Droplet digital PCR for verification of interspersed refuge in midge tolerant wheat varietal blends1

Analysis of bulk ground samples by droplet digital PCR (ddPCR) was investigated as an alternative to individual kernel testing for assessment of interspersed refuge in midge [Sitodiplosis mosellana (Géhin)] tolerant wheat (Triticum aestivum L.) varietal blends. Four genotyping assays were selected s...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Canadian journal of plant science 2017-04, Vol.97 (2), p.257-265
Hauptverfasser: Perry, D.J, Lee, S.-J
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 265
container_issue 2
container_start_page 257
container_title Canadian journal of plant science
container_volume 97
creator Perry, D.J
Lee, S.-J
description Analysis of bulk ground samples by droplet digital PCR (ddPCR) was investigated as an alternative to individual kernel testing for assessment of interspersed refuge in midge [Sitodiplosis mosellana (Géhin)] tolerant wheat (Triticum aestivum L.) varietal blends. Four genotyping assays were selected such that at least one assay was informative for each of 15 varietal blends registered for production in Canada. The assays were examined in DNA of each of the constituent varieties to assess intravarietal polymorphism and in DNA mixtures simulating each varietal blend. Seed mixtures corresponding to a range of refuge proportions in two different varietal blends were prepared and assessed by ddPCR on two different platforms (RainDrop Digital PCR System, RainDance Technologies, Billerica, MA, and QX200 AutoDG Droplet Digital PCR System, Bio-Rad Laboratories, Hercules, CA). Both systems yielded refuge estimates that were very close to the targeted proportions across the range simulated. Standard deviations among estimates made with the QX200 were, on average, about 60% greater than those among corresponding estimates made with the RainDrop system, but in either case, the coefficients of variation generally remained under 5%. For a ddPCR-based assessment of interspersed refuge in midge tolerant wheat varietal blends, any advantage held by the RainDrop system with respect to precision may be offset by higher throughput achievable with the QX200.
doi_str_mv 10.1139/cjps-2016-0223
format Article
fullrecord <record><control><sourceid>bioone</sourceid><recordid>TN_cdi_bioone_primary_10_1139_cjps_2016_0223</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>bioone_primary_10_1139_cjps_2016_0223</sourcerecordid><originalsourceid>FETCH-bioone_primary_10_1139_cjps_2016_02233</originalsourceid><addsrcrecordid>eNqVj8tKQzEQhoNY8HjZup4HMJpJRE_XVXEpxX1Im0k7JU0OSaz49p6AL-Di578wDHxC3KK6RzTLh-1hqlIrfJJKa3MmBlziKHE05lwMSqlRPmqtLsRlrYe5PuOoBuFfSp4iNfC84-YifKzWEHKBExUOvHWNc4IcgFOjUqdZ5KFQ-NrRvMGR_RxajlRcavC9J9fg5ApTf7aJlHzFa7EILla6-fMrcff2-rl6lxvOOZGdCh9d-bGobCexncR2EttJzD_PfwHJ51Hv</addsrcrecordid><sourcetype>Publisher</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Droplet digital PCR for verification of interspersed refuge in midge tolerant wheat varietal blends1</title><source>EZB-FREE-00999 freely available EZB journals</source><creator>Perry, D.J ; Lee, S.-J</creator><creatorcontrib>Perry, D.J ; Lee, S.-J</creatorcontrib><description>Analysis of bulk ground samples by droplet digital PCR (ddPCR) was investigated as an alternative to individual kernel testing for assessment of interspersed refuge in midge [Sitodiplosis mosellana (Géhin)] tolerant wheat (Triticum aestivum L.) varietal blends. Four genotyping assays were selected such that at least one assay was informative for each of 15 varietal blends registered for production in Canada. The assays were examined in DNA of each of the constituent varieties to assess intravarietal polymorphism and in DNA mixtures simulating each varietal blend. Seed mixtures corresponding to a range of refuge proportions in two different varietal blends were prepared and assessed by ddPCR on two different platforms (RainDrop Digital PCR System, RainDance Technologies, Billerica, MA, and QX200 AutoDG Droplet Digital PCR System, Bio-Rad