PoplarV1, Main, Exploration, bibRecord, 002E10

Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling.

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Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling.

Auteurs : Fabio Marroni [Italie] ; Sara Pinosio ; Eleonora Di Centa ; Irena Jurman ; Wout Boerjan ; Nicoletta Felice ; Federica Cattonaro ; Michele Morgante

Source :

The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2011.

RBID : pubmed:21554453

Descripteurs français

English descriptors

KwdEn :
- Alleles (MeSH), Base Sequence (MeSH), Chromosome Mapping (economics), Chromosome Mapping (methods), Chromosomes, Plant (genetics), Genetic Variation (genetics), Genome, Plant (genetics), Genome-Wide Association Study (economics), Genome-Wide Association Study (methods), Genotype (MeSH), High-Throughput Nucleotide Sequencing (methods), Lignin (biosynthesis), Mutation (MeSH), Phenotype (MeSH), Plant Proteins (genetics), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Sensitivity and Specificity (MeSH), Sequence Analysis, DNA (MeSH).
MESH :
- chemical , biosynthesis : Lignin.
- economics : Chromosome Mapping, Genome-Wide Association Study.
- genetics : Chromosomes, Plant, Genetic Variation, Genome, Plant, Plant Proteins, Polymorphism, Single Nucleotide, Populus.
- methods : Chromosome Mapping, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing.
- Alleles, Base Sequence, Genotype, Mutation, Phenotype, Sensitivity and Specificity, Sequence Analysis, DNA.

Abstract

Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.

DOI: 10.1111/j.1365-313X.2011.04627.x
PubMed: 21554453

Affiliations:

Italie

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Le document en format XML

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<author><name sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name>
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<author><name sortKey="Felice, Nicoletta" sort="Felice, Nicoletta" uniqKey="Felice N" first="Nicoletta" last="Felice">Nicoletta Felice</name>
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<author><name sortKey="Cattonaro, Federica" sort="Cattonaro, Federica" uniqKey="Cattonaro F" first="Federica" last="Cattonaro">Federica Cattonaro</name>
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<author><name sortKey="Jurman, Irena" sort="Jurman, Irena" uniqKey="Jurman I" first="Irena" last="Jurman">Irena Jurman</name>
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<author><name sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term>
<term>Base Sequence (MeSH)</term>
<term>Chromosome Mapping (economics)</term>
<term>Chromosome Mapping (methods)</term>
<term>Chromosomes, Plant (genetics)</term>
<term>Genetic Variation (genetics)</term>
<term>Genome, Plant (genetics)</term>
<term>Genome-Wide Association Study (economics)</term>
<term>Genome-Wide Association Study (methods)</term>
<term>Genotype (MeSH)</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
<term>Lignin (biosynthesis)</term>
<term>Mutation (MeSH)</term>
<term>Phenotype (MeSH)</term>
<term>Plant Proteins (genetics)</term>
<term>Polymorphism, Single Nucleotide (genetics)</term>
<term>Populus (genetics)</term>
<term>Sensitivity and Specificity (MeSH)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Allèles (MeSH)</term>
<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Cartographie chromosomique (méthodes)</term>
<term>Cartographie chromosomique (économie)</term>
<term>Chromosomes de plante (génétique)</term>
<term>Génome végétal (génétique)</term>
<term>Génotype (MeSH)</term>
<term>Lignine (biosynthèse)</term>
<term>Mutation (MeSH)</term>
<term>Phénotype (MeSH)</term>
<term>Polymorphisme de nucléotide simple (génétique)</term>
<term>Populus (génétique)</term>
<term>Protéines végétales (génétique)</term>
<term>Sensibilité et spécificité (MeSH)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>Séquençage nucléotidique à haut débit (méthodes)</term>
<term>Variation génétique (génétique)</term>
<term>Étude d'association pangénomique (méthodes)</term>
<term>Étude d'association pangénomique (économie)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Lignin</term>
</keywords>
<keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Lignine</term>
</keywords>
<keywords scheme="MESH" qualifier="economics" xml:lang="en"><term>Chromosome Mapping</term>
<term>Genome-Wide Association Study</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Plant</term>
<term>Genetic Variation</term>
<term>Genome, Plant</term>
<term>Plant Proteins</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes de plante</term>
<term>Génome végétal</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Populus</term>
<term>Protéines végétales</term>
<term>Variation génétique</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term>
<term>Genome-Wide Association Study</term>
<term>High-Throughput Nucleotide Sequencing</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie chromosomique</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Étude d'association pangénomique</term>
</keywords>
<keywords scheme="MESH" qualifier="économie" xml:lang="fr"><term>Cartographie chromosomique</term>
<term>Étude d'association pangénomique</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Alleles</term>
<term>Base Sequence</term>
<term>Genotype</term>
<term>Mutation</term>
<term>Phenotype</term>
<term>Sensitivity and Specificity</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Allèles</term>
<term>Analyse de séquence d'ADN</term>
<term>Génotype</term>
<term>Mutation</term>
<term>Phénotype</term>
<term>Sensibilité et spécificité</term>
<term>Séquence nucléotidique</term>
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<front><div type="abstract" xml:lang="en">Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.</div>
</front>
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<DateCompleted><Year>2012</Year>
<Month>04</Month>
<Day>27</Day>
</DateCompleted>
<DateRevised><Year>2012</Year>
<Month>05</Month>
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<JournalIssue CitedMedium="Internet"><Volume>67</Volume>
<Issue>4</Issue>
<PubDate><Year>2011</Year>
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<Title>The Plant journal : for cell and molecular biology</Title>
<ISOAbbreviation>Plant J</ISOAbbreviation>
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<ArticleTitle>Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling.</ArticleTitle>
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<Abstract><AbstractText>Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.</AbstractText>
<CopyrightInformation>© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Marroni</LastName>
<ForeName>Fabio</ForeName>
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</Author>
<Author ValidYN="Y"><LastName>Pinosio</LastName>
<ForeName>Sara</ForeName>
<Initials>S</Initials>
</Author>
<Author ValidYN="Y"><LastName>Di Centa</LastName>
<ForeName>Eleonora</ForeName>
<Initials>E</Initials>
</Author>
<Author ValidYN="Y"><LastName>Jurman</LastName>
<ForeName>Irena</ForeName>
<Initials>I</Initials>
</Author>
<Author ValidYN="Y"><LastName>Boerjan</LastName>
<ForeName>Wout</ForeName>
<Initials>W</Initials>
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<Author ValidYN="Y"><LastName>Felice</LastName>
<ForeName>Nicoletta</ForeName>
<Initials>N</Initials>
</Author>
<Author ValidYN="Y"><LastName>Cattonaro</LastName>
<ForeName>Federica</ForeName>
<Initials>F</Initials>
</Author>
<Author ValidYN="Y"><LastName>Morgante</LastName>
<ForeName>Michele</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>
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<ArticleDate DateType="Electronic"><Year>2011</Year>
<Month>07</Month>
<Day>11</Day>
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</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Plant J</MedlineTA>
<NlmUniqueID>9207397</NlmUniqueID>
<ISSNLinking>0960-7412</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
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</Chemical>
<Chemical><RegistryNumber>9005-53-2</RegistryNumber>
<NameOfSubstance UI="D008031">Lignin</NameOfSubstance>
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<CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Plant J. 2012 Feb;69(3):564</RefSource>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
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<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
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<MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName>
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<MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012680" MajorTopicYN="N">Sensitivity and Specificity</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
</MeshHeadingList>
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Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling.

Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling.

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Abstract

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