Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
Identifieur interne : 002B35 ( Pmc/Curation ); précédent : 002B34; suivant : 002B36Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
Auteurs : Shichen Wang [États-Unis] ; Debbie Wong [Australie] ; Kerrie Forrest [Australie] ; Alexandra Allen [Royaume-Uni] ; Shiaoman Chao [États-Unis] ; Bevan E. Huang [Australie] ; Marco Maccaferri [Italie] ; Silvio Salvi [Italie] ; Sara G. Milner [Italie] ; Luigi Cattivelli [Italie] ; Anna M. Mastrangelo [Italie] ; Alex Whan [Australie] ; Stuart Stephen [Australie] ; Gary Barker [Royaume-Uni] ; Ralf Wieseke [Allemagne] ; Joerg Plieske [Allemagne] ; Morten Lillemo [Norvège] ; Diane Mather [Australie] ; Rudi Appels [Australie] ; Rudy Dolferus [Australie] ; Gina Brown-Guedira [États-Unis] ; Abraham Korol [Israël] ; Alina R. Akhunova [États-Unis] ; Catherine Feuillet [France] ; Jerome Salse [France] ; Michele Morgante [Italie] ; Curtis Pozniak [Canada] ; Ming-Cheng Luo [États-Unis] ; Jan Dvorak [États-Unis] ; Matthew Morell [Australie] ; Jorge Dubcovsky [États-Unis] ; Martin Ganal [Allemagne] ; Roberto Tuberosa [Italie] ; Cindy Lawley [États-Unis] ; Ivan Mikoulitch [États-Unis] ; Colin Cavanagh [Australie] ; Keith J. Edwards [Royaume-Uni] ; Matthew Hayden [Australie] ; Eduard Akhunov [États-Unis]Source :
- Plant Biotechnology Journal [ 1467-7644 ] ; 2014.
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
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DOI: 10.1111/pbi.12183
PubMed: 24646323
PubMed Central: 4265271
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array</title>
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<author><name sortKey="Forrest, Kerrie" sort="Forrest, Kerrie" uniqKey="Forrest K" first="Kerrie" last="Forrest">Kerrie Forrest</name>
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<addr-line>Ås, Norway</addr-line>
</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Ås</wicri:regionArea>
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<author><name sortKey="Mather, Diane" sort="Mather, Diane" uniqKey="Mather D" first="Diane" last="Mather">Diane Mather</name>
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<author><name sortKey="Appels, Rudi" sort="Appels, Rudi" uniqKey="Appels R" first="Rudi" last="Appels">Rudi Appels</name>
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<addr-line>Murdoch, WA, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Murdoch, WA</wicri:regionArea>
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<author><name sortKey="Dolferus, Rudy" sort="Dolferus, Rudy" uniqKey="Dolferus R" first="Rudy" last="Dolferus">Rudy Dolferus</name>
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<country xml:lang="fr">Australie</country>
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<author><name sortKey="Brown Guedira, Gina" sort="Brown Guedira, Gina" uniqKey="Brown Guedira G" first="Gina" last="Brown-Guedira">Gina Brown-Guedira</name>
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<addr-line>Raleigh, NC, USA</addr-line>
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<country xml:lang="fr">États-Unis</country>
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<author><name sortKey="Korol, Abraham" sort="Korol, Abraham" uniqKey="Korol A" first="Abraham" last="Korol">Abraham Korol</name>
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<addr-line>Mount Carmel, Haifa, Israel</addr-line>
</nlm:aff>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Mount Carmel, Haifa</wicri:regionArea>
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</author>
<author><name sortKey="Akhunova, Alina R" sort="Akhunova, Alina R" uniqKey="Akhunova A" first="Alina R" last="Akhunova">Alina R. Akhunova</name>
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<addr-line>Manhattan, KS, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Manhattan, KS</wicri:regionArea>
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<author><name sortKey="Feuillet, Catherine" sort="Feuillet, Catherine" uniqKey="Feuillet C" first="Catherine" last="Feuillet">Catherine Feuillet</name>
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<addr-line>Clermont-Ferrand, France</addr-line>
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<country xml:lang="fr">France</country>
<wicri:regionArea>Clermont-Ferrand</wicri:regionArea>
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<author><name sortKey="Salse, Jerome" sort="Salse, Jerome" uniqKey="Salse J" first="Jerome" last="Salse">Jerome Salse</name>
