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Table 3 List of SNPs significantly associated with the studied traits

From: Genome-wide association study of agronomic traits in rice cultivated in temperate regions

    

structure

  

PCA

  

SNP

Loci number

Chr

Pos

p-value

q-values

% explained variance

p-value

q-values

% explained variance

H-1

1

7

26,125,810

   

8.53E-04

0.691

5.5

H-2

2

8

26,290,663

5.74E-05

0.098

8.0

1.54E-05

0.026

9.0

DH-1

3

4

15,171,082

2.33E-06

0.002

14.3

1.01E-05

0.009

12.5

DH-2

4

5

13,373,075

2.76E-05

0.014

8.9

6.75E-05

0.031

8.1

DH-3

5

6

7,249,825

6.91E-07

0.001

12.4

1.67E-07

0.000

13.5

DH-4

6

6

8,122,336

1.82E-04

0.058

7.2

7.18E-05

0.031

8.0

DH-5

7

6

11,002,220

   

7.12E-04

0.185

7.4

DH-6

7

6

11,018,229

1.94E-04

0.058

7.1

9.60E-05

0.033

7.7

DH-7

8

10

1,366,920

9.09E-04

0.181

7.2

   

DH-8

8

10

1,500,932

3.10E-04

0.078

6.7

   

DH-9

8

10

1,871,964

   

7.59E-04

0.185

5.8

PL-1

9

1

6,126,957

   

7.34E-05

0.054

7.7

PL-2

10

2

35,406,962

   

6.78E-04

0.119

5.8

PL-3

11

3

1,003,670

3.09E-04

0.081

6.7

6.48E-04

0.119

5.9

PL-4

12

3

19,250,700

   

6.99E-04

0.119

7.2

PL-5

12

3

19,349,943

9.37E-04

0.169

8.1

5.93E-04

0.119

8.5

PL-6

13

3

29,987,079

2.49E-04

0.081

6.8

8.55E-04

0.131

5.5

PL-7

14

4

4,758,113

3.15E-04

0.081

6.6

1.98E-04

0.084

6.9

PL-8

15

5

20,125,768

6.72E-04

0.136

5.9

   

PL-9

15

5

21,838,857

3.52E-04

0.081

6.5

   

PL-10

16

5

28,626,704

1.21E-05

0.020

11.3

1.43E-05

0.024

10.8

PL-11

17

7

6,375,823

6.80E-05

0.055

9.7

   

PL-12

18

8

24,250,565

   

3.15E-04

0.108

8.0

PL-13

19

9

19,877,778

   

9.50E-05

0.054

7.5

PL-14

20

10

17,376,318

1.19E-04

0.064

9.2

4.78E-04

0.119

7.6

GN-1

21

1

38,011,958

4,33E-04

0,064

6,4

   

GN-2

21

1

40,012,174

5,64E-04

0,070

6,1

   

GN-3

22

2

2,720,687

2,99E-04

0,056

6,7

   

GN-4

22

2

3,755,851

1,89E-04

0,044

7,1

   

GN-5

23

2

32,500,801

3,46E-04

0,056

8,1

   

GN-6

23

2

34,386,360

3,25E-04

0,056

6,6

   

GN-7

24

3

17,999,538

1,39E-04

0,044

7,4

   

GN-8

25

3

18,500,293

3,23E-05

0,013

8,7

9,63E-04

0,197

5,2

GN-9

26

3

19,125,149

3,23E-05

0,013

8,7

9,63E-04

0,197

5,2

GN-10

27

3

20,500,343

3,23E-05

0,013

8,7

9,63E-04

0,197

5,2

GN-11

28

3

20,875,010

3,23E-05

0,013

8,7

9,63E-04

0,197

5,2

GN-12

28

5

2,460,569

   

7,67E-04

0,197

5,2

GN-13

28

5

2,753,203

   

1,48E-04

0,197

6,6

GN-14

29

5

6,499,710

   

9,98E-04

0,197

6,5

GN-15

30

9

9,375,311

5,58E-04

0,070

6,2

9,06E-04

0,197

5,4

GN-16

31

11

15,123,344

1,87E-04

0,044

7,2

   

PN-1

32

2

7,879,224

9.94E-04

0.710

5.5

   

PN-2

33

3

30,752,398

2.15E-04

0.318

6.9

1.20E-04

0.171

6.5

  1. Associated SNPs to height (H), days to heading (DH), Panicle length (PL), number of grains per panicle (GN) and number of panicles (PN) according to population structure given by STRUCTURE program or by PCA analysis