Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus.
Identifieur interne : 002B67 ( Main/Exploration ); précédent : 002B66; suivant : 002B68Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus.
Auteurs : Michiharu Nakano [Japon] ; Takehiko Shimada ; Tomoko Endo ; Hiroshi Fujii ; Hirohisa Nesumi ; Masayuki Kita ; Masumi Ebina ; Tokurou Shimizu ; Mitsuo OmuraSource :
- Plant science : an international journal of experimental plant biology [ 1873-2259 ] ; 2012.
Descripteurs français
- KwdFr :
- ADN des plantes (analyse), Analyse de séquence d'ADN (MeSH), Apomixie (génétique), Cadres ouverts de lecture (MeSH), Chromosomes artificiels de bactérie (MeSH), Citrus (embryologie), Citrus (génétique), Données de séquences moléculaires (MeSH), Graines (embryologie), Graines (génétique), Génome végétal (MeSH), Génomique (MeSH), Haplotypes (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (génétique), Synténie (MeSH), Séquence nucléotidique (MeSH), Vitis (génétique).
- MESH :
- analyse : ADN des plantes.
- embryologie : Citrus, Graines.
- génétique : Apomixie, Citrus, Graines, Populus, Vitis.
- Analyse de séquence d'ADN, Cadres ouverts de lecture, Chromosomes artificiels de bactérie, Données de séquences moléculaires, Génome végétal, Génomique, Haplotypes, Polymorphisme de nucléotide simple, Synténie, Séquence nucléotidique.
English descriptors
- KwdEn :
- Apomixis (genetics), Base Sequence (MeSH), Chromosomes, Artificial, Bacterial (MeSH), Citrus (embryology), Citrus (genetics), DNA, Plant (analysis), Genome, Plant (MeSH), Genomics (MeSH), Haplotypes (MeSH), Molecular Sequence Data (MeSH), Open Reading Frames (MeSH), Polymorphism, Single Nucleotide (MeSH), Populus (genetics), Seeds (embryology), Seeds (genetics), Sequence Analysis, DNA (MeSH), Synteny (MeSH), Vitis (genetics).
- MESH :
- chemical , analysis : DNA, Plant.
- embryology : Citrus, Seeds.
- genetics : Apomixis, Citrus, Populus, Seeds, Vitis.
- Base Sequence, Chromosomes, Artificial, Bacterial, Genome, Plant, Genomics, Haplotypes, Molecular Sequence Data, Open Reading Frames, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Synteny.
Abstract
Polyembryony, in which multiple somatic nucellar cell-derived embryos develop in addition to the zygotic embryo in a seed, is common in the genus Citrus. Previous genetic studies indicated polyembryony is mainly determined by a single locus, but the underlying molecular mechanism is still unclear. As a step towards identification and characterization of the gene or genes responsible for nucellar embryogenesis in Citrus, haplotype-specific physical maps around the polyembryony locus were constructed. By sequencing three BAC clones aligned on the polyembryony haplotype, a single contiguous draft sequence consisting of 380 kb containing 70 predicted open reading frames (ORFs) was reconstructed. Single nucleotide polymorphism genotypes detected in the sequenced genomic region showed strong association with embryo type in Citrus, indicating a common polyembryony locus is shared among widely diverse Citrus cultivars and species. The arrangement of the predicted ORFs in the characterized genomic region showed high collinearity to the genomic sequence of chromosome 4 of Vitis vinifera and linkage group VI of Populus trichocarpa, suggesting that the syntenic relationship among these species is conserved even though V. vinifera and P. trichocarpa are non-apomictic species. This is the first study to characterize in detail the genomic structure of an apomixis locus determining adventitious embryony.
