Gene expression analysis between rainbow trout strains with different susceptibility to enteritis when reared on plant-based diets
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ABSTRACT:
ORGANISM(S): Oncorhynchus mykiss
PROVIDER: GSE79531 | GEO | 2017/09/05
SECONDARY ACCESSION(S): PRJNA316101
REPOSITORIES: GEO
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Project description:Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, liver RNA was examined for differential expression of long non-coding RNAs (lncRNAs) between commercial and selected trout strains when fed an alternative diet. These types of non-coding RNA have been previously shown to have a potential role in regulation of gene expression; however, most identified lncRNAs have not been functionally characterized and/or lack definition in many non-model organisms. Their roles in gene regulation and their responsiveness to dietary changes in trout are to be explored. After three months of rearing on a plant protein-based (PM) diet, liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the plant-diet tolerant selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then assembled into transcripts using Trinity. Assembled transcripts were then submitted to the Annocript pipeline to determine their potential as lncRNAs. RNA-seq reads were mapped to putative lncRNAs. Read-counts were used to assess differential expression between strains.
2018-04-10 | GSE85104 | GEO
Project description:Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain is resistant to development of soy-induced enteritis, an inflammatory intestinal pathology that occurs often in high-value carnivorous aquaculture species. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the homeostatic intestinal gene expression of the select strain to that of a commercial control line of trout. Samples were collected at early life stages known to be critical in the development of host-microbe interactions in the gut of rainbow trout. All female cohorts of both strains were reared alongside starting from eggs. Intestinal samples from 5 fish per group (2 fish strains; 2 developmental stages; 20 samples total) were used to generate mRNA selected stranded RNA-seq libraries for high throughput sequencing. Reads were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the two strains of trout and the developmental stages.
2020-12-15 | GSE156372 | GEO
Project description:Sustainable aquaculture, which entails proportional replacement of fish-based feed sources by plant-based ingredients, is impeded by the poor growth response frequently seen in fish fed high levels of plant ingredients. To evaluate the potential to improve, by means of early nutritional exposure, the growth of fish fed plant-based feed, rainbow trout swim-up fry were fed for 3 weeks either a plant-based diet (diet V, V-fish) or a diet containing fishmeal and fish oil as protein and fat source (diet M, M-fish). After this 3-week nutritional history period, all V- or M-fish received diet M for a 7-month intermediate growth phase. Both groups were then challenged by feeding diet V for 25 days during which voluntary feed intake, growth, and nutrient utilization were monitored (V-challenge). The results of the V-challenge showed a higher growth rate and higher feed intake in fish of nutritional history V compared to M (see PMID:24386155). To identify the molecular mechanisms that govern the enhancement of feed acceptance following early-feed exposure of diet V, we performed microarray expression analysis using swim-up fry collected at the end of early-feeding exposure (diet M and diet V), as well as brain and liver of juveniles sampled at the end of the V-challenge (M-his and V-his), and employing a rainbow trout microarray platform with 8 X 60K probes per slide. Persistently differentially expressed genes were identified by isolating probes that were differentially expressed (fold change ≥ 1.5 and p {nutritional history} ≤ 0.05), both at the end of the early exposure, and in either brain or liver of juvenile trout at the end of the V-challenge. Overall, 1787 (3-week + Brain) and 924 (3-week + Liver) mRNA probes were found to be persistently affected by nutritional history of early-feeding exposure. This positive response is encouraging as a potential strategy to improve the use of plant-based feed in fish, of interest in the field of fish farming and animal nutrition in general. Furthermore, the genes associated with mediating this positive early feeding effect, could serve as potential biomarkers to evaluate increasing acceptability of plant-based diets in fish farming.
2016-06-23 | GSE60010 | GEO
Project description:Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental viral infection using the CSF 220-90 isolate of Infectious Hematopoietic Necrosis virus (IHNv). At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with IHNv by static bath and one tank was mock challenged by static bath (Sham). Sampling was conducted at 4 days post challenge (dpc) (Early Infection) and 20 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. Infections were mild with mortality rates near 50% over the 21 day trial and no significant difference in mortality rates between the two strains of trout. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status.
2020-12-15 | GSE156595 | GEO
Project description:Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental bacterial infection with Flavobacterium psychrophilum (Fp) (CSF 259-93), the causative agent of bacterial cold water disease (BCWD) in salmonids. At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with Fp by intramuscular injection and one control tank was mock challenged by sham injection. Sampling was conducted at 5 days post challenge (dpc) (Early Infection) and 21 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. The select strain of trout showed significantly better survival rates (Log-Rank Test, p < 0.0001) over the 21 day infection period, with 70 and 95 % mortality among the select and commercial strain, respectively. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status.
