A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.
Identifieur interne : 002826 ( Main/Exploration ); précédent : 002825; suivant : 002827A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.
Auteurs : A. Geraldes [Canada] ; S P Difazio ; G T Slavov ; P. Ranjan ; W. Muchero ; J. Hannemann ; L E Gunter ; A M Wymore ; C J Grassa ; N. Farzaneh ; I. Porth ; A D Mckown ; O. Skyba ; E. Li ; M. Fujita ; J. Klápšt ; J. Martin ; W. Schackwitz ; C. Pennacchio ; D. Rokhsar ; M C Friedmann ; G O Wasteneys ; R D Guy ; Y A El-Kassaby ; S D Mansfield ; Q C B. Cronk ; J. Ehlting ; C J Douglas ; G A TuskanSource :
- Molecular ecology resources [ 1755-0998 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Populus.
- méthodes : Séquençage par oligonucléotides en batterie.
- classification : Cartographie chromosomique, Génotype, Polymorphisme de nucléotide simple, Populus.
English descriptors
- KwdEn :
- MESH :
- classification : Populus.
- genetics : Populus.
- methods : Oligonucleotide Array Sequence Analysis.
- Chromosome Mapping, Genotype, Polymorphism, Single Nucleotide.
Abstract
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.
DOI: 10.1111/1755-0998.12056
PubMed: 23311503
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Geraldes</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. geraldes@mail.ubc.ca</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Difazio, S P" sort="Difazio, S P" uniqKey="Difazio S" first="S P" last="Difazio">S P Difazio</name></author><author><name sortKey="Slavov, G T" sort="Slavov, G T" uniqKey="Slavov G" first="G T" last="Slavov">G T Slavov</name></author><author><name sortKey="Ranjan, P" sort="Ranjan, P" uniqKey="Ranjan P" first="P" last="Ranjan">P. Ranjan</name></author><author><name sortKey="Muchero, W" sort="Muchero, W" uniqKey="Muchero W" first="W" last="Muchero">W. Muchero</name></author><author><name sortKey="Hannemann, J" sort="Hannemann, J" uniqKey="Hannemann J" first="J" last="Hannemann">J. Hannemann</name></author><author><name sortKey="Gunter, L E" sort="Gunter, L E" uniqKey="Gunter L" first="L E" last="Gunter">L E Gunter</name></author><author><name sortKey="Wymore, A M" sort="Wymore, A M" uniqKey="Wymore A" first="A M" last="Wymore">A M Wymore</name></author><author><name sortKey="Grassa, C J" sort="Grassa, C J" uniqKey="Grassa C" first="C J" last="Grassa">C J Grassa</name></author><author><name sortKey="Farzaneh, N" sort="Farzaneh, N" uniqKey="Farzaneh N" first="N" last="Farzaneh">N. Farzaneh</name></author><author><name sortKey="Porth, I" sort="Porth, I" uniqKey="Porth I" first="I" last="Porth">I. Porth</name></author><author><name sortKey="Mckown, A D" sort="Mckown, A D" uniqKey="Mckown A" first="A D" last="Mckown">A D Mckown</name></author><author><name sortKey="Skyba, O" sort="Skyba, O" uniqKey="Skyba O" first="O" last="Skyba">O. Skyba</name></author><author><name sortKey="Li, E" sort="Li, E" uniqKey="Li E" first="E" last="Li">E. Li</name></author><author><name sortKey="Fujita, M" sort="Fujita, M" uniqKey="Fujita M" first="M" last="Fujita">M. Fujita</name></author><author><name sortKey="Klapst, J" sort="Klapst, J" uniqKey="Klapst J" first="J" last="Klápšt">J. Klápšt</name></author><author><name sortKey="Martin, J" sort="Martin, J" uniqKey="Martin J" first="J" last="Martin">J. Martin</name></author><author><name sortKey="Schackwitz, W" sort="Schackwitz, W" uniqKey="Schackwitz W" first="W" last="Schackwitz">W. Schackwitz</name></author><author><name sortKey="Pennacchio, C" sort="Pennacchio, C" uniqKey="Pennacchio C" first="C" last="Pennacchio">C. Pennacchio</name></author><author><name sortKey="Rokhsar, D" sort="Rokhsar, D" uniqKey="Rokhsar D" first="D" last="Rokhsar">D. Rokhsar</name></author><author><name sortKey="Friedmann, M C" sort="Friedmann, M C" uniqKey="Friedmann M" first="M C" last="Friedmann">M C Friedmann</name></author><author><name sortKey="Wasteneys, G O" sort="Wasteneys, G O" uniqKey="Wasteneys G" first="G O" last="Wasteneys">G O Wasteneys</name></author><author><name sortKey="Guy, R D" sort="Guy, R D" uniqKey="Guy R" first="R D" last="Guy">R D Guy</name></author><author><name sortKey="El Kassaby, Y A" sort="El Kassaby, Y A" uniqKey="El Kassaby Y" first="Y A" last="El-Kassaby">Y A El-Kassaby</name></author><author><name