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A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

Identifieur interne : 002467 ( Main/Exploration ); précédent : 002466; suivant : 002468

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

Auteurs : Wayne E. Clarke ; Erin E. Higgins ; Joerg Plieske [Allemagne] ; Ralf Wieseke [Allemagne] ; Christine Sidebottom ; Yogendra Khedikar ; Jacqueline Batley [Australie] ; Dave Edwards [Australie] ; Jinling Meng [République populaire de Chine] ; Ruiyuan Li [République populaire de Chine] ; Cynthia Taylor Lawley [États-Unis] ; Jérôme Pauquet [France] ; Benjamin Laga [Belgique] ; Wing Cheung ; Federico Iniguez-Luy [Chili] ; Emmanuelle Dyrszka [France] ; Stephen Rae [Belgique] ; Benjamin Stich [Allemagne] ; Rod J. Snowdon [Allemagne] ; Andrew G. Sharpe ; Martin W. Ganal [Allemagne] ; Isobel A. P. Parkin

Source :

RBID : PMC:5025514

Descripteurs français

English descriptors

Abstract

<bold>Key message</bold>

TheBrassica napusIllumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploidB. napusand its progenitor diploid genomes.

Abstract

A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.

Electronic supplementary material

The online version of this article (doi:10.1007/s00122-016-2746-7) contains supplementary material, which is available to authorized users.


Url:
DOI: 10.1007/s00122-016-2746-7
PubMed: 27364915
PubMed Central: 5025514


Affiliations:


