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Table 3 List of significant SNP associations, the genes tagged by significant SNPs and information from the genome wide analysis of sorghum germplasm under cold stress at seedling stage

From: Genome-wide association analysis of seedling traits in diverse Sorghum germplasm under thermal stress

Trait

SNP

FDR Adjusted p-Values*

R2 Value **

Nucleotide Variation

Distance to nearest gene (bp) ***

Nearest Gene ID

CSt_SFW

S6_57170126

0.008

10.73

C/G

(−)588

Sb06g028380

CSt_SFW

S6_57163269

0.008

10.26

A/G

149

Sb06g028370

CSt _SFW

S6_57302179

0.015

10.30

T/C

0

Sb06g028540

CSt _SFW

S6_57163127

0.015

12.62

A/G

291

Sb06g028370

CSt _SFW

S3_47228001

0.015

−17.48

T/C

1973

Sb03g023720

CSt _RFW

S3_59699677

0.000

0.06

T/A

930

Sb03g031320

CSt _SL

S6_5762763

0.171

8.75

T/A

768

Sb06g002877

CSt _RL

S2_73739699

0.001

−20.80

T/A

(−)127

Sb02g039680

CSt _RL

S9_8614594

0.001

−14.86

G/A

2098

Sb09g006020

CSt _RL

S2_56602226

0.001

−12.79

G/A

543

Sb02g023140

CSt _RL

S2_54575799

0.005

11.99

A/G

(+)889

Sb02g022120

CSt _RL

S4_60946340

0.005

−25.13

G/C

569

Sb04g030940

CSt _RL

S3_16201529

0.008

−16.12

G/C

495

Sb03g013220

CSt _RL

S2_56566217

0.010

12.65

C/G

(+)398

Sb02g023120

CSt_RL

S2_67807062

0.015

−12.04

C/A

-

-

CSt_RL

S2_72583772

0.015

14.48

C/T

(+)2810

Sb02g038300

CSt_RL

S2_72833569

0.015

12.10

C/T

(+)2150

Sb02g038630

CSt_RL

S2_54593968

0.019

13.13

A/G

(−)156

Sb02g022140

CSt_RL

S2_54593969

0.019

13.13

A/G

(−)157

Sb02g022140

CSt_RL

S5_1302419

0.019

5.84

C/G

(+)66

Sb05g001215

CSt_Anth_W−1

S1_8039999

0.022

−42.27

G/T

(−)104

Sb01g009310

CSt_Anth_W−1

S6_53967668

0.001

−5.71

T/C

77

Sb06g024943

CSt_Anth_W−1

S6_54057566

0.002

−19.29

G/C

(+)2144

Sb06g025060

CSt_Anth_W−1

S6_53978420

0.022

−20.33

G/C

661

Sb06g024960

CSt_Anth_W−1

S6_54030245

0.017

−13.36

G/A

(−)440

Sb06g025040

CSt_Anth_W−1

S6_53848121

0.023

−5.18

T/C

(+)4385

Sb06g024820

CSt_Anth_W−1

S6_53791123

0.019

5.21

T/C

(+)2883

Sb06g024740

CSt_Anth_W−1

S6_43169342

0.023

−47.53

A/G

108

Sb06g015560

CSt_Anth_W−1

S6_54030254

0.017

13.36

G/T

(−)449

Sb06g025040

CSt_Anth_W−1

S2_76203986

0.025

36.77

C/T

(−)2259

Sb02g042450

  1. *False Discovery Rate (FDR) values for the significantly associated SNP at p-value of 1E-06
  2. **Percent trait variation explained by the associated SNPs
  3. ***Distance to the nearest annotated gene coordinates in the reference genome
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BMC Plant Biology

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