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Table 3 Identified QTLs for the assessed salinity responsive traits

From: Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Trait

QTL

Chr

QTL interval (Mb)

Peak position (bp)

SNP Marker

F value

p value

Marker R2

PD18

qPD18_2.1

2

24.38–24.51

24,382,186

10,224,382,186

18.11

3.53E-05

0.1119

PD18

qPD18_4.1

4

17.08–17.09

17,083,910

10,417,083,910

19.43

1.87E-05

0.1134

PD18

qPD18_11.1

11

24.64–24.65

24,645,753

11,124,645,753

19.92

1.50E-05

0.1174

SES18

qSES18_2.1

2

24.38–24.51

24,382,186

10,224,382,186

20.23

1.31E-05

0.1255

SES18

qSES18_4.1

4

17.06–17.09

17,083,910

10,417,083,910

19.28

2.01E-05

0.1127

SES18

qSES18_11.1

11

24.64–24.65

24,645,753

11,124,645,753

20.89

9.55E-06

0.1234

SDW0

qSDW0_2.1

2

6.98–7.12

6,992,556

10,206,992,556

16.02

9.29E-05

0.092

SDW0

qSDW0_9.1

9

7.77–7.78

7,779,630

10,907,779,630

8.57

2.95E-04

0.1111

SNa+0

qSNa0_2.1

2

4.79–6.56

5,610,544

10,205,610,544

22.43

4.54E-06

0.1283

SNa+0

qSNa0_6.1

6

27.17–29.49

27,397,942

10,627,397,942

19.86

1.52E-05

0.12

SNa+0

qSNa0_8.1

8

21.49–21.51

21,498,898

10,821,498,898

16.21

8.59E-05

0.0997

SNa+0

qSNa0_8.2

8

26.56–26.57

26,568,663

10,826,568,663

10.12

7.13E-05

0.1225

SNa+0

qSNa0_9.1

9

6.77–7.42

7,411,725

10,907,411,725

16.83

6.47E-05

0.1043

SNa+12

qSNa12_4.1

4

20.33–20.57

20,374,274

10,420,374,274

11.62

1.91E-05

0.1427

SNa+12

qSNa12_10.1

10

14.91–16.19

15,893,435

11,015,893,435

16.29

8.30E-05

0.0988

SNa+D

qSNaD_5.1

5

10.28–11.25

10,287,595

10,510,287,595

17.9

3.83E-05

0.1062

SNa+D

qSNaD_6.1

6

23.74–23.85

23,820,480

10,623,820,480

16.49

7.53E-05

0.0984

SK+D

qSKD_1.1

1

32.96–38.59

38,584,909

10,138,584,909

20.12

1.33E-05

0.1155

SK+D

qSKD_2.1

2

24.49–25.43

24,686,915

10,224,686,915

30.49

1.23E-07

0.1754

SK+D

qSKD_2.2

2

28.40–28.92

28,694,339

10,228,694,339

24.25

1.97E-06

0.1391

SK+D

qSKD_3.1

3

3.69–3.81

3,805,384

10,303,805,384

28.01

3.69E-07

0.1611

SK+D

qSKD_4.1

4

4.49–4.72

4,509,563

10,404,509,563

30.72

4.08E-12

0.3525

SK+D

qSKD_12.1

12

16.55–17.62

16,556,527

11,216,556,527

18.41

2.95E-05

0.1056

SNa+/K+0

qSNa/K0_3.1

3

3.72–3.81

3,805,384

10,303,805,384

29.01

2.37E-07

0.168

SNa+/K+0

qSNa/K0_11.1

11

17.62–17.63

17,624,102

11,117,624,102

8.4

3.45E-04

0.1012

SNa+/K+D

qSNa/KD_3.1

3

23.88–24.08

24,079,731

10,324,079,731

15.67

1.10E-04

0.1019