Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L.
Identifieur interne : 002994 ( Main/Exploration ); précédent : 002993; suivant : 002995Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L.
Auteurs : Stephen R. Keller [États-Unis] ; Nicholas Levsen ; Matthew S. Olson ; Peter TiffinSource :
- Molecular biology and evolution [ 1537-1719 ] ; 2012.
Descripteurs français
- KwdFr :
- Adaptation physiologique (génétique), Déséquilibre de liaison (génétique), Facteurs temps (MeSH), Fleurs (génétique), Fleurs (physiologie), Gènes de plante (génétique), Génétique des populations (MeSH), Interaction entre gènes et environnement (MeSH), Modèles génétiques (MeSH), Polymorphisme de nucléotide simple (génétique), Populus (génétique), Populus (physiologie), Protéines CLOCK (génétique), Rythme circadien (génétique), Réseaux de régulation génique (génétique), Variation génétique (MeSH).
- MESH :
- génétique : Adaptation physiologique, Déséquilibre de liaison, Fleurs, Gènes de plante, Polymorphisme de nucléotide simple, Populus, Protéines CLOCK, Rythme circadien, Réseaux de régulation génique.
- physiologie : Fleurs, Populus.
- Facteurs temps, Génétique des populations, Interaction entre gènes et environnement, Modèles génétiques, Variation génétique.
English descriptors
- KwdEn :
- Adaptation, Physiological (genetics), CLOCK Proteins (genetics), Circadian Rhythm (genetics), Flowers (genetics), Flowers (physiology), Gene Regulatory Networks (genetics), Gene-Environment Interaction (MeSH), Genes, Plant (genetics), Genetic Variation (MeSH), Genetics, Population (MeSH), Linkage Disequilibrium (genetics), Models, Genetic (MeSH), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Populus (physiology), Time Factors (MeSH).
- MESH :
- chemical , genetics : CLOCK Proteins.
- genetics : Adaptation, Physiological, Circadian Rhythm, Flowers, Gene Regulatory Networks, Genes, Plant, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Populus.
- physiology : Flowers, Populus.
- Gene-Environment Interaction, Genetic Variation, Genetics, Population, Models, Genetic, Time Factors.
Abstract
Identifying the signature and targets of local adaptation is an increasingly important goal in empirical population genetics. Using data from 443 balsam poplar Populus balsamifera trees sampled from 31 populations, we tested for evidence of geographically variable selection shaping diversity at 27 homologues of the Arabidopsis flowering-time network. These genes are implicated in the control of seasonal phenology, an important determinant of fitness. Using 335 candidate and 412 reference single nucleotide polymorphisms (SNPs), we tested for evidence of local adaptation by searching for elevated population differentiation using F(ST)-based outlier analyses implemented in BayeScan or a Hierarchical Model in Arelquin and by testing for significant associations between allele frequency and environmental variables using BAYENV. A total of 46 SNPs from 14 candidate genes had signatures of local adaptation-either significantly greater population differentiation or significant covariance with one or more environmental variable relative to reference SNP distributions. Only 11 SNPs from two genes exhibited both elevated population differentiation and covariance with one or more environmental variables. Several genes including the abscisic acid gene ABI1B and the circadian clock genes ELF3 and GI5 harbored a large number of SNPs with signatures of local adaptation-with SNPs in GI5 strongly covarying with both latitude and precipitation and SNPs in ABI1B strongly covarying with temperature. In contrast to several other systems, we find little evidence that photoreceptors, including phytochromes, play an important role in local adaptation. Our results additionally show that detecting local adaptation is sensitive to the analytical approaches used and that model-based significance thresholds should be viewed with caution.
