ISIK, Fikret; BARTHOLOMÉ, Jérôme; FARJAT, Alfredo; CHANCEREL, Emilie; RAFFIN, Annie; SANCHEZ, Léopoldo; PLOMION, Christophe; BOUFFIER, Laurent

doi:10.1016/j.plantsci.2015.08.006

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ISIK, Fikret
Biodiversité, Gènes & Communautés [BioGeCo]

BARTHOLOMÉ, Jérôme
Biodiversité, Gènes & Communautés [BioGeCo]

FARJAT, Alfredo
North Carolina State University [Raleigh] [NC State]

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Article de revue

Ce document a été publié dans

Plant Science. 2016, vol. 242, p. 108-119

Elsevier

Résumé en anglais

A 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).< Réduire

Mots clés

pinus pinaster

Mots clés en anglais

linkage disequilibrium

tree breeding

genomic relationship

bayesian regression

DOI

http://dx.doi.org/10.1016/j.plantsci.2015.08.006

Projet Européen

Novel tree breeding strategies

Origine

Importé de hal

Unités de recherche

BioGeCo (Biodiversité Gènes & Communautés) - UMR 1202