Table 2. Genomic prediction accuracy in NAM-H.
| Cross-validation prediction accuracy (P-value) | Prediction accuracy (P-value) | Difference in prediction accuracy (P-value) | |||
|---|---|---|---|---|---|
| Training panel (Testers) | NAM-H (PHZ51) | Ames-H (PHZ51, B47) | Ames-H (PHZ51, B47) | Ames × PHZ51 (PHZ51 only) | Ames × B47 (B47 only) |
| Model | GBLUP | GBLUP | DGBLUP | GBLUP | GBLUP |
| DTS | 0.405 (2.2 × 10−11) | 0.331 (2.3 × 10−11) | −0.013 (0.21) | −0.028 (0.078) | −0.068 (2.7 × 10−3) |
| PH | 0.394 (1.4 × 10−10) | 0.235 (9.6 × 10−8) | +0.023 (0.021) | +0.014 (0.42) | −0.095 (8.5 × 10−5) |
| GY | 0.240 (2.2 × 10−9) | −0.001 (0.96) | −0.010 (0.33) | −0.018 (0.29) | +0.056 (0.014) |
Prediction accuracy: average correlation between observed and predicted phenotypes over the 24 populations in NAM-H; cross-validation prediction accuracy: leave-one-population-out prediction accuracy within NAM-H; difference in prediction accuracy: difference in cross-panel prediction accuracy between models (DGBLUP vs. GBLUP model in Ames-H) or between training sets (Ames × PHZ51 or Ames × B47 vs. Ames-H). Significance of average prediction accuracies (nonzero mean) and estimated differences in prediction accuracy (nonzero difference, paired by NAM-H population) was assessed by Student’s t-tests. Ames, North Central Regional Plant Introduction Station association panel; Ames-H, hybrid Ames panel; NAM, U.S. Nested Association Mapping panel; NAM-H, hybrid NAM panel; GBLUP, genomic best linear unbiased prediction; DGBLUP, dominance GBLUP; DTS, days to silking; PH, plant height; GY, grain yield adjusted for DTS.