A New Genotyping‐in‐Thousands‐by‐Sequencing Single Nucleotide Polymorphism Panel for Mixed‐Stock Analysis of Chum Salmon from Coastal Western Alaska: GENE MARKERS FOR IDENTIFICATION OF CHUM SALMON STOCKS (2024)

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Garrett J. McKinney

College of Fisheries and Ocean Sciences University of Alaska Fairbanks 17101 Point Lena Loop Road Juneau Alaska 99801 USA

School of Aquatic and Fishery Sciences University of Washington 1122 Northeast Boat Street, Box 355020 Seattle Washington 98195‐5020 USA

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Patrick D. Barry

College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, Alaska, 99801, USA

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Carita Pascal

School of Aquatic and Fishery Sciences, University of Washington, 1122 Northeast Boat Street, Box 355020, Seattle, Washington, 98195‐5020, USA

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James E. Seeb

School of Aquatic and Fishery Sciences, University of Washington, 1122 Northeast Boat Street, Box 355020, Seattle, Washington, 98195‐5020, USA

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School of Aquatic and Fishery Sciences, University of Washington, 1122 Northeast Boat Street, Box 355020, Seattle, Washington, 98195‐5020, USA

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Megan V. McPhee

College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, Alaska, 99801, USA

Corresponding author: mvmcphee@alaska.edu

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North American Journal of Fisheries Management, Volume 42, Issue 5, 1 October 2022, Pages 1134–1143, https://doi.org/10.1002/nafm.10805

Published:

01 October 2022

Article history

Received:

06 April 2022

Accepted:

11 June 2022

Published:

01 October 2022

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    Garrett J. McKinney, Patrick D. Barry, Carita Pascal, James E. Seeb, Lisa W. Seeb, Megan V. McPhee, A New Genotyping‐in‐Thousands‐by‐Sequencing Single Nucleotide Polymorphism Panel for Mixed‐Stock Analysis of Chum Salmon from Coastal Western Alaska: GENE MARKERS FOR IDENTIFICATION OF CHUM SALMON STOCKS, North American Journal of Fisheries Management, Volume 42, Issue 5, 1 October 2022, Pages 1134–1143, https://doi.org/10.1002/nafm.10805

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Abstract

Genetic stock identification is becoming increasingly important in the management of Chum Salmon Oncorhynchus keta from western Alaska due to frequent run failures in recent times. It has been notoriously difficult to distinguish populations of summer‐run Chum Salmon among four major regions in coastal western Alaska: Norton Sound, lower Yukon River, Kuskokwim River, and Nushagak River. Here we developed and evaluated a panel of single nucleotide polymorphism (SNP) markers designed to coamplify using the genotyping‐in‐thousands by sequencing (GT‐seq) method, which would greatly enhance the efficiency of genotyping samples from baseline populations and from mixed‐stock fisheries or incidental catches. We selected 479 SNPs in 355 amplicons from ~30,000 candidate SNPs for the GT‐seq panel. Evaluations using single‐stock and realistic fishery mixture simulations indicated that the panel was able to satisfactorily distinguish Norton Sound from the other regions to the south but was unable to distinguish among lower Yukon, Kuskokwim, and Nushagak rivers with accuracy >90%. The low degree of population structure among Chum Salmon in this region, described in previous studies and confirmed with tens of thousands of SNPs here, means that genetic stock identification will be inadequate to guide management decisions at the spatial scale desired by stakeholders and fishery managers in the region.

© 2022 American Fisheries Society (AFS)

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)

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