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Table 6 Prediction accuracies for wood quality and growth traits estimated with cross-validation sets built with individuals within full-sib families for wood quality and growth traits using ridge regression (RR) for subsets (SS) of SNPs from single-marker regression controlling for A or K , the largest absolute effects from the full model (RRA), the highest minor allele frequencies (HMAF), and a random selection (RAN) for various subpopulations of individuals

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

 

Accuracies obtained in cross-validation with various marker subsets

Trait†

Number of markers (m) and subpopulation*

Association tests using pedigree information‡(CVSSA)

Association tests using genotypic information₸(CVSSK)

Markers with largest absolute effects (CVSSRRA)

Markers chosen randomly (CVSSRAN)

Markers with highest minor allele frequencies (CVSSHMAF)

ADEN

m

640

404

600

600

600

 

BG1

0.76

0.78

0.74

0.78

0.78

 

BG1 → BG2

0.20

0.06

0.03

0.06

0.16

 

S1

0.74

0.77

0.74

0.71

0.73

 

S1 → S2

0.55

0.51

0.52

0.58

0.61

AMFA

m

406

359

600

600

600

 

BG1

0.74

0.78

0.72

0.75

0.74

 

BG1 → BG2

0.03

0.04

0.01

−0.12

0.11

 

S1

0.73

0.76

0.69

0.65

0.66

 

S1 → S2

0.51

0.54

0.44

0.55

0.52

HT17

m

476

426

600

600

600

 

BG1

0.64

0.70

0.69

0.56

0.57

 

BG1 → BG2

−0.03

−0.04

−0.07

0.00

−0.19

 

S1

0.72

0.77

0.74

0.63

0.64

 

S1 → S2

0.28

0.29

0.29

0.32

0.29

DBH17

m

482

403

600

600

600

 

BG1

0.56

0.61

0.58

0.49

0.51

 

BG1 → BG2

−0.12

−0.13

−0.25

−0.05

−0.23

 

S1

0.71

0.77

0.70

0.63

0.65

 

S1 → S2

0.17

0.18

0.18

0.22

0.20

MSE‡

 

0.025

0.024

0.023

0.024

0.023

  1. ‡Subset of significant SNPs (P < 0.05) identified after an association study using relatedness estimated with pedigree information.
  2. ₸Subset of significant SNPs (P < 0.05) identified after an association study using the realized genomic relationship matrix.
  3. †ADEN: average wood density; AMFA: average microfibril angle; HT17: 17-year height; DBH17: 17-year diameter at breast height.
  4. *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.
  5. ‡Mean standard error over cross-validation iterations and subpopulations.