Insertion site‐based polymorphism markers open new perspectives for genome saturation and marker‐assisted selection in wheat
Identifieur interne : 001042 ( Istex/Corpus ); précédent : 001041; suivant : 001043Insertion site‐based polymorphism markers open new perspectives for genome saturation and marker‐assisted selection in wheat
Auteurs : Etienne Paux ; Sébastien Faure ; Frédéric Choulet ; Delphine Roger ; Valérie Gauthier ; Jean-Pierre Martinant ; Pierre Sourdille ; François Balfourier ; Marie-Christine Le Paslier ; Aurélie Chauveau ; Mehmet Cakir ; Béatrice Gandon ; Catherine FeuilletSource :
- Plant Biotechnology Journal [ 1467-7644 ] ; 2010-02.
English descriptors
- KwdEn :
- Allele, Amplicon, Aneuploid, Anking, Appl, Assay, Biol, Biosystems, Biotechnology, Blackwell publishing, Bread wheat, Chinese spring, Chinese spring renan, Chromosome, Common wheat, Context sequence, Context sequences, Courtot, Courtot chinese spring, Curve analysis, Data points, Deletion, Deletion lines, Detection methods, Etienne, Etienne paux, European lines, Feuillet, Genet, Genetic, Genetic diversity, Genetic maps, Genetics, Genome, Genome saturation, Genomic, Genotype, Genotyping, Goldengate, Gupta, Hexaploid, Hexaploid wheat, High density, High level, Illumina, Illumina beadarray technology, Illumina goldengate assay, Inra, Inra journal compilation, Insertion, Insertion polymorphism, Isbp, Isbp markers, Isbpfinder, Isbps, Junction, Locus, Maize, Marker, Molecular markers, Multiplex system, Mutation, Paux, Plant biotechnology journal, Plant physiol, Polymorphic markers, Polymorphism, Presence absence, Presence absence polymorphism, Primer, Programme, Query, Renan, Saintenac, Same time, Sequence polymorphism, Sequencing, Snapshot, Snp, Sourdille, Success rate, Target loci, Theor, Throughput, Transposable, Transposable elements, Triticum aestivum, Unpublished data, Uorescence, Wheat, Wheat genome, Wheat lines, Worldwide bread wheat core collection.
- Teeft :
- Allele, Amplicon, Aneuploid, Anking, Appl, Assay, Biol, Biosystems, Biotechnology, Blackwell publishing, Bread wheat, Chinese spring, Chinese spring renan, Chromosome, Common wheat, Context sequence, Context sequences, Courtot, Courtot chinese spring, Curve analysis, Data points, Deletion, Deletion lines, Detection methods, Etienne, Etienne paux, European lines, Feuillet, Genet, Genetic, Genetic diversity, Genetic maps, Genetics, Genome, Genome saturation, Genomic, Genotype, Genotyping, Goldengate, Gupta, Hexaploid, Hexaploid wheat, High density, High level, Illumina, Illumina beadarray technology, Illumina goldengate assay, Inra, Inra journal compilation, Insertion, Insertion polymorphism, Isbp, Isbp markers, Isbpfinder, Isbps, Junction, Locus, Maize, Marker, Molecular markers, Multiplex system, Mutation, Paux, Plant biotechnology journal, Plant physiol, Polymorphic markers, Polymorphism, Presence absence, Presence absence polymorphism, Primer, Programme, Query, Renan, Saintenac, Same time, Sequence polymorphism, Sequencing, Snapshot, Snp, Sourdille, Success rate, Target loci, Theor, Throughput, Transposable, Transposable elements, Triticum aestivum, Unpublished data, Uorescence, Wheat, Wheat genome, Wheat lines, Worldwide bread wheat core collection.
Abstract
In wheat, the deployment of marker‐assisted selection has long been hampered by the lack of markers compatible with high‐throughput cost‐effective genotyping techniques. Recently, insertion site‐based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high‐throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot® Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP‐derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost‐effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker‐assisted selection.
