Table 1 True effects and statistical powers of 10 simulated QTL and Type 1 error rates for the modified LASSO method and GEMMA drawn from 100 replicated simulation experiments

From: Prediction and association mapping of agronomic traits in maize using multiple omic data

QTL

Chromosome

Position (bp)

Effect

R2a (%)

Statistical power (%)

     

LASSO

GEMMA-A b

GEMMA-B c

QTL-1

1

64 397 509

0.6137

2

36

2

0

QTL-2

1

217 180 912

0.4196

2

49

10

1

QTL-3

2

40 411 229

0.5500

4

68

5

0

QTL-4

3

28 354 373

0.9151

4

72

58

27

QTL-5

4

17 376 169

0.6681

6

95

89

58

QTL-6

5

11 600 672

1.1541

6

98

88

65

QTL-7

5

216 767 558

1.3985

8

99

98

91

QTL-8

6

142 446 480

0.7337

8

98

99

87

QTL-9

7

21 638 945

1.4079

10

99

100

100

QTL-10

8

172 759 416

1.5636

10

99

100

98

Type 1 error

    

0.00139

0.00446

0.00056

  1. Abbreviations: GEMMA, genome-wide efficient mixed model association; LASSO, least absolute shrinkage and selection operator; QTL, quantitative trait loci.
  2. aR2: Proportion of the total phenotypic variation explained by the QTL.
  3. bGEMMA-A: Bonferroni correction with P-value less than 1/m, where m is the total number of markers.
  4. cGEMMA-B: Bonferroni correction with P-value less than 0.05/m, where m is the total number of markers.
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