NDLI: Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters

Content Provider	Springer Nature Link
Author	Stetz, Jeffrey B. smith, Seth Sawaya, Michael A. Ramsey, Alan B. Amish, Stephen J. Schwartz, Michael K. Luikart, Gordon
Copyright Year	2016
Abstract	Many North American river otter (Lontra canadensis) populations are threatened or recovering but are difficult to study because they occur at low densities, it is difficult to visually identify individuals, and they inhabit aquatic environments that accelerate degradation of biological samples. Single nucleotide polymorphisms (SNPs) can improve our ability to monitor demographic and genetic parameters of difficult to study species. We used restriction site associated DNA (RAD) sequencing to discover 20,772 SNPs present in Montana, USA, river otter populations, including 14,512 loci that were also variable in at least one other population range-wide. After applying careful filtering criteria meant to minimize ascertainment bias and identify high quality, highly heterozygous (H $_{ o }$ = 0.2–0.50) SNPs, we developed and tested 52 independent SNP qPCR genotyping assays, including 41 that performed well with diluted DNA. The 41 loci provided high power for population assignment tests with only 1 misassignment (1.6 %) between closely neighboring populations. Our SNPs showed high power to differentiate individuals and assign them to population of origin, as well as strong concordance of genotypes from high and diluted concentrations of DNA, and between original RAD and the SNP qPCR array.
Starting Page	299
Ending Page	302
Page Count	4
File Format	PDF
ISSN	18777252
Journal	Conservation Genetics Resources
Volume Number	8
Issue Number	3
e-ISSN	18777260
Language	English
Publisher	Springer Netherlands
Publisher Date	2016-06-22
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Conservation genomics RAD Next generation sequencing River otter SNP Population monitoring Noninvasive genetic tagging Conservation Biology/Ecology Ecology Biodiversity Evolutionary Biology Plant Genetics & Genomics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Ecology, Evolution, Behavior and Systematics

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Data from: Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters (Dataset)

Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters

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