Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments.
Identifieur interne : 002674 ( Main/Exploration ); précédent : 002673; suivant : 002675Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments.
Auteurs : Wellington Muchero [États-Unis] ; Mitchell M. Sewell ; Priya Ranjan ; Lee E. Gunter ; Timothy J. Tschaplinski ; Tongming Yin ; Gerald A. TuskanSource :
- PloS one [ 1932-6203 ] ; 2013.
Descripteurs français
- KwdFr :
- Biomasse (MeSH), Cartographie physique de chromosome (MeSH), Croisements génétiques (MeSH), Environnement (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Interaction entre gènes et environnement (MeSH), Liaison génétique (MeSH), Locus de caractère quantitatif (MeSH), Lod score (MeSH), Phénotype (MeSH), Populus (croissance et développement), Populus (génétique).
- MESH :
- croissance et développement : Populus.
- génétique : Populus.
- Biomasse, Cartographie physique de chromosome, Croisements génétiques, Environnement, Gènes de plante, Génome végétal, Interaction entre gènes et environnement, Liaison génétique, Locus de caractère quantitatif, Lod score, Phénotype.
English descriptors
- KwdEn :
- Biomass (MeSH), Crosses, Genetic (MeSH), Environment (MeSH), Gene-Environment Interaction (MeSH), Genes, Plant (MeSH), Genetic Linkage (MeSH), Genome, Plant (MeSH), Lod Score (MeSH), Phenotype (MeSH), Physical Chromosome Mapping (MeSH), Populus (genetics), Populus (growth & development), Quantitative Trait Loci (MeSH).
- MESH :
- genetics : Populus.
- growth & development : Populus.
- Biomass, Crosses, Genetic, Environment, Gene-Environment Interaction, Genes, Plant, Genetic Linkage, Genome, Plant, Lod Score, Phenotype, Physical Chromosome Mapping, Quantitative Trait Loci.
Abstract
Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in a Populus trichocarpa × P. deltoides F(2) population. A genetic linkage map composed of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring biomass QTLs. Twelve intervals were identified, of which BM-1, BM-2, and BM-7 were identified in all three years for both height and diameter. One putative QTL, BM-7, and one suggestive QTL exhibited significant evidence of over-dominance in all three years for both traits. Conversely, QTLs BM-4 and BM-6 exhibited evidence of under-dominance in both environments for height and diameter. Seven of the nine QTLs were successfully anchored, and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions. Of the 3,031 genes located in genome-anchored QTL intervals, 1,892 had PFAM annotations. Of these, 1,313, representing 255 unique annotations, had at least one duplicate copy in a QTL interval identified on a separate scaffold. This observation suggests that some QTLs identified in this study may have shared the same ancestral sequence prior to the salicoid genome duplication in Populus.
DOI: 10.1371/journal.pone.0054468
PubMed: 23382900
PubMed Central: PMC3558514
Affiliations:
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Sewell</name></author><author><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name></author><author><name sortKey="Gunter, Lee E" sort="Gunter, Lee E" uniqKey="Gunter L" first="Lee E" last="Gunter">Lee E. Gunter</name></author><author><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name></author><author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. 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Tuskan</name></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biomass (MeSH)</term><term>Crosses, Genetic (MeSH)</term><term>Environment (MeSH)</term><term>Gene-Environment Interaction (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genetic Linkage (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Lod Score (MeSH)</term><term>Phenotype (MeSH)</term><term>Physical Chromosome Mapping (MeSH)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>Quantitative Trait Loci (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biomasse (MeSH)</term><term>Cartographie physique de chromosome (MeSH)</term><term>Croisements génétiques (MeSH)</term><term>Environnement (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Interaction entre gènes et environnement (MeSH)</term><term>Liaison génétique (MeSH)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Lod score (MeSH)</term><term>Phénotype (MeSH)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" 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>Biomass</term><term>Crosses, Genetic</term><term>Environment</term><term>Gene-Environment Interaction</term><term>Genes, Plant</term><term>Genetic Linkage</term><term>Genome, Plant</term><term>Lod Score</term><term>Phenotype</term><term>Physical Chromosome Mapping</term><term>Quantitative Trait Loci</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biomasse</term><term>Cartographie physique de chromosome</term><term>Croisements génétiques</term><term>Environnement</term><term>Gènes de plante</term><term>Génome végétal</term><term>Interaction entre gènes et environnement</term><term>Liaison génétique</term><term>Locus de caractère quantitatif</term><term>Lod score</term><term>Phénotype</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in a Populus trichocarpa × P. deltoides F(2) population. A genetic linkage map composed of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring biomass QTLs. Twelve intervals were identified, of which BM-1, BM-2, and BM-7 were identified in all three years for both height and diameter. One putative QTL, BM-7, and one suggestive QTL exhibited significant evidence of over-dominance in all three years for both traits. Conversely, QTLs BM-4 and BM-6 exhibited evidence of under-dominance in both environments for height and diameter. Seven of the nine QTLs were successfully anchored, and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions. Of the 3,031 genes located in genome-anchored QTL intervals, 1,892 had PFAM annotations. Of these, 1,313, representing 255 unique annotations, had at least one duplicate copy in a QTL interval identified on a separate scaffold. This observation suggests that some QTLs identified in this study may have shared the same ancestral sequence prior to the salicoid genome duplication in Populus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23382900</PMID><DateCompleted><Year>2013</Year><Month>08</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>1</Issue><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments.</ArticleTitle><Pagination><MedlinePgn>e54468</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0054468</ELocationID><Abstract><AbstractText>Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in a Populus trichocarpa × P. deltoides F(2) population. A genetic linkage map composed of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring biomass QTLs. Twelve intervals were identified, of which BM-1, BM-2, and BM-7 were identified in all three years for both height and diameter. One putative QTL, BM-7, and one suggestive QTL exhibited significant evidence of over-dominance in all three years for both traits. Conversely, QTLs BM-4 and BM-6 exhibited evidence of under-dominance in both environments for height and diameter. Seven of the nine QTLs were successfully anchored, and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions. Of the 3,031 genes located in genome-anchored QTL intervals, 1,892 had PFAM annotations. Of these, 1,313, representing 255 unique annotations, had at least one duplicate copy in a QTL interval identified on a separate scaffold. This observation suggests that some QTLs identified in this study may have shared the same ancestral sequence prior to the salicoid genome duplication in Populus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Muchero</LastName><ForeName>Wellington</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA. mucherow@ornl.gov</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sewell</LastName><ForeName>Mitchell M</ForeName><Initials>MM</Initials></Author><Author ValidYN="Y"><LastName>Ranjan</LastName><ForeName>Priya</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Gunter</LastName><ForeName>Lee E</ForeName><Initials>LE</Initials></Author><Author ValidYN="Y"><LastName>Tschaplinski</LastName><ForeName>Timothy J</ForeName><Initials>TJ</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></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>01</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018533" MajorTopicYN="Y">Biomass</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003433" MajorTopicYN="Y">Crosses, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName 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Gunter</name><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name><name sortKey="Sewell, Mitchell M" sort="Sewell, Mitchell M" uniqKey="Sewell M" first="Mitchell M" last="Sewell">Mitchell M. Sewell</name><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</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="Tennessee"><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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