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Table 2 SNPs for low-temperature germination-related traits detected in 222 maize inbred lines

From: Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seq approaches

SNP

Chromosome

Position

Bin

MAF

P value

Alleles

R2

Trait

SYN25470

1

60,897,507

1.04

0.34

6.50E-05

A/C

0.124

RVI

PZE-101120376

1

148,125,053

1.05

0.138

3.52E-06

A/C

0.265

RGI

PZE-101192647

1

238,680,213

1.08

0.111

3.53E-07

A/G

0.286

RRV

PUT-163a-88,747,038-4526

1

282,891,355

1.11

0.279

4.32E-05

A/C

0.127

KSRGR

PUT-163a-149,007,696-748

2

8,500,779

2.02

0.077

3.60E-05

A/G

0.159

RGR

SYN29778

2

17,713,628

2.03

0.318

6.89E-05

A/C

0.151

RRSA

PZE-102099570

2

114,621,446

2.05

0.361

2.95E-06

A/G

0.207

RGI

PZE-102100684

2

117,468,629

2.05

0.267

6.27E-05

A/C

0.182

RVI

SYN21841

2

219,117,623

2.08

0.253

3.73E-07

A/C

0.272

RRV

PZE-103072583

3

115,856,771

3.04

0.346

8.88E-05

A/G

0.149

RRSA

PZE-103094415

3

151,499,271

3.05

0.182

6.34E-05

A/G

0.135

RGL

PZE-104024779

4

28,770,811

4.04

0.095

8.24E-05

A/G

0.120

RRV

SYN30173

5

10,372,835

5.02

0.401

3.75E-05/7.50E-05

A/G

0.133/0.121

RGL/RSVI

PZE-105034900

5

19,776,726

5.03

0.089

2.34E-06/3.06E-05

A/C

0.209/0.165

RRV/RVI

PZE-106003222

6

4,152,307

6.00

0.141

2.15E-07

A/G

0.259

RRV

PZE-106097864

6

151,745,619

6.05

0.137

4.23E-05

A/G

0.159

RGI

PZE-106129965

6

168,030,463

6.08

0.382

1.96E-07

A/G

0.254

RRV

PZE-106130106

6

168,266,461

6.08

0.359

2.88E-07

A/G

0.267

RRV

SYN4961

7

7,156,626

7.01

0.144

3.602E-05

A/G

0.132

RSVI

PZE-107036384

7

56,177,181

7.02

0.257

1.70E-07

A/G

0.258

RRV

PZE-107098845

7

148,186,320

7.03

0.161

7.53E-05

A/G

0.127

RRL

PUT-163a-78,076,151-4108

8

1,508,965

8.00

0.282

9.95E-05

A/C

0.142

KSRSVI

PZE-108064544

8

113,952,611

8.04

0.141

2.79E-07

A/G

0.267

RRV

PZE-108068725

8

119,362,385

8.04

0.286

9.81E-05

A/C

0.145

RRSA

SYN26538

8

169,361,414

8.08

0.224

2.24E-07

A/G

0.259

RRV

PZE-109053558

9

89,605,923

9.03

0.4

5.64E-05/5.01E-05

A/G

0.134/0.136

XYRGR/XYRSVI

SYN5516

10

8,952,194

10.02

0.301

1.21E-06

A/G

0.250

RGI

PZE-110029252

10

50,842,298

10.03

0.128

9.84E-05

A/G

0.177

RRSA

PZE-110057591

10

110,369,493

10.04

0.113

4.24E-05

A/G

0.130

RVI

PZE-110060997

10

115,266,833

10.04

0.122

4.05E-05

A/G

0.132

XYRGL

  1. The location is indicated by the chromosome and base pair position. P values less than 10−4 corresponding to a 5% type I error are displayed in scientific notation. The frequency is indicated by the minor allele frequency (MAF). R2: the percentage of phenotypic variation
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BMC Plant Biology

ISSN: 1471-2229

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