Tree Genetics & Genomes

, Volume 9, Issue 1, pp 37–51 | Cite as

Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding

Original Paper

Abstract

We developed a simulation study to test the efficiency of genomic selection (GS) in the case of Eucalyptus breeding. We simulated a recurrent selection scheme for clone production over four breeding cycles. Scenarios crossing broad sense heritabilities (H2 = 0.6 and 0.1) and dominance to additive variance ratios (R = 0.1; 0.5; and 1) were compared. GS was performed with 1,000 SNPs and 22 QTLs per Morgan and tested against phenotypic selection (PS) based on best linear unbiased prediction of parents and clones. When the training population was made up of the first cycle progeny tests and the candidate populations were the progeny tests of three successive cycles, GS accuracy decreased with breeding cycles (e.g., from 0.9 to 0.4 with H2 = 0.6 and R = 0.1), whereas PS presented constant performances (accuracy of 0.8 with H2 = 0.6 and R = 0.1). When the training population set was updated by associating data of previous cycles, GS accuracy was improved from 25 % to 418 %, especially with H2 = 0.1. The GS model including dominance effects performed better in clone selection (genotypic value) when dominance effects were preponderant (R = 1), heritability was high (H2 = 0.6 and with an updated training set), but no improvement was detected for parent selection (breeding value). The genetic gains over cycles were lower with the GS method without updating the data set but, with an updated training set, were similar to PS. However, the genetic gain per unit time with GS was 1.5 to 3 times higher than with PS for breeding and clone populations. These results highlight the value of GS in Eucalyptus breeding.

Keywords

Genomic selection BLUP Eucalyptus Dominance variance Additive variance Selection accuracy Genetic gain 

Supplementary material

11295_2012_528_MOESM1_ESM.pptx (67 kb)
Fig. S1abc Change in selection method accuracy over cycles for breeding population with updating of the training set: influence of heritability (H2 = 0.6 and H2 = 0.1) and dominance to additive variance R ratio (R = 0.1, R = 0.5 and R = 1). For GS, the training population is constituted of the individuals of the cycle 1 progeny tests to predict the candidate populations of subsequent cycles. (PPTX 66 kb)
11295_2012_528_MOESM2_ESM.pptx (67 kb)
Fig. S1def (PPTX 66 kb)
11295_2012_528_MOESM3_ESM.pptx (67 kb)
Fig. S2abc Change in selection method accuracy over cycles for breeding population with updating of the training set: influence of heritability (H2 = 0.6 and H2 = 0.1) and dominance to additive variance R ratio (R = 0.1, R = 0.5 and R = 1). For GS, the training population is constituted of individuals of the cycle 1 progeny tests to predict the candidate populations of subsequent cycles. (PPTX 66 kb)
11295_2012_528_MOESM4_ESM.pptx (67 kb)
Fig. S2def (PPTX 66 kb)
11295_2012_528_MOESM5_ESM.docx (21 kb)
ESM 1(DOCX 21 kb)

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.CIRAD—AGAP Research unit 108 “Genetic improvement and adaptation of tropical and Mediterranean plants”Montpellier Cedex 5France

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