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122 results for “Oncorhynchus mykiss”
Underlying data - Digital Twin for Rainbow Trout (Oncorhynchus mykiss) land-based aquaculture
<p>Datasets for replicating Figures 5, 6, 7 and 8 of the article "Digital twins for land-based aquaculture: a case study for rainbow trout (<em>Oncorhynchus mykiss</em>)", by Adriano C. Lima, Edouard Royer, Matteo Bolzonella, and Roberto Pastres.</p>
Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams
<p>DNA were derived from fin tissue samples taken from individual trout captured from Little Jacks Creek, Big Jacks Creek , and Duncan Creek of the Owyhee mountains and Keithly Creek and Upper Mann Creek in the Hitt mountains of Western Idaho, United States. Fin tissues were collected from individual trout from each stream during monthly sampling events in June through October 2020. </p> <p><em>DNA Extraction:</em> Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.©). Small sections of fin tissue (≤ 25 mg) were collected from each sample. This was mixed with a digesting solution comprised of ultra-pure water, solid tissue buffer (Zymo Research Inc.©) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55°C in a water bath. We then aliquoted 100 µL of digestion supernatant and combined with 200 µL of genomic binding buffer (Zymo Research Inc.©). DNA was eluted in 50, 75, and 100 µL of elution buffer to determine which volume provided sufficient DNA concentration for genotyping. After it was determined all quantities produced suitable concentrations, going forward, 50 µL of elution buffer used.</p> <p><em>Genotyping:</em> Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery’s genetics research facility with the assistance of the Columbia River Intertribal Fish Commission (CRTFC). Genotyping protocols were as described in Campbell et al. (2015) and summarized below. First, samples were prepared for amplification via PCR by combining DNA extracts with a Qiagen Plus multiplex master mix and a species-specific pooled primer mix. This step added the Illumina sequencing primer sites to amplicons. Following the creation of the PCR cocktail, thermocycling was conducted for amplification. Amplified samples were then diluted 20-fold. Diluted samples were transferred to new 96-well PCR plates where two genetic indexes and barcodes provides a unique set of tagging primers to each well and plate. Tagged plates then underwent a second PCR step. After the second PCR, all DNA were transferred to Charm Biotech normalization plates where DNA was bound to wells, washed, and finally eluted. After normalization, all DNA was pooled together and a purification step using magnetized beads in two steps to selectively remove fragments of DNA that are both too large and too small for sequencing. Following purification, each plate was quantified via qPCR using Life Technologies QuantStudio 6 Flex Instrument (Life Technologies). Finally, sequencing was performed using an Illumina HiSeq 1500 instrument.</p> <p><strong>Ancillary peer-reviewed manuscripts:</strong><br> <em>Genotyping protocols</em><br> Campbell NR, Harmon SA, Narum SR. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour, 15: 855-867. https://doi.org/10.1111/1755-0998.12357<br> <em>SNP loci reference</em><br> Collins EE, Hargrove JS, Delomas TA, Narum SR. 2020. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecology and Evolution, 10(17): 9486-9502. https://doi.org/10.1002/ece3.6641 </p> <p><strong>Data Use</strong>:<br> <em>License</em>: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> <br> <em>Recommended Citation</em>: Wooding AP, Narum SR, Pradhan DS. 2022. Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7055582</p> <p>Funding for this project is provided by US National Science Foundation and Idaho EPSCoR through award: OIA-1757324 </p>