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<addr-line>Clermont-Ferrand, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Clermont-Ferrand</wicri:regionArea>
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</author>
<author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name>
<affiliation wicri:level="1"><nlm:aff id="au19"><institution>Department of Crop and Environmental Sciences, University of Udine, Via delle Scienze</institution>
<addr-line>Udine, Italy</addr-line>
</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Udine</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Pozniak, Curtis" sort="Pozniak, Curtis" uniqKey="Pozniak C" first="Curtis" last="Pozniak">Curtis Pozniak</name>
<affiliation wicri:level="1"><nlm:aff id="au20"><institution>Crop Development Centre and Department of Plant Sciences, University of Saskatchewan</institution>
<addr-line>Saskatoon, SK, Canada</addr-line>
</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Saskatoon, SK</wicri:regionArea>
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<author><name sortKey="Luo, Ming Cheng" sort="Luo, Ming Cheng" uniqKey="Luo M" first="Ming-Cheng" last="Luo">Ming-Cheng Luo</name>
<affiliation wicri:level="1"><nlm:aff id="au21"><institution>Department of Plant Sciences, University of California</institution>
<addr-line>Davis, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Davis, CA</wicri:regionArea>
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</author>
<author><name sortKey="Dvorak, Jan" sort="Dvorak, Jan" uniqKey="Dvorak J" first="Jan" last="Dvorak">Jan Dvorak</name>
<affiliation wicri:level="1"><nlm:aff id="au21"><institution>Department of Plant Sciences, University of California</institution>
<addr-line>Davis, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Davis, CA</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Morell, Matthew" sort="Morell, Matthew" uniqKey="Morell M" first="Matthew" last="Morell">Matthew Morell</name>
<affiliation wicri:level="1"><nlm:aff id="au9"><institution>Commonwealth Scientific and Industrial Research Organization, Plant Industry and Food Futures National Research Flagship</institution>
<addr-line>Canberra, ACT, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Canberra, ACT</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Dubcovsky, Jorge" sort="Dubcovsky, Jorge" uniqKey="Dubcovsky J" first="Jorge" last="Dubcovsky">Jorge Dubcovsky</name>
<affiliation wicri:level="1"><nlm:aff id="au21"><institution>Department of Plant Sciences, University of California</institution>
<addr-line>Davis, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Davis, CA</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="au22"><institution>Howard Hughes Medical Institute</institution>
<addr-line>Chevy Chase, MD, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Chevy Chase, MD</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ganal, Martin" sort="Ganal, Martin" uniqKey="Ganal M" first="Martin" last="Ganal">Martin Ganal</name>
<affiliation wicri:level="1"><nlm:aff id="au10"><institution>TraitGenetics GmbH</institution>
<addr-line>Gatersleben, Germany</addr-line>
</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Gatersleben</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Tuberosa, Roberto" sort="Tuberosa, Roberto" uniqKey="Tuberosa R" first="Roberto" last="Tuberosa">Roberto Tuberosa</name>
<affiliation wicri:level="1"><nlm:aff id="au6"><institution>Department of Agricultural Sciences, University of Bologna</institution>
<addr-line>Bologna, Italy</addr-line>
</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Bologna</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lawley, Cindy" sort="Lawley, Cindy" uniqKey="Lawley C" first="Cindy" last="Lawley">Cindy Lawley</name>
<affiliation wicri:level="1"><nlm:aff id="au23"><institution>Illumina Inc.</institution>
<addr-line>Hayward, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Hayward, CA</wicri:regionArea>
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<author><name sortKey="Mikoulitch, Ivan" sort="Mikoulitch, Ivan" uniqKey="Mikoulitch I" first="Ivan" last="Mikoulitch">Ivan Mikoulitch</name>
<affiliation wicri:level="1"><nlm:aff id="au23"><institution>Illumina Inc.</institution>
<addr-line>Hayward, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Hayward, CA</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Cavanagh, Colin" sort="Cavanagh, Colin" uniqKey="Cavanagh C" first="Colin" last="Cavanagh">Colin Cavanagh</name>
<affiliation wicri:level="1"><nlm:aff id="au9"><institution>Commonwealth Scientific and Industrial Research Organization, Plant Industry and Food Futures National Research Flagship</institution>
