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Genomic selection in maritime pine

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorISIK, Fikret
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBARTHOLOMÉ, Jérôme
hal.structure.identifierNorth Carolina State University [Raleigh] [NC State]
dc.contributor.authorFARJAT, Alfredo
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCHANCEREL, Emilie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorRAFFIN, Annie
hal.structure.identifierUnité de recherche Amélioration, Génétique et Physiologie Forestières [AGPF]
dc.contributor.authorSANCHEZ, Léopoldo
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBOUFFIER, Laurent
dc.date.issued2016
dc.identifier.issn0168-9452
dc.description.abstractEnA two-generation maritime pine (Pinus pinaster Ait.) breeding population (n = 661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r2 = 0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (View the MathML source). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM).
dc.language.isoen
dc.publisherElsevier
dc.subjectpinus pinaster
dc.subject.enlinkage disequilibrium
dc.subject.entree breeding
dc.subject.engenomic relationship
dc.subject.enbayesian regression
dc.title.enGenomic selection in maritime pine
dc.typeArticle de revue
dc.identifier.doi10.1016/j.plantsci.2015.08.006
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halInformatique [cs]/Modélisation et simulation
dc.description.sponsorshipEuropeNovel tree breeding strategies
bordeaux.journalPlant Science
bordeaux.page108-119
bordeaux.volume242
bordeaux.peerReviewedoui
hal.identifierhal-02635765
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02635765v1
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