Golden Trout Research Articles

Identification of single nucleotide polymorphisms in BMP-2 gene and their associations with productive traits in Rainbow Trout

Relevance. Aquaculture is occupying an increasingly important place in fish farming, as it allows obtaining more products per unit area. In recent years, special attention has been paid to the development of new breeds of Rainbow Trout in order to obtain fish forms adapted to aquaculture conditions. One of the significant breeding achievements is the Ropshinsky golden trout, characterized by attractive scale coloration. Taking into account the emergence of such forms of fish, research to identify genetic characteristics is of particular relevance. The BMP-2 gene is an important determinant of fish growth and development, so a comprehensive study of its structure will allow us to identify the most favorable genotypes in producers for their use in further selection and breeding.Results. The aim of the work is to identify single nucleotide polymorphisms (SNPs) in the studied gene and link their presence in parental forms with their productive traits. In particular, after sequencing, several SNPs were identified in different positions both in the intron and exon regions of the gene. The frequencies of occurrence of genotypes in parents were calculated and a number of quantitative traits were measured in the offspring numbered of 50 individuals from each crossing pair. In some cases, it was possible to establish statistically significant associations between the identified SNPs and productive traits in females and males — the parents of the resulting offspring. In females, an association was established between head length and SNP in one gene region, and in males, an association of another polymorphism with ejaculate volume has been demonstrated.

Evaluation of quality indices for functional products from fish enriched with selenium in conditions of aquaculture

Scientific and practical aspects are considered for development of functional nutrition products from fish raw materials after lifetime enrichment of the fish muscle tissue with selenium. Size-weight composition is investigated for rainbow golden trout grown in aquaculture, minerals and fatty acids content is determined for hot-smoked products of this species, and quality indicators and nutritional value are evaluated for both raw materials and the products to examine possibility of the enrichment with selenium by adding a selenium-containing preparation to fish feeds and to estimate effect of such feeding on commercial, nutritional and consumer properties of the products. The fish from the experimental group fed by the feeds with preparation Kormogran Selenium-3 had more valuable mineral and fatty acid composition of meat, higher yield of edible parts, and better organoleptic properties of smoked products in comparison with the control group. There is concluded that the lifetime enrichment of the trout tissues with selenium in aquaculture conditions is an effective technology for producing high-quality seafood for functional nutrition.

Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments.

Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size. In some lakes that were stocked decades ago, we find shifts in gill raker traits consistent with the hypothesis that trout have rapidly adapted to exploit available smaller-bodied zooplankton more effectively. We explore this morphological response in multiple lake populations across two species of trout (cutthroat trout, Oncorhynchus clarkii, and golden trout Oncorhynchus aguabonita) and examine the impact of resource availability on morphological variation in gill raker number among lakes. Furthermore, we present genetic data to provide evidence that historically stocked cutthroat trout populations likely derive from multiple population sources, and incorporate variation from genomic relatedness in our exploration of environmental predictors of feeding morphology. These findings describe rapid adaptation and eco-evolutionary interactions in trout and document an evolutionary response to novel, contemporary ecosystem change.

Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (Oncorhynchus chrysogaster and O. mykiss nelsoni)

In this study, the complete mitochondrial genomes of the Mexican golden trout, Oncorhynchus chrysogaster, and Nelson’s trout, O. mykiss nelsoni, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes (all with typical ‘cloverleaf’ secondary structures). The length of the D-loop regions was among the longest found in Salmonids, and mitochondrial synteny in both species was identical to that reported in other Salmonids. Selective pressure analysis in the PCGs indicated that purifying selection, mainly among cox and nd genes families, likely generated the main differences between the two studied species. Nine tRNA genes showed slight differences relative to other O. mykiss subspecies, which were identical between the two study taxa. The origin of the light-strand replication has a loop that was especially large in O. mykiss nelsoni. Phylogenetic analysis indicated that O. chrysogaster and O. mykiss nelsoni are sister species, contrary to the expectation that O. chrysogaster would cluster with O. gilae. As previous studies have suggested, O. chrysogaster and O. mykiss nelsoni share common ancestry with North American trout species.

Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River.