Url:
DOI: 10.1111/j.1467-7652.2009.00477.x
Links to Exploration step
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<front><div type="abstract" xml:lang="en">In wheat, the deployment of marker‐assisted selection has long been hampered by the lack of markers compatible with high‐throughput cost‐effective genotyping techniques. Recently, insertion site‐based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high‐throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot® Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP‐derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost‐effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker‐assisted selection.</div>
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<abstract>In wheat, the deployment of marker‐assisted selection has long been hampered by the lack of markers compatible with high‐throughput cost‐effective genotyping techniques. Recently, insertion site‐based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high‐throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot® Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP‐derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost‐effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker‐assisted selection.</abstract>
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<author xml:id="author-0000" role="corresp"><persName><forename type="first">Etienne</forename>
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<note type="foot">
These authors contributed equally to this work.</note>
<affiliation>* Correspondence (fax +33 473 62 44 53; e‐mail etienne.paux@clermont.inra.fr)</affiliation>
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<author xml:id="author-0001"><persName><forename type="first">Sébastien</forename>
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<affiliation>Note: † † These authors contributed equally to this work.</affiliation>
<note type="foot">
Current address: Genetics & Genomics in Cereals, BIOGEMMA, 8 rue des Frères Lumière, 63028 Clermont Ferrand cedex 2, France.</note>
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<author xml:id="author-0002"><persName><forename type="first">Frédéric</forename>
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<p>In wheat, the deployment of marker‐assisted selection has long been hampered by the lack of markers compatible with high‐throughput cost‐effective genotyping techniques. Recently, insertion site‐based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high‐throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, <hi rend="italic">IsbpFinder,</hi>
for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot<hi rend="superscript">®</hi>
Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP‐derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost‐effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker‐assisted selection.</p>
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*
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(fax +33 473 62 44 53; e‐mail <email>etienne.paux@clermont.inra.fr</email>
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<contentMeta><unparsedEditorialHistory>Received 17 July 2009; revised 15 October 2009; accepted 15 October 2009.</unparsedEditorialHistory>
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<titleGroup><title type="main">Insertion site‐based polymorphism markers open new perspectives for genome saturation and marker‐assisted selection in wheat</title>
<title type="shortAuthors"><i>Etienne Paux</i>
et al.</title>
<title type="short">ISBPs: new markers for wheat breeding</title>
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<supportingInformation><p><b>Table S1</b>
List of 157 sequenced ISBP markers, with sequence of origin and primers used for PCR amplification.</p>
<p><b>Table S2</b>
List of 25 ISBPs and 53 ISBP‐derived SNPs genotyped on Illumina platform. Each marker is associated with the name of the corresponding ISBP, the type of polymorphism (presence/absence or SNP), the design score, the context sequence as well as the ASO A, ASO B and LSO primers.</p>
<p><b>Table S3</b>
List of 46 European and 46 Australian wheat lines.</p>
<p>Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.</p>
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<p>In wheat, the deployment of marker‐assisted selection has long been hampered by the lack of markers compatible with high‐throughput cost‐effective genotyping techniques. Recently, insertion site‐based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high‐throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, <i>IsbpFinder,</i>
for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot<sup>®</sup>
Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP‐derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost‐effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker‐assisted selection.</p>
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These authors contributed equally to this work.</p>
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Current address: Genetics & Genomics in Cereals, BIOGEMMA, 8 rue des Frères Lumière, 63028 Clermont Ferrand cedex 2, France.</p>
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<abstract lang="en">In wheat, the deployment of marker‐assisted selection has long been hampered by the lack of markers compatible with high‐throughput cost‐effective genotyping techniques. Recently, insertion site‐based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high‐throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot® Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP‐derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost‐effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker‐assisted selection.</abstract>
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<note type="content"> Table S1 List of 157 sequenced ISBP markers, with sequence of origin and primers used for PCR amplification. Table S2 List of 25 ISBPs and 53 ISBP‐derived SNPs genotyped on Illumina platform. Each marker is associated with the name of the corresponding ISBP, the type of polymorphism (presence/absence or SNP), the design score, the context sequence as well as the ASO A, ASO B and LSO primers. Table S3 List of 46 European and 46 Australian wheat lines. Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Table S1 List of 157 sequenced ISBP markers, with sequence of origin and primers used for PCR amplification. Table S2 List of 25 ISBPs and 53 ISBP‐derived SNPs genotyped on Illumina platform. Each marker is associated with the name of the corresponding ISBP, the type of polymorphism (presence/absence or SNP), the design score, the context sequence as well as the ASO A, ASO B and LSO primers. Table S3 List of 46 European and 46 Australian wheat lines. Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Table S1 List of 157 sequenced ISBP markers, with sequence of origin and primers used for PCR amplification. Table S2 List of 25 ISBPs and 53 ISBP‐derived SNPs genotyped on Illumina platform. Each marker is associated with the name of the corresponding ISBP, the type of polymorphism (presence/absence or SNP), the design score, the context sequence as well as the ASO A, ASO B and LSO primers. Table S3 List of 46 European and 46 Australian wheat lines. Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Table S1 List of 157 sequenced ISBP markers, with sequence of origin and primers used for PCR amplification. Table S2 List of 25 ISBPs and 53 ISBP‐derived SNPs genotyped on Illumina platform. Each marker is associated with the name of the corresponding ISBP, the type of polymorphism (presence/absence or SNP), the design score, the context sequence as well as the ASO A, ASO B and LSO primers. Table S3 List of 46 European and 46 Australian wheat lines. Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.Supporting Info Item: Supporting info item - </note>
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