2020-12-15 | GSE156930 | GEO
Project description:Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an econmoical and sustainable protien replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth on plant based dits in rainbow trout Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation. Results: Microarray analysis of liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals grown on a fish meal or plant protein based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differntially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes were were ablet o map gene pathway and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential reaulation of genes related to cell oxidative stress, proliferation, growth, and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant based diet upregulated the expression of genes involved in immunoregulatroy processes. Genotyped samples linked to families that had 4 or more members sampled on each diet were identified and ranked according to average family weight on each diet. Size rankings corresponded to large (>750 g), medium (600-640 g), and small (<500 g). From these identified groups 2 families were chosen for microarray expression analysis that demonstrated individuals with growth differences between the two diets. Data for the two families used for analysis and slide arrangements are listed in table 3. The families compared for growth differences between diets used for this study only differed by one growth range, large fish on fish meal compared to medium fish on plant-based diet and medium sized fish on fishmeal diet compared to small fish on plant-based diet. This strategy to use size separation within family was an attempt to identify gene changes more specific to diet utilization than specific for growth differences.
2011-04-01 | E-GEOD-28310 | biostudies-arrayexpress
Project description:In mammals, increasing data suggests that there exists a complex and bi-directional relationship between thyroid and immune systems. However the existence of such interactions in fish is unknown. Here, we administered the biologically active hormone 3.3�.5-triiodo-L-thyronine (T3) and the anti-thyroid drug, propilthiouracil (PTU) to juvenile rainbow trout and examined the head kidney expression profile with a custom-made microarray enriched in immune-related genes. A seven day-experiment was performed. Fish were divided in 3 groups. First group received 20 µg/g fish feed of T3; second group received 5000 µg/g fish feed of PTU; third group served as control. After 7 days orally administering T3 or PTU, differentially expressed transcript levels from selected immune-related rainbow trout genes were studied in head kidney. Three groups were studied (T3-treated, PTU treated and control), each group having 4 biological replicates (each replicate consisting of 2 pooled fish).
2016-07-03 | E-GEOD-54422 | biostudies-arrayexpress
Project description:Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an econmoical and sustainable protien replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth on plant based dits in rainbow trout Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation. Results: Microarray analysis of liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals grown on a fish meal or plant protein based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differntially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes were were ablet o map gene pathway and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential reaulation of genes related to cell oxidative stress, proliferation, growth, and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant based diet upregulated the expression of genes involved in immunoregulatroy processes.
2011-04-01 | GSE28310 | GEO
Project description:The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such as growth. In the present study, the effects of dietary glycerol supplementation on the muscle and liver metabolomes of rainbow trout (Oncorhynchus mykiss) and European seabass (Dicentrarchus labrax) were evaluated. Fish juveniles were fed diets with 0%, 2.5%, and 5% glycerol. Muscle and liver aqueous fractions were extracted and 1H NMR spectra were acquired. Metabolite profiles derived from the 1H NMR signals were assessed using univariate and multivariate statistical analyses. The adenylate energy charge was determined in the muscle. For both species, the muscle metabolite profile showed more variability compared to that of the liver and was most perturbed by the 5.0% glycerol diet. For the liver metabolite profile, rainbow trout showed fewer differences compared to European seabass. No differences were observed in energy charge between experimental groups for either species. Thus, rainbow trout appeared to be less susceptible to tissue metabolite perturbations, compared to seabass, when the diet was supplemented with up to 5% glycerol.
2020-02-24 | MTBLS832 | MetaboLights
Project description:A critical problem facing all U. S. aquaculture is loss due to disease. In the past year alone, diseases accounted for 90% of all losses of trout intended for sale, greatly impacting the livelihood of our farmers. Previously, we focused on sustainable aquaculture efforts by evaluating the effects of dietary replacement (marine-based to plant-based protein sources) on rainbow trout. Through this effort, we developed a rainbow trout strain that thrives on an all plant-protein formulated diet (PSel/UI strain). In selecting for diet tolerance, we discovered this strain has also undergone positive selection for nonspecific disease resistance to Infectious Hematopoietic Necrosis Virus (IHNV). Therefore, the goal of this project was to determine the mechanisms behind this nonspecific immunity by performing a pathogen challenge and measuring several disease performance characteristics among PSel/UI and two other trout strains commonly used in the commercial aquaculture industry, one selected for disease resistance to these pathogens for several generations and the other completely unselected. We examined lysozyme activity changes in serum and innate gene expression using RNA-sequencing by sampling kidney, spleen, intestine, and liver at time zero and at 4, 12, 24, and 48 hours post-infection with IHNV. We then integrated innate gene expression with disease performance characteristics and made comparisons among strains to identify significant differentially expressed genes and compared with the genetic background of the fish. Through these objectives, we narrowed a set of candidate genes useful in the co-selection of two aquaculturally-important traits: enhanced nonspecific disease resistance with diet utilization. This project was supported by Agriculture and Food Research Initiative Competitive Grant no. USDA-NIFA-SRGP-006544 from the USDA National Institute of Food and Agriculture.
2024-05-16 | GSE188423 | GEO