Rainbow Trout, Oncorhynchus mykiss, exhibit high levels of phenotypic diversity leading to the recognition of numerous subspecies. A major distinction among Rainbow Trout subspecies exists between Coastal Rainbow Trout (O. m. irideus), which occurs west of the Cascade and Sierra Nevada mountain ranges, and interior Redband Trout (O. mykiss sspp.), largely distributed to the east. Interior Redband Trout are composed of three primary lineages and can share various outward, anatomical or physiological characteristics that are often symplesiomorphies or examples of convergence. We examine high-throughput DNA sequence data from Sacramento Redband Trout O. m. stonei from the Upper Pit and Upper McCloud Rivers along with representatives of Rainbow Trout and Golden Trout lineages to clarify the composition and relationships of the Sacramento Redband Trout. We find O. m. stonei to be polyphyletic, divided between populations in the Pit River and the Upper McCloud River. Redband Trout obtained from the Pit River are most-closely related to Great Basin Redband Trout O. m. newberrii and to fish of the Warner Lakes Basin and Surprise Valley within the O. m. newberrii lineage. The type specimen of O. m. stonei, collected from the Lower McCloud River, is phenotypically similar to Great Basin Redband Trout. We find as well that the isolated populations of trout in the Upper McCloud River Basin represent a lineage of Rainbow Trout now restricted to that region, are monophyletic and are not most closely related to the interior Redband Trout lineages of O. m. newberrii or O. m. gairdnerii. Furthermore, they are not represented by the type specimens of O. m. stonei or O. m. shasta. Consequently, we formally describe the McCloud River Redband Trout O. mykiss calisulat, new subspecies.

Morphological features and histological structure of the musculature of two trout phenotypic forms when reared in warm water of a power plant

The paper studies the effect of rearing in stocking ponds using the warm discharge water of the Smolensk NPP on the growth and trout meat quality. Some morphological indicators of trout cultivation are presented. The histological studies of the musculature of golden and typically colored trout are presented. It was revealed that the golden trout musculature grows with a predominance of hyperplasia of muscle fibers compared to the typically colored trout. It was shown that trout rearing using NPP cooling ponds does not lead to excessive accumulation internal fat and gives good results.

Metabolic responses of golden trout (Oncorhynchus mykiss aguabonita) after acute exposure to waterborne copper.

Despite the broad knowledge of copper-induced stress and toxicity, data on the physiological responses to acute copper exposure and the correlation of those activities to a generalized stress response are still limited. The present study aimed to assess the physiological responses of golden trout to overcome copper stress at concentrations of 60µg/L and 120µg/L after 96h, respectively. The activities of glucose-6-phosphate dehydrogenase (G6PD) phosphoenolpyruvate carboxykinase (PEPCK) and NADPH/NADP+ ratio were significantly increased, and metabolites including glucose 6-phosphate, fructose 1-phosphate and fatty acids significantly accumulated in fish liver, indicating that gluconeogenesis, the pentose-phosphate pathway, as well as alteration of the membrane fatty acid composition were activated to serve as a defense mechanism against 60µg/L of copper after 96h. After exposure to 120µg/L of copper for 96h, the NAD+ and ATP contents, the activities of enzymes in the glycolytic pathway (phosphofructokinase, PFK and pyruvate kinase, PK) and mitochondrial respiratory chain complex I decreased significantly in fish liver. In addition, carbohydrates and MDA accumulated in golden trout after 120µg/L copper treatment. These results indicated that 120µg/L of copper exposure may induce a metabolic stress in golden trout after 96h. The multi-marker approach allows us to reach a greater understanding of the effects of copper on physiological responses of golden trout.

Dietary supplementation of archaeal carotenoids improved antioxidative capacity and regulated immune‐related gene expression of golden trout Oncorhynchus mykiss against challenge

