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Table 6 Potential significant SNPs associated with root related traits

From: Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

Traits

Position

Methoda

Stage

Chr

P-value

-log10(P)

R2

Genotype

ARD

209,661,144

2

V2

Chr3

8.51E-08

7.07

0.100

G/A

ARD

159,805,368

2

V2

Chr6

8.32E-07

6.08

0.111

T/G

RBN

72,599,741

1

V1,V3

Chr1

3.31E-07

6.48

0.101

T/G

RBN

127,352,056

1

V2

Chr1

2.95E-07

6.53

0.115

T/C

RBN

1,707,072

1,3

V2

Chr2

4.37E-09

8.36

0.251

G/A

RBN

192,996,724

1

V2

Chr2

7.59E-08

7.12

0.151

 C/A

RBN

195,707,091

1

V2

Chr2

6.17E-08

7.21

0.152

 C/T

RBN

2,564,296

1

V2

Chr2

1.86E-07

6.73

0.108

 C/T

RBN

32,824,965

1

V2

Chr2

6.76E-08

7.17

0.107

G/C

RBN

171,057,172

2

V2

Chr3

4.68E-07

6.33

0.101

G/A

RBN

122,501,344

1

V1,V3

Chr4

8.91E-07

6.05

0.121

 C/T

RBN

87,176,006

1

V1,V3

Chr5

7.08E-07

6.15

0.123

 C/T

RBN

221,805,144

2

V2

Chr5

9.77E-07

6.01

0.134

G/A

RBN

178,455,944

2

V2

Chr5

2.29E-07

6.64

0.140

 C/T

RBN

205,892,847

2

V2

Chr5

2.82E-07

6.55

0.122

T/C

RBN

128,905,260

1

V2

Chr6

8.32E-07

6.08

0.114

G/A

RBN

162,388,475

2

V2

Chr6

7.08E-07

6.15

0.121

G/A

RBN

88,347,963

1

V1,V3

Chr8

7.41E-07

6.13

0.138

T/C

RBN

145,938,150

2

V2

Chr9

5.25E-07

6.28

0.150

G/A

RBN, SUA

58,218,452

2

V1,V3

Chr7

1.12E-15

14.95

0.302

 A/G

RBN,ROV, SUA

43,293,834

1

V1,V2

Chr2

1.29E-07

6.89

0.110

G/A

RDW

227,871,089

1

V2

Chr1

7.94E-07

6.10

0.140

 C/T

RDW

82,567,249

1

V2

Chr1

7.76E-07

6.11

0.140

 C/G

RDW

2,246,081

2

V2

Chr10

1.29E-11

10.89

0.223

G/A

RDW

191,539,297

2

V1,V3

Chr5

7.94E-07

6.10

0.160

G/C

RDW

82,882,718

2

V1,V3

Chr5

1.35E-07

6.87

0.063

 C/A

RDW

118,512,703

2

V2

Chr7

9.55E-07

6.02

0.113

 A/G

RDW,SUA

230,477,446

1

V1,V3

Chr1

8.91E-07

6.05

0.051

G/A

RDW/SDW

19,943,384

1

V2

Chr1

7.41E-09

8.13

0.160

 C/T

ROV

227,871,089

1

V1,V2,V3

Chr1

8.71E-07

6.06

0.140

 C/T

ROV

173,181,844

1

V2

Chr1

6.46E-07

6.19

0.120

G/A

ROV

150,754,726

1

V2

Chr2

8.32E-07

6.08

0.150

 A/T

ROV

166,210,299

1

V2

Chr2

5.01E-07

6.30

0.122

 C/T

ROV

21,486,113

1

V2

Chr2

1.70E-07

6.77

0.110

 C/T

ROV

187,822,582

2

V2

Chr3

2.82E-12

11.55

0.140

 C/T

ROV

12,060,838

2

V2

Chr3

1.00E-06

6.00

0.100

 A/G

ROV

241,936,576

1

V1,V2,V3

Chr4

9.77E-07

6.01

0.052

 C/G

ROV

118,806,068

1

V2

Chr5

9.55E-07

6.02

0.153

T/C

ROV

28,955,506

1

V2

Chr6

8.32E-07

6.08

0.054

G/A

ROV,SUA

82,882,718

2

V1,V2,V3

Chr5

7.94E-15

14.10

0.228

 C/A

SUA

227,871,089

1

V2

Chr1

9.55E-08

7.02

0.121

 C/T

SUA

1,707,072

1

V2

Chr2

3.55E-07

6.45

0.200

G/A

SUA

2,610,094

1

V2

Chr2

2.57E-08

7.59

0.121

 C/G

SUA

94,781,431

1

V2,V3

Chr3

7.94E-07

6.10

0.153

 C/T

SUA

7,141,374

2

V1,V3

Chr5

6.46E-08

7.19

0.152

G/A

SUA

217,144,020

2

V1,V3

Chr5

1.55E-12

11.81

0.160

 A/T

SUA

119,718,590

1

V2

Chr5

5.50E-07

6.26

0.150

 C/T

SUA

179,029,112

1

V2

Chr7

2.40E-07

6.62

0.145

 C/T

TRL

72,599,769

1

V1,V3

Chr1

4.68E-08

7.33

0.100

T/C

TRL

111,734,317

2

V2

Chr2

7.08E-07

6.15

0.128

 A/G

TRL

59,237,040

1

V2

Chr3

5.37E-08

7.27

0.134

G/A

TRL

241,936,576

1

V1,V3

Chr4

2.95E-07

6.53

0.061

 C/G

TRL

128,905,254

1

V2

Chr6

5.13E-07

6.29

0.106

G/A

  1. MAF minor allele frequency, R2 phenotypic contribution, Chr chromosome, RDW root dry weight, RDW/SDW root per shoot dry weight, TRL total root length, SUA surface area, ARD average root diameter, ROV root volume, RBN root branching number
  2. amethod 1-3 refers to EMMAX, FarmCPU, and MLM, respectively
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