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Table 2 Determination of loci for eating and cooking qualities in indica subpopulation

From: Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping

Traits

Associated Markers

Position (kb)

Chr.

MAF

2015

2016

Linked Gene

P value

R2 (%)

P value

R2 (%)

AC

RM170

1361

6

0.099

4.47E-06

7.67

6.74E-07

7.93

Wx linked

RM588

1612

6

0.025

3.29E-18

17.24

7.85E-18

15.83

Wx linked

Wx-S1

1765

6

0.346

3.53E-11

10.93

3.03E-10

9.4

Wxa/Wxb

Wx-S2

1765

6

0.012

1.35E-06

9.45

2.97E-06

8.43

(CT)n in Wx

GC

RM170

1361

6

0.099

  

1.83E-05

4.97

Wx linked

RM588

1612

6

0.025

7.77E-06

7.92

2.06E-08

7.15

Wx linked

Wx-S1

1765

6

0.346

  

3.84E-04

2.71

Wxa/Wxb

Wx-S2

1765

6

0.012

  

7.30E-04

4.43

(CT)n in Wx

ASV

SSIIa-S1

6747

6

0.457

3.10E-10

17.0

2.30E-04

7.83

SSIIa

SSIIa-S2

6747

6

0.012

2.71E-09

17.04

  

SSIIa

PV

RM588

1612

6

0.025

3.91E-04

8.48

  

Wx linked

Wx-S2

1765

6

0.012

9.84E-04

8.97

5.84E-04

9.89

(CT)n in Wx

RM412

30,328

6

0.438

  

3.51E-04

6.07

SBE1 linked

RM346

21,579

7

0.012

  

4.74E-04

8.22

 

BDV

RM170

1361

6

0.099

5.13E-04

5.72

7.45E-04

5.39

Wx linked

RM588

1612

6

0.025

8.79E-08

10.45

2.41E-05

7.41

Wx linked

Wx-S1

1765

6

0.346

8.81E-05

4.99

  

Wxa/Wxb

CPV

RM170

1361

6

0.099

4.18E-06

7.62

7.38E-05

5.98

Wx linked

SBV

RM170

1361

6

0.099

1.91E-06

7.26

7.92E-06

6.55

Wx linked

RM588

1612

6

0.025

4.42E-10

10.45

3.24E-08

8.96

Wx linked

Wx-S1

1765

6

0.346

5.18E-06

5.37

3.26E-05

4.49

Wxa/Wxb

Wx-S2

1765

6

0.012

9.26E-04

5.48

  

(CT)n in Wx

RM225

3417

6

0.013

  

6.40E-04

4.6

SS1 linked

CSV

RM170

1361

6

0.099

4.73E-06

8.23

8.80E-04

6.24

Wx linked

RM588

1612

6

0.025

4.57E-06

8.38

1.08E-05

9.42

Wx linked

Wx-S1

1765

6

0.346

2.47E-04

4.37

4.10E-04

4.78

Wxa/Wxb

RM3262

22,469

8

0.012

3.92E-04

4.09

   

RM216

5336

10

0.069

7.89E-04

5.27

   

PeT

RM488

24,808

1

0.013

1.06E-05

12.93

   

RM5473

31,676

4

0.075

5.11E-06

14.29

   

SSI-S1

3080

6

0.431

1.19E-08

17.82

  

SSI

SSIIa-S2

6747

6

0.012

  

8.14E-04

7.96

SSIIa

RM189

22,095

9

0.073

3.04E-05

11.8

   
  1. MAF Minor allele frequency
  2. R2 represents the proportion of phenotypic variation explained by each associated locus