Characterization of 13 single nucleotide polymorphism markers for chum salmon

Smith, Christian T.; Baker, Jason D.; Park, L.; Seeb, Lisa W.; Elfstrom, Carita M.; S, Abe; Seeb, James E.

doi:10.1111/j.1471-8286.2005.00903.x

Cited by 30 publications

(29 citation statements)

References 16 publications

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“…Variation was analyzed at 72 nuclear and 1 mitochondrial SNP with the primer and probe sequences outlined by Smith et al (2005aSmith et al ( , 2005bSmith et al ( , 2005cSmith et al ( , 2007, Miller et al (2008). A listing of all the SNPs surveyed is given in Table 2.…”

Section: Methodsmentioning

confidence: 99%

“…The repeatability of genotyping was evaluated by repeat PCR analysis and scoring of the genotypes of individual fish. Discrepancies in scoring were observed in 8 of the 15,360 genotypes scored across all loci, for a genotyping error rate of 0.05%.Variation was analyzed at 72 nuclear and 1 mitochondrial SNP with the primer and probe sequences outlined by Smith et al (2005a, 2005b, 2005c. A listing of all the SNPs surveyed is given in Table 2.…”

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confidence: 99%

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A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single‐Nucleotide Polymorphisms

2012

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The following questions were addressed in this study: (1) If a suite of 12-15 microsatellites were used in the genetic stock identification (GSI) of Chinook salmon Oncorhynchus tshawytscha, which microsatellites should be in the suite? (2) How many microsatellites are required to provide stock identification resolution equivalent to that of 72 single-nucleotide polymorphisms (SNPs)? (3) How many SNPs are required to replace the current microsatellite baselines used in GSI applications? (4) If additional GSI power is required for microsatellite baselines, what is the incremental increase provided by SNPs and microsatellites? The variation at 29 microsatellite loci and 73 SNP loci was surveyed in 60 populations of Chinook salmon in 16 regions in British Columbia. Microsatellites with more observed alleles provided more accurate estimates of stock composition than those with fewer alleles. The options available for improving the accuracy and precision of stock composition estimates for a 12-locus Fisheries and Oceans Canada (DFO) microsatellite suite range include adding either 4 microsatellites or 25 SNPs to the existing suite to achieve an overall population-specific accuracy of 86% across 60 populations. For the 13-locus Genetic Analysis of Pacific Salmon (GAPS) microsatellites, either 2 microsatellites or 20-25 SNPs can be added to the existing suite to achieve approximately 86% population-specific accuracy in estimated stock composition. The enhanced DFO (16 loci) and GAPS (15 loci) microsatellite baselines were projected to require 179 and 166 SNPs, respectively, for equivalent precision of the population-specific estimates. The level of regional accuracy of individual assignment available from the enhanced DFO and GAPS suites of microsatellites was projected to require 90 and 82 SNPs, respectively. The level of individual assignment to specific populations available from the enhanced DFO and GAPS suites of microsatellites was projected to require 137 and 121 SNPs, respectively.One key aspect of the management of Pacific salmon Oncorhynchus spp. fisheries is estimating the stock composition of mixed-stock fishery samples with enough resolution for effective management decisions, with the constraint that the estimates be timely and cost-effective. Prior to 2002, microsatellites had been successfully applied in sockeye salmon O. nerka fishery management in British Columbia, where the twin management objectives were to restrict exploitation of populations of conservation concern while enabling the harvest of abundant populations (Beacham et al. 2004). In 2002, this was precisely the Subject editor: Timothy King, U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia *Corresponding author: terry.beacham@dfo-mpo.gc.ca Received January 10, 2011; accepted August 22, 2011 dilemma confronting Canadian fishery managers in the management of the Chinook salmon O. tshawytscha fisheries off the Queen Charlotte Islands in northern British Columbia and the west coast of Vancouver Island in so...

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Section: Methodsmentioning

confidence: 99%

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A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single‐Nucleotide Polymorphisms

2012

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“…Although rarely used, SNPs have already proved as useful molecular tool in population genetic studies in salmonid taxa (e.g., Rengmark et al 2006;Smith et al 2005;Sušnik et al 2008). The set of SNPs presented in this study could represent effective means for genetic management of scarce and endangered trouts like marble trout, softmouth trout and several local stocks of brown trout, contaminated with non-native strains (e. g., with ''Atlantic'' hatchery strains).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 97%

A set of SNPs enabling identification of trouts and their hybrids in Salmo genus

Pustovrh

Snoj

Bajec

2010

Conservation Genet Resour

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We present a set of nuclear DNA SNPs enabling discrimination between Salmo marmoratus, S. obtusirostris and different evolutionary lineages of S. trutta. The loci containing SNPs were either isolated from marble trout nuclear DNA or inferred from literature. By comparing the joint sequences (ca. 5,830 bp) among 48 tested individuals, 127 substitutions and 8 indels were found. Forty-one of them, distributed across 16 loci, turned out as species or lineages specific. This set of SNP markers may be applied as molecular tool for genetic management purposes as well as in resolving phylogenetic and taxonomic uncertainties of different trout stocks.

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“…The popularity of SNP genotyping has increased with the emergence and widespread availability of technologies for whole-genome SNP identification (14) and has resulted in a growing number of SNP databases for a wide range of organisms, including humans (www.ncbi.nlm.nih.gov/projects/SNP). The shifting focus from discovery to utilization of SNP genotypes for cohort phenotype classification and segmentation has led to applications in human disease diagnostics (5,6); pharmacogenetics (7,8); blood typing (9,10); DNA fingerprinting for criminal or parental verification (11); fisheries management (12,13); plant and human pathogen detection and identification (14,15); and marker-assisted crop and animal breeding (1618). …”

Section: Introductionmentioning

confidence: 99%

A Nanoliter Fluidic Platform for Large-Scale Single Nucleotide Polymorphism Genotyping

et al. 2009

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Discovery, evaluation, and understanding the biological relevance of single nucleotide polymorphisms (SNPs) and their associated phenotypes is relevant to many applications, including human disease diagnostics, pathogen detection, and identification of genetic traits impacting agricultural practices, both in terms of food quality and production efficiency. Validation of putative SNP associations in large-scale cohorts is currently impeded by the technical challenges and high cost inherent in analyzing large numbers of samples using available SNP genotyping platforms. We describe in this report the implementation of the 5'-exonuclease, biallelic PCR assay for SNP genotyping (TaqMan) in a nanofluidic version of a high-density microplate. System performance was assessed using a panel of 32 TaqMan SNP genotyping assays targeted to human polymorphisms. This functional test of the nanoliter fluidic SNP genotyping platform delivered genotyping call rates and accuracies comparable to the same larger volume reactions in microplate systems.

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Characterization of 13 single nucleotide polymorphism markers for chum salmon

Cited by 30 publications

References 16 publications

A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single‐Nucleotide Polymorphisms

A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single‐Nucleotide Polymorphisms

A set of SNPs enabling identification of trouts and their hybrids in Salmo genus

A Nanoliter Fluidic Platform for Large-Scale Single Nucleotide Polymorphism Genotyping

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