Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae).
Identifieur interne : 003853 ( Main/Exploration ); précédent : 003852; suivant : 003854Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae).
Auteurs : P R K. Ingvarsson [Suède] ; M Victoria Garcia ; Virginia Luquez ; David Hall ; Stefan JanssonSource :
- Genetics [ 0016-6731 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Phytochrome.
- geographic : Europe.
- genetics : Flowers, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Populus.
- Base Sequence, Gene Frequency, Genotype, Phenotype, Population Dynamics.
Abstract
We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the "hinge region," close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.
DOI: 10.1534/genetics.107.082354
PubMed: 18245834
PubMed Central: PMC2323810
Affiliations:
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Ingvarsson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden. par.ingvarsson@emg.umu.se</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå</wicri:regionArea><wicri:noRegion>SE-901 87 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Garcia, M Victoria" sort="Garcia, M Victoria" uniqKey="Garcia M" first="M Victoria" last="Garcia">M Victoria Garcia</name></author><author><name sortKey="Luquez, Virginia" sort="Luquez, Virginia" uniqKey="Luquez V" first="Virginia" last="Luquez">Virginia Luquez</name></author><author><name sortKey="Hall, David" sort="Hall, David" uniqKey="Hall D" first="David" last="Hall">David Hall</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author></analytic><series><title level="j">Genetics</title><idno type="ISSN">0016-6731</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Europe (MeSH)</term><term>Flowers (genetics)</term><term>Gene Frequency (MeSH)</term><term>Genotype (MeSH)</term><term>Linkage Disequilibrium (genetics)</term><term>Phenotype (MeSH)</term><term>Phytochrome (genetics)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Population Dynamics (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Dynamique des populations (MeSH)</term><term>Déséquilibre de liaison (génétique)</term><term>Europe (MeSH)</term><term>Fleurs (génétique)</term><term>Fréquence d'allèle (MeSH)</term><term>Génotype (MeSH)</term><term>Phytochrome (génétique)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Populus (génétique)</term><term>Séquence nucléotidique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Phytochrome</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Europe</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Flowers</term><term>Linkage Disequilibrium</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Déséquilibre de liaison</term><term>Fleurs</term><term>Phytochrome</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Gene Frequency</term><term>Genotype</term><term>Phenotype</term><term>Population Dynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Dynamique des populations</term><term>Europe</term><term>Fréquence d'allèle</term><term>Génotype</term><term>Phénotype</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the "hinge region," close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18245834</PMID><DateCompleted><Year>2008</Year><Month>06</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0016-6731</ISSN><JournalIssue CitedMedium="Print"><Volume>178</Volume><Issue>4</Issue><PubDate><Year>2008</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Genetics</Title><ISOAbbreviation>Genetics</ISOAbbreviation></Journal><ArticleTitle>Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae).</ArticleTitle><Pagination><MedlinePgn>2217-26</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/genetics.107.082354</ELocationID><Abstract><AbstractText>We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the "hinge region," close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ingvarsson</LastName><ForeName>Pär K</ForeName><Initials>PK</Initials><AffiliationInfo><Affiliation>Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden. par.ingvarsson@emg.umu.se</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garcia</LastName><ForeName>M Victoria</ForeName><Initials>MV</Initials></Author><Author ValidYN="Y"><LastName>Luquez</LastName><ForeName>Virginia</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Hall</LastName><ForeName>David</ForeName><Initials>D</Initials></Author><Author 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