Download Supplement 1

Fig. S1 Selection of plant materials for DGE analysis. A, PCR amplification of hrf2 (1), part of the
pCAMBIAI1301 vector (2), and hptII (3). M: marker; P: positive control, pCAMBIAI1301::hrf2;
W, negative control (double distilled water); UT: negative control (untransformed plants); 1–6:
individual transgenic plants. B, RT-PCR analysis of hrf2 (1) and actin genes (2). M: marker; UT:
negative control (untransformed plants); 1–6: individual transgenic plants. C, Protein activity test
of transgenic plants. P: positive control (purified harpinXooc); UT: negative control (untransformed
plants); CK: lysis buffer; 1–4: individual transgenic plants.
Fig. S2 Distribution of total tags and distinct tags among different tag abundance
categories. (A) Distribution of total tags. Numbers in square brackets indicate the
range of copy numbers for a specific category of tags. For example, [2, 5] indicates
that all tags in this category are present in 2 to 5 copies. Numbers in parentheses
indicate the total tag copy number for all tags in that category. (B) Distribution of
distinct tags. Numbers in square brackets indicate the range of copy numbers for a
specific category of tags. Numbers in parentheses indicate the total number of types of
tags in that category.
Fig. S3 Gene expression levels in untransformed Y4 and transgenic T-4 rapeseed. The
upregulated and downregulated genes are shown in red and green, respectively. Genes
not exhibiting changes in expression are shown in blue. FDR ≤ 0.001, |log2Ratio |≥ 1.
Table S1 DEGs related to PCD in transgenic T-4 rapeseed
Effection on PCD a
Gene ID
Description
Log2Ratio
P-value
Bna39101002
Programmed cell death protein
1.36
3.15E-14
+
Bna39242408
HR-like lesion-inducing protein
1.58
0
+
Bna25434366
Development and cell death domain protein
1.18
2.46E-06
+
Bna39248523
Development and cell death domain protein
0.94
5.11E-08
+
Bna39239724
Disease resistance protein
2.07
6.43E-13
+
Bna38904688
Disease resistance-responsive family protein
1.89
1.15E-04
+
Bna36046487
Disease resistance protein
1.28
2.75E-14
+
Bna39276946
Disease resistance protein
0.12
3.88E-06
+
Bna38891812
ADP-ribosylation factor
2.15
6.44E-06
+
Bna39015143
ADP-ribosylation factor
1.72
4.47E-06
+
Bna39186766
Fasciclin-like arabinogalactan protein
2.12
2.10E-07
+
Bna25440452
Aspartic protease
0.58
1.07E-49
+/-
Bna39237556
Aspartic protease
0.37
1.56E-13
+/-
Bna39002684
OTU-like cysteine protease
1.14
1.65E-08
+/-
Bna35033042
Cathepsin B-like cysteine protease
0.85
6.18E-05
+/-
Bna39001308
Zinc finger protein LSD1
3.02
3.07E-07
-
Bna39277289
MLO1
0.52
1.32E-137
-
a ‘+’
represents genes with positive effects on plant PCD; ‘-’ represents genes with antagonistic effects on plant
PCD; ‘+/-’ represents genes that play ambiguous roles in plant PCD
Table S2 DEGs related to defense-related proteins, the phenylpropanoid defense pathway, and plant cell wall components in transgenic T-4 rapeseed