DOI: 10.1016/j.plantsci.2011.08.002
PubMed: 22195586
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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uniqKey="Endo T" first="Tomoko" last="Endo">Tomoko Endo</name></author><author><name sortKey="Fujii, Hiroshi" sort="Fujii, Hiroshi" uniqKey="Fujii H" first="Hiroshi" last="Fujii">Hiroshi Fujii</name></author><author><name sortKey="Nesumi, Hirohisa" sort="Nesumi, Hirohisa" uniqKey="Nesumi H" first="Hirohisa" last="Nesumi">Hirohisa Nesumi</name></author><author><name sortKey="Kita, Masayuki" sort="Kita, Masayuki" uniqKey="Kita M" first="Masayuki" last="Kita">Masayuki Kita</name></author><author><name sortKey="Ebina, Masumi" sort="Ebina, Masumi" uniqKey="Ebina M" first="Masumi" last="Ebina">Masumi Ebina</name></author><author><name sortKey="Shimizu, Tokurou" sort="Shimizu, Tokurou" uniqKey="Shimizu T" first="Tokurou" last="Shimizu">Tokurou Shimizu</name></author><author><name sortKey="Omura, Mitsuo" sort="Omura, Mitsuo" uniqKey="Omura M" first="Mitsuo" last="Omura">Mitsuo Omura</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date 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Shizuoka 424-0292, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Citrus Research, National Institute of Fruit Tree Science, Shizuoka 424-0292</wicri:regionArea><wicri:noRegion>Shizuoka 424-0292</wicri:noRegion></affiliation></author><author><name sortKey="Shimada, Takehiko" sort="Shimada, Takehiko" uniqKey="Shimada T" first="Takehiko" last="Shimada">Takehiko Shimada</name></author><author><name sortKey="Endo, Tomoko" sort="Endo, Tomoko" uniqKey="Endo T" first="Tomoko" last="Endo">Tomoko Endo</name></author><author><name sortKey="Fujii, Hiroshi" sort="Fujii, Hiroshi" uniqKey="Fujii H" first="Hiroshi" last="Fujii">Hiroshi Fujii</name></author><author><name sortKey="Nesumi, Hirohisa" sort="Nesumi, Hirohisa" uniqKey="Nesumi H" first="Hirohisa" last="Nesumi">Hirohisa Nesumi</name></author><author><name sortKey="Kita, Masayuki" sort="Kita, Masayuki" uniqKey="Kita M" first="Masayuki" last="Kita">Masayuki Kita</name></author><author><name sortKey="Ebina, Masumi" sort="Ebina, Masumi" uniqKey="Ebina M" first="Masumi" last="Ebina">Masumi Ebina</name></author><author><name sortKey="Shimizu, Tokurou" sort="Shimizu, Tokurou" uniqKey="Shimizu T" first="Tokurou" last="Shimizu">Tokurou Shimizu</name></author><author><name sortKey="Omura, Mitsuo" sort="Omura, Mitsuo" uniqKey="Omura M" first="Mitsuo" last="Omura">Mitsuo Omura</name></author></analytic><series><title level="j">Plant science : an international journal of experimental plant biology</title><idno type="eISSN">1873-2259</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Apomixis (genetics)</term><term>Base Sequence (MeSH)</term><term>Chromosomes, Artificial, Bacterial (MeSH)</term><term>Citrus (embryology)</term><term>Citrus (genetics)</term><term>DNA, Plant (analysis)</term><term>Genome, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Haplotypes (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Open Reading Frames (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (genetics)</term><term>Seeds (embryology)</term><term>Seeds (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Synteny (MeSH)</term><term>Vitis (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (analyse)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Apomixie (génétique)</term><term>Cadres ouverts de lecture (MeSH)</term><term>Chromosomes artificiels de bactérie (MeSH)</term><term>Citrus (embryologie)</term><term>Citrus (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Graines (embryologie)</term><term>Graines (génétique)</term><term>Génome végétal (MeSH)</term><term>Génomique (MeSH)</term><term>Haplotypes (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (génétique)</term><term>Synténie (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Vitis (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN des plantes</term></keywords><keywords scheme="MESH" qualifier="embryologie" xml:lang="fr"><term>Citrus</term><term>Graines</term></keywords><keywords scheme="MESH" qualifier="embryology" xml:lang="en"><term>Citrus</term><term>Seeds</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Apomixis</term><term>Citrus</term><term>Populus</term><term>Seeds</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Apomixie</term><term>Citrus</term><term>Graines</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Chromosomes, Artificial, Bacterial</term><term>Genome, Plant</term><term>Genomics</term><term>Haplotypes</term><term>Molecular Sequence Data</term><term>Open Reading Frames</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term><term>Synteny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cadres ouverts de lecture</term><term>Chromosomes artificiels de bactérie</term><term>Données de séquences moléculaires</term><term>Génome végétal</term><term>Génomique</term><term>Haplotypes</term><term>Polymorphisme de nucléotide simple</term><term>Synténie</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Polyembryony, in which multiple somatic nucellar cell-derived embryos develop in addition to the zygotic embryo in a seed, is common in the genus Citrus. Previous genetic studies indicated polyembryony is mainly determined by a single locus, but the underlying molecular mechanism is still unclear. As a step towards identification and characterization of the gene or genes responsible for nucellar embryogenesis in Citrus, haplotype-specific physical maps around the polyembryony locus were constructed. By sequencing three BAC clones aligned on the polyembryony haplotype, a single contiguous draft sequence consisting of 380 kb containing 70 predicted open reading frames (ORFs) was reconstructed. Single nucleotide polymorphism genotypes detected in the sequenced genomic region showed strong association with embryo type in Citrus, indicating a common polyembryony locus is shared among widely diverse Citrus cultivars and species. The arrangement of the predicted ORFs in the characterized genomic region showed high collinearity to the genomic sequence of chromosome 4 of Vitis vinifera and linkage group VI of Populus trichocarpa, suggesting that the syntenic relationship among these species is conserved even though V. vinifera and P. trichocarpa are non-apomictic species. This is the first study to characterize in detail the genomic structure of an apomixis locus determining adventitious embryony.