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Table 3 List of significant SNP markers (−log10 [p-value] ≥ 3) associated with different spike related traits using the individual environment and combined data

From: Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.)

Environment 1 (E1; 2017–18)

Environment 2 (E2; 2018–19)

Combined data (E1; 2017–18 and E2; 2018–19)

SNP

Id

Chr.

Pos.

P.value

Effect

SNP

Id

Chr.

Pos.

P.value

Effect

SNP

Id

Chr.

Pos.

P.value

Effect

GWPS

GWPS

GWPS

SNP_10127

1,094,714

5B

102

3.24E-04

0.84

SNP_109

980,521

5A

169

2.29E-04

0.82

SNP_5177

1,089,342

2D

25

4.09E-04

1.11

SNP_493

3,025,448

2B

156

5.57E-04

1.09

SNP_1671

1,011,353

6B

74

3.52E-04

0.83

SNP_493

3,025,448

2B

156

4.46E-04

1.11

SNP_5177

1,089,342

2D

25

5.97E-04

1.07

SNP_8417

1,076,441

2A

222

9.50E-04

1.33

SNP_109

980,521

5A

169

6.93E-04

0.68

SNP_8783

1,023,982

3A

18

7.99E-04

0.78

LTH

SNP_7209

1,006,397

4A

177

7.13E-04

0.76

SNP_5621

1,241,685

2B

155

9.91E-04

0.73

SNP_2448

1,059,739

1A

127

5.72E-05

−7.77

SNP_13995

1,228,280

1A

76

8.15E-04

0.92

LTH

SNP_2970

1,009,860

1A

175

4.29E-04

−4.29

LTH

SNP_1852

982,036

6A

175

9.09E-05

−3.24

SNP_12067

1,147,118

2A

132

8.93E-04

−5.51

SNP_2448

1,059,739

1A

127

8.05E-05

−6.15

SNP_8107

1,091,955

6A

173

1.88E-04

−3.35

SNP_1852

982,036

6A

175

9.07E-04

− 3.57

SNP_1800

3,025,720

6A

159

1.21E-04

−3.76

SNP_1869

1,093,162

6A

175

1.88E-04

−3.42

SNP_1800

3,025,720

6A

159

9.36E-04

3.91

SNP_1852

982,036

6A

175

4.73E-04

−3.03

SNP_2448

1,059,739

1A

127

6.60E-04

−4.53

NSPP

SNP_2933

1,091,284

6A

175

7.03E-04

−3.42

SNP_2933

1,091,284

6A

175

6.90E-04

−2.9

SNP_11101

1,011,157

3B

104

1.26E-04

−0.67

SNP_2970

1,009,860

1A

175

7.84E-04

−4.5

SNP_1800

3,025,720

6A

159

7.01E-04

−2.49

SNP_454

1,001,462

4B

64

2.09E-04

0.56

NSPP

SNP_5334

982,125

7B

184

7.34E-04

−2.71

SNP_10510

1,079,112

7A

304

2.18E-04

− 0.68

SNP_454

1,001,462

4B

64

1.04E-04

− 0.41

NSPP

SNP_4595

1,090,297

7B

70

5.69E-04

−0.63

SNP_4595

1,090,297

7B

70

2.91E-04

−0.34

SNP_6294

1,006,701

6A

33

6.69E-06

0.41

SNP_5062

3,064,849

7B

40

6.51E-04

0.38

SNP_11101

1,011,157

3B

104

3.63E-04

−0.38

SNP_2495

1,066,071

3B

298

5.34E-04

0.26

SNP_41

1,010,420

7B

134

9.18E-04

−0.39

SNP_11135

1,129,086

5B

106

4.14E-04

−0.36

SNP_13287

1,090,849

3B

156

7.46E-04

−0.21

NSPS

SNP_13287

1,090,849

3B

156

6.23E-04

0.37

SNP_598

1,106,300

2A

160

8.30E-04

0.28

SNP_4596

1,090,518

6A

183

4.78E-05

1.17

SNP_10864

1,262,277

4A

227

7.08E-04

0.3

NSPS

SNP_4839

1,077,393

2B

151

1.21E-04

1.09

SNP_10510

1,079,112

7A

304

7.54E-04

−0.3

SNP_4528

3,024,470

2B

164

3.03E-04

−0.49

SNP_13896

1,167,029

2B

164

2.19E-04

1.12

NSPS

SNP_1779

991,804

2A

89

4.31E-04

−0.48

SNP_813

1,087,368

1A

127

3.45E-04

1.23

SNP_813

1,087,368

1A

127

5.24E-05

0.89

SL

SNP_1766

1,077,298

6A

193

4.14E-04

0.74

SNP_1779

991,804

2A

89

3.19E-04

0.94

SNP_10587

992,268

3A

118

3.63E-04

−0.36

SNP_10039

1,058,522

5A

71

7.82E-04

0.74

SNP_13896

1,167,029

2B

164

3.26E-04

0.83

SNP_12221

1,002,874

6B

74

9.90E-04

−0.31

SNP_12996

1,067,398

2B

55

9.23E-04

−0.87

SNP_12996

1,067,398

2B

55

3.50E-04

−0.71

SLN

  

0

  

