Skip to main content

Table 4 Number of selected SNPs, number of tagged QTL, percentage of genetic variance explained, and accuracies of genomic and phenotype prediction under different π values, sampling distribution for the QTL effects and density of the marker panel using BayesB method. Standard errors of accuracies are listed between parentheses

From: High density marker panels, SNPs prioritizing and accuracy of genomic selection

  (1-π) =0.90 (1-π) =0.95 (1-π) =0.98 (1-π) =0.99
  Gamma1 Predefined2 Gamma Predefined Gamma Predefined Gamma Predefined
200 K marker density
# SNP 20 K 20 K 10 K 10 K 4 K 4 K 2 K 2 K
Tagged QTL3 78 98 63 97 54 94 48 91
% GV4 89.31 98.16 86.43 97.88 84.30 95.76 83.88 93.20
Acc_P5 0.473 0.463 0.478 0.471 0.489 0.487 0.499 0.500
  (0.018) (0.009) (0.018) (0.009) (0.018) (0.008) (0.018) (0.007)
Acc_G6 0.797 0.770 0.807 0.785 0.827 0.810 0.845 0.833
  (0.017) (0.008) (0.017) (0.007) (0.018) (0.007) (0.018) (0.005)
400 K marker density
# SNP 40K 40K 20 K 20 K 8 K 8 K 4 K 4 K
Tagged QTL 86 99 75 98 59 97 53 96
% GV 92.36 98.46 91.88 98.16 91.20 97.78 91.03 96.69
Acc_P 0.465 0.450 0.470 0.457 0.478 0.469 0.488 0.481
  (0.015) (0.018) (0.015) (0.018) (0.014) (0.018) (0.013) (0.019)
Acc_G 0.790 0.756 0.799 0.767 0.813 0.787 0.829 0.807
  (0.019) (0.013) (0.017) (0.013) (0.016) (0.014) (0.015) (0.014)
  1. 1 QTL effects sampled from a Gamma distribution, 2QTL effects pre-defined to explain at least 0.5% of genetic variance (GV), 3QTL with r2 > 0.7 with at least one selected SNP, 4 GV = Genetic Variance, 5 accuracy of phenotype prediction, 6accuracy of genomic prediction