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Table 1 Summary of DNA variation in nine genes involved in panicle development

From: Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice

Gene (bp)

Group

No. of nucleotide substitutions

No. of INDELs

π × 10−3

h

Hd

D

LAX1 (648)

Total

1

0

0.76

2

0.491

–

 

Indica

1

0

0.66

2

0.425

–

 

Japonica

1

0

0.14

2

0.091

–

 

Tong-il

1

0

0.62

2

0.400

–

APO1 (1299)

Total

12

3

2.02

3

0.533

−0.146

 

Indica

12

3

3.6

3

0.667

1.135

 

Japonica

0

0

–

–

–

–

 

Tong-il

2

1

0.62

2

0.400

−0.973

APO2 (1170)

Total

13

0

4.83

3

0.536

2.755**

 

Indica

13

0

4.33

3

0.602

1.329

 

Japonica

0

0

–

–

–

–

 

Tong-il

11

0

3.76

2

0.400

−1.200

DEP1 (1281)

Total

19

1

2.78

9

0.723

−1.251

 

Indica

9

0

2.38

7

0.854

0.647

 

Japonica

11

1

1.49

3

0.267

−1.320

 

Tong-il

6

0

2.03

3

0.700

−0.668

FON1 (2985)

Total

14

0

2.05

6

0.764

2.820**

 

Indica

6

0

0.99

4

0.731

2.321*

 

Japonica

12

0

2

3

0.552

2.812**

 

Tong-il

10

0

1.34

2

0.400

−1.193

GHD8 (903)

Total

16

6

6.16

9

0.812

1.605

 

Indica

15

6

4.07

7

0.866

−0.560

 

Japonica

11

1

1.54

3

0.495

−1.920*

 

Tong-il

11

3

7.13

3

0.800

1.527

GN1a (1706)

Total

8

4

1.44

8

0.790

0.948

 

Indica

5

2

0.98

6

0.801

0.526

 

Japonica

6

3

1.26

4

0.557

0.895

 

Tong-il

3

2

1.06

2

0.600

1.573

HD1 (1353)

Total

12

9

4.04

9

0.771

3.105**

 

Indica

10

8

3.07

6

0.760

1.503

 

Japonica

11

4

4.11

4

0.686

3.050***

 

Tong-il

12

4

4.08

3

0.700

−1.031

SP1 (1881)

Total

20

3

2.11

7

0.679

−0.436

 

Indica

7

0

1.33

4

0.696

0.756

 

Japonica

17

3

2.44

5

0.538

−0.105

 

Tong-il

3

0

0.65

2

0.400

−1.049

  1. S, Number of variable sites; π, Nucleotide diversity; h, Number of haplotypes; Hd, Haplotype diversity; D, Tajima’s D
  2. *, **, and ***, significant at p < 0.05, p < 0.01, and p < 0.001, respectively