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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

From: Genomic selection accuracies within and between environments and small breeding groups in white spruce

  

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

–

  1. †ADEN: average wood density; AMFA: average microfibril angle; HT17: 17-year height; DBH17: 17-year diameter at breast height.
  2. *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.
  3. ‡Mean standard error over cross-validation iterations and subpopulations.