SL

SNP_4596

1,090,518

6A

183

4.00E-04

0.56

SNP_241

985,588

5B

115

9.15E-04

0.29

SNP_12504

1,091,267

4A

107

5.10E-05

0.49

SNP_1766

1,077,298

6A

193

4.42E-04

−0.53

SLT

SNP_9403

3,027,359

7A

112

1.40E-04

0.41

SNP_5026

1,130,302

6A

71

6.36E-04

0.56

SNP_1870

981,078

5A

27

7.06E-04

2.21

SLN

SL

SLU

SNP_11184

1,120,035

1B

277

3.32E-05

−0.53

SNP_3859

1,192,931

7B

135

3.17E-04

0.27

SNP_5177

1,089,342

2D

25

1.64E-04

0.06

SNP_13306

1,128,418

6B

51

8.08E-05

−0.4

SNP_5909

1,040,130

6D

185

3.95E-04

−0.26

SNP_1870

981,078

5A

27

2.29E-04

−0.05

SNP_13877

1,206,584

6B

65

8.88E-05

−0.42

SNP_317

985,312

4B

58

5.37E-04

0.31

SNP_11011

3,064,643

5A

21

3.03E-04

−0.04

SNP_9637

1,227,916

3B

227

1.07E-04

−0.55

SNP_12504

1,091,267

4A

107

5.78E-04

0.31

SNP_10789

1,229,353

5A

29

5.46E-04

0.04

SNP_2980

1,118,663

2B

149

4.15E-04

−0.45

SNP_7958

1,211,711

6B

60

7.71E-04

0.46

SNP_10924

3,064,834

5B

102

5.83E-04

0.04

SNP_4799

3,064,625

5B

106

5.39E-04

0.25

SLN

SNP_14151

1,090,816

6A

1

6.88E-04

−0.03

SNP_3408

3,064,625

5B

106

6.90E-04

0.25

SNP_10880

1,210,090

1A

445

3.44E-08

0.21

SNP_3494

1,218,597

6A

167

9.25E-04

0.04

SLT

SNP_11184

1,120,035

1B

277

4.73E-08

−0.38

–

–

–

–

–

–

SNP_491

1,111,091

1B

451

3.50E-05

−3.68

SNP_13296

1,129,001

1D

231

1.01E-04

0.23

–

–

–

–

–

–

SNP_1105

1,093,432

1B

187

3.78E-05

−3.27

SNP_5061

1,126,012

2B

106

1.10E-04

0.15

–

–

–

–

–

–

SNP_11184

1,120,035

1B

277

4.08E-05

−3.44

SNP_1140

987,653

3B

117

1.14E-04

−0.16

–

–

–

–

–

–

SNP_1784

1,032,134

1B

262

6.88E-05

−2.63

SNP_8087

1,149,694

3D

292

1.46E-04

−0.15

–

–

–

–

–

–

SNP_2980

1,118,663

2B

149

2.24E-04

−3.64

SNP_13268

1,003,566

4A

242

1.89E-04

0.14

–

–

–

–

–

–

SNP_11490

1,094,450

3B

24

2.69E-04

3.07

SNP_1208

987,611

5A

161

2.15E-04

−0.15

–

–

–

–

–

–

SNP_6814

1,000,905

3B

34

8.27E-04

−2.81

SNP_4799

3,064,625

5B

106

2.53E-04

0.13

–

–

–

–

–

–

SNP_13306

1,128,418

6B

51

8.62E-04

−1.75

SNP_3886

3,064,747

5B

102

3.93E-04

0.1

–

–

–

–

–

–

SLU

SNP_1091

1,206,846

6A

103

4.07E-04

−0.24

–

–

–

–

