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Table 1 List of SNP identified on the QBPH4.1 sliding window (5.78–7.78 Mb) on chromosome 4. SI = SNP index; QS = QBPHS; QR = QBPHR; IndS = BPHS; IndR = BPHR; AAC = amino acid change; (−) = synonymous variant; (+) = missense variant or stop codon

From: Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population

Position

LOC identifier

gene product name

KASP-SNP marker

SNP S/R

SI in QS

SI in QR

SI in IndS

SI in IndR

SNP pos / CDS length

SNP effect

AAC

AAC position/protein length

5,806,676

LOC_Os04g10680

zinc finger, C3HC4 type domain containing protein

 

T/C

0.0

100.0

0.0

100.0

2071/3059

–

  

5,867,185

LOC_Os04g10800

inorganic phosphate transporter

 

A/G

NA

NA

0.0

100.0

534/1527

–

  

5,867,219

LOC_Os04g10800

inorganic phosphate transporter

R04005867219

G/C

0.0

85.0

0.0

100.0

568/1527

+

A > P

190/508

5,867,260

LOC_Os04g10800

inorganic phosphate transporter

 

T/C

0.9

82.9

0.0

100.0

609/1527

–

  

5,867,320

LOC_Os04g10800

inorganic phosphate transporter

 

T/G

0.0

80.0

0.0

100.0

669/1527

–

  

6,069,830

LOC_Os04g11165

gamma-thionin family domain containing protein

R04006069830

G/T

NA

NA

100.0

0.0

201/216

+

stop codon

67/71

6,069,877

LOC_Os04g11165

gamma-thionin family domain containing protein

R04006069877

A/G

0.0

81.0

0.0

81.0

154/216

+

C > R

52/71

6,069,900

LOC_Os04g11165

gamma-thionin family domain containing protein

R04006069900

A/G

0.0

81.0

0.0

81.0

131/216

+

I > T

44/71

6,263,052

LOC_Os04g11450

OsFBX118 - F-box domain containing protein

 

A/G

8.2

91.7

0.0

88.9

1011/1480

–

  

6,263,057

LOC_Os04g11450

OsFBX118 - F-box domain containing protein

R04006263057

G/C

91.8

4.0

100.0

0.0

922/1203

+

Q > E

308/400

6,263,087

LOC_Os04g11450

OsFBX118 - F-box domain containing protein

R04006263087

A/T

8.2

92.0

0.0

90.0

892/1203

+

Y > N

298/400

6,263,168

LOC_Os04g11450

OsFBX118 - F-box domain containing protein

R04006263168

C/G

38.8

96.9

0.0

96.8

811/1203

+

V > L

271/400

6,263,172

LOC_Os04g11450

OsFBX118 - F-box domain containing protein

 

T/A

36.7

96.5

0.0

96.0

891/1480

–

  

6,388,017

LOC_Os04g11660

OsFBX119 - F-box domain containing protein

R04006388017

C/A

16.7

97.7

16.7

97.7

837/1137

+

K > N

279/378

6,388,020

LOC_Os04g11660

OsFBX119 - F-box domain containing protein

 

A/G

16.7

97.7

16.7

97.7

916/1766

–

  

6,388,038

LOC_Os04g11660

OsFBX119 - F-box domain containing protein

 

G/T

13.5

100.0

0.0

100.0

898/1766

–

  

6,388,095

LOC_Os04g11660

OsFBX119 - F-box domain containing protein

R04006388095

G/C

10.8

100.0

0.0

100.0

759/1137

+

D > E

253/378

6,451,402

LOC_Os04g11780

resistance protein LR10

 

C/A

0.0

100.0

0.0

100.0

1110/1998

–

  

6,451,404

LOC_Os04g11780

resistance protein LR10

R04006451404

T/C

0.0

100.0

0.0

100.0

1112/1998

+

I > T

371/665

6,451,423

LOC_Os04g11780

resistance protein LR10

 

