Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).
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 9...
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ftdoajarticles:oai:doaj.org/article:08206640834f4e93895ecc9b651c6e03 2023-05-15T13:12:58+02:00 Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). Ida-Maria Blåhed Helena Königsson Göran Ericsson Göran Spong 2018-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0197364 https://doaj.org/article/08206640834f4e93895ecc9b651c6e03 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5976195?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0197364 https://doaj.org/article/08206640834f4e93895ecc9b651c6e03 PLoS ONE, Vol 13, Iss 5, p e0197364 (2018) Medicine R Science Q article 2018 ftdoajarticles https://doi.org/10.1371/journal.pone.0197364 2022-12-30T21:27:52Z 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 separate individuals with high confidence. Moreover, the autosomal SNPs were highly informative also for population level analyses. The potential applications of this SNP panel are thus many including investigations of population size, sex ratios, relatedness, reproductive success and population structure. Ideally, SNP-based studies could improve today's population monitoring and increase our knowledge about moose population dynamics. Article in Journal/Newspaper Alces alces Directory of Open Access Journals: DOAJ Articles PLOS ONE 13 5 e0197364 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
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Medicine R Science Q |
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Medicine R Science Q Ida-Maria Blåhed Helena Königsson Göran Ericsson Göran Spong Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). |
topic_facet |
Medicine R Science Q |
description |
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 separate individuals with high confidence. Moreover, the autosomal SNPs were highly informative also for population level analyses. The potential applications of this SNP panel are thus many including investigations of population size, sex ratios, relatedness, reproductive success and population structure. Ideally, SNP-based studies could improve today's population monitoring and increase our knowledge about moose population dynamics. |
format |
Article in Journal/Newspaper |
author |
Ida-Maria Blåhed Helena Königsson Göran Ericsson Göran Spong |
author_facet |
Ida-Maria Blåhed Helena Königsson Göran Ericsson Göran Spong |
author_sort |
Ida-Maria Blåhed |
title |
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). |
title_short |
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). |
title_full |
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). |
title_fullStr |
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). |
title_full_unstemmed |
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces). |
title_sort |
discovery of snps for individual identification by reduced representation sequencing of moose (alces alces). |
publisher |
Public Library of Science (PLoS) |
publishDate |
2018 |
url |
https://doi.org/10.1371/journal.pone.0197364 https://doaj.org/article/08206640834f4e93895ecc9b651c6e03 |
genre |
Alces alces |
genre_facet |
Alces alces |
op_source |
PLoS ONE, Vol 13, Iss 5, p e0197364 (2018) |
op_relation |
http://europepmc.org/articles/PMC5976195?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0197364 https://doaj.org/article/08206640834f4e93895ecc9b651c6e03 |
op_doi |
https://doi.org/10.1371/journal.pone.0197364 |
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PLOS ONE |
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13 |
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5 |
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e0197364 |
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