Salmon species identification via direct DNA sequencing of single amplicons
For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleot...
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| Veröffentlicht in: | Conservation genetics resources 2020-06, Vol.12 (2), p.285-291 |
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| creator | Beacham, Terry D. Wallace, Colin G. |
| description | For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleotide polymorphisms (SNPs) within two specific DNA amplicons was used to distinguish among coho salmon (
Oncorhynchus kisutch
), Chinook salmon (
Oncorhynchus tshawytscha
), sockeye salmon (
Oncorhynchus nerka
), chum salmon (
Oncorhynchus keta
), pink salmon (
Oncorhynchus gorbuscha
), masu salmon (
Oncorhynchus masou
), steelhead/rainbow trout (
Oncorhynchus mykiss
), cutthroat trout (
Oncorhynchus clarkii
), and Atlantic salmon (
Salmo salar
). A total of 2510 individuals was evaluated from a Pacific rim distribution of populations for sockeye salmon, chum salmon, and pink salmon, whereas masu salmon samples were genotyped only from Japanese populations. Coho salmon, Chinook salmon, steehead trout, cutthroat trout, and Atlantic salmon samples were genotyped only from North American populations. All individual salmonids genotyped were assigned with 100% accuracy to their respective species via diagnostic homozygous SNP genotypes for each species except for cutthroat trout, where no diagnostic SNP genotypes were observed in the two amplicons evaluated. |
| doi_str_mv | 10.1007/s12686-019-01102-1 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_2405160169</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2405160169</sourcerecordid><originalsourceid>FETCH-LOGICAL-c270t-ad68fffe6dac7b07f7436988da6206a3952745370c2678317b4015efb54090173</originalsourceid><addsrcrecordid>eNp9kE9LxDAQxYMouK5-AU8Bz9WZpE3a47L-RdGDeg7ZNFmydNOadAW_vdGK3jwMbxjemxl-hJwinCOAvEjIRC0KwCYXAitwj8ywlrKQTMD-b1-xQ3KU0gZA1JyxGbl_1t22DzQN1nibqG9tGL3zRo8-j9-9pq2P1oz08nFBk33b2WB8WNPe0ZS1s1Rvh86bPqRjcuB0l-zJj87J6_XVy_K2eHi6uVsuHgrDJIyFbkXtnLOi1UauQDpZctHUdasFA6F5UzFZVlyCYULWHOWqBKysW1UlNICSz8nZtHeIff4njWrT72LIJxUroUIBKJrsYpPLxD6laJ0aot_q-KEQ1Bc0NUFTGZr6hqYwh_gUStkc1jb-rf4n9Qn04G4V</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2405160169</pqid></control><display><type>article</type><title>Salmon species identification via direct DNA sequencing of single amplicons</title><source>SpringerLink Journals - AutoHoldings</source><creator>Beacham, Terry D. ; Wallace, Colin G.</creator><creatorcontrib>Beacham, Terry D. ; Wallace, Colin G.</creatorcontrib><description>For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleotide polymorphisms (SNPs) within two specific DNA amplicons was used to distinguish among coho salmon (
Oncorhynchus kisutch
), Chinook salmon (
Oncorhynchus tshawytscha
), sockeye salmon (
Oncorhynchus nerka
), chum salmon (
Oncorhynchus keta
), pink salmon (
Oncorhynchus gorbuscha
), masu salmon (
Oncorhynchus masou
), steelhead/rainbow trout (
Oncorhynchus mykiss
), cutthroat trout (
Oncorhynchus clarkii
), and Atlantic salmon (
Salmo salar
). A total of 2510 individuals was evaluated from a Pacific rim distribution of populations for sockeye salmon, chum salmon, and pink salmon, whereas masu salmon samples were genotyped only from Japanese populations. Coho salmon, Chinook salmon, steehead trout, cutthroat trout, and Atlantic salmon samples were genotyped only from North American populations. All individual salmonids genotyped were assigned with 100% accuracy to their respective species via diagnostic homozygous SNP genotypes for each species except for cutthroat trout, where no diagnostic SNP genotypes were observed in the two amplicons evaluated.