A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions
Identifieur interne : 000D02 ( Ncbi/Merge ); précédent : 000D01; suivant : 000D03A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions
Auteurs : Daniel Ioan P Curar [Suède, Roumanie] ; Monica L Cr Mioara P Curar [Suède, Roumanie] ; Nathaniel Street ; John Desmond Bussell [Suède, Australie] ; Tiberia Ioana Pop ; Laurent Gutierrez [Suède] ; Catherine Bellini [Suède, France]Source :
- Journal of Experimental Botany [ 0022-0957 ] ; 2012.
Abstract
The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes
Url:
DOI: 10.1093/jxb/err422
PubMed: 22282537
PubMed Central: 3346218
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A collection of INDEL markers for map-based cloning in seven <italic>Arabidopsis</italic> accessions</title><author><name sortKey="P Curar, Daniel Ioan" sort="P Curar, Daniel Ioan" uniqKey="P Curar D" first="Daniel Ioan" last="P Curar">Daniel Ioan P Curar</name><affiliation wicri:level="1"><nlm:aff id="aff1">Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå</wicri:regionArea><wicri:noRegion>SE-90183 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania</nlm:aff><country xml:lang="fr">Roumanie</country><wicri:regionArea>University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca</wicri:regionArea><wicri:noRegion>400372 Cluj Napoca</wicri:noRegion></affiliation></author><author><name sortKey="P Curar, Monica L Cr Mioara" sort="P Curar, Monica L Cr Mioara" uniqKey="P Curar M" first="Monica L Cr Mioara" last="P Curar">Monica L Cr Mioara P Curar</name><affiliation wicri:level="1"><nlm:aff id="aff1">Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå</wicri:regionArea><wicri:noRegion>SE-90183 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj 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Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78026 Versailles Cedex, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78026 Versailles Cedex</wicri:regionArea><wicri:noRegion>78026 Versailles Cedex</wicri:noRegion><wicri:noRegion>78026 Versailles Cedex</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22282537</idno><idno type="pmc">3346218</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346218</idno><idno type="RBID">PMC:3346218</idno><idno type="doi">10.1093/jxb/err422</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">002653</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002653</idno><idno type="wicri:Area/Pmc/Curation">002503</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">002503</idno><idno 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Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania</nlm:aff><country xml:lang="fr">Roumanie</country><wicri:regionArea>University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca</wicri:regionArea><wicri:noRegion>400372 Cluj Napoca</wicri:noRegion></affiliation></author><author><name sortKey="P Curar, Monica L Cr Mioara" sort="P Curar, Monica L Cr Mioara" uniqKey="P Curar M" first="Monica L Cr Mioara" last="P Curar">Monica L Cr Mioara P Curar</name><affiliation wicri:level="1"><nlm:aff id="aff1">Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå</wicri:regionArea><wicri:noRegion>SE-90183 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania</nlm:aff><country xml:lang="fr">Roumanie</country><wicri:regionArea>University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca</wicri:regionArea><wicri:noRegion>400372 Cluj Napoca</wicri:noRegion></affiliation></author><author><name sortKey="Street, Nathaniel" sort="Street, Nathaniel" uniqKey="Street N" first="Nathaniel" last="Street">Nathaniel Street</name></author><author><name sortKey="Bussell, John Desmond" sort="Bussell, John Desmond" uniqKey="Bussell J" first="John Desmond" last="Bussell">John Desmond Bussell</name><affiliation wicri:level="1"><nlm:aff id="aff1">Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå</wicri:regionArea><wicri:noRegion>SE-90183 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4">Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009</wicri:regionArea><wicri:noRegion>WA 6009</wicri:noRegion></affiliation></author><author><name sortKey="Pop, Tiberia Ioana" sort="Pop, Tiberia Ioana" uniqKey="Pop T" first="Tiberia Ioana" last="Pop">Tiberia Ioana Pop</name></author><author><name sortKey="Gutierrez, Laurent" sort="Gutierrez, Laurent" uniqKey="Gutierrez L" first="Laurent" last="Gutierrez">Laurent Gutierrez</name><affiliation wicri:level="1"><nlm:aff id="aff1">Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå</wicri:regionArea><wicri:noRegion>SE-90183 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Bellini, Catherine" sort="Bellini, Catherine" uniqKey="Bellini C" first="Catherine" last="Bellini">Catherine Bellini</name><affiliation wicri:level="1"><nlm:aff id="aff1">Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå</wicri:regionArea><wicri:noRegion>SE-90183 Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3">Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78026 Versailles Cedex, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78026 Versailles Cedex</wicri:regionArea><wicri:noRegion>78026 Versailles Cedex</wicri:noRegion><wicri:noRegion>78026 Versailles Cedex</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of Experimental Botany</title><idno type="ISSN">0022-0957</idno><idno type="eISSN">1460-2431</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes <italic>Arabidopsis thaliana</italic> an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg <italic>erecta</italic> (Col-0×L<italic>er</italic>-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and L<italic>er</italic>-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/L<italic>er</italic>-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used <italic>Arabidopsis</italic> accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alonso, Jm" uniqKey="Alonso J">JM Alonso</name></author><author><name sortKey="Ecker, Jr" uniqKey="Ecker J">JR Ecker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alonso Blanco, C" uniqKey="Alonso Blanco C">C Alonso-Blanco</name></author><author><name sortKey="Aarts, Mg" uniqKey="Aarts M">MG Aarts</name></author><author><name sortKey="Bentsink, L" uniqKey="Bentsink L">L Bentsink</name></author><author><name sortKey="Keurentjes, Jj" uniqKey="Keurentjes J">JJ Keurentjes</name></author><author><name sortKey="Reymond, M" uniqKey="Reymond M">M Reymond</name></author><author><name sortKey="Vreugdenhil, D" uniqKey="Vreugdenhil D">D Vreugdenhil</name></author><author><name sortKey="Koornneef, M" uniqKey="Koornneef M">M 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Stajich</name></author><author><name sortKey="Block, D" uniqKey="Block D">D Block</name></author><author><name sortKey="Boulez, K" uniqKey="Boulez K">K Boulez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Torjek, O" uniqKey="Torjek O">O Torjek</name></author><author><name sortKey="Berger, D" uniqKey="Berger D">D Berger</name></author><author><name sortKey="Meyer, Rc" uniqKey="Meyer R">RC Meyer</name></author><author><name sortKey="Mussig, C" uniqKey="Mussig C">C Mussig</name></author><author><name sortKey="Schmid, Kj" uniqKey="Schmid K">KJ Schmid</name></author><author><name sortKey="Rosleff Sorensen, T" uniqKey="Rosleff Sorensen T">T Rosleff Sorensen</name></author><author><name sortKey="Weisshaar, B" uniqKey="Weisshaar B">B Weisshaar</name></author><author><name sortKey="Mitchell Olds, T" uniqKey="Mitchell Olds T">T Mitchell-Olds</name></author><author><name sortKey="Altmann, T" uniqKey="Altmann T">T Altmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Uchida, N" uniqKey="Uchida N">N Uchida</name></author><author><name sortKey="Sakamoto, T" uniqKey="Sakamoto T">T Sakamoto</name></author><author><name sortKey="Kurata, T" uniqKey="Kurata T">T Kurata</name></author><author><name sortKey="Tasaka, M" uniqKey="Tasaka M">M Tasaka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ye, K" uniqKey="Ye K">K Ye</name></author><author><name sortKey="Schulz, Mh" uniqKey="Schulz M">MH Schulz</name></author><author><name sortKey="Long, Q" uniqKey="Long Q">Q Long</name></author><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R Apweiler</name></author><author><name sortKey="Ning, Z" uniqKey="Ning Z">Z Ning</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Exp Bot</journal-id><journal-id journal-id-type="iso-abbrev">J. Exp. Bot</journal-id><journal-id journal-id-type="hwp">jexbot</journal-id><journal-id journal-id-type="publisher-id">exbotj</journal-id><journal-title-group><journal-title>Journal of Experimental Botany</journal-title></journal-title-group><issn pub-type="ppub">0022-0957</issn><issn pub-type="epub">1460-2431</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22282537</article-id><article-id pub-id-type="pmc">3346218</article-id><article-id pub-id-type="doi">10.1093/jxb/err422</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Papers</subject></subj-group></article-categories><title-group><article-title>A collection of INDEL markers for map-based cloning in seven <italic>Arabidopsis</italic> accessions</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Păcurar</surname><given-names>Daniel Ioan</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="author-notes" rid="fn1">†</xref></contrib><contrib contrib-type="author"><name><surname>Păcurar</surname><given-names>Monica Lăcrămioara</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Street</surname><given-names>Nathaniel</given-names></name><xref ref-type="author-notes" rid="fn1">†</xref></contrib><contrib contrib-type="author"><name><surname>Bussell</surname><given-names>John Desmond</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Pop</surname><given-names>Tiberia