FIGURE 3 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 3 Salmo trutta fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with D50 and presence of wood. The trendline shows the relationship between S. trutta fry abundance and D50 in the three sites in which wood was absent () Wood () No Wood
FIGURE 5 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 5 Oncorhynchus mykiss fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with (a) velocity and (b) depth. A trendline shows the relationship between each habitat variable and the fry abundance data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
FIGURE 1 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 1 Fry site locations used to obtain abundance estimates or single-pass counts for Salmo trutta and Oncorhynchus mykiss in the upper Colorado River study section in Grand County, Colorado, downstream of Windy Gap Reservoir. The 20 15.2 m sites, sampled five times from July through October 2018, included one abundance estimation and four single-pass sites at the Sheriff Ranch, four single-pass sites at Kinney Creek, two abundance estimation and five single-pass sites in the Red Barn area and one abundance estimation and three single-pass sites at Hitching Post
FIGURE 2 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 2 Salmo trutta fry single-pass counts and associations with (a) D50, (b) depth and (c) velocity
FIGURE 4 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 4 Oncorhynchus mykiss fry counts from sites in which O. mykiss were or were not (i.e., natural reproduction) stocked and associations with (a) D50 and (b) velocity. A trendline shows the relationship between each habitat variable and the fry count data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
FIGURE 2 in The thermal dependence of the protein-sparing effect in rainbow trout (Oncorhynchus mykiss, Walbaum 1792)
FIGURE 2 Ammonia quotient (AQ) of rainbow trout (Oncorhynchus mykiss) fed three isonitrogenous diets with different energy contents [high energy (HE) = 20.50 MJ kg 1, medium energy (ME) = 18.76 MJ kg 1, low energy (LE) = 17.35 MJ kg 1) at five temperatures (12 C, 14 C, 16 C, 18 C, 20 C). A quadratic dependency model was used to analyse the data. Parabolas describe the quadratic dependency of AQ values on temperature. Calculated lowest AQ values for each parabola are marked with a cross (). Each data point represents the measurement of one tank with rainbow trout at each respective diet and temperature. (n = 3)
FIGURE 1 in The thermal dependence of the protein-sparing effect in rainbow trout (Oncorhynchus mykiss, Walbaum 1792)
FIGURE 1 Percentage of retainable energy (RE) relative to gross energy intake (GEI) of rainbow trout (Oncorhynchus mykiss) fed three isonitrogenous diets with different energy contents [high energy (HE) = 20.50 MJ kg 1, medium energy (ME) = 18.76 MJ kg 1, low energy (LE) = 17.35 MJ kg 1) at five temperatures (12 C, 14 C, 16 C, 18 C, 20 C). Each data point represents measurement of one tank with rainbow trout at each respective diet and temperature (n = 3)
Fig. 1 in Survival Of Embryos And Larvae Of The Rainbow Trout (Oncorhynchus Mykiss, Walbaum, 1792) Under Influence Of Optical Radiation At Various Temperature Regimes
Fig. 1. Linear dependencies of the probit (logit) effect of the death of rainbow trout larvae in vitro from the logarithm of days of fasting for various types of optical radiation at a temperature of 12 (a), 11 (b), 10 (c), 9 (d), 8(e) ° C.
