Differential DNA Methylation in Somatic and Sperm cells of Hatchery versus Wild (Natural-Origin) Steelhead Trout Populations
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ABSTRACT:
ORGANISM(S): Oncorhynchus mykiss
PROVIDER: GSE145887 | GEO | 2020/05/24
REPOSITORIES: GEO
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Project description:Background: Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish. Methods and Findings: This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1) 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2) testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i) sustained fast growth, ii) sustained slow growth, iii) accelerated growth, iv) decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish. Conclusions: Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex differentiation; however, an initial fast growth does not represent any advantage in terms of transcriptional fitness if later food becomes scarce.
2014-12-25 | GSE54362 | GEO
Project description:Although hydrogen sulfide is toxic to most organisms, a fish, Poecilia mexicana, has adapted to survive in environments with high levels of hydrogen sulfide. The epigenetic changes in response to this environmental stress were examined by assessing DNA methylation alterations in the nucleated red blood cells (RBC) in the fish. In addition to collecting wild males and females from sulfidic and non-sulfidic environments, wild males and females in these environments were collected and moved to a non-sulfidic environment in the laboratory and propagated for two generations in a non-sulfidic environment. We compared epimutations between sexes and field and laboratory populations. The F0 generation sulfidic wild fish were compared to the non-sulfidic wild fish and found to have significant differential DNA methylation regions (DMRs) in the RBC DNA. The F2 generation laboratory fish were also compared between the sulfidic and non-sulfidic populations, and a significant number of DMRs were also identified. The DMRs have stable generational inheritance in the absence of the sulfidic environment. The DMRs in the F0 generation wild fish had an over 80% overlap with the F2 generation laboratory non-sulfidic environment propagated fish. This is one of the first examples of epigenetic generational stability after the removal of an environmental stressor. The DMR associated genes were found to be relevant to sulfur toxicity and metabolism processes.
2020-12-09 | GSE157730 | GEO
Project description:Marker-assisted selective breeding of fish with higher levels of resistance towards specific pathogens has shown successful, but. However, the impact of host genotype on multiple pathogen infections are is still poorly investigated. This study examined the resistance in rainbow trout (Oncorhynchus mykis) towards infection with the eye fluke Diplostomum pseudospathaceum. We used genetically selected rainbow trout, carrying SNPs associated with resistance towards the parasitic ciliate Ichthyophthirius multifiliis, and exposed the fish to eye fluke cercariae. We showed that fish partly resistant to I. multifiliis were more susceptible to eye fluke invasion. Expression The expression of immune relevant genes (encoding innate and adaptive factors) was also affected as these genotypes responded less strongly to a secondary fluke infection. The complexity of genome architecture in disease resistance towards multiple pathogens is discussed. A total of 200 rainbow trout (body weight 14.3-17.7 g, body length 10.2-11.5 cm) were used for the study. Two groups of rainbow trout with high (QTL fish) and low (non-QTL fish) frequency of SNPs associated with I. multifiliis resistance, were hatched from eyed eggs at the disease free recirculated Bornholm Salmon Hatchery, Nexø, Denmark and subsequently reared to the fingerling stage. For this purpose, the first group (QTL-fish) was produced by using sperm from three male genotyped parents carrying SNPs AX-89947214 (Omy17) and AX-89960822 (Omy16), and the other group (non-QTL fish) was produced by using sperm from three other male parents negative for these SNPs. In both cases, sperm was used to fertilize a common pool of eggs stripped from a total of 30 outbred females. Processes of hatching and subsequent rearing of fry to the fingerling stage did not differ between groups of QTL fish and non-QTL fish. From each group (QTL and non-QTL fish) we randomly gathered 100 rainbow trout and transported them (3 h duration) from the hatchery to the infection facility at the University of Copenhagen. Fish were then accommodated and acclimatized 14 d in identical aerated glass tanks with internal biofilters (25 fish per 60 L water, total tank volume 80 L), which were placed in a temperature temperature-controlled room (water temperature constant at 12°C, pH 7.6). We used 30% water change per day to maintain ammonia levels below 0.25. Fish were fed by pelleted feed (1% of fish biomass per day). All fish were genotyped with respect to the two relevant QTLs, one on chomosome 16 and one on chromosome 17. Fish being double heterozugous were excluded from qPCR analysis.
2022-09-21 | GSE213738 | GEO
Project description:To identify gene expression differences between Oncorhynchus mykiss that migrate and those that reside in freshwater, we compared gill transcriptomes of fish prior to release from a hatchery with those of fish recaptured eight days post-release while all fish were still in freshwater, but some were captured next to the hatchery (non-migrants) and others were captured moving toward the ocean (migrants). The in-hatchery sampling method represents a highly similar environment for all the fish, and allows for the determination of activated genes predictive of smolting programs prior to release into streams. Morphological (e.g. color) and physiological (gill NaCl-ATPase activity) data were also obtained and correlated to gene expression differences to aid in predictions.
2014-03-04 | GSE48844 | GEO
Project description:We sequenced mRNA from embryonic heart of zebrafish larvae 4 days post fertilization, adult heart of 6-month-old WIK fish, and adult muscle of adult fish consisting of both fast-twitch and slow-twitch fibers.