<addr-line>Canberra, ACT, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Canberra, ACT</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Edwards, Keith J" sort="Edwards, Keith J" uniqKey="Edwards K" first="Keith J" last="Edwards">Keith J. Edwards</name>
<affiliation wicri:level="1"><nlm:aff id="au3"><institution>School of Biological Sciences, University of Bristol</institution>
<addr-line>Bristol, UK</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Bristol</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Hayden, Matthew" sort="Hayden, Matthew" uniqKey="Hayden M" first="Matthew" last="Hayden">Matthew Hayden</name>
<affiliation wicri:level="1"><nlm:aff id="au2"><institution>Department of Environment and Primary Industry, AgriBioSciences, La Trobe R&D Park</institution>
<addr-line>Bundoora, Vic., Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Bundoora, Vic.</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Akhunov, Eduard" sort="Akhunov, Eduard" uniqKey="Akhunov E" first="Eduard" last="Akhunov">Eduard Akhunov</name>
<affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Plant Pathology, Kansas State University</institution>
<addr-line>Manhattan, KS, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Manhattan, KS</wicri:regionArea>
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<series><title level="j">Plant Biotechnology Journal</title>
<idno type="ISSN">1467-7644</idno>
<idno type="eISSN">1467-7652</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Biotechnol J</journal-id>
<journal-id journal-id-type="iso-abbrev">Plant Biotechnol. J</journal-id>
<journal-id journal-id-type="publisher-id">pbi</journal-id>
<journal-title-group><journal-title>Plant Biotechnology Journal</journal-title>
</journal-title-group>
<issn pub-type="ppub">1467-7644</issn>
<issn pub-type="epub">1467-7652</issn>
<publisher><publisher-name>BlackWell Publishing Ltd</publisher-name>
<publisher-loc>Oxford, UK</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24646323</article-id>
<article-id pub-id-type="pmc">4265271</article-id>
<article-id pub-id-type="doi">10.1111/pbi.12183</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Shichen</given-names>
</name>
<xref ref-type="aff" rid="au1">1</xref>
<xref ref-type="corresp" rid="cor3">‡</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wong</surname>
<given-names>Debbie</given-names>
</name>
<xref ref-type="aff" rid="au2">2</xref>
<xref ref-type="corresp" rid="cor3">‡</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Forrest</surname>
<given-names>Kerrie</given-names>
</name>
<xref ref-type="aff" rid="au2">2</xref>
<xref ref-type="corresp" rid="cor3">‡</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Allen</surname>
<given-names>Alexandra</given-names>
</name>
<xref ref-type="aff" rid="au3">3</xref>
<xref ref-type="corresp" rid="cor3">‡</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chao</surname>
<given-names>Shiaoman</given-names>
</name>
<xref ref-type="aff" rid="au4">4</xref>
<xref ref-type="corresp" rid="cor3">‡</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Huang</surname>
<given-names>Bevan E</given-names>
</name>
<xref ref-type="aff" rid="au5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Maccaferri</surname>
<given-names>Marco</given-names>
</name>
<xref ref-type="aff" rid="au6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Salvi</surname>
<given-names>Silvio</given-names>
</name>
<xref ref-type="aff" rid="au6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Milner</surname>
<given-names>Sara G</given-names>
</name>
<xref ref-type="aff" rid="au6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cattivelli</surname>
<given-names>Luigi</given-names>
</name>
<xref ref-type="aff" rid="au7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mastrangelo</surname>
<given-names>Anna M</given-names>
</name>
<xref ref-type="aff" rid="au8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Whan</surname>
<given-names>Alex</given-names>
</name>
<xref ref-type="aff" rid="au9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stephen</surname>
<given-names>Stuart</given-names>
</name>
<xref ref-type="aff" rid="au9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Barker</surname>
<given-names>Gary</given-names>
</name>
<xref ref-type="aff" rid="au3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wieseke</surname>
<given-names>Ralf</given-names>
</name>
<xref ref-type="aff" rid="au10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Plieske</surname>
