Table 2 Summary of sequence divergence of six experimentally validated miRNA binding sites in the cultivated rice population. n, number of samples; S, number of segregating sites; π, average number of pairwise nucleotide differences per site between two sequences [43]; θ, the Watterson estimator of θ per basepair [42].

miR156

Os08g39890

29

5' flanking

1–197

197

5

5.75

6.46

Binding site

198–218

21

0

0

0

3' flanking

219–797

279

6

2.02

2.93

miR159

Os01g59660

29

5' flanking

1–455

455

1

0.15

0.56

Binding site

456–476

21

0

0

0

3' flanking

477–778

302

3

2.09

2.54

miR390

Os02g10100

27

5' flanking

1–212

212

2

2.53

2.45

Binding site

213–233

21

0

0

0

3' flanking

234–689

456

2

1.04

1.14

miR395

Os03g09930

24

5' flanking

1–36

36

1

2.38

7.65

Binding site

37–57

21

0

0

0

3' flanking

58–793

736

4

1.66

1.47

miR408

Os03g15340

25

5' flanking

1–27

27

0

0

0

Binding site

28–49

22

0

0

0

3' flanking

50–646

597

1

0.56

0.44

miR820a

Os03g02010

24

5' flanking

1–40

40

0

0

0

Binding site

41–61

21

0

0

0

3' flanking

62–610

549

2

1.79

0.98

Average

5' flanking

/

161.2

1.5

1.80

2.85

Binding site

/

21.2

0

0

0

3' flanking

/

536.5

3.0

1.53

1.58