</description><identifier>ISSN: 1877-7252</identifier><identifier>EISSN: 1877-7260</identifier><identifier>DOI: 10.1007/s12686-019-01102-1</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Genetics and Genomics ; Biodiversity ; Biomedical and Life Sciences ; Conservation Biology/Ecology ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Ecology ; Evolutionary Biology ; Forensic science ; Genetic diversity ; Life Sciences ; Methods and Resources Article ; Oncorhynchus gorbuscha ; Oncorhynchus keta ; Oncorhynchus kisutch ; Oncorhynchus masou ; Oncorhynchus mykiss ; Oncorhynchus nerka ; Oncorhynchus tshawytscha ; Plant Genetics and Genomics ; Salmo salar ; Salmon ; Salmonidae ; Single-nucleotide polymorphism ; Species ; Trout ; Wildlife conservation</subject><ispartof>Conservation genetics resources, 2020-06, Vol.12 (2), p.285-291</ispartof><rights>Crown 2019</rights><rights>Crown 2019.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c270t-ad68fffe6dac7b07f7436988da6206a3952745370c2678317b4015efb54090173</cites><orcidid>0000-0003-0987-8445</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12686-019-01102-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12686-019-01102-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Beacham, Terry D.</creatorcontrib><creatorcontrib>Wallace, Colin G.</creatorcontrib><title>Salmon species identification via direct DNA sequencing of single amplicons</title><title>Conservation genetics resources</title><addtitle>Conservation Genet Resour</addtitle><description>For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleotide polymorphisms (SNPs) within two specific DNA amplicons was used to distinguish among coho salmon (
Oncorhynchus kisutch
), Chinook salmon (
Oncorhynchus tshawytscha
), sockeye salmon (
Oncorhynchus nerka
), chum salmon (
Oncorhynchus keta
), pink salmon (
Oncorhynchus gorbuscha
), masu salmon (
Oncorhynchus masou
), steelhead/rainbow trout (
Oncorhynchus mykiss
), cutthroat trout (
Oncorhynchus clarkii
), and Atlantic salmon (
Salmo salar
). A total of 2510 individuals was evaluated from a Pacific rim distribution of populations for sockeye salmon, chum salmon, and pink salmon, whereas masu salmon samples were genotyped only from Japanese populations. Coho salmon, Chinook salmon, steehead trout, cutthroat trout, and Atlantic salmon samples were genotyped only from North American populations. All individual salmonids genotyped were assigned with 100% accuracy to their respective species via diagnostic homozygous SNP genotypes for each species except for cutthroat trout, where no diagnostic SNP genotypes were observed in the two amplicons evaluated.</description><subject>Animal Genetics and Genomics</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Conservation Biology/Ecology</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Ecology</subject><subject>Evolutionary Biology</subject><subject>Forensic science</subject><subject>Genetic diversity</subject><subject>Life Sciences</subject><subject>Methods and Resources Article</subject><subject>Oncorhynchus gorbuscha</subject><subject>Oncorhynchus keta</subject><subject>Oncorhynchus kisutch</subject><subject>Oncorhynchus masou</subject><subject>Oncorhynchus mykiss</subject><subject>Oncorhynchus nerka</subject><subject>Oncorhynchus tshawytscha</subject><subject>Plant Genetics and Genomics</subject><subject>Salmo salar</subject><subject>Salmon</subject><subject>Salmonidae</subject><subject>Single-nucleotide polymorphism</subject><subject>Species</subject><subject>Trout</subject><subject>Wildlife conservation</subject><issn>1877-7252</issn><issn>1877-7260</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kE9LxDAQxYMouK5-AU8Bz9WZpE3a47L-RdGDeg7ZNFmydNOadAW_vdGK3jwMbxjemxl-hJwinCOAvEjIRC0KwCYXAitwj8ywlrKQTMD-b1-xQ3KU0gZA1JyxGbl_1t22DzQN1nibqG9tGL3zRo8-j9-9pq2P1oz08nFBk33b2WB8WNPe0ZS1s1Rvh86bPqRjcuB0l-zJj87J6_XVy_K2eHi6uVsuHgrDJIyFbkXtnLOi1UauQDpZctHUdasFA6F5UzFZVlyCYULWHOWqBKysW1UlNICSz8nZtHeIff4njWrT72LIJxUroUIBKJrsYpPLxD6laJ0aot_q-KEQ1Bc0NUFTGZr6hqYwh_gUStkc1jb-rf4n9Qn04G4V</recordid><startdate>20200601</startdate><enddate>20200601</enddate><creator>Beacham, Terry D.</creator><creator>Wallace, Colin G.