Skip to main content

Table 3 A subset of SNPs significantly associated with 9 agronomic traits

From: Genomic consequences of selection and genome-wide association mapping in soybean

Trait

Chr.a

Positionb

MAF

Allele

P value

R2(%)

XP-CLR

Known locic

Grain yield

1

55794390

0.06

T/C

2.38 × 10-6

2.6

1.60

 
 

3

47136179

0.48

T/C

2.69 × 10-5

2.4

0.68

15-4

 

4

43653965

0.10

T/C

1.59 × 10-6

2.7

18.20d

12-2

 

8

39270868

0.21

T/C

5.50 × 10-8

4.5

4.25e

 
 

14

46260055

0.07

A/G

3.80 × 10-7

3.2

17.01d

3-4

Protein content

7

7058915

0.11

T/C

1.46 × 10-7

3.2

3.55

24-4

 

9

1195313

0.47

T/C

4.57 × 10-7

3.0

4.76e

 
 

10

47656484

0.14

T/C

2.88 × 10-5

2.0

9.02e

5-4

 

15

5312718

0.20

A/G

1.49 × 10-5

2.3

1.94

5-4

 

20

36078120

0.06

T/G

1.62 × 10-5

2.1

7.63e

26-5

Oil content

1

52863692

0.30

A/G

6.66 × 10-6

2.5

8.45e

24-21

 

6

14511997

0.08

A/G

1.23 × 10-5

2.4

8.93e

36-2

 

10

6572950

0.08

A/G

2.29 × 10-5

2.6

10.37d

 
 

11

1859395

0.06

T/C

7.63 × 10-6

2.3

2.10

 
 

14

5340642

0.16

A/G

7.23 × 10-7

2.9

4.14

2-6

Lodging

2

7785541

0.19

T/C

3.81 × 10-5

2.6

7.90e

7-1

 

10

44437412

0.13

A/C

4.96 × 10-6

2.3

9.02e

 
 

10

44723907

0.12

A/G

5.06 × 10-7

2.8

7.35e

20-6

 

10

44747924

0.12

A/G

1.85 × 10-6

2.6

7.35e

20-6

 

19

47672198

0.39

T/C

8.14 × 10-6

2.4

0.227

4-3

Plant height

8

10789902

0.18

T/C

6.84 × 10-6

2.3

4.82e

 
 

10

44444513

0.13

A/G

5.00 × 10-8

3.3

9.02e

E2

 

13

37624457

0.36

T/C

3.13 × 10-5

2.3

3.79

17-1

 

19

37391984

0.12

A/G

4.16 × 10-6

2.4

11.48d

 
 

19

47392861

0.37

T/C

2.75 × 10-6

2.5

0.69

5-10

Maturity date

7

8270118

0.30

A/G

4.61 × 10-5

1.9

2.90

2-1

 

10

5392194

0.21

T/C

7.56 × 10-6

2.3

0.81

 
 

10

44753351

0.12

T/C

5.83 × 10-19

8.4

7.35e

E2

 

18

59603446

0.06

A/G

5.9 × 10-5

1.9

0.19

29-8

 

19

47390815

0.37

T/C

9.21 × 10-13

5.5

0.69

E3

Seed-coat color

3

42959913

0.21

G/A

6.97 × 10-6

5.0

1.25

 
 

5

34734860

0.36

C/T

3.06 × 10-7

7.5

8.28e

CHS2

 

8

7589397

0.14

A/G

1.15 × 10-16

19.3

11.18d

CHS

 

8

8462762

0.12

T/G

1.30 × 10-19

23.3

7.52e

CHS

 

13

7681784

0.07

A/C

1.35 × 10-5

4.7

12.24d

 

Pubescence color

3

47244893

0.18

A/G

3.46 × 10-7

8.3

0.00

 
 

6

17567713

0.20

G/A

4.54 × 10-13

18.9

0.39

 
 

6

18118558

0.40

T/C

1.08 × 10-28

48.2

0.00

T

 

6

18583273

0.48

A/C

1.41 × 10-25

39.6

0.00

 

Flower color

13

2833623

0.44

T/C

1.37 × 10-11

12.2

0.00

 
 

13

3301099

0.45

C/T

2.93 × 10-29

39.1

0.00

 
 

13

3657853

0.44

G/A

7.63 × 10-35

46.4

0.19

W1

 

13

4198124

0.50

C/A

3.62 × 10-28

35.6

0.00

 
 

13

4559799

0.46

G/A

3.82 × 10-40

32.7

0.00

 
  1. aChr., chromosome; bPosition in base pairs for the peak SNP according to soybean reference sequence of Williams 82; cThe significant SNP located in one of the QTL intervals as reported in other studies (www.soybase.org) . dindicates a 1 % genome-wide cutoff level, eindicates a 5 % genome-wide cutoff level
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us