliability of EST-derived SNPs relatively low. Furthervalidation of EST-derived SNPs is therefore required. The objective of this work was toassess the quality of and to validate a large number of rainbow trout EST-derived SNPs. RESULTS: A panel of 1,152 EST-derived SNPs was selected from the INRA Sigenae SNP database andwas genotyped in standard and double haploid individuals from several populations using theIllumina GoldenGate BeadXpress assay. High-quality genotyping data were obtained for 958 SNPs representing a genotyping success rate of 83.2 %, out of which, 350 SNPs (36.5 %)were polymorphic in at least one population and were designated as true SNPs. They alsoproved to be a potential tool to investigate genetic diversity of the species, as the set of SNPsuccessfully sorted individuals into three main groups using STRUCTURE software.Functional annotations revealed 28 non-synonymous SNPs, out of which four substitutionswere predicted to affect protein functions. A subset of 223 true SNPs were polymorphic inthe two INRA mapping reference families and were integrated into the INRA microsatellitebasedlinkage map. CONCLUSIONS: Our results represent the first study of EST-derived SNPs validation in rainbow trout, aspecies whose genome sequences is not yet available. We designed several specific filters inorder to improve the genotyping yield. Nevertheless, our selection criteria should be furtherimproved in order to reduce the observed high rate of false positive SNPs which results fromthe occurrence of whole genome duplications.     

Rapid parallel evolution of standing variation in a single,complex, genomic region is associated with life history in steelhead/rainbow trout

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.     

Genetic divergence of sympatric resident and anadromous forms of Oncorhynchus mykiss in the Walla Walla River, U.S.A.

Genetic structure (six microsatellites) and gene flow were examined among anadromous (steelhead; n  = 326), resident (rainbow trout; n  = 52), and mixed ( n  = 407) Oncorhynchus mykiss life‐history forms collected from the major drainages the mainstem Walla Walla River and the Touchet River within the Walla Walla River sub‐basin, Washington, U.S.A. Genetic structure was detected between the two major drainages. Exact tests, F _ST, multi‐locus assignment tests and a neighbour‐joining dendrogram revealed genetic divergence between sympatric reference populations of adult steelhead and resident rainbow trout in the mainstem Walla Walla River, but not in the Touchet River. Tests of Hardy‐Weinberg equilibrium indicated anadromous and resident O. mykiss reference populations were in equilibrium, but many of the mixed life‐history collections were out of equilibrium. Populations out of equilibrium in the mainstem Walla Walla River appeared to be admixtures as confirmed by multi‐locus assignment tests. This is evidence of genetic divergence probably resulting from assortative mating between life‐history forms or out‐of‐basin stocking practices.     

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan(?) assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.     

Habitat diversity and species diversity: testing the competition hypothesis with juvenile salmonids

I experimentally tested two predictions of the hypothesis that the positive relationship between habitat diversity and species diversity arises from a reduction in the negative effects of interspecific competition. By allowing species to partition habitat and avoid competition, habitat diversity should 1) facilitate the addition of an ecologically intermediate species into an existing community, and 2) reduce the negative effects of that species on existing members of the community. I tested these predictions with juveniles of three sympatric salmonid species: coho salmon ( Oncorhynchus kisutch ), steelhead trout ( O. mykiss ), and cutthroat trout ( O. clarki ), which in natural streams occupy deep low-velocity pools, shallow high-velocity riffles, and intermediate habitats, respectively. I introduced two (coho and steelhead) and three species communities into each of three artificial stream habitats: pools, riffles, and diverse. The results provide partial support for the predictions. Cutthroat trout grew fastest in the diverse stream habitat. Though habitat diversity did not eliminate the negative effects of competition, in the three species community coho and steelhead grew as fast in the diverse habitat as in either homogeneous habitat. The results are consistent with data on species number and evenness from natural communities, where variation along other niche axes confounds the relationship between habitat diversity, interspecific competition, and species diversity.     

Modes of salmonid MHC class I and II evolution differ from the primate paradigm

Rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta) represent two salmonid genera separated for 15--20 million years. cDNA sequences were determined for the classical MHC class I heavy chain gene UBA and the MHC class II beta-chain gene DAB from 15 rainbow and 10 brown trout. Both genes are highly polymorphic in both species and diploid in expression. The MHC class I alleles comprise several highly divergent lineages that are represented in both species and predate genera separation. The class II alleles are less divergent, highly species specific, and probably arose after genera separation. The striking difference in salmonid MHC class I and class II evolution contrasts with the situation in primates, where lineages of class II alleles have been sustained over longer periods of time relative to class I lineages. The difference may arise because salmonid MHC class I and II genes are not linked, whereas in mammals they are closely linked. A prevalent mechanism for evolving new MHC class I alleles in salmonids is recombination in intron II that shuffles alpha 1 and alpha 2 domains into different combinations.     

不同倍性虹鳟幼鱼对急性温度胁迫的抗氧化响应

虹鳟属于冷水性鱼类,其生存的最适温度为12~18 ℃,温度胁迫是虹鳟在夏秋季养殖过程中经常遇到的问题.枫叶鲑和硬头鳟均为品质优良的虹鳟选育种.为探讨急性温度胁迫对两种倍性虹鳟抗氧化响应的影响,本研究选取二倍体枫叶鲑和三倍体硬头鳟幼鱼,分别在13、17、21和25 ℃下进行热应激试验.在达到目标温度后的0、1、6和12 h取样,之后将受试鱼恢复至13 ℃的适宜温度下培养,并在恢复培养的1、12、24和48 h后取样,测定受试鱼肝脏中超氧化物歧化酶(SOD)、过氧化氢酶(CAT)、谷胱甘肽过氧化物酶(GPx)的活性,以及脂质过氧化物(LPO)、丙二醛(MDA)和热激蛋白70(HSP70)含量.结果表明: 枫叶鲑和硬头鳟的3种抗氧化酶活性在17 ℃组没有出现显著升高;21 ℃组枫叶鲑和硬头鳟的SOD活性在热应激期间出现显著升高,但枫叶鲑的SOD活性在恢复过程中恢复到正常水平;25 ℃组枫叶鲑和硬头鳟的SOD、CAT和GPx的活性均显著提高;但在恢复试验进行24 h后,CAT和GPx的活性恢复到正常水平.枫叶鲑在17、21和25 ℃组HSP70的产生量显著高于13 ℃组,而硬头鳟仅在21和25 ℃组HSP70的产生量显著高于13 ℃组.通过整合生物标志物响应指标值对多种抗氧化参数进行分析,发现枫叶鲑在17和21 ℃组急性温度胁迫下的抗氧化响应显著高于硬头鳟,但在25 ℃组硬头鳟的抗氧化响应高于枫叶鲑.这表明不同倍性虹鳟幼鱼在不同温度急性胁迫下的抗氧化响应有所差异.