Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)

PloS One
Ida-Maria BlåhedGöran Spong

Abstract

Monitoring of wild animal populations is challenging, yet reliable information about population processes is important for both management and conservation efforts. Access to molecular markers, such as SNPs, enables population monitoring through genotyping of various DNA sources. We have developed 96 high quality SNP markers for individual identification of moose (Alces alces), an economically and ecologically important top-herbivore in boreal regions. Reduced representation libraries constructed from 34 moose were high-throughput de novo sequenced, generating nearly 50 million read pairs. About 50 000 stacks of aligned reads containing one or more SNPs were discovered with the Stacks pipeline. Several quality criteria were applied on the candidate SNPs to find markers informative on the individual level and well representative for the population. An empirical validation by genotyping of sequenced individuals and additional moose, resulted in the selection of a final panel of 86 high quality autosomal SNPs. Additionally, five sex-specific SNPs and five SNPs for sympatric species diagnostics are included in the panel. The genotyping error rate was 0.002 for the total panel and probability of identities were low enough to separat...Continue Reading

References

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Nov 22, 2013·PloS One·Anita J NormanGöran Spong
Sep 5, 2014·Molecular Ecology Resources·Jack PewTimothy R Frasier
Sep 12, 2015·Ecology and Evolution·Anita J Norman, Göran Spong
Sep 9, 2017·Scientific Reports·Alina von ThadenVioleta Muñoz-Fuentes

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Citations

May 7, 2020·Trends in Ecology & Evolution·Adam J SepulvedaGordon Luikart

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Methods Mentioned

BETA
genotyping
electrophoresis
PCR
PCA

Software Mentioned

related
Genepop
COANCESTRY
Plink
BioEdit
STRUCTURE
Stacks
GenAlEx
R
denovo

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