–

–

SNP_11184

1,120,035

1B

277

7.32E-05

0.06

SNP_10537

1,127,855

6B

153

4.20E-04

−0.15

–

–

–

–

–

–

SNP_5004

1,096,126

3B

161

1.41E-04

0.08

SNP_5909

1,040,130

6D

185

4.22E-04

−0.12

–

–

–

–

–

–

SNP_10924

3,064,834

5B

102

1.47E-04

0.1

SLT

–

–

–

–

–

–

SNP_4799

3,064,625

5B

106

1.89E-04

0.06

SNP_11184

1,120,035

1B

277

7.18E-05

−2.81

–

–

–

–

–

–

SNP_3408

3,064,625

5B

106

2.43E-04

−0.05

SNP_4799

3,064,625

5B

106

2.22E-04

1.48

–

–

–

–

–

–

SNP_13306

1,128,418

6B

51

4.17E-04

0.07

SNP_3408

3,064,625

5B

106

3.13E-04

1.44

–

–

–

–

–

–

SNP_5327

998,729

6D

186

4.73E-04

−0.05

SLU

–

–

–

–

–

–

SNP_10576

1,130,017

6D

187

8.58E-04

0.06

SNP_1792

1,209,199

1A

280

3.05E-08

0.04

–

–

–

–

–

–

SNP_8090

1,130,017

6D

187

8.59E-04

−0.05

SNP_11184

1,120,035

1B

277

9.56E-07

0.05

–

–

–

–

–

–

SNP_5909

1,040,130

6D

185

9.61E-04

0.05

SNP_8940

1,207,869

3A

201

2.01E-05

−0.03

–

–

–

–

–

–

–

–

–

–

–

–

SNP_2821

1,321,784

3B

162

5.84E-05

0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_3884

1,002,975

3B

254

1.04E-04

−0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_9866

1,256,184

3B

133

1.06E-04

0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_2796

1,083,825

4A

221

1.55E-04

−0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_6196

1,127,488

4A

39

1.61E-04

−0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_444

992,456

4A

129

1.89E-04

0.03

–

–

–

–

–

–

–

–

–

–

–

–

SNP_218

1,042,220

4B

90

4.63E-04

−0.03

–

–

–

–

–

–

–

–

–

–

–

–

SNP_652

990,542

5A

95

5.88E-04

−0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_10924

3,064,834

5B

102

6.04E-04

0.02

–

–

–

–

–

–

–

–

–

–

–

–

SNP_13218

1,209,264

6A

191

9.11E-04

−0.03

–

–

–

–

–

–

–

–

–

–

–

–

SNP_7430

1,127,751

7A

173

9.46E-04

0.02

  1. Chr: Chromosome, Pos: Position (cM), GWPS: Grain weight per spike, LTH: Lowest tiller height, NSPP: Number of spike per plant, SL: Spike length, NSPS: Number of spikelets per spike, SLN: Spike-layer number, SLT: Spike-layer thickness, SLU: Spike-layer uniformity
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