Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

The Delta Smelt Hypomesus transpacificus , listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Transactions of the American Fisheries Society (1900) 2015-07, Vol.144 (4), p.767-779
Hauptverfasser: Lew, Ryan M, Finger, Amanda J, Baerwald, Melinda R, Goodbla, Alisha, May, Bernie, Meek, Mariah H
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 779
container_issue 4
container_start_page 767
container_title Transactions of the American Fisheries Society (1900)
container_volume 144
creator Lew, Ryan M
Finger, Amanda J
Baerwald, Melinda R
Goodbla, Alisha
May, Bernie
Meek, Mariah H
description The Delta Smelt Hypomesus transpacificus , listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species. Received November 29, 2014; accepted March 30, 2015
doi_str_mv 10.1080/00028487.2015.1037016
format Article
fullrecord <record><control><sourceid>wiley_cross</sourceid><recordid>TN_cdi_crossref_primary_10_1080_00028487_2015_1037016</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>TAFS0767</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3297-f85ba4abb28613567fd5c3dabf3e57db3cee59a8513ff1e177a564e658141273</originalsourceid><addsrcrecordid>eNqNkNtO6zAQRSN0kOAAn4DwDwTsOL70nKeqXCVuUsuz5STj1iixwTaXfg2_iqOCxCNPezSz1x5pF8UhwccES3yCMa5kLcVxhQnLKyow4VvFLmG1LCVnkz8_5p3ib4yPGWGCy93i4yFat0S38J7KC3AQdLLeoTk8v4Brx1PyaBqjjQlpNPMuQnjdeC51alcQ1v_yYZ6dPZS3L20PPtkO0L3v14MPTysbB3SvHfTI-IDSCtD4J9kW3WinlzCAS8gbdOY67ZYQoEOn0KecOWTZL7aN7iMcfOlesTg_W8wuy-u7i6vZ9LpsaTURpZGs0bVumkpyQhkXpmMt7XRjKDDRNbQFYBMtGaHGECBCaMZr4EySmlSC7hVsE9sGH2MAo56CHXRYK4LVWLL6LlmNJauvkjP3f8O92R7Wv4PUYno-x4KPX482tNFe6WWwUT3Ms5VjnL2kqugnBZOMUA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt</title><source>Wiley Online Library</source><creator>Lew, Ryan M ; Finger, Amanda J ; Baerwald, Melinda R ; Goodbla, Alisha ; May, Bernie ; Meek, Mariah H</creator><creatorcontrib>Lew, Ryan M ; Finger, Amanda J ; Baerwald, Melinda R ; Goodbla, Alisha ; May, Bernie ; Meek, Mariah H</creatorcontrib><description>The Delta Smelt Hypomesus transpacificus , listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species. Received November 29, 2014; accepted March 30, 2015</description><identifier>ISSN: 1548-8659</identifier><identifier>ISSN: 0002-8487</identifier><identifier>EISSN: 1548-8659</identifier><identifier>DOI: 10.1080/00028487.2015.1037016</identifier><language>eng</language><publisher>Taylor &amp; Francis</publisher><subject>breeding stock ; chromosome mapping ; endangered species ; gene frequency ; genetic variation ; genotyping ; hatcheries ; high-throughput nucleotide sequencing ; Hypomesus transpacificus ; inbreeding ; linkage groups ; loci ; parentage ; pedigree ; progeny ; screening ; single nucleotide polymorphism</subject><ispartof>Transactions of the American Fisheries Society (1900), 2015-07, Vol.144 (4), p.767-779</ispartof><rights>2015 American Fisheries Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3297-f85ba4abb28613567fd5c3dabf3e57db3cee59a8513ff1e177a564e658141273</citedby><cites>FETCH-LOGICAL-c3297-f85ba4abb28613567fd5c3dabf3e57db3cee59a8513ff1e177a564e658141273</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1080%2F00028487.2015.1037016$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1080%2F00028487.2015.1037016$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27903,27904,45553,45554</link.rule.ids></links><search><creatorcontrib>Lew, Ryan M</creatorcontrib><creatorcontrib>Finger, Amanda J</creatorcontrib><creatorcontrib>Baerwald, Melinda R</creatorcontrib><creatorcontrib>Goodbla, Alisha</creatorcontrib><creatorcontrib>May, Bernie</creatorcontrib><creatorcontrib>Meek, Mariah H</creatorcontrib><title>Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt</title><title>Transactions of the American Fisheries Society (1900)</title><description>The Delta Smelt Hypomesus transpacificus , listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species. Received November 29, 2014; accepted March 30, 2015</description><subject>breeding stock</subject><subject>chromosome mapping</subject><subject>endangered species</subject><subject>gene frequency</subject><subject>genetic variation</subject><subject>genotyping</subject><subject>hatcheries</subject><subject>high-throughput nucleotide sequencing</subject><subject>Hypomesus transpacificus</subject><subject>inbreeding</subject><subject>linkage groups</subject><subject>loci</subject><subject>parentage</subject><subject>pedigree</subject><subject>progeny</subject><subject>screening</subject><subject>single