Archaeal carotenoids, as novel bioactive compound, are stronger free radical scavenger. The effects of archaea Halorubrum carotenoids on skin coloration, antioxidative status and immune-related genes expression of golden trout Oncorhynchus mykiss were investigated. In total, 420 fish (10.90 ± 0.06 g) were divided into three groups with four replicates, and fed with commercial diets containing 0 (Ctrl), 25 mg/kg (P25) and 50 mg archaeal carotenoids/kg feed (P50) for 8 weeks. Although no significant difference was observed on growth, the fish fed archaeal carotenoids had significantly higher yellowness and carotenoid content (p < 0.05) in skin. Compared with the Ctrl group, the total antioxidant capacity (T-AOC) in serum was significantly enhanced in the P25 and P50 groups (p < 0.05), but no significant difference on lysozyme activity was obtained (p > 0.05). In liver, the catalase activity significantly decreased in the P50 group (p < 0.05), but T-AOC and superoxide dismutase activity was not significantly regulated by archaeal carotenoids (p > 0.05). The significant improvement of liver glutathione peroxidase in P50 group was observed, while malondialdehyde content significantly decreased (p < 0.05). After ammonia exposure and Aeromonas hydrophilia challenge, higher survival was observed in the P25 and P50 groups, associating with reducing the expression of pro-inflammation cytokines il-1β, but enhancing the expression of anti-inflammation cytokines tgf-β and hsp70. However, ammonia stress and pathogenic challenge caused opposite trends in the expression of tnf-α. Our study confirmed the beneficial role of archaeal carotenoids on skin coloration, antioxidative and immune systems of golden trout, and provided evidence for the potential application of this novel carotenoid in health management of aquaculture.

Bacterial and parasite co-infection in Mexican golden trout (Oncorhynchus chrysogaster) by Aeromonas bestiarum, Aeromonas sobria, Plesiomonas shigelloides and Ichthyobodo necator

BackgroundBacterial infections are responsible of high economic losses in aquaculture. Mexican golden trout (Oncorhynchus chrysogaster) is a threatened native trout species that has been introduced in aquaculture both for species conservation and breeding for production and for which no studies of bacterial infections have been reported.Case presentationFish from juvenile stages of Mexican golden trout showed an infectious outbreak in a farm in co-culture with rainbow trout (Oncorhynchus mykiss), showing external puntiform red lesions around the mouth and caudal pedunculus resembling furuncles by Aeromonas spp. and causing an accumulated mortality of 91%. Isolation and molecular identification of bacteria from lesions and internal organs showed the presence of Aeromonas bestiarum, Aeromonas sobria, Plesiomonas shigelloides and Ichthyobodo necator isolated from a single individual. All bacterial isolates were resistant to amoxicillin-clavulanic acid and cefazoline. P. shigelloides was resistant to third generation β-lactamics.ConclusionsThis is the first report of coinfection by Aeromonas bestiarum, Aeromonas sobria, Plesiomonas shigelloides and Ichthyobodo necator in an individual of Mexican golden trout in co-culture with rainbow trout. Resistance to β-lactams suggests the acquisition of genetic determinants from water contamination by human- or livestock-associated activities.

Growth influence of juvenile golden trout (Oncorhynchus mykiss) in different osmotic conditions: implications for tissue histology, biochemical indicators, and genes transcription involved in GH/IGF system.

The objectives of this study were to evaluate the effects of different salinity levels on tissue histology, blood biochemistry, and genes transcription of the GH/IGF system in juvenile golden trout (Oncorhynchus mykiss). Five experimental salinity levels (0, 8, 16, 24, and 32‰) were selected to domesticate juvenile O. mykiss for 7 days. Histological characteristics changed with salinity, including higher ionocites area and epithelium thickness in gills, narrow lumen of collecting tubules in kidneys, and high numbers of goblet cells in the intestines. Similarly, increments in slits, degenerate hepatocytes, and individualization of hepatocytes have been shown in fish reared in the 32‰ salinity group. The lowest triglyceride (TG) and the highest level of total protein (TP) were detected in fish reared at the 32‰ group. The genes transcription of the GH/IGF system altered in response to the increase of salinity. The present results add to the understanding of the physiological responses of O. mykiss on salinity stress and would be helpful in formulating strategies to optimize the aquaculture of this species in environments with fluctuating patterns of salinity.

Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given (i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and (ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

Paleoecological and paleolandscape modeling support for pre-Columbian burning by Native Americans in the Golden Trout Wilderness Area, California, USA

Though people have used fire to alter landscapes across North America for millennia, there remains a debate whether Native Americans altered California’s mountainous forests to create an anthropogenic landscape. We use paleoecological reconstructions and paleolandscape modeling to test whether climate or Native Americans were the driving force of pre-historic forest composition change. Understanding pre-historic forests and land-use legacies becomes more critical in a warming climate as wildfires become deadlier and more extensive. We performed a sub-centennial pollen and charcoal reconstruction for the last 1200 years using standard techniques. We then used a forest succession model to quantitatively test drivers of change: climatic fires only, or the addition of Native American-set surface fires. Hypothesized periods of anthropogenic burning were inferred from the pollen record (more open canopy taxa than climatically expected). Modeled outputs were compared against the paleorecord to determine which drivers best explained changes in the empirical record. Periods of occupation from the archaeological record were compared to hypothesized periods of burning. Pollen and charcoal reconstructions showed intermittent periods inconsistent with climatic expectations. Modeled scenarios including surface fires set by Native Californians during these periods had the greatest correlation with the observed paleoecological record. Inferred periods of burning corresponded temporally with site used based on the archaeological record. California’s pre-historic forests were altered by the traditional use of fire as a tool by Native Americans. Modeled outputs hint that incorporating indigenous resources management practices could improve forest health and decrease the likelihood of catastrophic wildfires.

Genomic architecture and repertoire of the rainbow trout immunoglobulin light chain genes

The genomic loci encoding the four immunoglobulin light chains (IgL1, IgL2, IgL3, and IgL4) in the Swanson trout genome assembly were annotated in order to provide a measurement of the potential IgL repertoire. IgL1 and IgL3 gene segments are co-localized on chromosomes 21, 18, 15, and 7 while IgL2 and IgL4 were found on chromosomes 13 and 17, respectively. In total, 48 constant (CL), 87 variable (VL), and 59 joining (JL) productive genes are described. Pairwise alignment of the VL segments revealed that they belong to nine different families, three of which (kappa IV, V, and VI) are described for the first time in this study. VL and CL sequences on chromosome 15 and 21 and those on chromosomes 7 and 18 clustered together in phylogenetic analysis. PCR was used to examine IgL CL and VL genes in 9 lines of rainbow trout. IgL4 in the Hot Creek and Golden trout lines was missing 42 nucleotides resulting in a loss of 14 amino acids. The sigma IV variable family was completely absent from the Swanson, Arlee, Hot Creek, and wild type lines and silenced in the Skamania line with the addition of 176 bp mini-satellite insert. Similarly, the Whale Rock, Arlee, and wild type lines were all found to encode two sigma II products, a functional 252 bp product and a larger 425 bp product that contained a 172 bp insert. Results from this study indicate that there are genomic differences in IgL repertoire between different lines of trout that could affect humoral immune responses post vaccination and during disease.

First steps towards the identification of evolutionarily significant units in Mexican native trout: An assessment of microsatellite variation

In the remote high-elevation streams and rivers in the northwest of Mexico, there is an endemic and highly diverse group of native trout related to the rainbow trout lineage (Oncorhynchus mykiss). Currently, only two species have been formally described from this trout complex, the Mexican golden trout, O. chrysogaster, and the San Pedro Martir rainbow trout, O. m. nelsoni, but only the former occurs in the Sierra Madre Occidental (SMO). South and north of the O. chrysogaster range, there are other undescribed trout that have been recently discovered. Given the various human impacts on aquatic systems occupied by these Mexican native trout, the lack of taxonomic descriptions and the imminent risk of losing populations without their even being documented, we sought to infer a hierarchical population structure of the Mexican native trout, determine the geographic patterns of genetic diversity and gene flow among them, and identify evolutionarily significant units for a prompt conservation strategy. The allelic diversity across eleven microsatellite loci was used to assess genetic divergences of wild trout collected throughout its range in Mexico. Our results reject the old hypothesis that many of the trout in Mexico are introduced or translocated hatchery-reared rainbow trout and strongly support the new hypothesis of distinct genetic populations and lineages in the northwest of Mexico. According to the different statistical analysis of the genetic data, we distinguish between species and subspecies (O. chrysogaster, O. mykiss, and O. m. nelsoni) of the other regional lineages of undescribed trout (northern and southern) inhabiting the SMO. We also found a strong genetic substructure within these large clusters. We propose the presence of seven Evolutionarily Significant Units in the drainage basins of the SMO (two occur in the northern region, four in the southern, and one for the area of distribution of O. chrysogaster) and one in north-western Baja California. Based in microsatellite data a minimum gene flow among populations is evidenced, resulting the presence the highly divergent populations.

