Method | Scenariob | \( {\sigma}_g^2 \)(\( {\sigma}_{\varepsilon}^2 \)) | \( {\sigma}_e^2 \) | \( {\sigma}_{\alpha}^2\sum \limits_{j=1}^m2{p}_j\left(1-{p}_j\right) \) | 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, \( {\sigma}_{\varepsilon}^2 \) is the total genetic variance used in ssBR; \( {\sigma}_e^2 \) is the residual variance; \( {\sigma}_{\alpha}^2 \) is the marker variance; \( {\sigma}_{\alpha}^2\sum \limits_{j=1}^m2{p}_j\left(1-{p}_j\right) \) is used to calculate genetic variance via the estimated marker variance in ssBR, where pj 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; Pheno1 + 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 \( \frac{\sigma_{g\left(\varepsilon \right)}^2}{\left({\sigma}_{g\left(\varepsilon \right)}^2+{\sigma}_e^2\right)} \)
- 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