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Cross-species transferability and mapping of genomic and cDNA SSRs in pines

hal.structure.identifierBiodiversité, Gènes et Ecosystèmes [BioGeCo]
dc.contributor.authorCHAGNÉ, David
hal.structure.identifierBiodiversité, Gènes et Ecosystèmes [BioGeCo]
dc.contributor.authorCHAUMEIL, Philippe
hal.structure.identifierBiodiversité, Gènes et Ecosystèmes [BioGeCo]
dc.contributor.authorRAMBOER, Agnes
hal.structure.identifierUniversidad Politécnica de Madrid [UPM]
dc.contributor.authorCOLLADA, Carmen
hal.structure.identifierInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology [INIA]
dc.contributor.authorGUEVARA, Antonio
hal.structure.identifierInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology [INIA]
dc.contributor.authorCERVERA, M.T.
hal.structure.identifierIstituto di Genetica Vegetale, Sezione di Firenze
dc.contributor.authorVENDRAMIN, G.G.
hal.structure.identifierStation de physiologie végétale
dc.contributor.authorGARCIA, Virginie
hal.structure.identifierBiodiversité, Gènes et Ecosystèmes [BioGeCo]
dc.contributor.authorFRIGERIO, Jean-Marc
hal.structure.identifierNew Zealand Forest Research Institute
dc.contributor.authorECHT, C.
hal.structure.identifierNew Zealand Forest Research Institute
dc.contributor.authorRICHARDSON, T.
hal.structure.identifierBiodiversité, Gènes et Ecosystèmes [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2004
dc.identifier.issn0040-5752
dc.description.abstractEnTwo unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 51% in P. taeda and P. pinaster, respectively) and tended to be found within translated regions (76% in both species), whereas dinucleotide repeats were preferentially found within the 5'- and 3'-untranslated regions (75 and 65%, respectively). Fifty-three primer pairs amplifying a single PCR fragment in the source species (mainly P. taeda), were tested for amplification in six other pine species. The amplification rate with other pine species was high and corresponded with the phylogenetic distance between species, varying from 64.6% in P. canariensis to 94.2% in P. radiata. Genomic SSRs were found to be less transferable; 58 of the 107 primer pairs (i.e., 54%) derived from P. radiata amplified a single fragment in P. pinaster. Nine cDNA-SSRs were located to their chromosomes in two P. pinaster linkage maps. The level of polymorphism of these cDNA-SSRs was compared to that of previously and newly developed genomic-SSRs. Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles. This study suggests that useful SSR markers can be developed from pine ESTs
dc.language.isoen
dc.publisherSpringer Verlag
dc.subjectPINUS TAEDA
dc.subjectPINUS RADIATA
dc.subjectPINUS CANARIENSIS
dc.subject.enSIMPLE SEQUENCE REPEATS
dc.subject.enPIN MARITIME
dc.title.enCross-species transferability and mapping of genomic and cDNA SSRs in pines
dc.typeArticle de revue
dc.identifier.doi10.1007/s00122-004-1683-z
dc.subject.halSciences du Vivant [q-bio]/Génétique
bordeaux.journalTAG Theoretical and Applied Genetics
bordeaux.page1204-1214
bordeaux.volume19
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-02681281
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02681281v1
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