Laboratories, Hercules, CA). Both systems yielded refuge estimates that were very close to the targeted proportions across the range simulated. Standard deviations among estimates made with the QX200 were, on average, about 60% greater than those among corresponding estimates made with the RainDrop system, but in either case, the coefficients of variation generally remained under 5%. For a ddPCR-based assessment of interspersed refuge in midge tolerant wheat varietal blends, any advantage held by the RainDrop system with respect to precision may be offset by higher throughput achievable with the QX200.</description><identifier>ISSN: 0008-4220</identifier><identifier>EISSN: 1918-1833</identifier><identifier>DOI: 10.1139/cjps-2016-0223</identifier><language>eng</language><publisher>Canadian Science Publishing</publisher><subject>Application of Technology ; cécidomyie du blé ; droplet digital PCR ; interspersed refuge ; mélanges variétaux ; orange wheat blossom midge ; PCR numérique par gouttelettes ; refuge disséminé ; varietal blends</subject><ispartof>Canadian journal of plant science, 2017-04, Vol.97 (2), p.257-265</ispartof><rights>Copyright remains with the author(s)or their institution(s). Permission for reuse (free in most cases) can be obtained from RightsLink.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,782,786,27931,27932</link.rule.ids></links><search><creatorcontrib>Perry, D.J</creatorcontrib><creatorcontrib>Lee, S.-J</creatorcontrib><title>Droplet digital PCR for verification of interspersed refuge in midge tolerant wheat varietal blends1</title><title>Canadian journal of plant science</title><description>Analysis of bulk ground samples by droplet digital PCR (ddPCR) was investigated as an alternative to individual kernel testing for assessment of interspersed refuge in midge [Sitodiplosis mosellana (Géhin)] tolerant wheat (Triticum aestivum L.) varietal blends. Four genotyping assays were selected such that at least one assay was informative for each of 15 varietal blends registered for production in Canada. The assays were examined in DNA of each of the constituent varieties to assess intravarietal polymorphism and in DNA mixtures simulating each varietal blend. Seed mixtures corresponding to a range of refuge proportions in two different varietal blends were prepared and assessed by ddPCR on two different platforms (RainDrop Digital PCR System, RainDance Technologies, Billerica, MA, and QX200 AutoDG Droplet Digital PCR System, Bio-Rad Laboratories, Hercules, CA). Both systems yielded refuge estimates that were very close to the targeted proportions across the range simulated. Standard deviations among estimates made with the QX200 were, on average, about 60% greater than those among corresponding estimates made with the RainDrop system, but in either case, the coefficients of variation generally remained under 5%. For a ddPCR-based assessment of interspersed refuge in midge tolerant wheat varietal blends, any advantage held by the RainDrop system with respect to precision may be offset by higher throughput achievable with the QX200.</description><subject>Application of Technology</subject><subject>cécidomyie du blé</subject><subject>droplet digital PCR</subject><subject>interspersed refuge</subject><subject>mélanges variétaux</subject><subject>orange wheat blossom midge</subject><subject>PCR numérique par gouttelettes</subject><subject>refuge disséminé</subject><subject>varietal blends</subject><issn>0008-4220</issn><issn>1918-1833</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid/><recordid>eNqVj8tKQzEQhoNY8HjZup4HMJpJRE_XVXEpxX1Im0k7JU0OSaz49p6AL-Di578wDHxC3KK6RzTLh-1hqlIrfJJKa3MmBlziKHE05lwMSqlRPmqtLsRlrYe5PuOoBuFfSp4iNfC84-YifKzWEHKBExUOvHWNc4IcgFOjUqdZ5KFQ-NrRvMGR_RxajlRcavC9J9fg5ApTf7aJlHzFa7EILla6-fMrcff2-rl6lxvOOZGdCh9d-bGobCexncR2EttJzD_PfwHJ51Hv</recordid><startdate>201704</startdate><enddate>201704</enddate><creator>Perry, D.J</creator><creator>Lee, S.