sortKey="Mansfield, S D" sort="Mansfield, S D" uniqKey="Mansfield S" first="S D" last="Mansfield">S D Mansfield</name></author><author><name sortKey="Cronk, Q C B" sort="Cronk, Q C B" uniqKey="Cronk Q" first="Q C B" last="Cronk">Q C B. Cronk</name></author><author><name sortKey="Ehlting, J" sort="Ehlting, J" uniqKey="Ehlting J" first="J" last="Ehlting">J. Ehlting</name></author><author><name sortKey="Douglas, C J" sort="Douglas, C J" uniqKey="Douglas C" first="C J" last="Douglas">C J Douglas</name></author><author><name sortKey="Tuskan, G A" sort="Tuskan, G A" uniqKey="Tuskan G" first="G A" last="Tuskan">G A Tuskan</name></author></analytic><series><title level="j">Molecular ecology resources</title><idno type="eISSN">1755-0998</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping (MeSH)</term><term>Genotype (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie chromosomique (MeSH)</term><term>Génotype (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Séquençage par oligonucléotides en batterie (méthodes)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Séquençage par oligonucléotides en batterie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Genotype</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Cartographie chromosomique</term><term>Génotype</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23311503</PMID><DateCompleted><Year>2013</Year><Month>07</Month><Day>29</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1755-0998</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>2</Issue><PubDate><Year>2013</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Molecular ecology resources</Title><ISOAbbreviation>Mol Ecol Resour</ISOAbbreviation></Journal><ArticleTitle>A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.</ArticleTitle><Pagination><MedlinePgn>306-23</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/1755-0998.12056</ELocationID><Abstract><AbstractText>Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.</AbstractText><CopyrightInformation>© 2013 Blackwell Publishing Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Geraldes</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. geraldes@mail.ubc.ca</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Difazio</LastName><ForeName>S P</ForeName><Initials>SP</Initials></Author><Author ValidYN="Y"><LastName>Slavov</LastName><ForeName>G T</ForeName><Initials>GT</Initials></Author><Author ValidYN="Y"><LastName>Ranjan</LastName><ForeName>P</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Muchero</LastName><ForeName>W</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Hannemann</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Gunter</LastName><ForeName>L E</ForeName><Initials>LE</Initials></Author><Author ValidYN="Y"><LastName>Wymore</LastName><ForeName>A M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Grassa</LastName><ForeName>C J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Farzaneh</LastName><ForeName>N</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Porth</LastName><ForeName>I</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>McKown</LastName><ForeName>A D</ForeName><Initials>AD</Initials></Author><Author ValidYN="Y"><LastName>Skyba</LastName><ForeName>O</ForeName><Initials>O</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>E</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Fujita</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Klápště</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Schackwitz</LastName><ForeName>W</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Pennacchio</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Rokhsar</LastName><ForeName>D</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Friedmann</LastName><ForeName>M C</ForeName><Initials>MC</Initials></Author><Author ValidYN="Y"><LastName>Wasteneys</LastName><ForeName>G O</ForeName><Initials>GO</Initials></Author><Author ValidYN="Y"><LastName>Guy</LastName><ForeName>R D</ForeName><Initials>RD</Initials></Author><Author ValidYN="Y"><LastName>El-Kassaby</LastName><ForeName>Y A</ForeName><Initials>YA</Initials></Author><Author ValidYN="Y"><LastName>Mansfield</LastName><ForeName>S D</ForeName><Initials>SD</Initials></Author><Author