Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
Identifieur interne : 001877 ( Ncbi/Curation ); précédent : 001876; suivant : 001878Characterization 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.
Url:
DOI: 10.1111/pbi.12183
PubMed: 24646323
PubMed Central: 4265271
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</nlm:aff>
<country xml:lang="fr">Australie</country>
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<author><name sortKey="Edwards, Keith J" sort="Edwards, Keith J" uniqKey="Edwards K" first="Keith J" last="Edwards">Keith J. Edwards</name>
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<addr-line>Bristol, UK</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Bristol</wicri:regionArea>
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<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>
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<author><name sortKey="Akhunov, Eduard" sort="Akhunov, Eduard" uniqKey="Akhunov E" first="Eduard" last="Akhunov">Eduard Akhunov</name>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Kansas</region>
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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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<addr-line>Manhattan, KS, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Manhattan, KS</wicri:regionArea>
<placeName><region type="state">Kansas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wong, Debbie" sort="Wong, Debbie" uniqKey="Wong D" first="Debbie" last="Wong">Debbie Wong</name>
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</nlm:aff>
<country xml:lang="fr">Australie</country>
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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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<author><name sortKey="Allen, Alexandra" sort="Allen, Alexandra" uniqKey="Allen A" first="Alexandra" last="Allen">Alexandra Allen</name>
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<addr-line>Bristol, UK</addr-line>
</nlm:aff>
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<author><name sortKey="Chao, Shiaoman" sort="Chao, Shiaoman" uniqKey="Chao S" first="Shiaoman" last="Chao">Shiaoman Chao</name>
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<author><name sortKey="Huang, Bevan E" sort="Huang, Bevan E" uniqKey="Huang B" first="Bevan E" last="Huang">Bevan E. Huang</name>
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<author><name sortKey="Maccaferri, Marco" sort="Maccaferri, Marco" uniqKey="Maccaferri M" first="Marco" last="Maccaferri">Marco Maccaferri</name>
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<addr-line>Bologna, Italy</addr-line>
</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Bologna</wicri:regionArea>
</affiliation>
</author>
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</nlm:aff>
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<wicri:regionArea>Bologna</wicri:regionArea>
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<addr-line>Fiorenzuola d'arda, Italy</addr-line>
</nlm:aff>
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</author>
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</nlm:aff>
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<wicri:regionArea>Foggia</wicri:regionArea>
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</author>
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<addr-line>Bristol, UK</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Bristol</wicri:regionArea>
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</author>
<author><name sortKey="Wieseke, Ralf" sort="Wieseke, Ralf" uniqKey="Wieseke R" first="Ralf" last="Wieseke">Ralf Wieseke</name>
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</nlm:aff>
<country xml:lang="fr">Allemagne</country>
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<author><name sortKey="Plieske, Joerg" sort="Plieske, Joerg" uniqKey="Plieske J" first="Joerg" last="Plieske">Joerg Plieske</name>
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</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Gatersleben</wicri:regionArea>
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</author>
<author><name sortKey="Lillemo, Morten" sort="Lillemo, Morten" uniqKey="Lillemo M" first="Morten" last="Lillemo">Morten Lillemo</name>
<affiliation wicri:level="1"><nlm:aff id="au12"><institution>Department of Plant Sciences, Norwegian University of Life Sciences</institution>
<addr-line>Ås, Norway</addr-line>
</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Ås</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mather, Diane" sort="Mather, Diane" uniqKey="Mather D" first="Diane" last="Mather">Diane Mather</name>
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<addr-line>Urrbrae, SA, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
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</nlm:aff>
<country xml:lang="fr">Australie</country>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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</placeName>
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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>
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<addr-line>Manhattan, KS, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<addr-line>Clermont-Ferrand, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
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<addr-line>Clermont-Ferrand, France</addr-line>
</nlm:aff>
<country xml:lang="fr">France</country>
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</author>
<author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name>
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<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>
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</author>
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<addr-line>Davis, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<addr-line>Davis, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Davis, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
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<author><name sortKey="Morell, Matthew" sort="Morell, Matthew" uniqKey="Morell M" first="Matthew" last="Morell">Matthew Morell</name>
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<addr-line>Canberra, ACT, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Canberra, ACT</wicri:regionArea>
<wicri:noRegion>ACT</wicri:noRegion>
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</author>
<author><name sortKey="Dubcovsky, Jorge" sort="Dubcovsky, Jorge" uniqKey="Dubcovsky J" first="Jorge" last="Dubcovsky">Jorge Dubcovsky</name>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Maryland</region>
</placeName>
</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="2"><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>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Mikoulitch, Ivan" sort="Mikoulitch, Ivan" uniqKey="Mikoulitch I" first="Ivan" last="Mikoulitch">Ivan Mikoulitch</name>
<affiliation wicri:level="2"><nlm:aff id="au23"><institution>Illumina Inc.</institution>
<addr-line>Hayward, CA, USA</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Cavanagh, Colin" sort="Cavanagh, Colin" uniqKey="Cavanagh C" first="Colin" last="Cavanagh">Colin Cavanagh</name>
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<addr-line>Canberra, ACT, Australia</addr-line>
</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Canberra, ACT</wicri:regionArea>
<wicri:noRegion>ACT</wicri:noRegion>
</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>
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</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>
<wicri:noRegion>Vic.</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Akhunov, Eduard" sort="Akhunov, Eduard" uniqKey="Akhunov E" first="Eduard" last="Akhunov">Eduard Akhunov</name>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Kansas</region>
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</analytic>
<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>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Akhunov, E" uniqKey="Akhunov E">E Akhunov</name>
</author>
<author><name sortKey="Nicolet, C" uniqKey="Nicolet C">C Nicolet</name>
</author>
<author><name sortKey="Dvorak, J" uniqKey="Dvorak J">J Dvorak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Albrechtsen, A" uniqKey="Albrechtsen A">A Albrechtsen</name>
</author>
<author><name sortKey="Nielsen, Fc" uniqKey="Nielsen F">FC Nielsen</name>
</author>
<author><name sortKey="Nielsen, R" uniqKey="Nielsen R">R Nielsen</name>
</author>
</analytic>
</biblStruct>
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