Table 3.
The corresponding predictive abilities for GS analyses in Table 2, calculated as the correlation between the raw phenotype (juvenile height: HTJ) and their genomic estimated breeding values (GEBVs) or deregressed genomic estimated breeding values (GDEBVs)
| Analysis | Predictive ability (SE) | |||
|---|---|---|---|---|
| ABLUP | RR-BLUP | GRR | Bayes-B | |
| r (HTJ, HTJ GEBVs) | 0.71 (0.003) | 0.43 (0.0004) | 0.42 (0.0006) | 0.43 (0.0007) |
| EBV < 201 | 0.10 (0.002) | 0.07 (0.002) | 0.07 (0.003) | |
| EBV < 202 | 0.04 (0.002) | −0.01 (0.003) | −0.01 (0.003) | |
| EBV < 203 | −0.10 (0.003) | −0.12 (0.004) | −0.09 (0.003) | |
| EBV > 201 | 0.05 (0.002) | 0.03 (0.002) | 0.07 (0.004) | |
| EBV > 202 | 0.04 (0.002) | 0.01 (0.002) | 0.07 (0.003) | |
| EBV > 203 | 0.15 (0.004) | 0.12 (0.005) | 0.59 (0.0004) | |
| r (HTJ, HTJ GDEBVs) | 0.06 (0.008) | 0.009 (0.007) | 0.40 (0.003) | |
| EBV < 201 | −0.20 (0.006) | −0.21 (0.005) | −0.04 (0.006) | |
| EBV < 202 | −0.22 (0.005) | −0.25 (0.005) | −0.15 (0.007) | |
| EBV < 203 | −0.21 (0.006) | −0.20 (0.006) | −0.21 (0.006) | |
| EBV > 201 | 0.23 (0.004) | 0.31 (0.005) | 0.20 (0.005) | |
| EBV > 202 | 0.19 (0.005) | 0.22 (0.005) | 0.16 (0.006) | |
| EBV > 203 | 0.15 (0.007) | 0.11 (0.007) | 0.07 (0.010) | |
| r (HTJ, HT35 GEBVs) | 0.24 (0.005) | 0.21 (0.001) | 0.21 (0.001) | 0.22 (0.002) |
| EBV < 201 | −0.19 (0.001) | −0.13 (0.002) | −0.09 (0.005) | |
| EBV < 202 | −0.23 (0.001) | −0.17 (0.002) | −0.14 (0.004) | |
| EBV < 203 | −0.10 (0.002) | −0.07 (0.002) | −0.06 (0.004) | |
| EBV > 201 | −0.03 (0.001) | −0.04 (0.001) | −0.09 (0.002) | |
| EBV > 202 | −0.03 (0.0009) | −0.05 (0.001) | −0.07 (0.002) | |
| EBV > 203 | −0.04 (0.001) | −0.04 (0.002) | −0.06 (0.001) | |
| r (HTJ, HT35 GDEBVs) | −0.17 (0.005) | −0.13 (0.004) | 0.04 (0.006) | |
| EBV < 201 | −0.18 (0.003) | −0.13 (0.003) | −0.13 (0.003) | |
| EBV < 202 | −0.18 (0.003) | −0.18 (0.003) | −0.18 (0.003) | |
| EBV < 203 | −0.05 (0.003) | −0.03 (0.004) | −0.05 (0.004) | |
| EBV > 201 | 0.08 (0.005) | 0.13 (0.004) | 0.003 (0.004) | |
| EBV > 202 | 0.09 (0.005) | 0.09 (0.006) | −0.01 (0.003) | |
| EBV > 203 | 0.15 (0.005) | 0.15 (0.005) | 0.06 (0.006) | |
Results for the validation set as a whole are in bold (N = 136), below each are the results for each of the two clusters EBV < 20 (N = 83) and EBV > 20 (N = 53), with indices representing different training set composition: 1 all genotyped F1 individuals; 2 all genotyped F1 individuals minus the parents of the opposing cluster; 3 only the F1 parents of the cluster in question