Table 3 Selected PHYB-specific regulated genes

 CCA-B1

Traes_7BL_998EC9F74.2

29,787

13,084

Circadian clock output

 LHY-B

Traes_6BL_2F2381640.1

126

43

Circadian clock output

 FT-like_chr3-A

Traes_3AS_4310A2281.1

4

44

PEBP-family

 FT-like_chr3-B

TRAES3BF053100340CFD_t1

2

303

PEBP-family

 FT-like_chr6-A

Traes_6AL_66B24F155.1

21

138

PEBP-family

 FT-like_chr2-A

Traes_2AL_2F198B97C.1

0

10

PEBP-family

 FT-like_chr5-1-A

Traes_5AL_96274800D.1

1

95

PEBP-family

 FT-like_chr5-2-A

Traes_5AL_EFB6E50C9.2

179

27

PEBP-family

 FPF-like-A1

Traes_2AS_329CCD131.1

63

7,688

Flowering promotion

 FPF-like-B1

Traes_2BS_EA4D55C79.1

35

3,503

Flowering promotion

 FPF-like-B2

Traes_2BL_600226046.1

140

1,538

Flowering promotion

 FPF-like-A3

Traes_6AS_447C71E5B.1

13

70

Flowering promotion

 FPF-like-A4

Traes_5AL_6FD9AE7EB.1

91

7

Flowering promotion

 VIL-A2

Traes_6AS_DF6C22BF3.1

1,315

539

Vernalization

 VIL-B2

Traes_6BS_2B746261B.1

1,030

337

Vernalization

 TAR-A2

Traes_3AS_FF5C06A87.1

26

94

Auxin biosynthesis

 TAR-B2

td-k55_contig_11729

559

1609

Auxin biosynthesis

 IAA-A12

td-k61_contig_15261

1

20

AUX/IAA

 IAA-B12

Traes_5BL_9301BD154.1

41

143

AUX/IAA

 IAA-B15

Traes_1BS_8A19C460B.1

191

440

AUX/IAA

 IAA-A16

Traes_3AS_771897131.2

71

163

AUX/IAA

 IAA-B17

Traes_7BL_74071485F.2

1,041

1,859

AUX/IAA

 IAA-A19

Traes_1AL_859346448.1

380

689

AUX/IAA

 ARF-B6

Traes_6BS_BD894AD26.1

335

88

ARF

 ARF-B9

contig33661

16

0

ARF

 ARF-B17

Traes_7BL_66296695F.1

2,071

493

ARF

 WAT1-like-A1

td-k25_contig_69900

3

16

Auxin transport

 WAT1-like-B2

Traes_5BL_CBB9D7E7F.1

552

114

Auxin transport

 PIN3-like-B

Traes_6BL_F93C57B09.1

69

152

Auxin transport

 GA20ox-A1

Traes_4AL_FABDF4EDA.1

77

423

GA biosynthesis

 GA20ox-B2

td-k51_contig_72276

20

2,482

GA biosynthesis

 GA20ox-A4

Traes_1AL_3A716350F.2

4

229

GA biosynthesis

 GA20ox-B4

Traes_1BL_32506F819.1

8

219

GA biosynthesis

 GA2ox-A6

Traes_2AL_BA387175F.1

2

37

GA catabolism

 GA2ox-A11

Traes_4AS_7DC625FF5.1

3

47

GA catabolism

 GA2ox-B11

Traes_4BL_63EFE8C91.1

1

36

GA catabolism

 ACC synthase-A

Traes_4AL_A5B9F7B36.1

2

28

Ethylene biosynthesis

 ACC oxidase-B

Traes_5BL_6AAC89B49.1

164

857

Ethylene biosynthesis

 BZR1-like-A

Traes_3AS_5A6A80EA5.1

153

916

BR signaling

 BZR1-like-B

td-k21_contig_21617

113

681

BR signaling

 PYL4-like-A1

Traes_4AS_72BEF89AC.1

115

19

ABA signaling

 PYL4-like-B1

Traes_4BL_E43C1BB11.1

322

80

ABA signaling

 PYL4-like-B2

Traes_2BS_6428AA6CC.1

323

146

ABA signaling

Transcription factors

 PIF-B3

Traes_1BS_D1FCBFBE8.1

35

3,065

bHLH

 bHLH47-like1-A

Traes_2AS_9AEA9BDEA.1

87

5,046

bHLH

 bHLH47-like2-A

Traes_2AS_C4568AE60.1

606

1,740

bHLH

 PIL1-like-A

Traes_5AL_85F3BE385.2

323

698

bHLH

 BIM-A2

Traes_5AL_0D4BDDDCD.1

93

248

bHLH

 BIM-B2

Traes_5BL_AAC9C7238.2

615

1,453

Bhlh

 ATHB2-A

Traes_2AL_EF9549D16.1

24

640

Homeobox domain

 ATHB2-B

Traes_2BL_02479C76A.1

4

332

Homebox domain

 SPL14-like-A

Traes_7AS_FB2A769B5.1

93

182

SPL

 SPL14-like-B

Traes_7BS_7ACA0B10A.2

36

128

SPL

Growth and cell elongation

 XTH-like-B

Traes_4BS_64FB912EE.1

18

103

Cell elongation

 LNG-1-like-A

Traes_2AS_2C93BAE62.1

204

1,102

Cell elongation

 LNG-2-like-A

td-k25_contig_4862

0

23

Cell elongation

 PROG –A1

td-k41_contig_81185

90

502

Vegetative growth

 PROG –B1

td-k41_contig_81185

16

173

Vegetative growth

 BSH-B

Traes_1BS_E09101AE8.1

296

640

Vegetative growth

 GT-A1

Traes_4AS_1EA23DE08.1

11

92

Vegetative growth

 TZP-A

Traes_3AL_5006FA990.1

1,766

694

Architecture

 TZP-B

isotig04736

7,439

2,774

Architecture

Cold tolerance

 ICE-B41

td-k35_contig_73009

103

12

CBF induction

 WCOR413-A

Traes_5AL_F7649C79D.1

31

125

Cold response

 WCS19a-B

Traes_2BL_6382E3EFF.1

1

23

Cold response

 WCOR14-B

td-k25_contig_47404

5

208

Cold response

 WCOR15-A

Traes_2AL_079988C38.1

18

1,025

Cold response