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Table 5 Summary of the main QTLs (−log10(Pval) ≥ 8) identified for the three traits

From: Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies

Trait

QTL

Chr

Pos

Lower Limit

Upper Limit

R2

Effect

Log

Minor All

Major All

MAF

EnvMax

Nb DiffEnv

DTA

95

3

158,974,594

158,943,646

159,005,990

0.15

1.27

10.03

G

C

0.41

Ner13R

19

plantHT

21

2

130,441,738

129,971,437

130,912,039

0.15

−6.74

9.21

A

G

0.14

Cam12W

3

71

6

6,614,012

6,593,785

6,636,807

0.13

−4.76

8.39

G

A

0.18

Cam12R

2

72

6

6,807,230

6,793,841

6,837,747

0.14

−4.87

8.77

T

G

0.18

Cam12R

2

78

6

20,330,595

12,258,527

20,758,095

0.27

−8.99

17.31

C

T

0.26

Cam12W

4

79

6

22,905,376

21,037,721

23,951,687

0.19

−5.45

11.42

T

G

0.31

Cam12R

3

80

6

25,3178,25

24,184,017

26,606,537

0.13

−4.41

8.17

T

C

0.2

Cam12R

2

81

6

28,130,108

26,695,327

28,659,766

0.16

−5.14

9.84

C

G

0.44

Cam12R

2

94

6

101,482,646

101,463,249

101,501,936

0.14

−5.98

8.22

T

A

0.17

Cam12W

2

110

8

12,782,777

12,767,198

12,798,330

0.19

−7.67

12.44

C

T

0.22

Cam12W

3

GY

65

3

141,621,777

140,505,559

144,210,207

0.12

0.42

8.13

A

C

0.27

Gai12W

5

85

3

187,028,970

186,994,852

187057,772

0.12

−0.48

8.49

A

C

0.28

Kar12W

1

120

6

5,155,708

5,131,927

5,177,694

0.12

−0.58

8.24

C

T

0.42

Cam12W

2

122

6

5,638,516

5,623,945

5,659,803

0.12

−0.57

8.11

T

G

0.23

Cam12W

2

124

6

5,871,000

5,855,407

5,887,383

0.12

−0.56

8.4

T

G

0.42

Cam12W

2

127

6

6,612,654

6,593,785

6,636,807

0.16

−0.65

10.44

C

A

0.32

Cam12W

2

128

6

6,807,462

6,793,841

6,837,747

0.12

−0.54

8.41

A

C

0.26

Cam12W

2

129

6

6,890,199

6,878,877

6,930,838

0.12

0.63

8.06

T

A

0.48

Cam12W

3

130

6

7,046,773

7,027,497

7,088,575

0.13

0.62

8.71

A

G

0.4

Cam12W

3

131

6

7,159,714

7,113,662

7,200,479

0.12

0.59

8.24

T

C

0.39

Cam12W

3

135

6

18,528,943

12,258,527

29,438,316

0.28

−0.78

18.7

G

C

0.31

Cam12W

6

147

6

101,482,646

101,463,249

101,501,936

0.22

−0.65

15.04

T

A

0.17

Cam12W

5

173

8

12,782,777

12,767,198

12,798,330

0.17

−0.61

11.8

C

T

0.22

Cam12W

4

  1. “Pos” indicates the physical position in base pair of the SNP with the strongest association on the V2 of reference genome. LowerLimit and UpperLimit indicate the lower and upper physical limits estimated by LD windows (LD_win) for each QTL. The proportion of the variance explained (R2), the effect of the major allele (Effect) as outputted by FastLMM, −log10(Pval) (Log), the minor and major alleles (Minor All and Major All) and the minor allele frequency (MAF) of the most significant SNP within the QTL are shown. The following columns represent environment for which the most associated QTL was observed (EnvMax) and the number of different environments in which QTL are detected (NbDiffEnv) are shown. Note that QTLs 71–72 for the plant height and QTLs 129–130 for the grain yield are genetically close (< 1 cM) and display high mean LD (r2K > 0.5). Hence, QTLs 71–72 and 129–130 can potentially be merged