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 : 002429 ( PubMed/Checkpoint ); précédent : 002428; suivant : 002430A 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 [Canada] ; Erin E. Higgins [Canada] ; Joerg Plieske [Allemagne] ; Ralf Wieseke [Allemagne] ; Christine Sidebottom [Canada] ; Yogendra Khedikar [Canada] ; 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 [Canada] ; Federico Iniguez-Luy [Chili] ; Emmanuelle Dyrszka [France] ; Stephen Rae [Belgique] ; Benjamin Stich [Allemagne] ; Rod J. Snowdon [Allemagne] ; Andrew G. Sharpe [Canada] ; Martin W. Ganal [Allemagne] ; Isobel A P. Parkin [Canada]Source :
- TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik [ 1432-2242 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Plant.
- genetics : Brassica napus.
- Chromosome Mapping, Diploidy, Genetic Markers, Genome, Plant, Genotyping Techniques, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Tetraploidy.
Abstract
The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. 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.
DOI: 10.1007/s00122-016-2746-7
PubMed: 27364915
Affiliations:
- Allemagne, Australie, Belgique, Canada, Chili, France, République populaire de Chine, États-Unis
- District de Cologne, Rhénanie-du-Nord-Westphalie
- Cologne
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Snowdon</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.</nlm:affiliation><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 wicri:level="1"><nlm:affiliation>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9</wicri:regionArea><wicri:noRegion>S7N 0W9</wicri:noRegion></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:affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</nlm:affiliation><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>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 wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea><wicri:noRegion>S7N 0X2</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27364915</idno><idno type="pmid">27364915</idno><idno type="doi">10.1007/s00122-016-2746-7</idno><idno type="wicri:Area/PubMed/Corpus">001838</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001838</idno><idno type="wicri:Area/PubMed/Curation">001815</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001815</idno><idno type="wicri:Area/PubMed/Checkpoint">001815</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001815</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">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.</title><author><name sortKey="Clarke, Wayne E" sort="Clarke, Wayne E" uniqKey="Clarke W" first="Wayne E" last="Clarke">Wayne E. Clarke</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea><wicri:noRegion>S7N 0X2</wicri:noRegion></affiliation></author><author><name sortKey="Higgins, Erin E" sort="Higgins, Erin E" uniqKey="Higgins E" first="Erin E" last="Higgins">Erin E. Higgins</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea><wicri:noRegion>S7N 0X2</wicri:noRegion></affiliation></author><author><name sortKey="Plieske, Joerg" sort="Plieske, Joerg" uniqKey="Plieske J" first="Joerg" last="Plieske">Joerg Plieske</name><affiliation wicri:level="1"><nlm:affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</nlm:affiliation><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>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Wieseke, Ralf" sort="Wieseke, Ralf" uniqKey="Wieseke R" first="Ralf" last="Wieseke">Ralf Wieseke</name><affiliation wicri:level="1"><nlm:affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</nlm:affiliation><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>Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Sidebottom, Christine" sort="Sidebottom, Christine" uniqKey="Sidebottom C" first="Christine" last="Sidebottom">Christine Sidebottom</name><affiliation wicri:level="1"><nlm:affiliation>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9</wicri:regionArea><wicri:noRegion>S7N 0W9</wicri:noRegion></affiliation></author><author><name sortKey="Khedikar, Yogendra" sort="Khedikar, Yogendra" uniqKey="Khedikar Y" first="Yogendra" last="Khedikar">Yogendra Khedikar</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea><wicri:noRegion>S7N 0X2</wicri:noRegion></affiliation></author><author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009</wicri:regionArea><wicri:noRegion>6009</wicri:noRegion></affiliation></author><author><name sortKey="Edwards, Dave" sort="Edwards, Dave" uniqKey="Edwards D" first="Dave" last="Edwards">Dave Edwards</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009</wicri:regionArea><wicri:noRegion>6009</wicri:noRegion></affiliation></author><author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name><affiliation wicri:level="1"><nlm:affiliation>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:affiliation><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, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Li, Ruiyuan" sort="Li, Ruiyuan" uniqKey="Li R" first="Ruiyuan" last="Li">Ruiyuan Li</name><affiliation wicri:level="1"><nlm:affiliation>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:affiliation><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, 430070</wicri:regionArea><wicri:noRegion>430070</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="1"><nlm:affiliation>Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA, 92121, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA, 92121</wicri:regionArea><wicri:noRegion>92121</wicri:noRegion></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:affiliation>BIOGEMMA 6, chemin des Panedautes, 31700, Mondonville, France.