<given-names>Joerg</given-names>
</name>
<xref ref-type="aff" rid="au10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>International Wheat Genome Sequencing Consortium</surname>
<given-names></given-names>
</name>
<xref ref-type="aff" rid="au11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lillemo</surname>
<given-names>Morten</given-names>
</name>
<xref ref-type="aff" rid="au12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mather</surname>
<given-names>Diane</given-names>
</name>
<xref ref-type="aff" rid="au13">13</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Appels</surname>
<given-names>Rudi</given-names>
</name>
<xref ref-type="aff" rid="au14">14</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dolferus</surname>
<given-names>Rudy</given-names>
</name>
<xref ref-type="aff" rid="au9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Brown-Guedira</surname>
<given-names>Gina</given-names>
</name>
<xref ref-type="aff" rid="au15">15</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Korol</surname>
<given-names>Abraham</given-names>
</name>
<xref ref-type="aff" rid="au16">16</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Akhunova</surname>
<given-names>Alina R</given-names>
</name>
<xref ref-type="aff" rid="au17">17</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Feuillet</surname>
<given-names>Catherine</given-names>
</name>
<xref ref-type="aff" rid="au18">18</xref>
<xref ref-type="corresp" rid="cor2">†</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Salse</surname>
<given-names>Jerome</given-names>
</name>
<xref ref-type="aff" rid="au18">18</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Morgante</surname>
<given-names>Michele</given-names>
</name>
<xref ref-type="aff" rid="au19">19</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pozniak</surname>
<given-names>Curtis</given-names>
</name>
<xref ref-type="aff" rid="au20">20</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Luo</surname>
<given-names>Ming-Cheng</given-names>
</name>
<xref ref-type="aff" rid="au21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dvorak</surname>
<given-names>Jan</given-names>
</name>
<xref ref-type="aff" rid="au21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Morell</surname>
<given-names>Matthew</given-names>
</name>
<xref ref-type="aff" rid="au9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dubcovsky</surname>
<given-names>Jorge</given-names>
</name>
<xref ref-type="aff" rid="au21">21</xref>
<xref ref-type="aff" rid="au22">22</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ganal</surname>
<given-names>Martin</given-names>
</name>
<xref ref-type="aff" rid="au10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tuberosa</surname>
<given-names>Roberto</given-names>
</name>
<xref ref-type="aff" rid="au6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lawley</surname>
<given-names>Cindy</given-names>
</name>
<xref ref-type="aff" rid="au23">23</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mikoulitch</surname>
<given-names>Ivan</given-names>
</name>
<xref ref-type="aff" rid="au23">23</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cavanagh</surname>
<given-names>Colin</given-names>
</name>
<xref ref-type="aff" rid="au9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Edwards</surname>
<given-names>Keith J</given-names>
</name>
<xref ref-type="aff" rid="au3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hayden</surname>
<given-names>Matthew</given-names>
</name>
<xref ref-type="aff" rid="au2">2</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Akhunov</surname>
<given-names>Eduard</given-names>
</name>
<xref ref-type="aff" rid="au1">1</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<aff id="au1"><label>1</label>
<institution>Department of Plant Pathology, Kansas State University</institution>
<addr-line>Manhattan, KS, USA</addr-line>
</aff>
<aff id="au2"><label>2</label>
<institution>Department of Environment and Primary Industry, AgriBioSciences, La Trobe R&D Park</institution>
<addr-line>Bundoora, Vic., Australia</addr-line>
</aff>
<aff id="au3"><label>3</label>
<institution>School of Biological Sciences, University of Bristol</institution>
<addr-line>Bristol, UK</addr-line>
</aff>
<aff id="au4"><label>4</label>
<institution>US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory</institution>
<addr-line>Fargo, ND, USA</addr-line>
</aff>
<aff id="au5"><label>5</label>
<institution>Commonwealth Scientific and Industrial Research Organization, Computational Informatics and Food Futures National Research Flagship</institution>
