Skip to main content
. 2017 Feb 1;49:17. doi: 10.1186/s12711-017-0293-6

Table 1.

Accuracy of genomic prediction for BCWD survival DAYS in rainbow trout

Modela Training sample Testing sample
Phenotyped fish Genotyped fish Effective SNPs h2 b Genotyped fish Predictive abilityc Biasd
P-BLUP 7893 0 0 0.37 0 0.34 0.86
ssGBLUP 7893 1473 35,636 0.33 930 0.63 0.99
wssGBLUP2 7893 1473 35,623 0.33 930 0.67 0.71
wssGBLUP3 7893 1473 35,623 0.33 930 0.65 0.65
BayesB 1473 1473 35,636 0.23 930 0.71 1.16

aThe estimated breeding values (EBV) were estimated with a pedigree-based animal model (P-BLUP); and the genomic EBV (GEBV) were estimated with three genomic selection (GS) models: single-step GBLUP (ssGBLUP), weighted ssGBLUP (wssGBLUP) and Bayesian method BayesB. The wssGBLUP2 and wssGBLUP3 corresponds to iteration 2 and 3, respectively

bFor the GS models, h2 is the proportion of phenotypic variance explained by the markers. For the P-BLUP model, h2 is the trait narrow-sense heritability estimated from pedigree and phenotypic records

cThe predictive ability of EBV PAEBV or GEBV PAGEBV was defined as the correlation of mid-parent EBV or GEBV with MPP from each PTF: PAEBV=CORRMPP,MidparentEBV; PAGEBV=CORRMPP,MidparentGEBV

dThe bias of EBV BiasEBV or GEBV BiasGEBV was defined as the regression coefficient of performance MPP on predicted mid-parent EBV or GEBV: BiasEBV=REGRESMPP,MidparentEBV;BiasGEBV=REGRESMPP,MidparentGEBV