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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.