Evaluating Microsatellite Markers for Parentage-Based Tagging of Hatchery Burbot

Ashton, Neil K.; Campbell, Matthew R.; Anders, Paul J.; Powell, Madison S.; Cain, Kenneth D.

doi:10.3955/046.090.0303

Cited by 10 publications

(13 citation statements)

References 43 publications

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“…Steele 2013;Beacham et al 2017). This level of accuracy can have many applications other than analysis of mixed-stock fishery samples, ranging from PBT being increasingly applied in both natural and hatchery settings (Sekino et al 2005;Denson et al 2012;Ashton et al 2016), and has provided valuable information on individual reproductive success, effective population size, and proportion of hatchery-origin individuals in salmon escapements (Abadia-Cardosa et al 2013;Ford et al 2015, Hinrichsen et al 2016.…”

Section: Discussionmentioning

confidence: 99%

Population and individual identification of Chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

Beacham

Wallace

MacConnachie

et al. 2018

Can. J. Fish. Aquat. Sci.

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A study was undertaken to evaluate whether a parentage-based tagging (PBT) and genetic stock identification (GSI) program has the potential to emulate the results from an existing coded-wire tag (CWT) assessment program in British Columbia. A PBT–GSI approach was used to identify Chinook salmon (Oncorhynchus tshawytscha) to specific populations and brood years where 36 241 individuals from 45 populations were genotyped at 321 single nucleotide polymorphisms (SNPs). Known-origin and known-age age 1 juveniles from seven test populations were assigned via PBT (two parental genotypes required, 538 of 656 juveniles assigned; one parental genotype required, 636 of 656 juveniles assigned) with a minimum accuracy of 99.9%. Assignment accuracy via PBT of 1026 ages 1, 2, or 3 Chinook salmon returning to nine populations in 2015 or 2016 (two parental genotypes required, 556 of 1026 individuals assigned; one parental genotype required, 898 of 1026 individuals assigned) was a minimum of 99.8%. A PBT–GSI or PBT system of identification may provide an alternate cost-effective method of identification in the assessment and conservation of Canadian-origin Chinook salmon relative to the existing CWT program, thereby providing very high resolution of mixed-stock fishery samples containing both hatchery-origin (adipose fin clipped) and wild-origin (unclipped) populations.

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Section: Discussionmentioning

confidence: 99%

Population and individual identification of Chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

Beacham

Wallace

MacConnachie

et al. 2018

Can. J. Fish. Aquat. Sci.

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“…Microsatellites have been the most common codominant genetic marker for studies of parentage and kinship in fish populations and have recently been investigated for PBT of supplementation Burbot in the Kootenai River (Ashton et al. ). In the Ashton et al.…”

Section: Purpose Of Sample Collection Sample Locations Latitude/lonmentioning

confidence: 99%

“…In the Ashton et al. () study, supplementation broodstock were screened with 14 microsatellite loci previously developed for Burbot (Sanetra and Meyer ). That screening, which involved multiplexes of four panels, indicated low levels of genetic diversity within supplementation broodstock and high false‐assignment rates during parentage testing (19.0%).…”

Section: Purpose Of Sample Collection Sample Locations Latitude/lonmentioning

confidence: 99%

Development and Application of Single‐Nucleotide Polymorphism (SNP) Genetic Markers for Conservation Monitoring of Burbot Populations

Campbell

LaGrange

et al. 2019

Trans Am Fish Soc

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The transboundary (Idaho, USA; and British Columbia, Canada) population of Burbot Lota lota native to the Kootenai River basin once provided a popular sport and commercial fishery and has been culturally significant to the Kootenai Tribe of Idaho for millennia. However, the population has experienced significant declines over the last 30 years, due primarily to habitat loss and alteration caused by water storage and diversion. By the late 1990s, the population was considered functionally extinct, with estimates of fewer than 50 Burbot in the wild and little to no recruitment, prompting an ongoing international recovery effort. As part of these recovery efforts, managers have been actively developing a hatchery supplementation program to rebuild the population and support future tribal subsistence harvest and recreational fisheries. Although supplementation breeding programs have the potential to rapidly rebuild depleted natural populations, careful genetic management is critical. To monitor genetic diversity and potential inbreeding in the broodstock and to provide parentage-based tagging of supplementation offspring, we developed a set (N = 96) of highly variable single-nucleotide polymorphism (SNP) genetic markers. The subset of 96 SNP markers was developed from a larger suite of 6,517 SNPs that were discovered by using restriction site-associated DNA sequencing. This cost-efficient technology allows for the rapid discovery of thousands of SNP markers in species that have not been extensively studied previously or for which there are little existing DNA sequence data. We demonstrated high accuracy (>99%) of our SNP set for parentage and individual identification through simulated and empirical tests. The SNP marker set provides a powerful new tool for managing broodstock and for monitoring and genetically tagging Burbot to track the growth, survival, and movement of released individuals.

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“…In addition, genetic tracking methods allow for life-long marker retention, no minimum size for tagging, nonlethal detection, and high resolution differentiation of individuals. In addition to tracking individuals, genetic methods can also yield relevant data on the relatives of sequenced individuals [26][27][28][29], thus allowing the potential assessment of population structure [29][30][31][32]. A small number of independently segregating microsatellite markers have been successfully used in pedigree reconstruction, but are constrained by inflexibility between species and difficulty designing markers [32,33].…”

Section: Introductionmentioning

confidence: 99%

“…In addition to tracking individuals, genetic methods can also yield relevant data on the relatives of sequenced individuals [26][27][28][29], thus allowing the potential assessment of population structure [29][30][31][32]. A small number of independently segregating microsatellite markers have been successfully used in pedigree reconstruction, but are constrained by inflexibility between species and difficulty designing markers [32,33]. Single nucleotide polymorphisms (SNP) are being increasingly used as genetic tags because they are high-throughput, have low genotyping error, and their cost of detection is continuously decreasing [29,30,34,35].…”

Section: Introductionmentioning

confidence: 99%

Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids

et al. 2020

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Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.

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Evaluating Microsatellite Markers for Parentage-Based Tagging of Hatchery Burbot

Cited by 10 publications

References 43 publications

Population and individual identification of Chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

Population and individual identification of Chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

Development and Application of Single‐Nucleotide Polymorphism (SNP) Genetic Markers for Conservation Monitoring of Burbot Populations

Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids

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