Table 5.
Prediction accuracies for wood quality and growth traits estimated with cross-validation sets built with full-sib families, using pedigree (CV2-A), ridge regression (CV2-RR) or both (CV2-RRA) sources of information with all SNPs ( m = 6,932) and various subpopulations of individuals
| Cross-validation | |||||
|---|---|---|---|---|---|
| Trait† | Subpopulation* | Pedigree (CV2-A) | Markers (CV2-RR) | Markers and pedigree (CV2-RRA) | Relative efficiency markers/pedigree (%) |
| ADEN | BG1 | 0.57 | 0.59 | 0.62 | 104 |
| BG1 → BG2 | 0.10 | 0.10 | 0.19 | – | |
| S1 | 0.71 | 0.63 | 0.69 | 89 | |
| S1 → S2 | 0.59 | 0.53 | 0.57 | 90 | |
| AMFA | BG1 | 0.55 | 0.36 | 0.47 | 65 |
| BG1 → BG2 | 0.13 | 0.04 | 0.05 | – | |
| S1 | 0.62 | 0.52 | 0.61 | 84 | |
| S1 → S2 | 0.52 | 0.41 | 0.50 | 79 | |
| HT17 | BG1 | 0.44 | 0.33 | 0.42 | 75 |
| BG1 → BG2 | −0.01 | −0.01 | −0.01 | – | |
| S1 | 0.66 | 0.55 | 0.64 | 83 | |
| S1 → S2 | 0.33 | 0.22 | 0.29 | 67 | |
| DBH17 | BG1 | 0.30 | 0.29 | 0.34 | 97 |
| BG1 → BG2 | 0.13 | −0.06 | −0.07 | – | |
| S1 | 0.53 | 0.48 | 0.53 | 91 | |
| S1 → S2 | 0.23 | 0.15 | 0.20 | 65 | |
| MSE‡ | 0.081 | 0.075 | 0.074 | – | |
†ADEN: average wood density; AMFA: average microfibril angle; HT17: 17-year height; DBH17: 17-year diameter at breast height.
*BG1: both training and testing sets from breeding group 1; BG1 → BG2: training sets from breeding group 1 and testing sets from breeding group 2; S1: both training and testing sets from site 1; S1 → S2: training sets from site 1 and testing sets from site 2.
‡Mean standard error over cross-validation iterations and subpopulations.