<addr-line>Dutton Park, Qld, Australia</addr-line>
</aff>
<aff id="au6"><label>6</label>
<institution>Department of Agricultural Sciences, University of Bologna</institution>
<addr-line>Bologna, Italy</addr-line>
</aff>
<aff id="au7"><label>7</label>
<institution>Consiglio per la Ricerca e la sperimentazione in Agricoltura, Genomics Research Centre</institution>
<addr-line>Fiorenzuola d'arda, Italy</addr-line>
</aff>
<aff id="au8"><label>8</label>
<institution>Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre</institution>
<addr-line>Foggia, Italy</addr-line>
</aff>
<aff id="au9"><label>9</label>
<institution>Commonwealth Scientific and Industrial Research Organization, Plant Industry and Food Futures National Research Flagship</institution>
<addr-line>Canberra, ACT, Australia</addr-line>
</aff>
<aff id="au10"><label>10</label>
<institution>TraitGenetics GmbH</institution>
<addr-line>Gatersleben, Germany</addr-line>
</aff>
<aff id="au11"><label>11</label>
<institution>IWGSC</institution>
<addr-line>Bethesda, MD, USA</addr-line>
</aff>
<aff id="au12"><label>12</label>
<institution>Department of Plant Sciences, Norwegian University of Life Sciences</institution>
<addr-line>Ås, Norway</addr-line>
</aff>
<aff id="au13"><label>13</label>
<institution>Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide</institution>
<addr-line>Urrbrae, SA, Australia</addr-line>
</aff>
<aff id="au14"><label>14</label>
<institution>Murdoch University</institution>
<addr-line>Murdoch, WA, Australia</addr-line>
</aff>
<aff id="au15"><label>15</label>
<institution>US Department of Agriculture–Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory</institution>
<addr-line>Raleigh, NC, USA</addr-line>
</aff>
<aff id="au16"><label>16</label>
<institution>Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa</institution>
<addr-line>Mount Carmel, Haifa, Israel</addr-line>
</aff>
<aff id="au17"><label>17</label>
<institution>K-State Integrated Genomics Facility, Kansas State University</institution>
<addr-line>Manhattan, KS, USA</addr-line>
</aff>
<aff id="au18"><label>18</label>
<institution>INRA – Université Blaise Pascal, UMR 1095, Genetics Diversity and Ecophysiology of Cereals</institution>
<addr-line>Clermont-Ferrand, France</addr-line>
</aff>
<aff id="au19"><label>19</label>
<institution>Department of Crop and Environmental Sciences, University of Udine, Via delle Scienze</institution>
<addr-line>Udine, Italy</addr-line>
</aff>
<aff id="au20"><label>20</label>
<institution>Crop Development Centre and Department of Plant Sciences, University of Saskatchewan</institution>
<addr-line>Saskatoon, SK, Canada</addr-line>
</aff>
<aff id="au21"><label>21</label>
<institution>Department of Plant Sciences, University of California</institution>
<addr-line>Davis, CA, USA</addr-line>
</aff>
<aff id="au22"><label>22</label>
<institution>Howard Hughes Medical Institute</institution>
<addr-line>Chevy Chase, MD, USA</addr-line>
</aff>
<aff id="au23"><label>23</label>
<institution>Illumina Inc.</institution>
<addr-line>Hayward, CA, USA</addr-line>
</aff>
</contrib-group>
<author-notes><corresp id="cor1">* <italic>Correspondence</italic>
(Tel +61 3 9032 7084; fax +61 3 9032 7000; email <email>matthew.hayden@dpi.vic.gov.au</email>
) and (Tel 785 532 1342; fax 785 532 5692; email <email>eakhunov@ksu.edu</email>
)
</corresp>
<corresp id="cor2">† Present address: Bayer, Research & Development, 3500 Paramount Parkway, Morrisville, NC, 27560, USA.
</corresp>
<corresp id="cor3">‡ These authors made equal contribution.
</corresp>
<fn><p>Accession numbers: SRX191136</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>8</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>20</day>
<month>3</month>
<year>2014</year>
</pub-date>
<volume>12</volume>
<issue>6</issue>
<fpage>787</fpage>
<lpage>796</lpage>
<history><date date-type="received"><day>29</day>
<month>10</month>
<year>2013</year>
</date>
<date date-type="rev-recd"><day>29</day>
<month>1</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>05</day>
<month>2</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© 2014 The Authors <italic>Plant Biotechnology Journal</italic>
published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.</p>
</abstract>
<kwd-group><kwd>single nucleotide polymorphism</kwd>
<kwd>polyploid wheat</kwd>
<kwd>wheat iSelect array</kwd>
<kwd>genotyping</kwd>
<kwd>high-density map</kwd>
<kwd>genetic diversity</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
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