nucleotide polymorphism</subject><issn>1548-8659</issn><issn>0002-8487</issn><issn>1548-8659</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNqNkNtO6zAQRSN0kOAAn4DwDwTsOL70nKeqXCVuUsuz5STj1iixwTaXfg2_iqOCxCNPezSz1x5pF8UhwccES3yCMa5kLcVxhQnLKyow4VvFLmG1LCVnkz8_5p3ib4yPGWGCy93i4yFat0S38J7KC3AQdLLeoTk8v4Brx1PyaBqjjQlpNPMuQnjdeC51alcQ1v_yYZ6dPZS3L20PPtkO0L3v14MPTysbB3SvHfTI-IDSCtD4J9kW3WinlzCAS8gbdOY67ZYQoEOn0KecOWTZL7aN7iMcfOlesTg_W8wuy-u7i6vZ9LpsaTURpZGs0bVumkpyQhkXpmMt7XRjKDDRNbQFYBMtGaHGECBCaMZr4EySmlSC7hVsE9sGH2MAo56CHXRYK4LVWLL6LlmNJauvkjP3f8O92R7Wv4PUYno-x4KPX482tNFe6WWwUT3Ms5VjnL2kqugnBZOMUA</recordid><startdate>201507</startdate><enddate>201507</enddate><creator>Lew, Ryan M</creator><creator>Finger, Amanda J</creator><creator>Baerwald, Melinda R</creator><creator>Goodbla, Alisha</creator><creator>May, Bernie</creator><creator>Meek, Mariah H</creator><general>Taylor &amp; Francis</general><scope>FBQ</scope><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>201507</creationdate><title>Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt</title><author>Lew, Ryan M ; Finger, Amanda J ; Baerwald, Melinda R ; Goodbla, Alisha ; May, Bernie ; Meek, Mariah H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3297-f85ba4abb28613567fd5c3dabf3e57db3cee59a8513ff1e177a564e658141273</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>breeding stock</topic><topic>chromosome mapping</topic><topic>endangered species</topic><topic>gene frequency</topic><topic>genetic variation</topic><topic>genotyping</topic><topic>hatcheries</topic><topic>high-throughput nucleotide sequencing</topic><topic>Hypomesus transpacificus</topic><topic>inbreeding</topic><topic>linkage groups</topic><topic>loci</topic><topic>parentage</topic><topic>pedigree</topic><topic>progeny</topic><topic>screening</topic><topic>single nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lew, Ryan M</creatorcontrib><creatorcontrib>Finger, Amanda J</creatorcontrib><creatorcontrib>Baerwald, Melinda R</creatorcontrib><creatorcontrib>Goodbla, Alisha</creatorcontrib><creatorcontrib>May, Bernie</creatorcontrib><creatorcontrib>Meek, Mariah H</creatorcontrib><collection>AGRIS</collection><collection>CrossRef</collection><jtitle>Transactions of the American Fisheries Society (1900)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lew, Ryan M</au><au>Finger, Amanda J</au><au>Baerwald, Melinda R</au><au>Goodbla, Alisha</au><au>May, Bernie</au><au>Meek, Mariah H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt</atitle><jtitle>Transactions of the American Fisheries Society (1900)</jtitle><date>2015-07</date><risdate>2015</risdate><volume>144</volume><issue>4</issue><spage>767</spage><epage>779</epage><pages>767-779</pages><issn>1548-8659</issn><issn>0002-8487</issn><eissn>1548-8659</eissn><abstract>The Delta Smelt Hypomesus transpacificus , listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species. Received November 29, 2014; accepted March 30, 2015</abstract><pub>Taylor &amp; Francis</pub><doi>10.1080/00028487.2015.1037016</doi><tpages>13</tpages></addata></record>
fulltext fulltext
identifier ISSN: 1548-8659
ispartof Transactions of the American Fisheries Society (1900), 2015-07, Vol.144 (4), p.767-779
issn 1548-8659
0002-8487
1548-8659
language eng
recordid cdi_crossref_primary_10_1080_00028487_2015_1037016
source Wiley Online Library
subjects breeding stock
chromosome mapping
endangered species
gene frequency
genetic variation
genotyping
hatcheries
high-throughput nucleotide sequencing
Hypomesus transpacificus
inbreeding
linkage groups
loci
parentage
pedigree
progeny
screening
single nucleotide polymorphism
title Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-22T20%3A40%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-wiley_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Using%20Next-Generation%20Sequencing%20to%20Assist%20a%20Conservation%20Hatchery:%20a%20Single-Nucleotide%20Polymorphism%20Panel%20for%20the%20Genetic%20Management%20of%20Endangered%20Delta%20Smelt&rft.jtitle=Transactions%20of%20the%20American%20Fisheries%20Society%20(1900)&rft.au=Lew,%20Ryan%20M&rft.date=2015-07&rft.volume=144&rft.issue=4&rft.spage=767&rft.epage=779&rft.pages=767-779&rft.issn=1548-8659&rft.eissn=1548-8659&rft_id=info:doi/10.1080/00028487.2015.1037016&rft_dat=%3Cwiley_cross%3ETAFS0767%3C/wiley_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/&rfr_iscdi=true