Dataset for "Diets supplemented with Saccharina latissima influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (Oncorhynchus mykiss) fillet composition" (doi.org/10.1016/j.fct.2020.111332)
<p>Dataset corresponding to the following article:</p> <p>Ferreira, M., Larsen, B.K., Granby, K., Cunha, S.C., Monteiro, C., Fernandes, J.O., Nunes, M.L., Marques, A., Dias, J., Cunha, I., Castro, L.F.C., Valente, L.M.P., 2020. Diets supplemented with <em>Saccharina latissima </em>influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (<em>Oncorhynchus mykiss</em>) fillet composition. Food Chem. Toxicol. 140, 111332. <a href="https://doi.org/10.1016/j.fct.2020.111332">https://doi.org/10.1016/j.fct.2020.111332</a></p>
Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)
<p>Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding the traits associated with population divergence. We used genome-wide data to identify genomic regions associated with a key trait that distinguishes two ecotypes of rainbow trout (Oncorhynchus mykiss) – insectivores and piscivores – that coexist in Kootenay Lake, southeastern British Columbia, for the non-breeding portion of the year. "Gerrards" are large-bodied (breeding maturity at >60cm) piscivores that spawn 50km north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data covering 60 percent of the genome to assess the level of genomic divergence between ecotypes, test for genotype-phenotype associations, and identify loci that may play functional or selective roles in their divergence. Analysis of nearly seven million SNPs provided a genome-wide mean FST estimate of 0.18, indicating a high level of reproductive isolation between populations. The window-based FST analysis did not reveal "islands" of genomic differentiation; however, the window with highest FST estimate did include a gene associated with insulin secretion. Although we explored the use of the "Local score" approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (20 percent). Gene Ontology (GO) analysis identified several growth processes as enriched in genes occurring in the 200 most divergent genomic windows, indicating the importance of genetically-based growth and growth-related metabolic functions in the divergence of these ecotypes. In spite of their sympatric coexistence, a high degree of genomic differentiation separates the populations of piscivores and insectivores, indicating little to no contemporary genetic exchange between ecotypes. Our results further indicate that the large body piscivorous 27 phenotype is likely not due to one or a few loci of large effect, rather it may be controlled by several loci of small effect, thus highlighting the power of whole-genome low-coverage sequencing in phenotypic association studies.</p>
Data from: Personality determines population-level effects of microplastics consumption in a modelled population of stream-dwelling rainbow trout (Oncorhynchus mykiss)
<p>Microplastics in freshwater habitats are consumed by fish, including stream-dwelling salmonids, which can alter food consumption or negatively affect swimming and foraging behaviour. As population-level effects are largely unknown, a simulated population of stream-dwelling rainbow trout (<em>Oncorhynchus mykiss</em>) was created using the agent-based model 'inSTREAM 7' to model population-level effects (biomass) of behavioural changes caused by microplastics consumption. Individual fish were assigned all possible combinations of two personality traits (dominance, boldness/shyness), and consumed microplastics while foraging, while their abundance, body size, and microplastics consumption were tracked for three different life stages (fry, juvenile, adult) for a 10-year simulation period. Three additive scenarios were explored: a low-impact scenario with decreased food consumption, a medium-impact scenario with added lower swimming speed, and a high-impact scenario with added reductions in prey capture efficiency. Each was tested with microplastics concentrations of 0%, 1% (i.e., current levels), and 3% (i.e., future levels) of drift food. Overall, microplastics consumption did not strongly affect trout population abundance. Dominant adult trout consumed disproportionally more microplastics than all other fish, especially with higher microplastics concentrations. Different personality types were affected differently in the three scenarios: dominant and bold adults were smaller when food consumption was reduced, shy and subordinate adults were smaller when swimming speed was lowered, and all dominant adults, regardless of boldness, were smaller when foraging efficiency was impeded, with dominant and bold fry also less abundant in this scenario. However, effects on fish body size were only found with microplastic concentrations of 3%, indicating these outcomes can be prevented, as current levels of microplastics pollution are unlikely to affect salmonid body size. Nevertheless, microplastics ingestion represents an additional stressor that may potentially interact with a myriad of anthropogenic impacts that already affect wild salmonid populations.</p>
Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)
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Differences in gene expression between high and low tolerance rainbow trout (Oncorhynchus mykiss) to acute thermal stress
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Quantifying component mortality estimates of out-migrating juvenile steelhead (<em>Oncorhynchus mykiss</em>)
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Data from: Personality determines population-level effects of microplastics consumption in a modelled population of stream-dwelling rainbow trout (Oncorhynchus mykiss)
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Data from: Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?
Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of O. mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 SNPs on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident-genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.
Determining the upper thermal tolerance of Athabasca rainbow trout (Oncorhynchus mykiss) across naturally varying stream temperatures in the Athabasca River watershed
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Genotype data from: Extent of stream habitat and hybridization influence levels of genetic diversity in Redband Trout (<em>Oncorhynchus mykiss gairdneri</em>) populations
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