</nlm:affiliation><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></author><author><name sortKey="Laga, Benjamin" sort="Laga, Benjamin" uniqKey="Laga B" first="Benjamin" last="Laga">Benjamin Laga</name><affiliation wicri:level="1"><nlm:affiliation>Bayer BioScience NV, 9052, Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Bayer BioScience NV, 9052, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Cheung, Wing" sort="Cheung, Wing" uniqKey="Cheung W" first="Wing" last="Cheung">Wing Cheung</name><affiliation wicri:level="1"><nlm:affiliation>DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC, J3B 6X3, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC, J3B 6X3</wicri:regionArea><wicri:noRegion>J3B 6X3</wicri:noRegion></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:affiliation>Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco, Chile.</nlm:affiliation><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:affiliation>Syngenta France SAS, 12 Chemin de l'hobit, B.P. 27, 31790, Saint-Sauveur, France.</nlm:affiliation><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:affiliation>Bayer BioScience NV, 9052, Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Bayer BioScience NV, 9052, Ghent</wicri:regionArea><wicri:noRegion>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:affiliation>Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.</nlm:affiliation><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:affiliation>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.</nlm:affiliation><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 wicri:level="1"><nlm:affiliation>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9</wicri:regionArea><wicri:noRegion>S7N 0W9</wicri:noRegion></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:affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</nlm:affiliation><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>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 wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea><wicri:noRegion>S7N 0X2</wicri:noRegion></affiliation></author></analytic><series><title level="j">TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</title><idno type="eISSN">1432-2242</idno><imprint><date when="2016" type="published">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">The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. 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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27364915</PMID><DateCreated><Year>2016</Year><Month>09</Month><Day>17</Day></DateCreated><DateCompleted><Year>2017</Year><Month>01</Month><Day>05</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-2242</ISSN><JournalIssue CitedMedium="Internet"><Volume>129</Volume><Issue>10</Issue><PubDate><Year>2016</Year><Month>Oct</Month></PubDate></JournalIssue><Title>TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</Title><ISOAbbreviation>Theor. Appl. Genet.</ISOAbbreviation></Journal><ArticleTitle>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.</ArticleTitle><Pagination><MedlinePgn>1887-99</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00122-016-2746-7</ELocationID><Abstract><AbstractText Label="KEY MESSAGE" NlmCategory="CONCLUSIONS">The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Clarke</LastName><ForeName>Wayne E</ForeName><Initials>WE</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Higgins</LastName><ForeName>Erin E</ForeName><Initials>EE</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Plieske</LastName><ForeName>Joerg</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wieseke</LastName><ForeName>Ralf</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sidebottom</LastName><ForeName>Christine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Khedikar</LastName><ForeName>Yogendra</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Batley</LastName><ForeName>Jacqueline</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Edwards</LastName><ForeName>Dave</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Jinling</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Ruiyuan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawley</LastName><ForeName>Cynthia Taylor</ForeName><Initials>CT</Initials><AffiliationInfo><Affiliation>Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA, 92121, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pauquet</LastName><ForeName>Jérôme</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>BIOGEMMA 6, chemin des Panedautes, 31700, Mondonville, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>SYNGENTA France SAS, 346, route des Pasquiers, 84260, Sarrians, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Laga</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Bayer BioScience NV, 9052, Ghent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheung</LastName><ForeName>Wing</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC, J3B 6X3, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iniguez-Luy</LastName><ForeName>Federico</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco, Chile.