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22195586</PMID><DateCompleted><Year>2012</Year><Month>09</Month><Day>27</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-2259</ISSN><JournalIssue CitedMedium="Internet"><Volume>183</Volume><PubDate><Year>2012</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Plant science : an international journal of experimental plant biology</Title><ISOAbbreviation>Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus.</ArticleTitle><Pagination><MedlinePgn>131-42</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plantsci.2011.08.002</ELocationID><Abstract><AbstractText>Polyembryony, in which multiple somatic nucellar cell-derived embryos develop in addition to the zygotic embryo in a seed, is common in the genus Citrus. Previous genetic studies indicated polyembryony is mainly determined by a single locus, but the underlying molecular mechanism is still unclear. As a step towards identification and characterization of the gene or genes responsible for nucellar embryogenesis in Citrus, haplotype-specific physical maps around the polyembryony locus were constructed. By sequencing three BAC clones aligned on the polyembryony haplotype, a single contiguous draft sequence consisting of 380 kb containing 70 predicted open reading frames (ORFs) was reconstructed. Single nucleotide polymorphism genotypes detected in the sequenced genomic region showed strong association with embryo type in Citrus, indicating a common polyembryony locus is shared among widely diverse Citrus cultivars and species. The arrangement of the predicted ORFs in the characterized genomic region showed high collinearity to the genomic sequence of chromosome 4 of Vitis vinifera and linkage group VI of Populus trichocarpa, suggesting that the syntenic relationship among these species is conserved even though V. vinifera and P. trichocarpa are non-apomictic species. This is the first study to characterize in detail the genomic structure of an apomixis locus determining adventitious embryony.</AbstractText><CopyrightInformation>Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nakano</LastName><ForeName>Michiharu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Citrus Research, National Institute of Fruit Tree Science, Shizuoka 424-0292, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shimada</LastName><ForeName>Takehiko</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Endo</LastName><ForeName>Tomoko</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Fujii</LastName><ForeName>Hiroshi</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Nesumi</LastName><ForeName>Hirohisa</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Kita</LastName><ForeName>Masayuki</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Ebina</LastName><ForeName>Masumi</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Shimizu</LastName><ForeName>Tokurou</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Omura</LastName><ForeName>Mitsuo</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>AB573149</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>08</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>Ireland</Country><MedlineTA>Plant Sci</MedlineTA><NlmUniqueID>9882015</NlmUniqueID><ISSNLinking>0168-9452</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D060832" MajorTopicYN="N">Apomixis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D022202" MajorTopicYN="N">Chromosomes, Artificial, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002957" MajorTopicYN="N">Citrus</DescriptorName><QualifierName UI="Q000196" MajorTopicYN="N">embryology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012639" MajorTopicYN="N">Seeds</DescriptorName><QualifierName UI="Q000196" MajorTopicYN="N">embryology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026801" MajorTopicYN="Y">Synteny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D027843" MajorTopicYN="N">Vitis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2011</Year><Month>03</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2011</Year><Month>07</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2011</Year><Month>08</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>12</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>12</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>9</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22195586</ArticleId><ArticleId IdType="pii">S0168-9452(11)00223-8</ArticleId><ArticleId IdType="doi">10.1016/j.plantsci.2011.08.002</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country></list><tree><noCountry><name sortKey="Ebina, Masumi" sort="Ebina, Masumi" uniqKey="Ebina M" first="Masumi" last="Ebina">Masumi Ebina</name><name sortKey="Endo, Tomoko" sort="Endo, Tomoko" uniqKey="Endo T" first="Tomoko" last="Endo">Tomoko Endo</name><name sortKey="Fujii, Hiroshi" sort="Fujii, Hiroshi" uniqKey="Fujii H" first="Hiroshi" last="Fujii">Hiroshi Fujii</name><name sortKey="Kita, Masayuki" sort="Kita, Masayuki" uniqKey="Kita M" first="Masayuki" last="Kita">Masayuki Kita</name><name sortKey="Nesumi, Hirohisa" sort="Nesumi, Hirohisa" uniqKey="Nesumi H" first="Hirohisa" last="Nesumi">Hirohisa Nesumi</name><name sortKey="Omura, Mitsuo" sort="Omura, Mitsuo" uniqKey="Omura M" first="Mitsuo" last="Omura">Mitsuo Omura</name><name sortKey="Shimada, Takehiko" sort="Shimada, Takehiko" uniqKey="Shimada T" first="Takehiko" last="Shimada">Takehiko Shimada</name><name sortKey="Shimizu, Tokurou" sort="Shimizu, Tokurou" uniqKey="Shimizu T" first="Tokurou" last="Shimizu">Tokurou Shimizu</name></noCountry><country name="Japon"><noRegion><name sortKey="Nakano, Michiharu" sort="Nakano, Michiharu" uniqKey="Nakano M" first="Michiharu" last="Nakano">Michiharu Nakano</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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