In:
PLOS ONE, Public Library of Science (PLoS), Vol. 15, No. 11 ( 2020-11-11), p. e0239221-
Abstract:
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.
Type of Medium:
Online Resource
ISSN:
1932-6203
DOI:
10.1371/journal.pone.0239221
DOI:
10.1371/journal.pone.0239221.g001
DOI:
10.1371/journal.pone.0239221.g002
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10.1371/journal.pone.0239221.g003
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10.1371/journal.pone.0239221.g004
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10.1371/journal.pone.0239221.g005
DOI:
10.1371/journal.pone.0239221.t001
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10.1371/journal.pone.0239221.s001
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10.1371/journal.pone.0239221.s002
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10.1371/journal.pone.0239221.s003
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10.1371/journal.pone.0239221.s004
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10.1371/journal.pone.0239221.s005
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10.1371/journal.pone.0239221.s006
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10.1371/journal.pone.0239221.s007
DOI:
10.1371/journal.pone.0239221.s008
DOI:
10.1371/journal.pone.0239221.s009
DOI:
10.1371/journal.pone.0239221.s010
DOI:
10.1371/journal.pone.0239221.s011
DOI:
10.1371/journal.pone.0239221.s012
DOI:
10.1371/journal.pone.0239221.s013
DOI:
10.1371/journal.pone.0239221.s014
DOI:
10.1371/journal.pone.0239221.s015
DOI:
10.1371/journal.pone.0239221.s016
DOI:
10.1371/journal.pone.0239221.s017
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2020
detail.hit.zdb_id:
2267670-3
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