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dyrszka</LastName><ForeName>Emmanuelle</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Syngenta France SAS, 12 Chemin de l'hobit, B.P. 27, 31790, Saint-Sauveur, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rae</LastName><ForeName>Stephen</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Bayer BioScience NV, 9052, Ghent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stich</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Snowdon</LastName><ForeName>Rod J</ForeName><Initials>RJ</Initials><AffiliationInfo><Affiliation>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sharpe</LastName><ForeName>Andrew G</ForeName><Initials>AG</Initials><AffiliationInfo><Affiliation>National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ganal</LastName><ForeName>Martin W</ForeName><Initials>MW</Initials><AffiliationInfo><Affiliation>TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parkin</LastName><ForeName>Isobel A P</ForeName><Initials>IA</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>06</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Theor Appl Genet</MedlineTA><NlmUniqueID>0145600</NlmUniqueID><ISSNLinking>0040-5752</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, 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napus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="Y">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004171" MajorTopicYN="N">Diploidy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060005" MajorTopicYN="Y">Genotyping Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D057891" MajorTopicYN="N">Tetraploidy</DescriptorName></MeshHeading></MeshHeadingList><CoiStatement>The authors MWG, RW, and JP have competing commercial interests as members of TraitGenetics GmbH which is a company that offers marker development and analysis (including this array) for commercial purposes. This does not alter the authors’ adherence to sharing data.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>04</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>06</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>7</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>7</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>1</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27364915</ArticleId><ArticleId IdType="doi">10.1007/s00122-016-2746-7</ArticleId><ArticleId IdType="pii">10.1007/s00122-016-2746-7</ArticleId><ArticleId IdType="pmc">PMC5025514</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>Belgique</li><li>Canada</li><li>Chili</li><li>France</li><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>District de Cologne</li><li>Rhénanie-du-Nord-Westphalie</li></region><settlement><li>Cologne</li></settlement></list><tree><country name="Canada"><noRegion><name sortKey="Clarke, Wayne E" sort="Clarke, Wayne E" uniqKey="Clarke W" first="Wayne E" last="Clarke">Wayne E. Clarke</name></noRegion><name sortKey="Cheung, Wing" sort="Cheung, Wing" uniqKey="Cheung W" first="Wing" last="Cheung">Wing Cheung</name><name sortKey="Higgins, Erin E" sort="Higgins, Erin E" uniqKey="Higgins E" first="Erin E" last="Higgins">Erin E. Higgins</name><name sortKey="Khedikar, Yogendra" sort="Khedikar, Yogendra" uniqKey="Khedikar Y" first="Yogendra" last="Khedikar">Yogendra Khedikar</name><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><name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G" last="Sharpe">Andrew G. Sharpe</name><name sortKey="Sidebottom, Christine" sort="Sidebottom, Christine" uniqKey="Sidebottom C" first="Christine" last="Sidebottom">Christine Sidebottom</name></country><country name="Allemagne"><noRegion><name sortKey="Plieske, Joerg" sort="Plieske, Joerg" uniqKey="Plieske J" first="Joerg" last="Plieske">Joerg Plieske</name></noRegion><name sortKey="Ganal, Martin W" sort="Ganal, Martin W" uniqKey="Ganal M" first="Martin W" last="Ganal">Martin W. Ganal</name><name sortKey="Snowdon, Rod J" sort="Snowdon, Rod J" uniqKey="Snowdon R" first="Rod J" last="Snowdon">Rod J. Snowdon</name><name sortKey="Stich, Benjamin" sort="Stich, Benjamin" uniqKey="Stich B" first="Benjamin" last="Stich">Benjamin Stich</name><name sortKey="Wieseke, Ralf" sort="Wieseke, Ralf" uniqKey="Wieseke R" first="Ralf" last="Wieseke">Ralf Wieseke</name></country><country name="Australie"><noRegion><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name></noRegion><name sortKey="Edwards, Dave" sort="Edwards, Dave" uniqKey="Edwards D" first="Dave" last="Edwards">Dave Edwards</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name></noRegion><name sortKey="Li, Ruiyuan" sort="Li, Ruiyuan" uniqKey="Li R" first="Ruiyuan" last="Li">Ruiyuan Li</name></country><country name="États-Unis"><noRegion><name sortKey="Lawley, Cynthia Taylor" sort="Lawley, Cynthia Taylor" uniqKey="Lawley C" first="Cynthia Taylor" last="Lawley">Cynthia Taylor Lawley</name></noRegion></country><country name="France"><noRegion><name sortKey="Pauquet, Jerome" sort="Pauquet, Jerome" uniqKey="Pauquet J" first="Jérôme" last="Pauquet">Jérôme Pauquet</name></noRegion><name sortKey="Dyrszka, Emmanuelle" sort="Dyrszka, Emmanuelle" uniqKey="Dyrszka E" first="Emmanuelle" last="Dyrszka">Emmanuelle Dyrszka</name></country><country name="Belgique"><noRegion><name sortKey="Laga, Benjamin" sort="Laga, Benjamin" uniqKey="Laga B" first="Benjamin" last="Laga">Benjamin Laga</name></noRegion><name sortKey="Rae, Stephen" sort="Rae, Stephen" uniqKey="Rae S" first="Stephen" last="Rae">Stephen Rae</name></country><country name="Chili"><noRegion><name sortKey="Iniguez Luy, Federico" sort="Iniguez Luy, Federico" uniqKey="Iniguez Luy F" first="Federico" last="Iniguez-Luy">Federico Iniguez-Luy</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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