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Rice

Table 1 Significant associations between SNP genotypes and blast resistance in the analyzed rice accessions

From: Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Category

MTA

ID

Peak Marker/Region (bp)

Chr.

-log10(p)

#SNP

Associated region (bp)

Peak marker R2 a

LD block (bp)

SNP alleles at peak markerb

Average blast score

Allelic frequence (%)

      

Start

End

Size

 

Start-End

  

Total

K1

K2

Adm.

Field

BRF01

S1_32855693

1

4.369

1

–

–

–

6.23%

32,855,693-33,101,889

A

7.39

93.5

92.0

100.0

90.9

G

5.26

6.5

8.0

0.0

9.1

Field

BRF04

S4_31566281

4

14.594

31

31,257,415

32,476,401

1,218,986

19.54%

–

T

7.59

91.4

96.4

75.9

91.7

G

3.23

8.6

3.6

24.1

8.3

Field

BRF06–1

S6_10184497

6

5.889

17

10,108,408

11,927,672

1,819,264

7.77%

–

C

7.60

92.4

94.4

92.2

74.2

A

4.52

7.6

5.6

7.8

25.8

Field

BRF06–2

S6_29136506

6

3.963

1

–

–

–

5.08%

–

A

7.06

58.8

57.4

59.6

64.9

G

7.44

41.2

42.6

40.4

35.1

Field

BRF07

S7_23126442

7

4.723

1

–

–

–

6.18%

–

A

7.35

94.5

92.3

100.0

100.0

G

4.95

5.5

7.7

0.0

0.0

Field

BRF10

S10_14442878

10

4.450

2

14,421,776

14,442,878

21,102

5.79%

–

G

6.75

58.6

47.9

79.3

83.8

A

7.86

41.4

52.1

20.7

16.2

Field

BRF11–1

S11_27464620

11

5.476

28

26,482,681

27,672,972

1,190,291

7.26%

26,090,712-28,791,205

C

7.57

91.7

99.5

72.4

83.8

T

4.12

8.3

0.5

27.6

16.2

Field

BRF11–2

S11_28957771

11

6.304

2

28,900,124

28,957,771

57,647

8.43%

28,807,359-29,018,344

T

7.64

83.8

91.3

56.9

86.5

G

5.05

16.2

8.7

43.1

13.5

Growth chamber

BRGC01

S1_1719121

1

3.872

1

–

–

–

5.65%

 

A

3.48

80.4

97.9

26.4

68.6

G

2.71

19.6

2.1

73.6

31.4

Growth chamber

BRGC06

S6_10390066

6

6.068

20

9,906,359

10,685,711

779,352

9.55%

 

C

3.51

89.1

94.7

86.5

63.9

T

2.00

10.9

5.3

13.5

36.1

Growth chamber

BRGC07

S7_22505151

7

4.167

1

–

–

–

6.14%

 

G

3.41

92

90.4

92.5

100.0

A

2.47

8

9.6

7.5

0.0

Growth chamber

BRGC11–1

S11_25555354

11

4.413

5

24,811,878

25,555,354

743,476

6.03%

24,068,338-26,090,282

T

3.54

87

97.3

67.3

61.1

G

1.95

13

2.7

32.7

38.9

Growth chamber

BRGC11–2

S11_27672972

11

5.975

25

26,482,681

28,167,315

1,684,634

8.34%

26,090,712-28,791,205

C

3.47

92.4

97.9

75.5

88.9

T

1.65

7.58

2.1

24.5

11.1

Growth chamber

BRGC11–3

S11_28957771

11

7.143

34

28,809,430

29,007,377

197,947

11.54%

28,807,359-29,018,344

T

3.54

84.1

91.0

58.5

86.1

G

2.25

15.9

9.0

41.5

13.9

  1. For each trait, the peak marker (SNP with the highest p-value) is reported. avariance explained by the marker/region; bMajor allele is written in bold letters
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