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Table 3 Loci detected for eating and cooking qualities in Panel 1 and Panel 2

From: Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.)

Trait

  

Panel1

Panel 2

Chr.

Position

P value

MAFa

R squareb

P value

MAFa

R squareb

AAC

6

1765761

5.29 × 10−11

0.436

0.152

   

6

1585864

   

9.21 × 10−8

0.052

0.231

9

19310549

   

2.32 × 10−7

0.143

0.214

PRO

5

12559930

1.57 × 10−7

0.110

0.242

   

11

22563596

2.47 × 10−6

0.092

0.190

   

PV

1

5102566

   

6.31 × 10−5

0.155

0.118

2

29640874

7.77 × 10−5

0.136

0.118

   

5

7944999

   

4.15 × 10−5

0.086

0.125

6

1666386

2.86 × 10−5

0.177

0.133

   

7

16503569

   

1.62 × 10−5

0.194

0.139

HPV

1

3541593

   

1.72 × 10−5

0.164

0.169

1

27287504

3.51 × 10−5

0.082

0.127

   

2

29640874

5.22 × 10−5

0.136

0.121

   

5

7944999

   

2.88 × 10−5

0.086

0.159

6

1750498

5.19 × 10−6

0.141

0.157

   

7

16506178

   

2.63 × 10−5

0.181

0.161

11

27792076

   

6.92 × 10−6

0.147

0.186

CPV

1

3541593

   

4.78 × 10−6

0.164

0.178

4

27772775

1.59 × 10−5

0.336

0.130

   

6

1750498

3.78 × 10−5

0.141

0.118

   

7

16506178

   

4.68 × 10−6

0.181

0.178

9

15417525

2.31 × 10−5

0.282

0.125

   

11

192690

4.16 × 10−5

0.136

0.116

   

BD

2

8596549

   

5.57 × 10−5

0.138

0.102

6

1765761

1.16 × 10−5

0.441

0.183

   

6

1985864

   

9.85 × 10−5

0.052

0.095

SB

4

24056499

   

1.09 × 10−6

0.125

0.165

6

1765761

2.39 × 10−8

0.441

0.261

   

CS

1

30627943

1.98 × 10−5

0.214

0.111

   

6

1765761

2.41 × 10−6

0.441

0.138

   

9

15474876

2.19 × 10−5

0.277

0.110

   

11

24255295

1.96 × 10−5

0.118

0.111

   

PeT

2

24259382

   

7.68 × 10−5

0.086

0.115

2

27305077

1.11 × 10-5

0.055

0.131

   

3

33893179

1.12 × 10−5

0.068

0.131

   

6

21443081

8.35 × 10−6

0.059

0.135

   

10

23087051

9.69 × 10−6

0.132

0.133

   

PTemp

6

6757255

1.54 × 10−8

0.491

0.217

   

6

21712093

1.11 × 10−6

0.118

0.155

   

8

9459681

   

4.28 × 10−5

0.233

0.141

  1. a: MAF: minor allele frequency; b: R square was calculated by R square of model with SNP minus R square of model without SNP