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Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCHANCEREL, Emilie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLEPOITTEVIN, Camille
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierCenter for Plant Systems Biology [PSB Center]
dc.contributor.authorLIN, Yao-Cheng
hal.structure.identifierInstituto de Ecologia
dc.contributor.authorJARAMILLO-CORREA, Juan Pablo
hal.structure.identifierUniversity of California [Davis] [UC Davis]
dc.contributor.authorECKERT, Andrew J.
hal.structure.identifierUniversity of California [Davis] [UC Davis]
dc.contributor.authorWEGRZYN, Jill L.
hal.structure.identifierCommissariat à l'énergie atomique et aux énergies alternatives [CEA]
dc.contributor.authorZELENIKA, Diana
hal.structure.identifierCommissariat à l'énergie atomique et aux énergies alternatives [CEA]
dc.contributor.authorBOLAND, Anne
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFRIGERIO, Jean-Marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCHAUMEIL, Philippe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGARNIER‐GÉRÉ, Pauline
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBOURY, Christophe
hal.structure.identifierInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology [INIA]
dc.contributor.authorGRIVET, Delphine
hal.structure.identifierDepartment of Forest Ecology and GeneticsForest Research Centre
dc.contributor.authorGONZÁLEZ-MARTÍNEZ, Santiago C.
hal.structure.identifierCenter for Plant Systems Biology [PSB Center]
dc.contributor.authorROUZÉ, Pierre
hal.structure.identifierCenter for Plant Systems Biology [PSB Center]
dc.contributor.authorVAN DE PEER, Yves
hal.structure.identifierUniversity of California [Davis] [UC Davis]
dc.contributor.authorNEALE, David B.
hal.structure.identifierInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology [INIA]
dc.contributor.authorCERVERA, Maria T.
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2011
dc.identifier.issn1471-2164
dc.description.abstractEn*Background : Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe. *Results : We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. *Conclusions : Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.
dc.language.isoen
dc.publisherBioMed Central
dc.subjectPINUS TAEDA
dc.subjectCARTOGRAPHIE GENETIQUE
dc.subjectPIN A L'ENCENS
dc.subjectPOLYMORPHISME NUCLÉOTIDIQUE SIMPLE
dc.subjectEXTRACTION D'ADN
dc.subject.enPIN MARITIME
dc.title.enDevelopment and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-12-368
dc.subject.halSciences du Vivant [q-bio]/Génétique
bordeaux.journalBMC Genomics
bordeaux.page14 p.
bordeaux.volume12
bordeaux.peerReviewedoui
hal.identifierhal-02649406
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02649406v1
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