Table 2.

Comparison of genomic prediction accuracy between the stepwise linear mixed model (StepLMM) and genomic best linear unbiased prediction (GBLUP) based on WTCCC simulated data

${\mathit{h}}^2$	${\widehat{\mathit{h}}}^2$	${\widehat{\mathit{h}}}_{\mathit{q}}^2/{\widehat{\mathit{h}}}^{2^{\text{a}}}$	$r_{qtl}^{\text{b}}$	$r_{poly}^{\text{c}}$	$r_{StepLMM}^{\text{d}}$	$r_{GBLUP}^{\text{e}}$	$b_{StepLMM}^{\text{f}}$	$b_{GBLUP}^{\text{g}}$
0.25	0.25 (0.009)	0.68 (0.026)	0.71 (0.010)	0.27 (0.009)	0.75 (0.007)	0.49 (0.008)	0.89 (0.011)	1.16 (0.055)
0.50	0.52 (0.007)	0.81 (0.013)	0.87 (0.004)	0.23 (0.006)	0.90 (0.002)	0.71 (0.002)	0.94 (0.005)	1.04 (0.042)
0.75	0.76 (0.004)	0.92 (0.007)	0.95 (0.002)	0.18 (0.007)	0.96 (0.001)	0.86 (0.001)	0.98 (0.002)	1.01 (0.022)

^aProportion of phenotypic variance explained by the QTL in the models, $h_q^2=\frac{{\mathit{\sigma }}_q^2}{{\mathit{\sigma }}_q^2+{\mathit{\sigma }}_g^2+{\mathit{\sigma }}_e^2}$

^bCorrelation between true breeding values and genetic values explained by QTL detected with StepLMM

^cCorrelation between true breeding values and genetic values excluding QTL detected with StepLMM

^dCorrelation between true breeding values and genomic breeding values estimated with StepLMM

^eCorrelation between true breeding values and genomic breeding values estimated with GBLUP

^fRegression coefficient of the true on the estimated breeding values with StepLMM

^gRegression coefficient of the true on the estimated breeding values with GBLUP