Effects of chronic exposure of waterborne copper on the antioxidant system and tissue accumulation in golden trout (Oncorhynchus mykiss aguabonita).

We assessed the acute and chronic effects of copper (Cu2+) on the antioxidant system in golden trout (Oncorhynchus mykiss aguabonita). The median lethal concentration after 96h was determined as 0.24mgL-1. We then used 0.06 (L) and 0.12mgL-1 (H) Cu2+ to assess the responses of the antioxidant system to long-term exposure. The activities of superoxide dismutase, catalase, glutathione-S-transferase, glutathione peroxidase, glutathione reductase, reduced glutathione, and oxidized glutathione were measured in gill and liver tissue after 24 and 72h and 7, 14, 21, and 28days of exposure, as well as after 16days of recovery in Cu2+-free water. Cu2+ accumulated to a greater extent in the liver than in the gill (0.61-0.75mgkg-1 vs. 24.0-69.9mgkg-1 in L group and 0.98-1.47mgkg-1 vs. 33.3-66.03mgkg-1 in H group). In the gill, we observed increases in the activities of superoxide dismutase, catalase, and glutathione peroxidase, as well as in the concentrations of reduced glutathione and oxidized glutathione. In the liver of L group, we observed increases in glutathione reductase activity and in the levels of reduced glutathione and oxidized glutathione. In L group, the activity of superoxide dismutase and reduced glutathione content increased after 24h and then decreased over time, while catalase and glutathione reductase activity and oxidized glutathione levels increased. Data from the recovery period indicated that higher concentrations of Cu2+ may induce irreversible oxidative damage to the gill of golden trout.

Effects of different durations of fasting/re-feeding bouts on growth, biochemical and histological changes in the digestive tract of Gansu golden trout (Oncorhynchus mykiss)

This study was conducted to explore the outcomes of starvation/re-feeding techniques on growth performance, liver antioxidant activities, and histological changes of the gastrointestinal organs of Gansu golden trout. A total of 225 juveniles were divided into 5 treatment groups; the control group (N&lt;sub&gt;0&lt;/sub&gt;) was routinely fed every day while the other groups (N&lt;sub&gt;7&lt;/sub&gt;, N&lt;sub&gt;14&lt;/sub&gt;, N&lt;sub&gt;21&lt;/sub&gt;, and N&lt;sub&gt;28&lt;/sub&gt;) were starved for 7, 14, 21, and 28 days, respectively and after the starvation session, each group was re-fed for 28 days. Compensatory growth was statistically recorded in N&lt;sub&gt;14&lt;/sub&gt;. Weight gain rate and feeding ratio were the highest in the N&lt;sub&gt;14&lt;/sub&gt; group, while specific growth rate and feeding conversion ratio showed significant increases in the fish groups exposed to longer starvation periods. Liver antioxidant activities showed a significant increase and decrease in malondialdehyde and superoxide dismutase levels in N&lt;sub&gt;21&lt;/sub&gt; and N&lt;sub&gt;28&lt;/sub&gt;, respectively, which returned to normal levels after re-feeding. Stomach, intestine, and liver showed histological alterations in all groups and the severity was correlated with the fasting periods. Those changes were restored to a certain degree after feeding was resumed. The compensation by group N&lt;sub&gt;14&lt;/sub&gt; presents potential for economic usefulness of the fasting/re-feeding strategy in Gansu golden trout.

The interplay of riverscape features and exotic introgression on the genetic structure of the Mexican golden trout (Oncorhynchus chrysogaster), a simulation approach