ValidYN="Y"><LastName>Cronk</LastName><ForeName>Q C B</ForeName><Initials>QC</Initials></Author><Author ValidYN="Y"><LastName>Ehlting</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>C J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>G A</ForeName><Initials>GA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>01</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol Resour</MedlineTA><NlmUniqueID>101465604</NlmUniqueID><ISSNLinking>1755-098X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>11</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>12</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23311503</ArticleId><ArticleId IdType="doi">10.1111/1755-0998.12056</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Colombie-Britannique </li></region><settlement><li>Vancouver</li></settlement><orgName><li>Université de la Colombie-Britannique</li></orgName></list><tree><noCountry><name sortKey="Cronk, Q C B" sort="Cronk, Q C B" uniqKey="Cronk Q" first="Q C B" last="Cronk">Q C B. Cronk</name><name sortKey="Difazio, S P" sort="Difazio, S P" uniqKey="Difazio S" first="S P" last="Difazio">S P Difazio</name><name sortKey="Douglas, C J" sort="Douglas, C J" uniqKey="Douglas C" first="C J" last="Douglas">C J Douglas</name><name sortKey="Ehlting, J" sort="Ehlting, J" uniqKey="Ehlting J" first="J" last="Ehlting">J. Ehlting</name><name sortKey="El Kassaby, Y A" sort="El Kassaby, Y A" uniqKey="El Kassaby Y" first="Y A" last="El-Kassaby">Y A El-Kassaby</name><name sortKey="Farzaneh, N" sort="Farzaneh, N" uniqKey="Farzaneh N" first="N" last="Farzaneh">N. Farzaneh</name><name sortKey="Friedmann, M C" sort="Friedmann, M C" uniqKey="Friedmann M" first="M C" last="Friedmann">M C Friedmann</name><name sortKey="Fujita, M" sort="Fujita, M" uniqKey="Fujita M" first="M" last="Fujita">M. Fujita</name><name sortKey="Grassa, C J" sort="Grassa, C J" uniqKey="Grassa C" first="C J" last="Grassa">C J Grassa</name><name sortKey="Gunter, L E" sort="Gunter, L E" uniqKey="Gunter L" first="L E" last="Gunter">L E Gunter</name><name sortKey="Guy, R D" sort="Guy, R D" uniqKey="Guy R" first="R D" last="Guy">R D Guy</name><name sortKey="Hannemann, J" sort="Hannemann, J" uniqKey="Hannemann J" first="J" last="Hannemann">J. Hannemann</name><name sortKey="Klapst, J" sort="Klapst, J" uniqKey="Klapst J" first="J" last="Klápšt">J. Klápšt</name><name sortKey="Li, E" sort="Li, E" uniqKey="Li E" first="E" last="Li">E. Li</name><name sortKey="Mansfield, S D" sort="Mansfield, S D" uniqKey="Mansfield S" first="S D" last="Mansfield">S D Mansfield</name><name sortKey="Martin, J" sort="Martin, J" uniqKey="Martin J" first="J" last="Martin">J. Martin</name><name sortKey="Mckown, A D" sort="Mckown, A D" uniqKey="Mckown A" first="A D" last="Mckown">A D Mckown</name><name sortKey="Muchero, W" sort="Muchero, W" uniqKey="Muchero W" first="W" last="Muchero">W. Muchero</name><name sortKey="Pennacchio, C" sort="Pennacchio, C" uniqKey="Pennacchio C" first="C" last="Pennacchio">C. Pennacchio</name><name sortKey="Porth, I" sort="Porth, I" uniqKey="Porth I" first="I" last="Porth">I. Porth</name><name sortKey="Ranjan, P" sort="Ranjan, P" uniqKey="Ranjan P" first="P" last="Ranjan">P. Ranjan</name><name sortKey="Rokhsar, D" sort="Rokhsar, D" uniqKey="Rokhsar D" first="D" last="Rokhsar">D. Rokhsar</name><name sortKey="Schackwitz, W" sort="Schackwitz, W" uniqKey="Schackwitz W" first="W" last="Schackwitz">W. Schackwitz</name><name sortKey="Skyba, O" sort="Skyba, O" uniqKey="Skyba O" first="O" last="Skyba">O. Skyba</name><name sortKey="Slavov, G T" sort="Slavov, G T" uniqKey="Slavov G" first="G T" last="Slavov">G T Slavov</name><name sortKey="Tuskan, G A" sort="Tuskan, G A" uniqKey="Tuskan G" first="G A" last="Tuskan">G A Tuskan</name><name sortKey="Wasteneys, G O" sort="Wasteneys, G O" uniqKey="Wasteneys G" first="G O" last="Wasteneys">G O Wasteneys</name><name sortKey="Wymore, A M" sort="Wymore, A M" uniqKey="Wymore A" first="A M" last="Wymore">A M Wymore</name></noCountry><country name="Canada"><region name="Colombie-Britannique "><name sortKey="Geraldes, A" sort="Geraldes, A" uniqKey="Geraldes A" first="A" last="Geraldes">A. Geraldes</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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