PoplarV1, Main, Exploration, bibRecord, 003564

Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome.

Identifieur interne : 003564 ( Main/Exploration ); précédent : 003563; suivant : 003565

Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome.

Auteurs : T M Yin [République populaire de Chine] ; X Y Zhang [République populaire de Chine] ; L E Gunter [République populaire de Chine] ; S X Li [République populaire de Chine] ; S D Wullschleger [République populaire de Chine] ; M R Huang [République populaire de Chine] ; G A Tuskan [République populaire de Chine]

Source :

The New phytologist [ 1469-8137 ] ; 2009.

RBID : pubmed:19121044

Descripteurs français

English descriptors

KwdEn :
- Analysis of Variance (MeSH), Chromosome Mapping (MeSH), Databases, Genetic (MeSH), Genetic Variation (MeSH), Genome, Plant (MeSH), Microsatellite Repeats (MeSH), Minisatellite Repeats (MeSH), Nucleic Acid Amplification Techniques (MeSH), Populus (genetics), RNA (MeSH), Regression Analysis (MeSH).
MESH :
- chemical : RNA.
- genetics : Populus.
- Analysis of Variance, Chromosome Mapping, Databases, Genetic, Genetic Variation, Genome, Plant, Microsatellite Repeats, Minisatellite Repeats, Nucleic Acid Amplification Techniques, Regression Analysis.

Abstract

In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.

DOI: 10.1111/j.1469-8137.2008.02663.x
PubMed: 19121044

Affiliations:

République populaire de Chine

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<author><name sortKey="Tuskan, G A" sort="Tuskan, G A" uniqKey="Tuskan G" first="G A" last="Tuskan">G A Tuskan</name>
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<series><title level="j">The New phytologist</title>
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<term>Chromosome Mapping (MeSH)</term>
<term>Databases, Genetic (MeSH)</term>
<term>Genetic Variation (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Microsatellite Repeats (MeSH)</term>
<term>Minisatellite Repeats (MeSH)</term>
<term>Nucleic Acid Amplification Techniques (MeSH)</term>
<term>Populus (genetics)</term>
<term>RNA (MeSH)</term>
<term>Regression Analysis (MeSH)</term>
</keywords>
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<term>Analyse de régression (MeSH)</term>
<term>Analyse de variance (MeSH)</term>
<term>Bases de données génétiques (MeSH)</term>
<term>Cartographie chromosomique (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Populus (génétique)</term>
<term>Répétitions microsatellites (MeSH)</term>
<term>Répétitions minisatellites (MeSH)</term>
<term>Techniques d'amplification d'acides nucléiques (MeSH)</term>
<term>Variation génétique (MeSH)</term>
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</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" xml:lang="en"><term>Analysis of Variance</term>
<term>Chromosome Mapping</term>
<term>Databases, Genetic</term>
<term>Genetic Variation</term>
<term>Genome, Plant</term>
<term>Microsatellite Repeats</term>
<term>Minisatellite Repeats</term>
<term>Nucleic Acid Amplification Techniques</term>
<term>Regression Analysis</term>
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<term>Analyse de variance</term>
<term>Bases de données génétiques</term>
<term>Cartographie chromosomique</term>
<term>Génome végétal</term>
<term>Répétitions microsatellites</term>
<term>Répétitions minisatellites</term>
<term>Techniques d'amplification d'acides nucléiques</term>
<term>Variation génétique</term>
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<front><div type="abstract" xml:lang="en">In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.</div>
</front>
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<Abstract><AbstractText>In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.</AbstractText>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yin</LastName>
<ForeName>T M</ForeName>
<Initials>TM</Initials>
<AffiliationInfo><Affiliation>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA;The Key Lab of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, China.</Affiliation>
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<Author ValidYN="Y"><LastName>Zhang</LastName>
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</AffiliationInfo>
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</AffiliationInfo>
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</AffiliationInfo>
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<MeshHeading><DescriptorName UI="D021141" MajorTopicYN="N">Nucleic Acid Amplification Techniques</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D012313" MajorTopicYN="Y">RNA</DescriptorName>
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<MeshHeading><DescriptorName UI="D012044" MajorTopicYN="N">Regression Analysis</DescriptorName>
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<tree><country name="République populaire de Chine"><noRegion><name sortKey="Yin, T M" sort="Yin, T M" uniqKey="Yin T" first="T M" last="Yin">T M Yin</name>
</noRegion>
<name sortKey="Gunter, L E" sort="Gunter, L E" uniqKey="Gunter L" first="L E" last="Gunter">L E Gunter</name>
<name sortKey="Huang, M R" sort="Huang, M R" uniqKey="Huang M" first="M R" last="Huang">M R Huang</name>
<name sortKey="Li, S X" sort="Li, S X" uniqKey="Li S" first="S X" last="Li">S X Li</name>
<name sortKey="Tuskan, G A" sort="Tuskan, G A" uniqKey="Tuskan G" first="G A" last="Tuskan">G A Tuskan</name>
<name sortKey="Wullschleger, S D" sort="Wullschleger, S D" uniqKey="Wullschleger S" first="S D" last="Wullschleger">S D Wullschleger</name>
<name sortKey="Zhang, X Y" sort="Zhang, X Y" uniqKey="Zhang X" first="X Y" last="Zhang">X Y Zhang</name>
</country>
</tree>
</affiliations>
</record>

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{{Explor lien
   |wiki=    Bois
   |area=    PoplarV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:19121044
   |texte=   Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome.
}}

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Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome.

Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome.

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