AbstractAimWe explored the factors between riverscape features and exotic introgression of cultured rainbow trout (Oncorhynchus mykiss) that drive the current genetic structure in the endemic Mexican golden trout (Oncorhynchus chrysogaster) using a riverscape genetics simulator.LocationSierra Madre Occidental, Northwest Mexico, North America.MethodsWe created a system model for Mexican golden trout to test various scenarios for the effect of riverscape resistance and rainbow trout introgression on the native genetic structure of the Mexican golden trout. Individual genotypes were used to initialize the model and were based upon empirical allele frequencies from three genetically and spatially distinct groups in the study area. The geographical location of the simulated populations was defined using a species distribution model. We included hypotheses for movement of riverine distance and riverscape resistance. We evaluated model performance by conducting population and landscape genetics analyses on the simulation outputs.ResultsThe most plausible scenario included riverscape resistance without introgression, which presented a spatial genetic structure matching the observed riverscape genetic structure and fitting expected general life‐history patterns for high elevation trout streams. In addition, temperature, precipitation, hydrology and topography were the most important variables influencing species occurrence and dispersal.Main conclusionThis work presents one of the first empirically derived simulation studies of introgression. It highlights the importance of considering riverscape resistance (i.e. hydroclimatic and topographical gradient effects) in models of spatial genetic structure and introgression. Moreover, our modelling suggests that what we characterize as riverscape resistance is acting as a boundary against exotic introgression. The results of this study could help to develop management strategies that preserve native gene pools.

Genome-wide genetic analysis of cultured rainbow trout ( Oncorhynchus mykiss ) populations in China

PDF HTML阅读 XML下载 导出引用 引用提醒 国内虹鳟代表性养殖群体的高通量SNP芯片检测及遗传分析 DOI: 作者: 作者单位: 1. 中国水产科学研究院, 农业部水生动物基因组学重点实验室, 渔业生物技术北京市重点实验室, 北京 100141;2. 中国水产科学研究院黑龙江水产研究所, 黑龙江 哈尔滨 150070;3. 四川农业大学 动物科技学院, 四川 雅安 625014;4. National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV 25430, USA;5. 厦门大学 海洋与地球学院, 福建省海洋生物资源开发利用协同创新中心, 福建 厦门 361102 作者简介: 赵紫霞(1983-),女,博士,副研究员,从事水产生物技术研究. 通讯作者: 中图分类号: S917 基金项目: 国家科技支撑计划项目（2015BAD25B01）；中国水产科学研究院基本科研业务费专项（2015C007）. Genome-wide genetic analysis of cultured rainbow trout (Oncorhynchus mykiss) populations in China Author: Affiliation: 1. Key Laboratory of Aquatic Genomics, Ministry of Agriculture;Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China;2. Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China;3. College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, China;4. National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV 25430, USA;5. Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources;College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:本研究旨在对国内虹鳟（）代表性养殖群体开展全基因组水平的遗传评估。利用57K单核苷酸多态性（single nucleotide polymorphism，SNP）芯片，检测了来自不同地域的6个虹鳟养殖群体样本共计48尾，包括黑龙江虹鳟、黑龙江金鳟、四川虹鳟、四川金鳟、北京虹鳟和北京金鳟，共获得有效SNP位点50201个，在中国虹鳟中的多态比例达到97.7%，表明该芯片虽然基于美国和挪威虹鳟群体设计，但对中国群体同样具有良好的适用性。各群体最小等位基因频率均值为0.240~0.267，与国外主流养殖群体相近，黑龙江虹鳟、四川虹鳟和北京虹鳟群体内遗传多样性丰富，多态位点比例为83.6%~84.9%，与国外主流养殖群体相近，而黑龙江金鳟、四川金鳟和北京金鳟，多态位点比例相对较低，在60.2%~76.9%范围内。应用6个中国虹鳟群体和2个美国虹鳟群体数据开展系统发育分析、主成分分析和群体遗传结构STRUCTURE分析，结果显示8个群体可分为3个祖源类群，其中3个金鳟群体为遗传联系较紧密的一个类群，黑龙江虹鳟和北京虹鳟为一个类群，而四川虹鳟与2个美国虹鳟群体为一个类群，部分中国养殖群体中有显著离群个体存在，表明群体遗传背景不均一。本研究表明，高密度SNP芯片在我国虹鳟养殖群体遗传分析中具有广泛的应用前景，能够为种质资源评估、本土化良种培育、制种和引种工作提供基因组水平的参考信息。 Abstract:The present study aimed to perform a genome-wide genetic evaluation of representative aquaculture populations of rainbow trout () in China. A 57K single nucleotide polymorphism (SNP) array that was designed by the National Center for Cool and Cold Water Aquaculture (NCCCWA) was used to genotype 48 individuals from six aquaculture populations, which included the Heilongjiang rainbow trout (1HLJ), Heilongjiang golden trout (2gHLJ), Sichuan rainbow trout (3SC), Sichuan golden trout (4gSC), Beijing rainbow trout (5BJ), and Beijing golden trout (6gBJ). A total of 50,201 SNPs were successfully genotyped using a >97% call rate threshold, and the overall rate of polymorphism was 97.7%, which indicated that the SNP array was suitable for analyzing the Chinese rainbow trout populations, even though it was designed using USA and Norwegian populations. The average minor allele frequency of each population was between 0.240 and 0.267, which is similar to that reported for other major aquaculture populations. Genetic diversity was high in the 1HLJ, 3SC, and 5BJ populations, with rates of polymorphism ranging from 83.6% to 84.9%, which is similar to reported for other major aquaculture populations. However, genetic diversity was relatively low in the 2gHLJ, 4gSC, and 6gBJ populations, with rates of polymorphism ranging from 60.2% to 76.9%. Phylogenetic, principal components, and STRUCTURE analyses, which were performed using genotype data from the six Chinese populations and two USA populations, indicated that the eight populations could be clustered into three groups. The three golden trout groups and the 1HLJ and 5BJ populations formed respective clusters, whereas the 3SC population was placed in a third cluster with the two USA populations. Outliers were identified for the 3SC, 4gSC, and 6gBJ populations, which suggested that the populations possessed inhomogeneous genetic backgrounds. Together, these results demonstrate the promising potential of high-density SNP arrays for the genetic analysis of Chinese rainbow trout populations and that such analyses could provide genomic data for plasm resource evaluation, localized strain breeding, high-quality fry production, and reasonable foreign strain introduction. 参考文献 相似文献 引证文献

