Table 2 Genomic selection analyses based on all marker information (4,993 SNPs) and following different schemes of model building and application. “Pedigree” indicates that only pedigree information was used for prediction after model calibrations, which is also referred to as the conventional breeding approach in the body of the text; “Markers” indicates that SNP information was used for prediction. All results are from cross-validations using 10 replicates on randomly-selected trees not included in model fitting, but from the same families used to fit models. The first scheme considered all 734 trees from the two sites combined. Models in other schemes were trained on one site only and whether applied on the same or on the other site, respectively. For comparative purposes, the “Site_mean” scheme represents the mean of 5 models run on 359 trees corresponding to the mean number of trees per site. Model accuracy is the correlation between the cross-validated estimated breeding value (using independent sets of trees) and the “true” reference breeding value. The predictive ability is the correlation between the predicted and the actual phenotypes. Genetic gains are given in absolute values and percentages are given in brackets. Gain estimates are based on predicted phenotypes and a selection intensity of 5%. Annual gain estimates were based on assumptions of a conventional breeding cycle length of 28 years for pedigree selection (“Pedigree”), and a shortened cycle length of 9 years for selection with markers (“Markers”), with 4 years for crosses and production of seedlots that are full-siblings to the training population, followed by 1 year for selection of individuals using markers and genomic selection models, and 4 years for vegetative propagation of selected individuals for seedling production

Wood density

Combined sites

0.89 (0.03)

0.84 (0.02)

0.45 (0.09)

0.49 (0.07)

34.74 (0.08)

35.63 (0.09)

Site1

0.80 (0.08)

0.77 (0.06)

0.34 (0.16)

0.38 (0.12)

35.90 (0.09)

31.87 (0.08)

Site2

0.88 (0.05)

0.82 (0.10)

0.52 (0.15)

0.56 (0.12)

26.25 (0.06)

29.48 (0.07)

Site_mean

0.85 (0.05)

0.81 (0.05)

0.42 (0.18)

0.43 (0.16)

30.15 (0.07)

28.55 (0.07)

Site1 → 2

0.79 (0.05)

0.77 (0.08)

0.42 (0.16)

0.44 (0.19)

24.60 (0.06)

21.47 (0.05)

Site2 → 1

0.85 (0.04)

0.80 (0.08)

0.36 (0.13)

0.39 (0.11)

40.02 (0.10)

45.46 (0.11)

Height

Combined sites

0.88 (0.03)

0.86 (0.03)

0.56 (0.08)

0.57 (0.07)

105.17 (0.13)

104.57 (0.13)

Site1

0.84 (0.05)

0.81 (0.04)

0.51 (0.11)

0.51 (0.11)

53.95 (0.07)

52.17 (0.07)

Site2

0.88 (0.02)

0.85 (0.03)

0.58 (0.09)

0.58 (0.12)

82.89 (0.10)

78.69 (0.10)

Site_mean

0.85 (0.05)

0.83 (0.05)

0.55 (0.12)

0.55 (0.12)

87.00 (0.11)

84.56 (0.11)

Site1 → 2

0.84 (0.03)

0.83 (0.04)

0.56 (0.12)

0.56 (0.13)

75.93 (0.09)

74.56 (0.09)

Site2 → 1

0.85 (0.04)

0.84 (0.03)

0.51 (0.11)

0.52 (0.11)

63.67 (0.08)

62.31 (0.08)

Diameter (DBH)

Combined sites

0.86 (0.03)

0.83 (0.04)

0.45 (0.06)

0.43 (0.07)

16.65 (0.14)

14.81 (0.13)

Site1

0.76 (0.08)

0.74 (0.08)

0.38 (0.15)

0.34 (0.15)

12.09 (0.10)

10.15 (0.09)

Site2

0.87 (0.02)

0.82 (0.04)

0.53 (0.05)

0.48 (0.08)

14.70 (0.13)

13.18 (0.12)

Site_mean

0.82 (0.05)

0.79 (0.06)

0.45 (0.09)

0.42 (0.11)

13.44 (0.12)

11.84 (0.10)

Site1 → 2

0.76 (0.05)

0.75 (0.05)

0.43 (0.09)

0.43 (0.10)

10.99 (0.10)

9.65 (0.08)

Site2 → 1

0.80 (0.05)

0.78 (0.05)

0.33 (0.13)

0.34 (0.12)

16.09 (0.14)

13.75 (0.12)

Microfibril angle^c

Combined sites

0.88 (0.03)

0.84 (0.04)

0.51 (0.11)

0.51 (0.10)

−2.71 (−0.15)

−2.78 (−0.15)

Site1

0.83 (0.06)

0.79 (0.04)

0.47 (0.15)

0.45 (0.13)

−2.47 (−0.12)

−2.29 (−0.11)

Site2

0.86 (0.04)

0.82 (0.04)

0.54 (0.16)

0.52 (0.15)

−1.72 (−0.11)

−1.80 (−0.12)

Site_mean

0.84 (0.06)

0.80 (0.05)

0.48 (0.15)

0.48 (0.14)

−1.84 (−0.11)

−1.80 (−0.11)

Site1 → 2

0.80 (0.03)

0.76 (0.04)

0.48 (0.13)

0.47 (0.12)

−2.05 (−0.13)

−1.95 (−0.12)

Site2 → 1

0.84 (0.04)

0.81 (0.04)

0.44 (0.13)

0.45 (0.11)

−2.14 (−0.10)

−2.16 (−0.10)