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A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.

dc.contributor.authorDURAND, Jérôme
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODÉNÈS, Catherine
dc.contributor.authorCHANCEREL, Emilie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFRIGERIO, Jean-Marc
dc.contributor.authorVENDRAMIN, Giovanni
hal.structure.identifierDipartimento di Biotecnologie Agrarie
dc.contributor.authorSEBASTIANI, Federico
dc.contributor.authorBUONAMICI, Anna
dc.contributor.authorGAILING, Oliver
dc.contributor.authorKOELEWIJN, Hans-Peter
dc.contributor.authorVILLANI, Fiorella
dc.contributor.authorMATTIONI, Claudia
dc.contributor.authorCHERUBINI, Marcello
dc.contributor.authorGOICOECHEA, Pablo G
dc.contributor.authorHERRÁN, Ana
dc.contributor.authorIKARAN, Ziortza
hal.structure.identifierCentre de Bioinformatique de Bordeaux [CBIB]
dc.contributor.authorCABANÉ, Cyril
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorUENO, Saneyoshi
dc.contributor.authorALBERTO, Florian
dc.contributor.authorDUMOULIN, Pierre-Yves
dc.contributor.authorGUICHOUX, Erwan
hal.structure.identifierCentre de Bioinformatique de Bordeaux [CBIB]
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorDE DARUVAR, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2010
dc.identifier.issn1471-2164
dc.description.abstractEnBACKGROUND: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). RESULTS: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. CONCLUSION: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
dc.language.isoen
dc.publisherBioMed Central
dc.subjectQUERCUS ROBUR
dc.subjectQUERCUS PETRAEA
dc.subjectCHENE ROUVRE
dc.subjectQUERCUS SESSILIFLORA
dc.subjectCARTOGRAPHIE GENETIQUE
dc.subject.enCHENE
dc.subject.enCHENE PEDONCULE
dc.subject.meshChromosome Mapping
dc.subject.meshCost-Benefit Analysis
dc.subject.meshData Mining
dc.subject.meshExpressed Sequence Tags
dc.subject.meshGenetic Markers
dc.subject.meshGenome, Plant
dc.subject.meshMicrosatellite Repeats
dc.subject.meshMinisatellite Repeats
dc.subject.meshPolymorphism, Genetic
dc.subject.meshQuercus
dc.title.enA fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-11-570
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
bordeaux.journalBMC Genomics
bordeaux.page570
bordeaux.volume11
bordeaux.issue570
bordeaux.peerReviewedoui
hal.identifierhal-00645935
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00645935v1
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