2017-05-01 | GSE85416 | GEO
Project description:Previous studies examining the reproductive health of alligators in Florida lakes indicate that a variety of developmental and health impacts can be attributed to environmental quality and exposures to environmental contaminants. A number of these environmental contaminants have been shown to disrupt normal endocrine signaling. The potential that these environmental toxicants may influence epigenetic status and correlate to the health abnormalities was investigated in the current study. The red blood cell (RBC) (erythrocyte) in the alligator is nucleated so was used as an easily purified marker cell to investigate epigenetic programming. RBCs were collected from adult male alligators captured at three sites in Florida, each characterized by varying degrees of contamination. While Lake Woodruff (WO) has remained relatively pristine, Lake Apopka (AP) and Merritt Island (MI) convey exposures to different suites of contaminants. DNA was isolated and methylated DNA immunoprecipitation (MeDIP) was used to isolate methylated DNA that was then analyzed in a competitive hybridization using a genome-wide alligator tiling array for a MeDIP-Chip analysis. Pairwise comparisons of alligators from AP and MI to WO revealed alterations in the DNA methylome. The AP vs. WO comparison identified 85 differential DNA methylation regions (DMRs) with ≥3 adjacent oligonucleotide tiling array probes and 15,451 DMRs with a single oligo probe analysis. The MI vs. WO comparison identified 75 DMRs with the ≥3 oligo probe and 17,411 DMRs with the single oligo probe analysis. There was negligible overlap between the DMRs identified in AP vs. WO and MI vs. WO comparisons. In both comparisons DMRs were primarily associated with CpG deserts which are regions of low CpG density (1-2 CpG/100bp). Although the alligator genome is not fully annotated, gene associations were identified and correlated to major gene functional categories and pathways. Observations demonstrate that environmental quality is associated with epigenetic programming and status in the alligator. The epigenetic alterations may provide biomarkers to assess the environmental exposures and health impacts on these populations of alligators.
2016-08-27 | GSE82318 | GEO
Project description:The sustainable development of modern aquaculture must rely on a significant reduction of the fish meal (FM) used in aquafeed formulations. However, FM substitution with alternative ingredients in diets for carnivorous fish species often showed reduced nutrient absorption, significantly perturbed metabolisms and histological changes at both hepatic and intestinal level. In the present study, adult rainbow trout (Oncorhynchus mykiss) were fed three different experimental aquafeed formulations. A control diet with higher FM content (27.3%) than two test formulations in which fish meal was substituted with two more sustainable and promising alternatives: insect meal (Hermetia illucens larvae=10.1%, FM=11.6%) and poultry by-products meal (PBM=14.8%; FM=11.7%). Combined metabolomics and proteomics analyses of fish liver, together with histological examination of liver and intestine demonstrated that a well balanced formulation of nutrients in the three diets allowed high metabolic compatibility of either substitutions, paving the way for innovative and sustainable use of novel raw materials for the fish feed industry. Results show that the main metabolic pathways of nutrient absorption and catabolism were essentially unaltered by alternative feed ingredients, and also histological alterations were negligible. It is demonstrated that substitution of fish meal with sustainable alternatives does not impact on fish metabolism, given proper efforts are put in fulfilling nutritional requirements of rainbow trout.
2022-07-18 | PXD033201 | Pride
Project description:Embryonic development rate is a key trait significantly associated and genetically linked with both growth rate and sexual maturity in rainbow trout. To identify candidate genes underlying embryonic development rate, whole genome expression microarray analyses were conducted using embryos from a fourth generation backcross family; each backcross generation involved the introgression of the fast-developing alleles for the major development rate QTL (from the Clearwater clonal line [CW]) into a slow-developing clonal line (Oregon State University [OSU]). Embryos were collected at 15, 19, and 28 days post-fertilization. Microsatellite markers (One112ADFG, OMM1009 and OmyFGT12TUF) linked to the major embryonic development rate QTL region were used to determine the QTL genotype. The sex marker OMY-Y1 was used to determine the genotypic sex of each embryo. cDNA from 48 individual embryos were used for microarray expression analysis. An ANOVA modeling approach was used to detect differential gene expression between embryos possessing fast-developing genotypes and slow-developing genotypes. A total of 182 features have been identified with significant differences between embryonic development rate genotypes. Quantitative PCR was conducted on ten representative genes using the rainbow trout homologous sequences and microarray results were validated.
2009-11-12 | GSE13570 | GEO
Project description:To identify gene expression differences between Oncorhynchus mykiss that migrate and those that reside in freshwater, we compared gill transcriptomes of fish prior to release from a hatchery with those of fish recaptured eight days post-release while all fish were still in freshwater, but some were captured next to the hatchery (non-migrants) and others were captured moving toward the ocean (migrants). The in-hatchery sampling method represents a highly similar environment for all the fish, and allows for the determination of activated genes predictive of smolting programs prior to release into streams. Morphological (e.g. color) and physiological (gill NaCl-ATPase activity) data were also obtained and correlated to gene expression differences to aid in predictions. Gill tissue was sampled for transcriptome profiling 13 days prior to two different releases from the hatchery (total sampled within hatchery n = 19). Samples were also taken eight days after the two releases near-hatchery (total in-creek n = 20) or migrating towards the ocean but still in freshwater (second release only n = 20). Finally, 48 days after the second release a final set of resident fish were sampled near the hatchery (n =10). In terms of time after release, the most parallel comparison is the second 8 day post release sample in-creek and migrating. Although all samples were obtained in freshwater, the samples with the most similar local environment are the pre-release samples.
2014-03-04 | E-GEOD-48844 | biostudies-arrayexpress