Table 2.

Mean (SD) of the “true” variance components and heritability in the base (founder) population (P-base) and the base population for the genomic phase^a and estimates of variance components and heritabilities from P-AM, ssGBLUP, and ssBR based on three scenarios of phenotyping^b

Method	Scenariob	${\sigma }_g^2$(${\sigma }_{\epsilon }^2$)	${\sigma }_e^2$	${\sigma }_{\alpha }^2\sum _{j=1}^{m}2p_j\left(1-p_j\right)$	h2c
True VCs in P-base		3.59 (0.03)	5.05 (0.09)	–	0.42 (0.004)
True VCs in G-base		2.82 (0.09)	5.10 (0.07)	–	0.36 (0.009)
P-AM	Pheno1	3.62 (0.12)	5.02 (0.02)	–	0.42 (0.009)
	Pheno1 + 2	3.52 (0.06)	5.07 (0.03)	–	0.41 (0.004)
	Pheno2	3.19 (0.20)*	5.21 (0.10)	–	0.38 (0.018)*
ssGBLUP	Pheno1	2.99 (0.12)***	5.54 (0.01)***	–	0.35 (0.009)***
	Pheno1 + 2	3.39 (0.06)***	5.17 (0.03)	–	0.40 (0.009)***
	Pheno2	3.36 (0.15)***	5.19 (0.05)	–	0.39 (0.013)*
ssBR	Pheno1	3.44 (0.15)	5.10 (0.04)	4.20 (0.10)***	0.40 (0.012)
	Pheno1 + 2	3.14 (0.10)***	5.24 (0.02)*	3.71 (0.11)	0.37 (0.008)***
	Pheno2	2.99 (0.20)	5.27 (0.06)**	2.97 (0.09)	0.36 (0.017)

^aP-AM: traditional pedigree-based animal model; ssGBLUP: single-step genomic BLUP; ssBR: single-step Bayesian regression. ${\sigma }_g^2$ is the genetic variance used in P-AM, ${\sigma }_{\epsilon }^2$ is the total genetic variance used in ssBR; ${\sigma }_e^2$ is the residual variance; ${\sigma }_{\alpha }^2$ is the marker variance; ${\sigma }_{\alpha }^2\sum _{j=1}^{m}2p_j\left(1-p_j\right)$ is used to calculate genetic variance via the estimated marker variance in ssBR, where p_j is the observed allele frequency at locus j, and m is the total number of markers

^bPheno₁: phenotypes from only the conventional phase (1–20 years) were used; Pheno_1 + 2: phenotypes from both the conventional phase and genomic selection phase (1–35 years) were used; Pheno₂: phenotypes from only the genomic selection phase were used (21–35 years)

^cHeritabilities (h²) from P-AM, ssGBLUP, and ssBR calculated as $\frac{{\sigma }_{g\left(\epsilon \right)}^2}{\left({\sigma }_{g\left(\epsilon \right)}^2+{\sigma }_e^2\right)}$

The significance test was performed to determine whether the estimated parameter differs from the simulated parameter. ^* significant at P < 0.01; ^** significant at P < 0.005; ^*** significant at P < 0.001