A/T

0.0

100.0

0.0

100.0

1131/1998

+

E > D

377/665

6,451,424

LOC_Os04g11780

resistance protein LR10

R04006451424

C/A

0.0

100.0

0.0

100.0

1132/1998

+

L > M

378/665

6,451,469

LOC_Os04g11780

resistance protein LR10

R04006451469

G/A

2.9

100.0

2.9

100.0

1177/1998

+

V > I

393/665

6,451,485

LOC_Os04g11780

resistance protein LR10

R04006451485

A/G

2.9

100.0

2.9

100.0

1193/1998

+

K > R

398/665

6,451,495

LOC_Os04g11780

resistance protein LR10

R04006451495

T/G

2.9

100.0

2.9

100.0

1203/1998

+

D > E

401/665

6,455,216

LOC_Os04g11790

OsFBX120 - F-box domain containing protein

 

T/C

25.0

98.3

0.0

95.8

827/1461

–

  

6,455,225

LOC_Os04g11790

OsFBX120 - F-box domain containing protein

 

C/T

75.0

1.6

100.0

4.2

818/1461

–

  

6,593,508

LOC_Os04g12010

glycosyltransferase

 

G/T

24.3

96.6

0.0

94.5

1455/1774

–

  

6,593,541

LOC_Os04g12010

glycosyltransferase

 

G/A

22.2

96.7

0.0

94.8

1422/1774

–

  

6,659,796

LOC_Os04g12110

expressed protein

 

C/A

NA

NA

100.0

0.0

1818/1839

–

  

6,659,820

LOC_Os04g12110

expressed protein

 

G/A

75.9

0.0

75.9

0.0

1794/1839

–

  

6,659,826

LOC_Os04g12110

expressed protein

 

A/G

100.0

11.1

100.0

11.1

1788/1839

–

  

6,659,838

LOC_Os04g12110

expressed protein

 

A/G

100.0

11.1

100.0

11.1

1776/1839

–

  

6,659,844

LOC_Os04g12110

expressed protein

R04006659844

C/A

75.9

0.0

75.9

0.0

1770/1839

+

R > S

590/612

6,659,845

LOC_Os04g12110

expressed protein

R04006659845

C/G

75.9

0.0

75.9

0.0

1769/1839

+

R > T

590/612

6,659,847

LOC_Os04g12110

expressed protein

 

G/T

75.5

0.0

75.5

0.0

1767/1839

–

  

6,659,872

LOC_Os04g12110

expressed protein

R04006659872

C/T

88.6

5.3

100.0

7.4

1742/1839

+

C > Y

581/612

6,659,873

LOC_Os04g12110

expressed protein

R04006659873

A/T

88.6

5.3

100.0

7.4

1741/1839

+

C > S

581/612

6,659,874

LOC_Os04g12110

expressed protein

 

A/G

88.6

5.3

100.0

7.4

1740/1839

–

  

6,659,877

LOC_Os04g12110

expressed protein

 

A/C

88.6

5.3

100.0

7.4

1737/1839

–

  

6,659,884

LOC_Os04g12110

expressed protein

R04006659884

G/C

89.1

5.3

100.0

7.4

1730/1839

+

S > C

577/612

6,659,915

LOC_Os04g12110

expressed protein

R04006659915

T/C

88.9

5.4

100.0

7.4

1699/1839

+

I > V

567/612

6,925,203

LOC_Os04g12530

amino acid transporter family protein

R04006925203

T/G

0.0

80.0

0.0

80.0

404/612

+

D > A

135/203

6,925,208

LOC_Os04g12530

amino acid transporter family protein

 

C/G

NA

NA

0.0

75.0

399/612

–

  

6,925,211

LOC_Os04g12530

amino acid transporter family protein

 

C/G

NA

NA

0.0

71.4

396/612

–

  

6,968,050

LOC_Os04g12580

receptor-like protein kinase (OsLecRK3)

OsLecRK3-SNP

A/G

NA

NA

0.0

100.0

990/2346

–

  

6,977,171

LOC_Os04g12600

receptor-like protein kinase

 

G/A

96.6

0.0

96.6

0.0

2079/2415

–

  

6,978,761

LOC_Os04g12600

receptor-like protein kinase

 

C/T

100.0

0.0

100.0

0.0

489/2415

–

 Â