Defense-related proteins
Gene ID
Description
Bna52590269
Pathogenesis-related protein PR1-3
0.36
2.78E-07
Bna39248888
Pathogenesis-related family protein 1
0.33
4.34E-12
Bna39162989
Chitinase
8.84
1.06E-08
Bna38995176
Chitinase
0.34
8.22E-20
Bna25500170
Basic endochitinase CHB4
0.32
4.00E-305
Bna38911151
Chitinase
0.11
2.09E-07
Thaumatin-like, PR-5
Bna25470693
Pathogenesis-related thaumatin family protein
0.90
2.69E-18
Protease inhibitor, PR-6
Bna39165915
Cysteine protease inhibitor CPI-1
1.79
0
Bna39164360
Protease inhibitor
9.56
7.75E-14
Bna39204491
protease inhibitor
9.08
3.98E-10
Bna39249683
Protease inhibitor
5.89
1.11E-06
Bna39292123
Protease inhibitor
2.88
1.51E-09
Bna39069238
Protease inhibitor
1.46
1.34E-06
Bna39242999
Protease inhibitor
0.83
1.59E-59
Bna39170555
Protease inhibitor
0.22
1.06E-15
Bna25413960
Peroxidase
2.37
1.21E-95
Bna39219121
Peroxidase
2.26
1.71E-20
Bna36046061
Peroxidase
2.17
0
Bna36045118
Peroxidase
2.12
6.43E-13
Ribonuclease, PR-10
Bna38972235
Ribonuclease H2 subunit C
2.74
5.54E-05
Defensin, PR-12
Bna39218572
Defensin-like protein 2
10.48
0
Bna39152633
Defensin-like protein 2
4.31
3.95E-05
Bna39167627
Defensin-like protein 1
2.15
0
Pathogenesis-related protein, PR-1
Chitinase, PR-3
Peroxidase, PR-9
Log2Ratio
P-value
Lioid transfer protein, PR-14
Bna39234498
Defensin 1.2
1.73
3.75E-13
Bna39298875
Defensin
0.27
3.37E-29
Bna53136534
Plant defensin PDF1.3
0.73
1.12E-05
Bna39237828
Lipid transfer protein
8.12
1.46E-05
Bna39234607
Lipid transfer protein 5
2.47
0
Bna36045110
Nonspecific lipid-transfer protein precursor-like
2.04
1.8E-04
protein
Oxalic acid oxidase; OXO, PR-15
Polygalacturonase inhibitory
Bna38885837
Lipid transfer protein
1.77
0
Bna39243338
Lipid transfer protein
0.57
0
Bna39240733
Lipid transfer protein
0.35
5.59E-45
Bna32888249
Nonspecific lipid-transfer protein 3
0.34
1.64E-25
Bna39171614
Nonspecific lipid-transfer protein precursor
0.33
2.85E-189
Bna39250032
Nonspecific lipid-transfer protein 6
0.32
1.08E-37
Bna39256299
Lipid transfer protein
0.30
3.66E-87
Bna39162760
Oxalic acid oxidase
1.56
2.84E-14
Bna39267991
Oxalic acid oxidase
1.01
9.68E-09
Bna39206653
Polygalacturonase inhibitory protein
3.93
3.95E-05
Bna25484467
Polygalacturonase inhibitor protein
3.50
1.29E-05
Bna36045639
Myrosinase
2.81
2.21E-08
Bna25477544
Myrosinase
1.48
1.40E-13
Bna25494861
Myrosinase-associated protein
10.14
0
Bna39244710
Myrosinase-associated protein
9.82
0
Bna25494844
Myrosinase-associated protein
9.62
2.04E-14
Bna39249134
Myrosinase-associated protein
9.28
1.49E-11
protein, PGIP
Myrosinase
Myrosinase-associated protein,
MyAP
Myrosinase-binding protein
Phenylpropanoid defence pathway
Plant cell wall components
Pectin acetylesterase
Pectin esterase
Cellulose synthase
Expansin
Bna25419266
Myrosinase-associated protein
0.43
9.53E-07
Bna25477510
Myrosinase-binding protein
4.68
5.62E-13
Bna39282653
