Table 3 Conserved miRNAs differentially expressed in developing wheat grain and their predicted target gene functions

Relative abundance during grain filling stages (RAGS)

tae-miR9674b-5p

13,242

14,580

19,780

2.10E-05

14,337

14,831

20,374

3.32E-06

SCF ubiquitin ligase complex; calcium-dependent protein kinase 20-like

tae-miR160

3696

6919

5125

3.34E-07

4129

6157

5376

5.90E-05

serine carboxypeptidase; transcription factor; Auxin reponse factor

ata-miR166a-3p

9081

2818

4010

1.05E-08

8443

3171

4564

9.00E-09

kinesin-1-like protein PSS1; transport

tae-miR159a

5372

1381

2706

1.28E-06

5191

1110

5056

2.89E-07

MYB; 40D repeat

Relative abundance at early stage(RAES)

osa-miR171a

1235

113

58

1.10E-09

1299

172

42

2.73E-07

DELLA proteins RGL2; malate dehydrogenase

ata-miR172c-3p

162

104

0

1.65E-05

180

63

0

5.64E-06

cytokinin response factor1; DnaJ

ata-miR396a-5p

1869

967

964

4.70E-07

1726

1085

762

1.40E-07

phosphatidylinositol 4-phosphate 5-kinase 1; glutamate dehydrogenase; response to GA

ata-miR396c-5p

144

16

7

4.11E-06

134

22

3

2.34E-04

GTPase activity; HSP protein; RPM1

ata-miR396e-5p

2264

772

709

7.40E-08

2366

931

722

2.87E-07

transcription factor TFIID; ribonuclease P activity

ata-miR393-5p_L-1R + 1

325

45

37

6.88E-07

331

44

41

1.64E-07

auxin-activated signaling; protein TRANSPORT INHIBITOR RESPONSE 1; LRR kinase

ata-miR167f-3p_L-1R + 1

61

26

19

5.86E-04

57

48

9

2.89E-04

ubiquitin ligase complex; lysosomal alpha-mannosidase

ata-miR169e-5p

38

5

2

1.23E-06

63

5

1

8.42E-05

serine-type endopeptidase; peptidase

osa-miR168a-5p

108

84

72

4.97E-03

110

78

73

5.45E-03

WRKY; Cul4-RING E3 ubiquitin ligase;

osa-miR168a-3p_L-3

115

50

23

1.79E-04

162

47

39

5.70E-05

ubiquitin domain-containing protein DSK2b

ata-miR169g-3p_L + 1R-1

250

7

0

4.17E-07

326

17

0

5.98E-06

ubiquitin protein ligase; RPM protein

osa-miR171e-5p_2ss2GA21AG

344

12

0

1.51E-06

361

19

5

9.00E-10

protein binding

osa-miR530-5p_L + 1

126

61

0

3.00E-04

134

109

30

8.85E-05

SCF ubiquitin ligase complex; fructose-bisphosphate aldolase

ata-miR5168-3p

5692

638

454

2.00E-10

5409

559

511

0.00E+ 00

kinesin-1-like protein PSS1; Transcription factor;

osa-miR530-5p_R + 1

52

36

0

3.00E-04

52

49

16

1.45E-03

fructose-bisphosphate aldolase; HSP70;

osa-miR159a.1_L + 1

86

15

41

9.85E-03

94

9

85

8.26E-05

MYB; WS40 repeat protein

tae-miR9776_L-1R + 1_1ss18AG

190

167

145

3.54E-03

215

158

143

6.85E-03

cell division; O-methyltransferase

osa-miR166g-3p_L + 1_1ss21TC

118

14

16

1.10E-05

97

24

28

9.90E-06

transcription factor; transport

tae-miR171a

696

125

126

1.00E-10

770

156

193

3.80E-06

DELLA protein RGL2-like; malate dehydrogenase

ata-miR394-5p

286

42

98

3.46E-06

354

47

141

3.40E-09

SCF ubiquitin ligase complex; glutathione transferase activity

ata-miR9772a-5p_L-2R + 2

47

21

16

1.17E-04

40

30

20

1.13E-02

SCF ubiquitin ligase complex

Relative abundance at middle stage(RAMS)

ata-miR528-5p

39

46

3

4.89E-04

28

38

23

1.99E-02

lectin-rich repeat receptor kinase

bdi-miR531_L-4R + 1_1ss5CT

17

33

18

7.10E-03

12

38

23

1.27E-02

NAD(P)H dehydrogenase; ABC transporter

ata-miR172b-3p

22

66

34

1.65E-05

26

36

20

1.35E-02

Cytokinin response factor; chaperone binding;

tae-miR1127b-3p_1ss12TC

7

18

4

3.57E-02

2

26

13

2.84E-04

UDP-glucuronate decarboxylase; SCF ubiquitin ligase complex

tae-miR9652-5p

3

28

0

3.46E-02

0

18

10

2.63E-02

retrograde transport

tae-miR167c-5p

681

793

595

4.30E-02

638

790

336

2.95E-05

SCF ubiquitin ligase complex

tae-miR9657a-3p

37

124

91

6.02E-05

23

87

68

5.70E-05

serine-type endopeptidase inhibitor activity; amino acid transport; WRKY

tae-miR9655-3p

21

1031

312

4.10E-07

0

1099

333

2.78E-07

L-fucosidase; SCF ubiquitin ligase complex

tae-miR9658-3p

24

37

20

1.10E-02

19

53

15

4.54E-04

SCF ubiquitin ligase complex; RPM1

Relative abundance at later stage (RALS)

bdi-miR156h-3p_L + 1

32

110

207

5.24E-04

23

103

219

9.19E-06

WRKY transcription factor

zma-miR156d-3p_L + 1_1ss9TC

5

50

114

5.71E-05

9

28

64

3.78E-06

catalytic activity

ata-miR167b-5p

111

576

889

1.38E-06

124

634

648

4.41E-07

SCF ubiquitin ligase complex

tae-miR319

179

227

682

3.93E-06

130

199

1018

1.94E-06

MYB transcription factor; Dnaj protein

osa-miR827

34

174

1002

7.10E-09

41

566

682

2.09E-07

SPX-domain-containing genes

tae-miR408_L-1

28

207

213

6.71E-06

25

127

204

6.88E-05

L-ascorbate oxidase; LPEAT1-like

tae-miR9666a-3p

0

439

4812

0.00E+ 00

0

492

911

3.68E-07

Alternative splicing regulator; regulatory protein NPR5

tae-miR9666b-3p

3

213

674

4.59E-07

0

255

318

1.46E-07

DNA-directed RNA polymerase II subunit 1

tae-miR9664–3p_L-1

15

29

55

4.78E-03

0

62

151

1.67E-07

RPM1 protein; zinc finger CCCH domain-containing; glucosidase

hvu-miR399

0

24

66

2.40E-05

0

54

62

2.18E-05

NB-ARC domain; glucosyltransferase

lus-miR159b_R + 1_1ss21CT

101

42

150

9.28E-04

78

22

179

2.10E-04

MYB

osa-miR319a-3p.2-3p_R + 1

387

210

608

1.23E-05

507

193

537

3.02E-05

SCF ubiquitin ligase complex; MYB