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Table 3 SNP loci significantly associated with eight traits of Brassica napus under Al toxicity stress

From: Integration of GWAS and transcriptome analyses to identify SNPs and candidate genes for aluminum tolerance in rapeseed (Brassica napus L.)

Traits

SNP

Chromosome

Position

P value

R2/%

Allele

GLM

MLM

RFWAG

Bn-A04-p2852490

A04

2,852,490

2.07E-06

11.32

T/A

 
 

Bn-A04-p9422509

A04

9,422,509

3.86E-06

11.25

G/A

 

RRD

Bn-A01-p8185115

A01

8,185,115

9.87E-08 ~ 7.34E-07

14.02

T/C

 

Bn-A01-p11875598

A01

11,875,598

3.18E-06

10.26

C/T

 
 

Bn-C03-p23403794

C03

23,403,794

4.33E-06

9.25

G/A

 

RRFW

Bn-A03-p16212704

A03

16,212,704

3.81E-06

11.07

T/A

 
 

Bn-A06-p18721845

A06

18,721,845

4.24E-06

10.07

C/T

 
 

Bn-A08-p15773789

A08

15,773,789

4.21E-06

9.61

T/C

 
 

Bn-A10-p5162750

A10

5,162,750

3.54E-06

11.83

G/A

 
 

Bn-C02-p15705371

C02

15,705,371

3.97E-06

10.59

C/T

 
 

Bn-C02-p16911048

C02

16,911,048

3.40E-07 ~ 2.87E-08

14.00 ~ 14.36

C/T

 

Bn-C03-p56785277

C03

56,785,277

4.90E-06 ~ 3.86E-06

9.64 ~ 10.74

C/T

 

Bn-C03-p56785578

C03

56,785,578

4.57E-06 ~ 3.62E-06

9.69 ~ 10.82

A/G

RRE

Bn-A03-p10703126

A03

10,703,126

7.74E-07 ~ 3.62E-06

10.51 ~ 10.63

G/C

 

Bn-A03-p10703167

A03

10,703,167

7.03E-07 ~ 3.35E-06

10.57 ~ 10.70

T/C

 

Bn-A10-p9658437

A10

9,658,437

4.09E-06

11.63

A/T

 
 

Bn-C02-p18429273

C02

18,429,273

2.57E-06

11.14

T/G

 
 

Bn-C04-p17161440

C04

17,161,440

4.72E-06

10.91

G/A

 
 

Bn-C06-p30829548

C06

30,829,548

3.77E-06

10.17

C/T

 
 

Bn-C09-p13036538

C09

13,036,538

2.84E-06

9.97

G/A

 

RTRSA

Bn-A01-p8185115

A01

8,185,115

2.16E-06

12

T/C

 
 

Bn-A02-p18627325

A02

18,627,325

2.38E-06

11.42

A/C

 
 

Bn-A02-p18627333

A02

18,627,333

2.50E-06

11.64

A/T

 
 

Bn-A02-p18627380

A02

18,627,380

1.10E-06

12.1

C/T

 
 

Bn-A09-p6718215

A09

6,718,215

3.98E-06

8.22

C/T

 
 

Bn-C02-p12430774

C02

12,430,774

3.61E-06

9.73

T/C

 
 

Bn-C02-p26059415

C02

26,059,415

2.31E-07 ~ 2.16E-06

11.11 ~ 11.70

G/C

RTRT

Bn-A03-p5766579

A03

5,766,579

4.56E-06

11.34

T/C

 
 

Bn-A03-p14798182

A03

14,798,182

4.23E-06

10.92

A/C

 
 

Bn-A04-p9422509

A04

9,422,509

8.05E-07 ~ 1.72E-07

13.83 ~ 14.07

G/A

 

Bn-A08-p3750050

A08

3,750,050

4.54E-06

10.46

T/G

 
 

Bn-A08-p3750315

A08

3,750,315

3.78E-06

10.67

A/G

 
 

Bn-C03-p16673270

C03

16,673,270

1.01E-06

12.68

C/A

 

RTRV

Bn-A06-p17634684

A06

17,634,684

4.12E-06

9.23%

G/T

 
 

Bn-A06-p17634738

A06

17,634,738

4.92E-06

9.07%

A/T

 
 

Bn-C04-p4409586

C04

4,409,586

3.39E-06

9.15

G/A

 
 

Bn-C05-p15402975

C05

15,402,975

4.41E-06 ~ 2.46E-06

9.49 ~ 9.98

G/A

 

Bn-C05-p15403018

C05

15,403,018

3.94E-06 ~ 2.79E-06

9.40 ~ 10.08

A/C

RTRL

Bn-A01-p8185115

A01

8,185,115

2.97E-07 ~ 1.18E-06

13.63 ~ 14.52

T/C

 

Bn-A01-p11875598

A01

11,875,598

4.27E-06

10.21%

C/T

 
 

Bn-A06-p10959923

A06

10,959,923

4.35E-06

9.60%

C/T

 
 

Bn-A09-p8460525

A09

8,460,525

2.43E-06

9.95%

C/T

 
 

Bn-C02-p26059415

C02

26,059,415

7.20E-08 ~ 4.05E-07

12.33 ~ 12.49

G/C

  1. Note: R2 is the percentage of phenotypic variance explained by the SNP. indicates the GLM model detecting the significantly associated-trait SNP locus. indicates the MLM model detecting the significantly associated-trait SNP locus