Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)
Identifieur interne : 000A67 ( Main/Exploration ); précédent : 000A66; suivant : 000A68Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)
Auteurs : Manosh Kumar Biswas [République populaire de Chine] ; Qiang Xu [République populaire de Chine] ; Christoph Mayer [Allemagne] ; Xiuxin Deng [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
English descriptors
- KwdEn :
- Chromosome Mapping, Chromosomes, Plant, Citrus sinensis (genetics), Computational Biology, Databases, Nucleic Acid, Gene Frequency, Genome, Plant, Genome-Wide Association Study, Genotype, High-Throughput Nucleotide Sequencing, Microsatellite Repeats (genetics), Molecular Sequence Annotation, Polymorphism, Genetic, Reproducibility of Results.
- MESH :
- genetics : Citrus sinensis, Microsatellite Repeats.
- Chromosome Mapping, Chromosomes, Plant, Computational Biology, Databases, Nucleic Acid, Gene Frequency, Genome, Plant, Genome-Wide Association Study, Genotype, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Polymorphism, Genetic, Reproducibility of Results.
Abstract
Sweet orange (
Url:
DOI: 10.1371/journal.pone.0104182
PubMed: 25148383
PubMed Central: 4141690
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (<italic>Citrus sinensis</italic>)</title><author><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author><author><name sortKey="Mayer, Christoph" sort="Mayer, Christoph" uniqKey="Mayer C" first="Christoph" last="Mayer">Christoph Mayer</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Forschungsmuseum Alexander Koenig, Bonn, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Forschungsmuseum Alexander Koenig, Bonn</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Cologne</region><settlement type="city">Bonn</settlement></placeName></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25148383</idno><idno type="pmc">4141690</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141690</idno><idno type="RBID">PMC:4141690</idno><idno type="doi">10.1371/journal.pone.0104182</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000210</idno><idno type="wicri:Area/Pmc/Curation">000210</idno><idno type="wicri:Area/Pmc/Checkpoint">000810</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000311</idno><idno type="wicri:Area/PubMed/Curation">000311</idno><idno type="wicri:Area/PubMed/Checkpoint">000311</idno><idno type="wicri:Area/Ncbi/Merge">001813</idno><idno type="wicri:Area/Ncbi/Curation">001813</idno><idno type="wicri:Area/Ncbi/Checkpoint">001813</idno><idno type="wicri:Area/Main/Merge">000A68</idno><idno type="wicri:Area/Main/Curation">000A67</idno><idno type="wicri:Area/Main/Exploration">000A67</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (<italic>Citrus sinensis</italic>)</title><author><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author><author><name sortKey="Mayer, Christoph" sort="Mayer, Christoph" uniqKey="Mayer C" first="Christoph" last="Mayer">Christoph Mayer</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Forschungsmuseum Alexander Koenig, Bonn, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Forschungsmuseum Alexander Koenig, Bonn</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Cologne</region><settlement type="city">Bonn</settlement></placeName></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China</addr-line></nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping</term><term>Chromosomes, Plant</term><term>Citrus sinensis (genetics)</term><term>Computational Biology</term><term>Databases, Nucleic Acid</term><term>Gene Frequency</term><term>Genome, Plant</term><term>Genome-Wide Association Study</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Microsatellite Repeats (genetics)</term><term>Molecular Sequence Annotation</term><term>Polymorphism, Genetic</term><term>Reproducibility of Results</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Microsatellite Repeats</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Chromosomes, Plant</term><term>Computational Biology</term><term>Databases, Nucleic Acid</term><term>Gene Frequency</term><term>Genome, Plant</term><term>Genome-Wide Association Study</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Annotation</term><term>Polymorphism, Genetic</term><term>Reproducibility of Results</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Sweet orange (<italic>Citrus sinensis</italic>) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their <italic>in silico</italic> PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of <italic>C. sinensis</italic> with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Weber, Jl" uniqKey="Weber J">JL Weber</name></author><author><name sortKey="Wong, C" uniqKey="Wong C">C Wong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kruglyak, S" uniqKey="Kruglyak S">S Kruglyak</name></author><author><name sortKey="Durrett, Rt" uniqKey="Durrett R">RT Durrett</name></author><author><name sortKey="Schug, Md" uniqKey="Schug M">MD Schug</name></author><author><name sortKey="Aquadro, Cf" uniqKey="Aquadro C">CF Aquadro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Richard, Gf" uniqKey="Richard G">GF Richard</name></author><author><name sortKey="Kerrest, A" uniqKey="Kerrest A">A Kerrest</name></author><author><name sortKey="Dujon, B" uniqKey="Dujon B">B 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Wierdl</name></author><author><name sortKey="Dominska, M" uniqKey="Dominska M">M Dominska</name></author><author><name sortKey="Petes, Td" uniqKey="Petes T">TD Petes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cavagnaro, Pf" uniqKey="Cavagnaro P">PF Cavagnaro</name></author><author><name sortKey="Chung, Sm" uniqKey="Chung S">SM Chung</name></author><author><name sortKey="Manin, S" uniqKey="Manin S">S Manin</name></author><author><name sortKey="Yildiz, M" uniqKey="Yildiz M">M Yildiz</name></author><author><name sortKey="Ali, A" uniqKey="Ali A">A Ali</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Ly" uniqKey="Zhang L">LY Zhang</name></author><author><name sortKey="Bernard, M" uniqKey="Bernard M">M Bernard</name></author><author><name sortKey="Leroy, P" uniqKey="Leroy P">P Leroy</name></author><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C Feuillet</name></author><author><name sortKey="Sourdille, P" uniqKey="Sourdille P">P Sourdille</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhao, H" uniqKey="Zhao H">H Zhao</name></author><author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name></author><author><name sortKey="You, Fm" uniqKey="You F">FM You</name></author><author><name sortKey="Luo, M" uniqKey="Luo M">M Luo</name></author><author><name sortKey="Peng, J" uniqKey="Peng J">J Peng</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>République populaire de Chine</li></country><region><li>District de Cologne</li><li>Rhénanie-du-Nord-Westphalie</li></region><settlement><li>Bonn</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name></noRegion><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></country><country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Mayer, Christoph" sort="Mayer, Christoph" uniqKey="Mayer C" first="Christoph" last="Mayer">Christoph Mayer</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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