</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FE</scope><scope>8FH</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><orcidid>https://orcid.org/0000-0003-0987-8445</orcidid></search><sort><creationdate>20200601</creationdate><title>Salmon species identification via direct DNA sequencing of single amplicons</title><author>Beacham, Terry D. ; Wallace, Colin G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c270t-ad68fffe6dac7b07f7436988da6206a3952745370c2678317b4015efb54090173</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biodiversity</topic><topic>Biomedical and Life Sciences</topic><topic>Conservation Biology/Ecology</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Ecology</topic><topic>Evolutionary Biology</topic><topic>Forensic science</topic><topic>Genetic diversity</topic><topic>Life Sciences</topic><topic>Methods and Resources Article</topic><topic>Oncorhynchus gorbuscha</topic><topic>Oncorhynchus keta</topic><topic>Oncorhynchus kisutch</topic><topic>Oncorhynchus masou</topic><topic>Oncorhynchus mykiss</topic><topic>Oncorhynchus nerka</topic><topic>Oncorhynchus tshawytscha</topic><topic>Plant Genetics and Genomics</topic><topic>Salmo salar</topic><topic>Salmon</topic><topic>Salmonidae</topic><topic>Single-nucleotide polymorphism</topic><topic>Species</topic><topic>Trout</topic><topic>Wildlife conservation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Beacham, Terry D.</creatorcontrib><creatorcontrib>Wallace, Colin G.</creatorcontrib><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection (ProQuest)</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science 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><jtitle>Conservation genetics resources</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Beacham, Terry D.</au><au>Wallace, Colin G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Salmon species identification via direct DNA sequencing of single amplicons</atitle><jtitle>Conservation genetics resources</jtitle><stitle>Conservation Genet Resour</stitle><date>2020-06-01</date><risdate>2020</risdate><volume>12</volume><issue>2</issue><spage>285</spage><epage>291</epage><pages>285-291</pages><issn>1877-7252</issn><eissn>1877-7260</eissn><abstract>For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleotide polymorphisms (SNPs) within two specific DNA amplicons was used to distinguish among coho salmon (
Oncorhynchus kisutch
), Chinook salmon (
Oncorhynchus tshawytscha
), sockeye salmon (
Oncorhynchus nerka
), chum salmon (
Oncorhynchus keta
), pink salmon (
Oncorhynchus gorbuscha
), masu salmon (
Oncorhynchus masou
), steelhead/rainbow trout (
Oncorhynchus mykiss
), cutthroat trout (
Oncorhynchus clarkii
), and Atlantic salmon (
Salmo salar
). A total of 2510 individuals was evaluated from a Pacific rim distribution of populations for sockeye salmon, chum salmon, and pink salmon, whereas masu salmon samples were genotyped only from Japanese populations. Coho salmon, Chinook salmon, steehead trout, cutthroat trout, and Atlantic salmon samples were genotyped only from North American populations. All individual salmonids genotyped were assigned with 100% accuracy to their respective species via diagnostic homozygous SNP genotypes for each species except for cutthroat trout, where no diagnostic SNP genotypes were observed in the two amplicons evaluated.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s12686-019-01102-1</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0003-0987-8445</orcidid></addata></record> |
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| ispartof | Conservation genetics resources, 2020-06, Vol.12 (2), p.285-291 |
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| subjects | Animal Genetics and Genomics Biodiversity Biomedical and Life Sciences Conservation Biology/Ecology Deoxyribonucleic acid DNA DNA sequencing Ecology Evolutionary Biology Forensic science Genetic diversity Life Sciences Methods and Resources Article Oncorhynchus gorbuscha Oncorhynchus keta Oncorhynchus kisutch Oncorhynchus masou Oncorhynchus mykiss Oncorhynchus nerka Oncorhynchus tshawytscha Plant Genetics and Genomics Salmo salar Salmon Salmonidae Single-nucleotide polymorphism Species Trout Wildlife conservation |
| title | Salmon species identification via direct DNA sequencing of single amplicons |
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