Patterns and dynamics of vegetation recovery following grazing cessation in the California golden trout habitat

AbstractIn 1978, the Golden Trout Wilderness area was established to protect the California golden trout (Oncorhynchus mykiss aguabonita)—a vulnerable subspecies of the rainbow trout that is endemic to California—and its habitat, which is currently restricted to a few streams within high‐elevation meadows in the Sierra Nevada Mountain Range. Because of the deleterious effects of livestock grazing on riparian vegetation in the golden trout habitat (occurring since the 1800s), meadow restoration activities were initiated in 1991, including cattle exclusion. There has been renewed discussion about re‐opening these public lands to livestock grazing, and impact assessment studies are needed to inform decision makers about the potential consequences. Thus, we estimated the recovery potential of the golden trout habitat by measuring the height of riparian vegetation within areas that have been grazed vs. closed to grazing (“rested”) since 1991. We found that cattle exclusion is effective at favoring riparian vegetation growth, but that vegetation recovery from grazing could take several decades in these sensitive habitats as some “rested” areas have yet to recover to full vegetation height, even after 25 yr of rest.

Using stable isotope analysis to assess the effects of hypolimnetic oxygenation on diet in a mixed cold- and warmwater fish community

Line-diffuser hypolimnetic oxygenation was initiated in North Twin Lake, Washington, in 2009 to mitigate reductions in Rainbow Trout (Oncorhynchus mykiss) and Brook Trout (Salvelinus fontinalis) habitat due to temperature-dissolved oxygen “habitat squeeze”. Previous studies demonstrated that trout populations rapidly expanded into increased hypolimnetic habitat within the first few years of oxygenation and previous short-term diet analyses indicated an effect on fish diet; however, the long-term effects on fish ecology have yet to be established. In this study, stable isotope analysis of fish liver tissue suggests relatively few differences in feeding ecology of principal coldwater fish species in North Twin Lake compared to unoxygenated South Twin Lake. When compared between lakes, Rainbow Trout and Brook Trout diets contained similar proportions of Daphnia, Chironomidae, and Chaoboridae. Littoral and epilimnetic-focused Golden Shiner (Notemigonus crysoleucas) diets were also similar between lakes. Observed similarities between Golden Shiner and trout diets suggest the effects of interspecific competition between salmonids and non-salmonids may be limiting trout growth and survival. Fisheries managers should therefore consider both habitat limitations and interspecific competition when managing for coldwater fish species in mesotrophic, dimictic lakes.