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Le document en format XML

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<nlm:aff id="Aff5">National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan</wicri:regionArea>
<wicri:noRegion>Wuhan</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Lawley, Cynthia Taylor" sort="Lawley, Cynthia Taylor" uniqKey="Lawley C" first="Cynthia Taylor" last="Lawley">Cynthia Taylor Lawley</name>
<affiliation wicri:level="2">
<nlm:aff id="Aff6">Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>Illumina, Inc., 9885 Towne Centre Drive, San Diego</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Pauquet, Jerome" sort="Pauquet, Jerome" uniqKey="Pauquet J" first="Jérôme" last="Pauquet">Jérôme Pauquet</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff7">BIOGEMMA 6, chemin des Panedautes, 31700 Mondonville, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>BIOGEMMA 6, chemin des Panedautes, 31700 Mondonville</wicri:regionArea>
<wicri:noRegion>31700 Mondonville</wicri:noRegion>
<wicri:noRegion>31700 Mondonville</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="Aff13">SYNGENTA France SAS, 346, route des Pasquiers, 84260 Sarrians, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>SYNGENTA France SAS, 346, route des Pasquiers, 84260 Sarrians</wicri:regionArea>
<wicri:noRegion>84260 Sarrians</wicri:noRegion>
<wicri:noRegion>84260 Sarrians</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Laga, Benjamin" sort="Laga, Benjamin" uniqKey="Laga B" first="Benjamin" last="Laga">Benjamin Laga</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff8">Bayer BioScience NV, 9052 Ghent, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Bayer BioScience NV, 9052 Ghent</wicri:regionArea>
<wicri:noRegion>9052 Ghent</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Cheung, Wing" sort="Cheung, Wing" uniqKey="Cheung W" first="Wing" last="Cheung">Wing Cheung</name>
<affiliation>
<nlm:aff id="Aff9">DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC J3B 6X3 Canada</nlm:aff>
<wicri:noCountry code="subfield">QC J3B 6X3 Canada</wicri:noCountry>
</affiliation>
</author>
<author>
<name sortKey="Iniguez Luy, Federico" sort="Iniguez Luy, Federico" uniqKey="Iniguez Luy F" first="Federico" last="Iniguez-Luy">Federico Iniguez-Luy</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff10">Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco, Chile</nlm:aff>
<country xml:lang="fr">Chili</country>
<wicri:regionArea>Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco</wicri:regionArea>
<wicri:noRegion>Temuco</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Dyrszka, Emmanuelle" sort="Dyrszka, Emmanuelle" uniqKey="Dyrszka E" first="Emmanuelle" last="Dyrszka">Emmanuelle Dyrszka</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff11">Syngenta France SAS, 12 Chemin de l’hobit, B.P. 27, 31790 Saint-Sauveur, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Syngenta France SAS, 12 Chemin de l’hobit, B.P. 27, 31790 Saint-Sauveur</wicri:regionArea>
<wicri:noRegion>31790 Saint-Sauveur</wicri:noRegion>
<wicri:noRegion>31790 Saint-Sauveur</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Rae, Stephen" sort="Rae, Stephen" uniqKey="Rae S" first="Stephen" last="Rae">Stephen Rae</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff8">Bayer BioScience NV, 9052 Ghent, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Bayer BioScience NV, 9052 Ghent</wicri:regionArea>
<wicri:noRegion>9052 Ghent</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Stich, Benjamin" sort="Stich, Benjamin" uniqKey="Stich B" first="Benjamin" last="Stich">Benjamin Stich</name>
<affiliation wicri:level="3">
<nlm:aff id="Aff12">Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region>
<region type="district" nuts="2">District de Cologne</region>
<settlement type="city">Cologne</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Snowdon, Rod J" sort="Snowdon, Rod J" uniqKey="Snowdon R" first="Rod J." last="Snowdon">Rod J. Snowdon</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff14">Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen</wicri:regionArea>
<wicri:noRegion>Giessen</wicri:noRegion>
<wicri:noRegion>Giessen</wicri:noRegion>
<wicri:noRegion>Giessen</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G." last="Sharpe">Andrew G. Sharpe</name>
<affiliation>
<nlm:aff id="Aff3">National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9 Canada</nlm:aff>
<wicri:noCountry code="subfield">S7N 0W9 Canada</wicri:noCountry>
</affiliation>
</author>
<author>
<name sortKey="Ganal, Martin W" sort="Ganal, Martin W" uniqKey="Ganal M" first="Martin W." last="Ganal">Martin W. Ganal</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff2">TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466 Gatersleben, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466 Gatersleben</wicri:regionArea>
<wicri:noRegion>06466 Gatersleben</wicri:noRegion>
<wicri:noRegion>06466 Gatersleben</wicri:noRegion>
<wicri:noRegion>06466 Gatersleben</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name>
<affiliation>
<nlm:aff id="Aff1">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada</nlm:aff>
<wicri:noCountry code="subfield">SK S7N 0X2 Canada</wicri:noCountry>
</affiliation>
</author>
</analytic>
<series>
<title level="j">TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik</title>
<idno type="ISSN">0040-5752</idno>
<idno type="eISSN">1432-2242</idno>
<imprint>
<date when="2016">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="KwdEn" xml:lang="en">
<term>Brassica napus (genetics)</term>
<term>Chromosome Mapping</term>
<term>DNA, Plant (genetics)</term>
<term>Diploidy</term>
<term>Genetic Markers</term>
<term>Genome, Plant</term>
<term>Genotyping Techniques</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Sequence Analysis, DNA</term>
<term>Tetraploidy</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>ADN des plantes (génétique)</term>
<term>Analyse de séquence d'ADN</term>
<term>Brassica napus (génétique)</term>
<term>Cartographie chromosomique</term>
<term>Diploïdie</term>
<term>Génome végétal</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Techniques de génotypage</term>
<term>Tétraploïdie</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>DNA, Plant</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Brassica napus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>ADN des plantes</term>
<term>Brassica napus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Chromosome Mapping</term>
<term>Diploidy</term>
<term>Genetic Markers</term>
<term>Genome, Plant</term>
<term>Genotyping Techniques</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Sequence Analysis, DNA</term>
<term>Tetraploidy</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de séquence d'ADN</term>
<term>Cartographie chromosomique</term>
<term>Diploïdie</term>
<term>Génome végétal</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Techniques de génotypage</term>
<term>Tétraploïdie</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<sec>
<title>
<bold>Key message</bold>
</title>
<p>
<bold>The</bold>
<bold>
<italic>Brassica napus</italic>
</bold>
<bold>Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid</bold>
<bold>
<italic>B. napus</italic>
</bold>
<bold>and its progenitor diploid genomes.</bold>
</p>
</sec>
<sec>
<title>Abstract</title>
<p>A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid
<italic>Brassica napus</italic>
. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of
<italic>B. napus</italic>
material. This genome specificity was supported by the analysis of the diploid ancestors of
<italic>B. napus,</italic>
whereby 26,504 and 29,720 markers were scorable in
<italic>B. oleracea</italic>
and
<italic>B. rapa</italic>
, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid
<italic>B. napus</italic>
population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the
<italic>B. napus</italic>
nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in
<italic>B. napus</italic>
and its progenitor genomes.</p>
</sec>
<sec>
<title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1007/s00122-016-2746-7) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
<back>
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