A little SNP of this, a little SNP of that: The discovery of 116 single nucleotide polymorphism markers to enable the ra
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TECHNICAL NOTE
A little SNP of this, a little SNP of that: The discovery of 116 single nucleotide polymorphism markers to enable the rapid identification of individual Pacific walrus (Odobenus rosmarus divergens) Geoffrey M. Cook1,2 · Daniel J. Prince3 · Sean M. O’Rourke3 · Timothy L. King4 · Michael R. Miller3 · Cara J. Lewis2 · Michael S. Eackles4 · Patrick R. Lemons5 · Suresh A. Sethi2,6 · Jeffrey B. Olsen2 · John K. Wenburg2 Received: 17 October 2019 / Accepted: 4 June 2020 © Springer Nature B.V. 2020
Abstract We developed single nucleotide polymorphism (SNP) markers to support a genetics-based capture-mark-recapture (CMR) project implemented for the management of Pacific walrus (Odobenus rosmarus divergens). Using a combination of Restriction-site Associated DNA sequencing (RADSeq) and genome resequencing, 57,504 single nucleotide variants were identified from Pacific walrus DNA. RADSeq was performed on genomic DNA from 192 walruses (63 males; 94 females; 35 unknown sex) whereas genome resequencing was performed on 41 individual walruses (21 males, 20 females). All read mappings were subjected to quality-based variant detection and screened for SNPs. These efforts generated a pool of 909 putative SNPs from which 217 unique TaqMan® assays were developed for validation. Ultimately, 116 validated, biallelic SNPs were combined to create a genetic tag for identifying individual walrus during the multi-year CMR project. Conversion to a 116-SNP TaqMan® OpenArray® enabled use of a high-throughput genotyping qPCR platform, which expedited accurate discrimination of individual walrus and reduced the probability of genotyping errors, thereby providing improved resolution for assessing the size and demographic rates of this population. Keywords Conservation genomics · RAD sequencing · Pacific walrus · SNP · Capture mark recapture · Endangered species act
Deceased: Timothy L. King. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01156-6) contains supplementary material, which is available to authorized users. * Geoffrey M. Cook [email protected] 1
Department of Biology and Health Science, New England College, 98 Bridge Street, Henniker, NH 03242, USA
2
Conservation Genetics Laboratory, U.S. Fish & Wildlife Service, 1011 E. Tudor Road, Anchorage, AK 99503, USA
3
Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
4
U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA
5
Marine Mammals Management, U.S. Fish & Wildlife Service, 1011 E. Tudor Road, Anchorage, AK 99503, USA
6
Department of Natural Resources, Cornell University, Ithaca, NY 14853, USA
The Pacific walrus (Odobenus rosmarus divergens) is an ice-associated pinniped inhabiting the subarctic and arctic continental shelf waters of the Bering and Chukchi seas. Over the past three decades, the extent of sea ice habitat vital to Pacific walruses has declined (Douglas 2010; Perovich and Richter-Me
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