Ioana</given-names></name><xref ref-type="author-notes" rid="fn1">†</xref></contrib><contrib contrib-type="author"><name><surname>Gutierrez</surname><given-names>Laurent</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="author-notes" rid="fn2">‡</xref></contrib><contrib contrib-type="author"><name><surname>Bellini</surname><given-names>Catherine</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="author-notes" rid="fn1">†</xref></contrib></contrib-group><aff id="aff1"><label>1</label>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden</aff><aff id="aff2"><label>2</label>University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania</aff><aff id="aff3"><label>3</label>Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78026 Versailles Cedex, France</aff><aff id="aff4"><label>4</label>Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009, Australia</aff><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed. E-mail: <email>Daniel.Pacurar@plantphys.umu.se</email></corresp><fn id="fn1"><label>†</label><p>Present address: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden.</p></fn><fn id="fn2"><label>‡</label><p>Present address: Centre de Ressources Régionales en Biologie Moléculaire, Université de Picardie Jules Verne, F-80039 Amiens, France.</p></fn></author-notes><pub-date pub-type="ppub"><month>4</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>25</day><month>1</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>25</day><month>1</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>63</volume><issue>7</issue><fpage>2491</fpage><lpage>2501</lpage><history><date date-type="received"><day>19</day><month>10</month><year>2011</year></date><date date-type="accepted"><day>24</day><month>11</month><year>2011</year></date></history><permissions><copyright-statement>© 2012 The Author(s).</copyright-statement><copyright-year>2012</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p><license-p>This paper is available online free of all access charges (see <ext-link ext-link-type="uri" xlink:href="http://jxb.oxfordjournals.org/open_access.html">http://jxb.oxfordjournals.org/open_access.html</ext-link> for further details)</license-p></license></permissions><abstract><p>The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes <italic>Arabidopsis thaliana</italic> an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg <italic>erecta</italic> (Col-0×L<italic>er</italic>-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and L<italic>er</italic>-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/L<italic>er</italic>-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used <italic>Arabidopsis</italic> accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.</p></abstract><counts><page-count count="11"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>Australie</li><li>France</li><li>Roumanie</li><li>Suède</li></country></list><tree><noCountry><name sortKey="Pop, Tiberia Ioana" sort="Pop, Tiberia Ioana" uniqKey="Pop T" first="Tiberia Ioana" last="Pop">Tiberia Ioana Pop</name><name sortKey="Street, Nathaniel" sort="Street, Nathaniel" uniqKey="Street N" first="Nathaniel" last="Street">Nathaniel Street</name></noCountry><country name="Suède"><noRegion><name sortKey="P Curar, Daniel Ioan" sort="P Curar, Daniel Ioan" uniqKey="P Curar D" first="Daniel Ioan" last="P Curar">Daniel Ioan P Curar</name></noRegion><name sortKey="Bellini, Catherine" sort="Bellini, Catherine" uniqKey="Bellini C" first="Catherine" last="Bellini">Catherine Bellini</name><name sortKey="Bussell, John Desmond" sort="Bussell, John Desmond" uniqKey="Bussell J" first="John Desmond" last="Bussell">John Desmond Bussell</name><name sortKey="Gutierrez, Laurent" sort="Gutierrez, Laurent" uniqKey="Gutierrez L" first="Laurent" last="Gutierrez">Laurent Gutierrez</name><name sortKey="P Curar, Monica L Cr Mioara" sort="P Curar, Monica L Cr Mioara" uniqKey="P Curar M" first="Monica L Cr Mioara" last="P Curar">Monica L Cr Mioara P Curar</name></country><country name="Roumanie"><noRegion><name sortKey="P Curar, Daniel Ioan" sort="P Curar, Daniel Ioan" uniqKey="P Curar D" first="Daniel Ioan" last="P Curar">Daniel Ioan P Curar</name></noRegion><name sortKey="P Curar, Monica L Cr Mioara" sort="P Curar, Monica L Cr Mioara" uniqKey="P Curar M" first="Monica L Cr Mioara" last="P Curar">Monica L Cr Mioara P Curar</name></country><country name="Australie"><noRegion><name sortKey="Bussell, John Desmond" sort="Bussell, John Desmond" uniqKey="Bussell J" first="John Desmond" last="Bussell">John Desmond Bussell</name></noRegion></country><country name="France"><noRegion><name sortKey="Bellini, Catherine" sort="Bellini, Catherine" uniqKey="Bellini C" first="Catherine" last="Bellini">Catherine Bellini</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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