Afficher la notice abrégée

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCHANCEREL, Emilie
hal.structure.identifierUniversity of Wisconsin-Madison
dc.contributor.authorENDELMAN, Jeffrey
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLAMY, Jean-Baptiste
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorMANDROU, Eric
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierHelixVenture
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorEHRENMANN, François
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierDepartment of Forestry and Environmental Resources
dc.contributor.authorISIK, Fikret
hal.structure.identifierBiometris
dc.contributor.authorBINK, Marco C. A. M.
hal.structure.identifierBiometris
dc.contributor.authorVAN HEERWAARDEN, Joost
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBOUFFIER, Laurent
dc.date.issued2014
dc.identifier.issn1471-2164
dc.description.abstractEnBackground: The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results: Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H-e) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H-e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions: These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species.
dc.language.isoen
dc.publisherBioMed Central
dc.subject.enPinus pinaster; genetic diversity; linkage disequilibrium; recombination; linkage map; domestication; breeding program; forest tree; genomics; genomic selection
dc.title.enGenome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-15-171
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalBMC Genomics
bordeaux.page17 p.
bordeaux.volume15
bordeaux.peerReviewedoui
hal.identifierhal-02636858
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02636858v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=BMC%20Genomics&rft.date=2014&rft.volume=15&rft.spage=17%20p.&rft.epage=17%20p.&rft.eissn=1471-2164&rft.issn=1471-2164&rft.au=PLOMION,%20Christophe&CHANCEREL,%20Emilie&ENDELMAN,%20Jeffrey&LAMY,%20Jean-Baptiste&MANDROU,%20Eric&rft.genre=article


Fichier(s) constituant ce document

FichiersTailleFormatVue

Il n'y a pas de fichiers associés à ce document.

Ce document figure dans la(les) collection(s) suivante(s)

Afficher la notice abrégée