DOI: 10.1093/molbev/mss121
PubMed: 22513286
Affiliations:
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Using data from 443 balsam poplar Populus balsamifera trees sampled from 31 populations, we tested for evidence of geographically variable selection shaping diversity at 27 homologues of the Arabidopsis flowering-time network. These genes are implicated in the control of seasonal phenology, an important determinant of fitness. Using 335 candidate and 412 reference single nucleotide polymorphisms (SNPs), we tested for evidence of local adaptation by searching for elevated population differentiation using F(ST)-based outlier analyses implemented in BayeScan or a Hierarchical Model in Arelquin and by testing for significant associations between allele frequency and environmental variables using BAYENV. A total of 46 SNPs from 14 candidate genes had signatures of local adaptation-either significantly greater population differentiation or significant covariance with one or more environmental variable relative to reference SNP distributions. Only 11 SNPs from two genes exhibited both elevated population differentiation and covariance with one or more environmental variables. Several genes including the abscisic acid gene ABI1B and the circadian clock genes ELF3 and GI5 harbored a large number of SNPs with signatures of local adaptation-with SNPs in GI5 strongly covarying with both latitude and precipitation and SNPs in ABI1B strongly covarying with temperature. In contrast to several other systems, we find little evidence that photoreceptors, including phytochromes, play an important role in local adaptation. Our results additionally show that detecting local adaptation is sensitive to the analytical approaches used and that model-based significance thresholds should be viewed with caution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22513286</PMID><DateCompleted><Year>2013</Year><Month>02</Month><Day>06</Day></DateCompleted><DateRevised><Year>2012</Year><Month>09</Month><Day>26</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>29</Volume><Issue>10</Issue><PubDate><Year>2012</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L.</ArticleTitle><Pagination><MedlinePgn>3143-52</MedlinePgn></Pagination><Abstract><AbstractText>Identifying the signature and targets of local adaptation is an increasingly important goal in empirical population genetics. Using data from 443 balsam poplar Populus balsamifera trees sampled from 31 populations, we tested for evidence of geographically variable selection shaping diversity at 27 homologues of the Arabidopsis flowering-time network. These genes are implicated in the control of seasonal phenology, an important determinant of fitness. Using 335 candidate and 412 reference single nucleotide polymorphisms (SNPs), we tested for evidence of local adaptation by searching for elevated population differentiation using F(ST)-based outlier analyses implemented in BayeScan or a Hierarchical Model in Arelquin and by testing for significant associations between allele frequency and environmental variables using BAYENV. A total of 46 SNPs from 14 candidate genes had signatures of local adaptation-either significantly greater population differentiation or significant covariance with one or more environmental variable relative to reference SNP distributions. Only 11 SNPs from two genes exhibited both elevated population differentiation and covariance with one or more environmental variables. Several genes including the abscisic acid gene ABI1B and the circadian clock genes ELF3 and GI5 harbored a large number of SNPs with signatures of local adaptation-with SNPs in GI5 strongly covarying with both latitude and precipitation and SNPs in ABI1B strongly covarying with temperature. In contrast to several other systems, we find little evidence that photoreceptors, including phytochromes, play an important role in local adaptation. Our results additionally show that detecting local adaptation is sensitive to the analytical approaches used and that model-based significance thresholds should be viewed with caution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Keller</LastName><ForeName>Stephen R</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, University of Minnesota, MN, USA. skeller@umces.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Levsen</LastName><ForeName>Nicholas</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Olson</LastName><ForeName>Matthew S</ForeName><Initials>MS</Initials></Author><Author ValidYN="Y"><LastName>Tiffin</LastName><ForeName>Peter</ForeName><Initials>P</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>2012</Year><Month>04</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>EC 2.3.1.48</RegistryNumber><NameOfSubstance UI="D056926">CLOCK Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="N">Adaptation, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056926" MajorTopicYN="N">CLOCK Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002940" MajorTopicYN="N">Circadian Rhythm</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D035264" MajorTopicYN="N">Flowers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059647" MajorTopicYN="N">Gene-Environment Interaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013997" MajorTopicYN="N">Time Factors</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>2</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22513286</ArticleId><ArticleId IdType="pii">mss121</ArticleId><ArticleId IdType="doi">10.1093/molbev/mss121</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Minnesota</li></region></list><tree><noCountry><name sortKey="Levsen, Nicholas" sort="Levsen, Nicholas" uniqKey="Levsen N" first="Nicholas" last="Levsen">Nicholas Levsen</name><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name><name sortKey="Tiffin, Peter" sort="Tiffin, Peter" uniqKey="Tiffin P" first="Peter" last="Tiffin">Peter Tiffin</name></noCountry><country name="États-Unis"><region name="Minnesota"><name sortKey="Keller, Stephen R" sort="Keller, Stephen R" uniqKey="Keller S" first="Stephen R" last="Keller">Stephen R. Keller</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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