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...
Gespeichert in:
| Veröffentlicht in: | PloS one 2018-05, Vol.13 (5), p.e0197364-e0197364 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0197364 |
|---|---|
| container_issue | 5 |
| container_start_page | e0197364 |
| container_title | PloS one |
| container_volume | 13 |
| creator | Blåhed, Ida-Maria Königsson, Helena Ericsson, Göran Spong, Göran |
| 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. |
| doi_str_mv | 10.1371/journal.pone.0197364 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_2047226585</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A540865578</galeid><doaj_id>oai_doaj_org_article_08206640834f4e93895ecc9b651c6e03</doaj_id><sourcerecordid>A540865578</sourcerecordid><originalsourceid>FETCH-LOGICAL-c730t-5c78d4e8da257edd13d8e68a85a8825fd62f0ff4471f2649bf70843b3747ce7e3</originalsourceid><addsrcrecordid>eNqNk11v0zAUhiMEYmPwDxBEQkLbRYsTf-ZmUjW-Kk0MMeDWcuzj1iONi50U-u9xaDc1aBcoUk7k85w3Pq99sux5gaYF5sWbG9-HVjXTtW9hioqKY0YeZMdFhcsJKxF-ePB9lD2J8QYhigVjj7OjshKEU0aOsx9vXdR-A2Gbe5tff_occ-tD7lrjNs70qsmdgbZz1mnVOd_m9TYPYHoNJsV1gJiyu0yEnz202rWLQWrlfYT8dNZoiLka3mdPs0dWNRGe7eNJ9u39u68XHyeXVx_mF7PLieYYdROquTAEhFEl5WBMgY0AJpSgSoiSWsNKi6wlhBe2ZKSqLUeC4BpzwjVwwCfZy53uuvFR7n2KskSElyWjgiZiviOMVzdyHdxKha30ysm_Cz4spAqd0w1IJErEGEECE0ugwqKioHVVM1poBggnrclOK_6CdV-P1GLT1yoMQUaQFU1aiT_f766vV2B08i-oZlQ2zrRuKRd-I2nFWVENmz_dCwSfHI-dXKUzhKZRLfh-12dVEoqLhL76B73fjT21UKlh11qf_qsHUTmjqXNGKReJmt5DpcfAyul0Ca1L66OCs1FBYjr43S1UH6OcX3_5f_bq-5h9fcAuQTXdMvqmHy5hHINkB-rgYwxg70wukBxm6NYNOcyQ3M9QKntxeEB3RbdDg_8AgX4XhA</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2047226585</pqid></control><display><type>article</type><title>Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Blåhed, Ida-Maria ; Königsson, Helena ; Ericsson, Göran ; Spong, Göran</creator><contributor>Apollonio, Marco</contributor><creatorcontrib>Blåhed, Ida-Maria ; Königsson, Helena ; Ericsson, Göran ; Spong, Göran ; Sveriges lantbruksuniversitet ; Apollonio, Marco</creatorcontrib><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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0197364</identifier><identifier>PMID: 29847564</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Alces alces ; Animal populations ; Animals ; Bioinformatics ; Biology and Life Sciences ; Breeding success ; Conservation ; Deer - genetics ; Deoxyribonucleic acid ; DNA ; Ecology ; Ecosystems ; Empirical analysis ; Environmental studies ; Female ; Genetic aspects ; Genetic Markers ; Genetics ; Genetik ; Genomes ; Genotyping ; Identification ; Information processing ; Male ; Markers ; Molecular chains ; Monitoring ; Moose ; People and places ; Polymorphism, Single Nucleotide ; Population ; Population number ; Population structure ; Population studies ; Representations ; Reproduction ; Research and Analysis Methods ; Sex ; Sex Characteristics ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Species Specificity ; Stacks ; Sympatric populations ; Wildlife conservation</subject><ispartof>PloS one, 2018-05, Vol.13 (5), p.e0197364-e0197364</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Blåhed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 Blåhed et al 2018 Blåhed et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c730t-5c78d4e8da257edd13d8e68a85a8825fd62f0ff4471f2649bf70843b3747ce7e3</citedby><cites>FETCH-LOGICAL-c730t-5c78d4e8da257edd13d8e68a85a8825fd62f0ff4471f2649bf70843b3747ce7e3</cites><orcidid>0000-0002-9977-2996</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976195/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976195/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2101,2927,23865,27923,27924,53790,53792,79471,79472</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29847564$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/95820$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><contributor>Apollonio, Marco</contributor><creatorcontrib>Blåhed, Ida-Maria</creatorcontrib><creatorcontrib>Königsson, Helena</creatorcontrib><creatorcontrib>Ericsson, Göran</creatorcontrib><creatorcontrib>Spong, Göran</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)</title><title>PloS one</title><addtitle>PLoS One</addtitle><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.</description><subject>Alces alces</subject><subject>Animal populations</subject><subject>Animals</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Breeding success</subject><subject>Conservation</subject><subject>Deer - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecology</subject><subject>Ecosystems</subject><subject>Empirical analysis</subject><subject>Environmental studies</subject><subject>Female</subject><subject>Genetic aspects</subject><subject>Genetic Markers</subject><subject>Genetics</subject><subject>Genetik</subject><subject>Genomes</subject><subject>Genotyping</subject><subject>Identification</subject><subject>Information processing</subject><subject>Male</subject><subject>Markers</subject><subject>Molecular chains</subject><subject>Monitoring</subject><subject>Moose</subject><subject>People and places</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population number</subject><subject>Population structure</subject><subject>Population studies</subject><subject>Representations</subject><subject>Reproduction</subject><subject>Research and Analysis Methods</subject><subject>Sex</subject><subject>Sex