-J</creator><general>Canadian Science Publishing</general><scope/></search><sort><creationdate>201704</creationdate><title>Droplet digital PCR for verification of interspersed refuge in midge tolerant wheat varietal blends1</title><author>Perry, D.J ; Lee, S.-J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-bioone_primary_10_1139_cjps_2016_02233</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Application of Technology</topic><topic>cécidomyie du blé</topic><topic>droplet digital PCR</topic><topic>interspersed refuge</topic><topic>mélanges variétaux</topic><topic>orange wheat blossom midge</topic><topic>PCR numérique par gouttelettes</topic><topic>refuge disséminé</topic><topic>varietal blends</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Perry, D.J</creatorcontrib><creatorcontrib>Lee, S.-J</creatorcontrib><jtitle>Canadian journal of plant science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Perry, D.J</au><au>Lee, S.-J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Droplet digital PCR for verification of interspersed refuge in midge tolerant wheat varietal blends1</atitle><jtitle>Canadian journal of plant science</jtitle><date>2017-04</date><risdate>2017</risdate><volume>97</volume><issue>2</issue><spage>257</spage><epage>265</epage><pages>257-265</pages><issn>0008-4220</issn><eissn>1918-1833</eissn><abstract>Analysis of bulk ground samples by droplet digital PCR (ddPCR) was investigated as an alternative to individual kernel testing for assessment of interspersed refuge in midge [Sitodiplosis mosellana (Géhin)] tolerant wheat (Triticum aestivum L.) varietal blends. Four genotyping assays were selected such that at least one assay was informative for each of 15 varietal blends registered for production in Canada. The assays were examined in DNA of each of the constituent varieties to assess intravarietal polymorphism and in DNA mixtures simulating each varietal blend. Seed mixtures corresponding to a range of refuge proportions in two different varietal blends were prepared and assessed by ddPCR on two different platforms (RainDrop Digital PCR System, RainDance Technologies, Billerica, MA, and QX200 AutoDG Droplet Digital PCR System, Bio-Rad Laboratories, Hercules, CA). Both systems yielded refuge estimates that were very close to the targeted proportions across the range simulated. Standard deviations among estimates made with the QX200 were, on average, about 60% greater than those among corresponding estimates made with the RainDrop system, but in either case, the coefficients of variation generally remained under 5%. For a ddPCR-based assessment of interspersed refuge in midge tolerant wheat varietal blends, any advantage held by the RainDrop system with respect to precision may be offset by higher throughput achievable with the QX200.</abstract><pub>Canadian Science Publishing</pub><doi>10.1139/cjps-2016-0223</doi><tpages>9</tpages></addata></record>
fulltext fulltext
identifier ISSN: 0008-4220
ispartof Canadian journal of plant science, 2017-04, Vol.97 (2), p.257-265
issn 0008-4220
1918-1833
language eng
recordid cdi_bioone_primary_10_1139_cjps_2016_0223
source EZB-FREE-00999 freely available EZB journals
subjects Application of Technology
cécidomyie du blé
droplet digital PCR
interspersed refuge
mélanges variétaux
orange wheat blossom midge
PCR numérique par gouttelettes
refuge disséminé
varietal blends
title Droplet digital PCR for verification of interspersed refuge in midge tolerant wheat varietal blends1
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-09T10%3A50%3A14IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-bioone&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Droplet%20digital%20PCR%20for%20verification%20of%20interspersed%20refuge%20in%20midge%20tolerant%20wheat%20varietal%20blends1&rft.jtitle=Canadian%20journal%20of%20plant%20science&rft.au=Perry,%20D.J&rft.date=2017-04&rft.volume=97&rft.issue=2&rft.spage=257&rft.epage=265&rft.pages=257-265&rft.issn=0008-4220&rft.eissn=1918-1833&rft_id=info:doi/10.1139/cjps-2016-0223&rft_dat=%3Cbioone%3Ebioone_primary_10_1139_cjps_2016_0223%3C/bioone%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