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17 results for “Oncorhynchus kisutch”
Fig. 1 in Catch of Coho Salmon (Oncorhynchus kisutch) Infected with the Freshwater Parasite Salvelinema walkeri (Nematoda: Cystidicolidae) in the Gulf of Alaska in the Early Winter
Fig. 1. Locations of salmonid collection along a south-north transect (from 44°32′N to 52°06′N along ca. 145°W) in the Gulf of Alaska in mid-December 1992 and those of salmonids infected with Salvelinema walkeri in marine and estuarine waters based in this and past papers. Open circles, catch locations of infected salmonids; closed circles, locations with salmonid catch; and crosses, locations without salmonid catch. Location 1, 52°06′N, 145°56′W (this paper); location 2, the Columbia River estuary (Claxton et al. 2013); location 3, off Newport, Oregon (Olson 1978); locations 4 and 5, the Strait of Georgia near Nanoose (Margolis 1967a) and Nanaimo (Ekbaum 1935, 1936; Margolis 1967a), respectively; and locations 6–10, Cowichan Bay, Satellite Channel, the Strait of Juan de Fuca, Sechelt Inlet, and Howe Sound, respectively (Godfrey 1968).
Re-evaluating coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data
<p><span>Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history, and genetic variation using microsatellite markers as indirect measures of local adaptation. Genomic datasets have the potential to improve the definition of CUs by reducing variance around estimates of population genetic parameters, thereby increasing the power to detect more subtle patterns of population genetic structure and by providing an opportunity to incorporate adaptive information more directly with the identification of variants putatively under selection. We used one of the largest genomic datasets recently published for a non-model species, comprising 5,662 individual Coho salmon (<em>Oncorhynchus kisutch</em>) from 149 sampling locations and a total of 24,542 high-quality SNPs obtained using genotyping-by-sequencing and mapped to the Coho salmon reference genome to 1) evaluate the current delineation of CUs for Coho in Canada and 2) compare patterns of population structure observed using neutral and outlier loci from genotype-environment association analyses to determine whether separate CUs that capture adaptive diversity are needed. Our results reflected CU boundaries on the whole, with the majority of sampling locations managed in the same CU clustering together within genetic groups. However, additional groups not currently represented by CUs were also uncovered. We observed considerable overlap in the genetic clusters identified using neutral or candidate loci, indicating a general congruence in patterns of genetic variation driven by local adaptation and gene flow in this species. Consequently, we suggest that the current CU boundaries for Coho salmon are largely well-suited for meeting the Canadian Wild Salmon Policy's objective of defining biologically distinct groups, but we highlight specific areas where CU boundaries may be refined.</span></p>
Data from: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch
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Re-evaluating coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data
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Data from: Genomic predictions and genome-wide association study of resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAD sequencing
Piscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming, and current treatments have been ineffective for the control of this disease. Genetic improvement for P. salmonis resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping of hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against P. salmonis in a farmed coho salmon population and to identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. A total of 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) were experimentally challenged against P. salmonis and their genotypes were assayed using ddRAD sequencing. A total of 9,389 SNPs markers were identified in the population. These markers were used to test genomic selection models and compare different GWAS methodologies for resistance measured as day of death (DD) and binary survival (BIN). Genomic selection models showed higher accuracies than the traditional pedigree-based best linear unbiased prediction (PBLUP) method, for both DD and BIN. The models showed an improvement of up to 95% and 155% respectively over PBLUP. One SNP related with B-cell development was identified as a potential functional candidate associated with resistance to P. salmonis defined as DD.
Data from: Tryptophan and Cortisol modulate the Kynurenine and Serotonin transcriptional pathway in the kidney of Oncorhynchus kisutch
<p>Aquaculture fish are kept for long-periods in sea cages or tanks. Consequently, accumulated stress causes the fish to present serious problems with critical economic losses. Fish food has been supplemented to reduce the stress, using many compoment as amino acids such as tryptophan. This study aims to determine the transcriptional effect of tryptophan and cortisol on primary cell cultures of salmon head and posterior kidney. Our results indicate activation of the kynurenine pathway and serotonin activity when stimulated with tryptophan and cortisol. 95% of tryptophan is degraded by the kynurenine pathway, indicating the relevance of knowing how this pathway is activated and if stress levels associated with fish culture trigger its activation. Additionally, it is essential to know the consequence of increasing kynurenic acid "KYNA" levels in the short and long term, and even during the fish ontogeny.</p>
Oncorhynchus kisutch genetic stock ID SNP baseline
<p>Genetic stock identification (GSI) <span>using genotypes produced from genotyping-by-sequencing of SNP loci</span> has become the gold standard for stock identification in Pacific salmon, which are found in mixed stocks in the ocean. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and promise real-time, in-field stock identification on variable batch sizes. Here we evaluate utility and comparability to established GSI platforms of at-sea stock identification of coho salmon <i>Oncorhynchus kisutch</i> based on targeted SNP amplicon sequencing on the minION platform during a high-sea winter expedition to the Gulf of Alaska. As long read sequencers are not optimized for short amplicons, we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach by providing mobile small batch genotyping to diverse stakeholders.</p>
Data for: Sex-specific differences in swimming, aerobic metabolism, and recovery from exercise in adult coho salmon (Oncorhynchus kisutch) across ecologically relevant temperatures
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Seasonal dynamics of juvenile coho salmon (Oncorhynchus kisutch) in wetlands of the North Thompson River, British Columbia
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Data from: Genomic predictions and genome-wide association study of resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAD sequencing
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Oncorhynchus kisutch genetic stock ID SNP baseline
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Differential Gene Expression in Liver, Gill and Olfactory Tissues of Coho Salmon (Oncorhynchus kisutch) after Acclimation to Salinity.
GEO Series GSE67461. Salmo salar; Oncorhynchus kisutch. 48 samples. Type: Expression profiling by array.
Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [brain]
GEO Series GSE123304. Oncorhynchus kisutch; Salmo salar. 206 samples. Type: Expression profiling by array.
Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [muscle]
GEO Series GSE123306. Oncorhynchus kisutch; Salmo salar. 221 samples. Type: Expression profiling by array.
Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [liver]
GEO Series GSE123307. Oncorhynchus kisutch; Salmo salar. 226 samples. Type: Expression profiling by array.
Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [gill]
GEO Series GSE123305. Oncorhynchus kisutch; Salmo salar. 82 samples. Type: Expression profiling by array.
Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments
GEO Series GSE123308. Oncorhynchus kisutch; Salmo salar. 735 samples. Type: Expression profiling by array.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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