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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)

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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.

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This study was funded by the U.S. Fish and Wildlife Service, the USGS Ecosystems Mission Area, and the Department of Animal Science and College of Agricultural and Environmental Sciences at the University of California, Davis. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service.

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Correspondence to Geoffrey M. Cook.

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All procedures followed the guidelines of the American Society of Mammalogists (Sikes et al. 2016) and were approved by the U.S. Fish and Wildlife Service Region 7 Animal Care and Use Committee (2011-02, 2017-01) and conducted under a Marine Mammal Protection Act permit (MA039386-2).

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Cook, G.M., Prince, D.J., O’Rourke, S.M. et al. 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). Conservation Genet Resour 12, 555–565 (2020).

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