A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.
Identifieur interne : 003723 ( Main/Exploration ); précédent : 003722; suivant : 003724A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.
Auteurs : Derek R. Drost [États-Unis] ; Evandro Novaes ; Carolina Boaventura-Novaes ; Catherine I. Benedict ; Ryan S. Brown ; Tongming Yin ; Gerald A. Tuskan ; Matias KirstSource :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2009.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Cartographie chromosomique (méthodes), Données de séquences moléculaires (MeSH), Génome végétal (MeSH), Génotype (MeSH), Polymorphisme génétique (MeSH), Populus (génétique), Répétitions microsatellites (MeSH), Sondes d'ADN (MeSH), Séquence nucléotidique (MeSH), Séquençage par oligonucléotides en batterie (méthodes).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Plant.
- chemical : DNA Probes.
- genetics : Populus.
- methods : Chromosome Mapping, Oligonucleotide Array Sequence Analysis.
- Base Sequence, Genome, Plant, Genotype, Microsatellite Repeats, Molecular Sequence Data, Polymorphism, Genetic.
Abstract
Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.
DOI: 10.1111/j.1365-313X.2009.03828.x
PubMed: 19220791
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Tuskan</name></author><author><name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Chromosome Mapping (methods)</term><term>DNA Probes (MeSH)</term><term>DNA, Plant (genetics)</term><term>Genome, Plant (MeSH)</term><term>Genotype (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Polymorphism, Genetic (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Cartographie chromosomique (méthodes)</term><term>Données de séquences moléculaires (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génotype (MeSH)</term><term>Polymorphisme génétique (MeSH)</term><term>Populus (génétique)</term><term>Répétitions microsatellites (MeSH)</term><term>Sondes d'ADN (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquençage par oligonucléotides en batterie (méthodes)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Probes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie chromosomique</term><term>Séquençage par oligonucléotides en batterie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Genome, Plant</term><term>Genotype</term><term>Microsatellite Repeats</term><term>Molecular Sequence Data</term><term>Polymorphism, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Génome végétal</term><term>Génotype</term><term>Polymorphisme génétique</term><term>Répétitions microsatellites</term><term>Sondes d'ADN</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. 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Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Drost</LastName><ForeName>Derek R</ForeName><Initials>DR</Initials><AffiliationInfo><Affiliation>Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Novaes</LastName><ForeName>Evandro</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Boaventura-Novaes</LastName><ForeName>Carolina</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Benedict</LastName><ForeName>Catherine I</ForeName><Initials>CI</Initials></Author><Author ValidYN="Y"><LastName>Brown</LastName><ForeName>Ryan S</ForeName><Initials>RS</Initials></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Tongming</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials></Author><Author ValidYN="Y"><LastName>Kirst</LastName><ForeName>Matias</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>02</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015342">DNA Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Plant J. 2009 Dec;60(5):929</RefSource></CommentsCorrections><CommentsCorrections RefType="CommentIn"><RefSource>G3 (Bethesda). 2013 Apr 9;3(4):617-631</RefSource><PMID Version="1">23550116</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015342" MajorTopicYN="N">DNA Probes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="N">Polymorphism, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>2</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>2</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>8</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19220791</ArticleId><ArticleId IdType="pii">TPJ3828</ArticleId><ArticleId IdType="doi">10.1111/j.1365-313X.2009.03828.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><noCountry><name sortKey="Benedict, Catherine I" sort="Benedict, Catherine I" uniqKey="Benedict C" first="Catherine I" last="Benedict">Catherine I. Benedict</name><name sortKey="Boaventura Novaes, Carolina" sort="Boaventura Novaes, Carolina" uniqKey="Boaventura Novaes C" first="Carolina" last="Boaventura-Novaes">Carolina Boaventura-Novaes</name><name sortKey="Brown, Ryan S" sort="Brown, Ryan S" uniqKey="Brown R" first="Ryan S" last="Brown">Ryan S. Brown</name><name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name><name sortKey="Novaes, Evandro" sort="Novaes, Evandro" uniqKey="Novaes E" first="Evandro" last="Novaes">Evandro Novaes</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name></noCountry><country name="États-Unis"><region name="Floride"><name sortKey="Drost, Derek R" sort="Drost, Derek R" uniqKey="Drost D" first="Derek R" last="Drost">Derek R. 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