Characteristics</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Species Specificity</subject><subject>Stacks</subject><subject>Sympatric populations</subject><subject>Wildlife conservation</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11v0zAUhiMEYmPwDxBEQkLbRYsTf-ZmUjW-Kk0MMeDWcuzj1iONi50U-u9xaDc1aBcoUk7k85w3Pq99sux5gaYF5sWbG9-HVjXTtW9hioqKY0YeZMdFhcsJKxF-ePB9lD2J8QYhigVjj7OjshKEU0aOsx9vXdR-A2Gbe5tff_occ-tD7lrjNs70qsmdgbZz1mnVOd_m9TYPYHoNJsV1gJiyu0yEnz202rWLQWrlfYT8dNZoiLka3mdPs0dWNRGe7eNJ9u39u68XHyeXVx_mF7PLieYYdROquTAEhFEl5WBMgY0AJpSgSoiSWsNKi6wlhBe2ZKSqLUeC4BpzwjVwwCfZy53uuvFR7n2KskSElyWjgiZiviOMVzdyHdxKha30ysm_Cz4spAqd0w1IJErEGEECE0ugwqKioHVVM1poBggnrclOK_6CdV-P1GLT1yoMQUaQFU1aiT_f766vV2B08i-oZlQ2zrRuKRd-I2nFWVENmz_dCwSfHI-dXKUzhKZRLfh-12dVEoqLhL76B73fjT21UKlh11qf_qsHUTmjqXNGKReJmt5DpcfAyul0Ca1L66OCs1FBYjr43S1UH6OcX3_5f_bq-5h9fcAuQTXdMvqmHy5hHINkB-rgYwxg70wukBxm6NYNOcyQ3M9QKntxeEB3RbdDg_8AgX4XhA</recordid><startdate>20180530</startdate><enddate>20180530</enddate><creator>Blåhed, Ida-Maria</creator><creator>Königsson, Helena</creator><creator>Ericsson, Göran</creator><creator>Spong, Göran</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-9977-2996</orcidid></search><sort><creationdate>20180530</creationdate><title>Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)</title><author>Blåhed, Ida-Maria ; Königsson, Helena ; Ericsson, Göran ; Spong, Göran</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c730t-5c78d4e8da257edd13d8e68a85a8825fd62f0ff4471f2649bf70843b3747ce7e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Alces alces</topic><topic>Animal populations</topic><topic>Animals</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Breeding success</topic><topic>Conservation</topic><topic>Deer - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Ecology</topic><topic>Ecosystems</topic><topic>Empirical analysis</topic><topic>Environmental studies</topic><topic>Female</topic><topic>Genetic aspects</topic><topic>Genetic Markers</topic><topic>Genetics</topic><topic>Genetik</topic><topic>Genomes</topic><topic>Genotyping</topic><topic>Identification</topic><topic>Information processing</topic><topic>Male</topic><topic>Markers</topic><topic>Molecular chains</topic><topic>Monitoring</topic><topic>Moose</topic><topic>People and places</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population</topic><topic>Population number</topic><topic>Population structure</topic><topic>Population studies</topic><topic>Representations</topic><topic>Reproduction</topic><topic>Research and Analysis Methods</topic><topic>Sex</topic><topic>Sex Characteristics</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Species Specificity</topic><topic>Stacks</topic><topic>Sympatric populations</topic><topic>Wildlife conservation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Blåhed, Ida-Maria</creatorcontrib><creatorcontrib>Königsson, Helena</creatorcontrib><creatorcontrib>Ericsson, Göran</creatorcontrib><creatorcontrib>Spong, Göran</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Blåhed, Ida-Maria</au><au>Königsson, Helena</au><au>Ericsson, Göran</au><au>Spong, Göran</au><au>Apollonio, Marco</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-05-30</date><risdate>2018</risdate><volume>13</volume><issue>5</issue><spage>e0197364</spage><epage>e0197364</epage><pages>e0197364-e0197364</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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 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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29847564</pmid><doi>10.1371/journal.pone.0197364</doi><tpages>e0197364</tpages><orcidid>https://orcid.org/0000-0002-9977-2996</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2018-05, Vol.13 (5), p.e0197364-e0197364 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2047226585 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Alces alces Animal populations Animals Bioinformatics Biology and Life Sciences Breeding success Conservation Deer - genetics Deoxyribonucleic acid DNA Ecology Ecosystems Empirical analysis Environmental studies Female Genetic aspects Genetic Markers Genetics Genetik Genomes Genotyping Identification Information processing Male Markers Molecular chains Monitoring Moose People and places Polymorphism, Single Nucleotide Population Population number Population structure Population studies Representations Reproduction Research and Analysis Methods Sex Sex Characteristics Single nucleotide polymorphisms Single-nucleotide polymorphism Species Specificity Stacks Sympatric populations Wildlife conservation |
| title | Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-08T22%3A42%3A48IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Discovery%20of%20SNPs%20for%20individual%20identification%20by%20reduced%20representation%20sequencing%20of%20moose%20(Alces%20alces)&rft.jtitle=PloS%20one&rft.au=Bl%C3%A5hed,%20Ida-Maria&rft.aucorp=Sveriges%20lantbruksuniversitet&rft.date=2018-05-30&rft.volume=13&rft.issue=5&rft.spage=e0197364&rft.epage=e0197364&rft.pages=e0197364-e0197364&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0197364&rft_dat=%3Cgale_plos_%3EA540865578%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2047226585&rft_id=info:pmid/29847564&rft_galeid=A540865578&rft_doaj_id=oai_doaj_org_article_08206640834f4e93895ecc9b651c6e03&rfr_iscdi=true |