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Table 3 Number of selected SNPs, number of tagged QTLs, percentage of genetic variance explained, and accuracies of genomic and phenotype prediction under different quantile of the distribution of FST scores, sampling distribution for the QTL effects and density of the marker panel using the proposed method. Standard errors of accuracies are listed between parentheses

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

  All SNPs 97.5 quantile1 99.0 quantile 99.5 quantile
  Gamma2 Predefined3 Gamma Predefined Gamma Predefined Gamma Predefined
200 K SNP marker panel
Selected SNP 200 K 200 K 4932 5620 1956 2171 935 1076
Tagged QTL4 95 97 33 69 18 47 13 31
% GV5 91.29 98.60 83.70 71.27 73.57 49.69 64.08 35.10
Acc_P6 0.462 0.445 0.503 0.490 0.472 0.415 0.434 0.359
  (0.018) (0.012) (0.017) (0.014) (0.015) (0.018) (0.028) (0.032)
Acc_G7 0.777 0.741 0.853 0.830 0.797 0.704 0.725 0.617
  (0.017) (0.012) (0.019) (0.023) (0.017) (0.031) (0.037) (0.026)
400 K SNP marker panel
Selected SNP 400 K 400 K 10,173 10,651 3586 4646 2078 2037
Tagged QTL 95 99 38 74 20 53 13 34
% GV 96.73 99.01 84.03 75.09 73.83 56.66 66.12 43.79
Acc_P 0.456 0.438 0.506 0.485 0.473 0.433 0.448 0.350
  (0.015) (0.017) (0.014) (0.017) (0.029) (0.021) (0.039) (0.028)
Acc_G 0.775 0.735 0.860 0.813 0.807 0.722 0.765 0.685
  (0.020) (0.012) (0.015) (0.012) (0.041) (0.025) (0.059) (0.052)
  1. 1quantile of the distribution of the FST scores, 2QTL effects sampled from a Gamma distribution, 3QTL effects pre-defined to explain at least 0.5% of genetic variance (GV), 4QTL with r2 > 0.7 with at least one selected SNP, 5GV = Genetic Variance, 6accuracy of phenotype prediction, 7accuracy of genomic prediction