Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping
Identifieur interne : 001F96 ( Main/Exploration ); précédent : 001F95; suivant : 001F97Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping
Auteurs : François L. Luro [France] ; Gilles Costantino [France] ; Javier Terol [Espagne] ; Xavier Argout [France] ; Thierry Allario [France] ; Patrick Wincker [France] ; Manuel Talon [France] ; Patrick Ollitrault [France] ; Raphael Morillon [France]Source :
- BMC Genomics [ 1471-2164 ] ; 2008.
Abstract
During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences.
Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten
Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus.
Url:
DOI: 10.1186/1471-2164-9-287
PubMed: 18558001
PubMed Central: 2435559
Affiliations:
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Luro</name><affiliation wicri:level="1"><nlm:aff id="I1">INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao</wicri:regionArea><wicri:noRegion>20230 San Nicolao</wicri:noRegion><wicri:noRegion>20230 San Nicolao</wicri:noRegion></affiliation></author><author><name sortKey="Costantino, Gilles" sort="Costantino, Gilles" uniqKey="Costantino G" first="Gilles" last="Costantino">Gilles Costantino</name><affiliation wicri:level="1"><nlm:aff id="I1">INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao</wicri:regionArea><wicri:noRegion>20230 San Nicolao</wicri:noRegion><wicri:noRegion>20230 San Nicolao</wicri:noRegion></affiliation></author><author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name><affiliation wicri:level="1"><nlm:aff id="I2">Centro de Genomica, Instituto Valenciano de Investigationes Agrarias, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigationes Agrarias, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Argout, Xavier" sort="Argout, Xavier" uniqKey="Argout X" first="Xavier" last="Argout">Xavier Argout</name><affiliation wicri:level="1"><nlm:aff id="I3">CIRAD AMIS, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD AMIS, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Allario, Thierry" sort="Allario, Thierry" uniqKey="Allario T" first="Thierry" last="Allario">Thierry 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'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18558001</idno><idno type="pmc">2435559</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435559</idno><idno type="RBID">PMC:2435559</idno><idno type="doi">10.1186/1471-2164-9-287</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000964</idno><idno type="wicri:Area/Pmc/Curation">000963</idno><idno type="wicri:Area/Pmc/Checkpoint">001045</idno><idno type="wicri:Area/Ncbi/Merge">000848</idno><idno type="wicri:Area/Ncbi/Curation">000848</idno><idno type="wicri:Area/Ncbi/Checkpoint">000848</idno><idno 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Luro</name><affiliation wicri:level="1"><nlm:aff id="I1">INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao</wicri:regionArea><wicri:noRegion>20230 San Nicolao</wicri:noRegion><wicri:noRegion>20230 San Nicolao</wicri:noRegion></affiliation></author><author><name sortKey="Costantino, Gilles" sort="Costantino, Gilles" uniqKey="Costantino G" first="Gilles" last="Costantino">Gilles Costantino</name><affiliation wicri:level="1"><nlm:aff id="I1">INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao</wicri:regionArea><wicri:noRegion>20230 San Nicolao</wicri:noRegion><wicri:noRegion>20230 San Nicolao</wicri:noRegion></affiliation></author><author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name><affiliation wicri:level="1"><nlm:aff id="I2">Centro de Genomica, Instituto Valenciano de Investigationes Agrarias, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigationes Agrarias, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Argout, Xavier" sort="Argout, Xavier" uniqKey="Argout X" first="Xavier" last="Argout">Xavier Argout</name><affiliation wicri:level="1"><nlm:aff id="I3">CIRAD AMIS, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD AMIS, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Allario, Thierry" sort="Allario, Thierry" uniqKey="Allario T" first="Thierry" last="Allario">Thierry Allario</name><affiliation wicri:level="1"><nlm:aff id="I4">UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Wincker, Patrick" sort="Wincker, Patrick" uniqKey="Wincker P" first="Patrick" last="Wincker">Patrick Wincker</name><affiliation wicri:level="1"><nlm:aff id="I5">Genoscope, CNS, Evry, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Genoscope, CNS, Evry</wicri:regionArea><placeName><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><affiliation wicri:level="1"><nlm:aff id="I3">CIRAD AMIS, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD AMIS, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name><affiliation wicri:level="1"><nlm:aff id="I4">UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Morillon, Raphael" sort="Morillon, Raphael" uniqKey="Morillon R" first="Raphael" last="Morillon">Raphael Morillon</name><affiliation wicri:level="1"><nlm:aff id="I4">UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UPR 'Amélioration génétique d'espèces à multiplication végétative', CIRAD, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences.</p></sec><sec><title>Results</title><p>Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten <italic>Citrus </italic>species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis.</p></sec><sec><title>Conclusion</title><p>Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Espagne</li><li>France</li></country><settlement><li>Montpellier</li><li>Évry (Essonne)</li></settlement></list><tree><country name="France"><noRegion><name sortKey="Luro, Francois L" sort="Luro, Francois L" uniqKey="Luro F" first="François L" last="Luro">François L. Luro</name></noRegion><name sortKey="Allario, Thierry" sort="Allario, Thierry" uniqKey="Allario T" first="Thierry" last="Allario">Thierry Allario</name><name sortKey="Argout, Xavier" sort="Argout, Xavier" uniqKey="Argout X" first="Xavier" last="Argout">Xavier Argout</name><name sortKey="Costantino, Gilles" sort="Costantino, Gilles" uniqKey="Costantino G" first="Gilles" last="Costantino">Gilles Costantino</name><name sortKey="Morillon, Raphael" sort="Morillon, Raphael" uniqKey="Morillon R" first="Raphael" last="Morillon">Raphael Morillon</name><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><name sortKey="Wincker, Patrick" sort="Wincker, Patrick" uniqKey="Wincker P" first="Patrick" last="Wincker">Patrick Wincker</name></country><country name="Espagne"><noRegion><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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