Myrosinase-binding protein
0.72
7.53E-06
Bna39230744
Myrosinase-binding protein
0.24
5.80E-09
Bna39230798
Myrosinase-binding protein
0.18
2.61E-25
Bna25439452
4-coumarate—CoA ligase, 4CL
4.12
1.08E-04
Bna38432659
Flavanone 3-hydroxylase, F3H
0.36
4.06E-12
Bna39206171
Flavone synthase, FNS
0.14
1.61E-11
Bna38994658
Caffeic acid 3-O-methyltransferase, COMT
0.12
7.22E-05
Bna39168141
Pectin acetylesterase
10.43
0
Bna39250453
Pectin acetylesterase family protein
1.12
1.18E-11
Bna39254181
Pectin esterase like protein
2.59
1.18E-04
Bna25464532
Pectin esterase family protein
1.05
6.51E-06
Bna39298688
Cellulose synthase
0.31
4.27E-21
Bna39163311
Cellulose synthase-like protein B3
0.25
3.18E-16
Bna39170396
ATEXPA10, Arabidopsis Thaliana Expansin A
4.78
2.21E-08
1.29
3.40E-07
3.71
1.09E-04
2.79
3.88E-06
2.37
1.07E-05
1.80
1.26E-06
10
Bna39004961
ATEXLB1, Arabidopsis Thaliana Expansin-like
B1
Hydroxyproline-rich glycoprotein,
Bna37283313
HRGP
Late embryogenesis abundant
hydroxyproline-rich glycoprotein
Bna39186972
Hydroxyproline-rich glycoprotein family
protein
Bna39184710
Hydroxyproline-rich glycoprotein family
protein
Bna39167482
Hydroxyproline-rich glycoprotein family
protein
Proline-rich protein, PRP
Glycine-rich protein, GRP
Arabinogalactanprotein, AGP
Bna39140702
Proline-rich family protein
2.31
0
Bna38922708
Proline-rich family protein
1.62
3.75E-05
Bna32888220
Glycine-rich protein
3.21
3.95E-05
Bna39199521
Glycine-rich protein
2.13
7.49E-05
Bna39237806
Glycine rich protein-like
1.93
3.02E-05
Bna39230134
Glycine-rich protein
1.72
0
Bna39166293
Glycine-rich protein 23
1.58
1.23E-12
Bna39297845
Glycine-rich protein
0.84
4.18E-13
Bna25466355
Glycine-rich protein
0.59
4.13E-36
Bna36047368
Arabinogalactan-protein
8.20
7.59E-06
Bna39186766
Fasciclin-like arabinogalactan protein
2.12
2.10E-07
Table S3 DEGs related to plant hormone biosynthesis, catabolism, and signal transduction in
transgenic T-4 rapeseed
Gene ID
Description
Fold
P-value
SA biosynthesis
Bna39167207
Isochorismate synthase 2, ICS2
1.32
2.69E-07
SA signalling
Bna39248803
NPR1-like protein 3, NPR3
0.66
1.07E-04
JA biosynthesis
Bna39187958
Phospholipase family protein
2.09
2.00E-10
Bna52587885
Phospholipase A2-alpha
1.75
9.16E-09
Bna39173182
Lipoxygenase, LOX
8.79
2.05E-08
Bna39169601
Lipoxygenase
4.23
1.08E-04
Bna25485078
Lipoxygenase 2
1.93
0
Bna39250058
12-oxophytodienoate reductase, OPR
2.38
3.49E-14
Bna39186998
Enoyl-CoA hydratase
1.49
6.29E-07
Bna39297304
Thiolase
1.57
8.45E-06
Bna25477588
2-hydroxyacyl-CoA dehydrogenase
0.58
1.37E-21
Bna52594427
protein TIFY 7; Jasmonate ZIM-domain protein
2.89
4.26E-05
Bna52593600
protein TIFY 10B; Jasmonate ZIM-domain
2.86
1.51E-13
2.73
1.30E-05
change
JA signalling
protein
Bna39238037
protein TIFY 11B; Jasmonates ZIM-domain
protein
ET biosynthesis
Bna39163192
ACC oxidase
1.68
6.40E-05
ET signalling
Bna39188380
APETALA2 and EREBP, ethylene responsive
9.49
2.89E-13
element binding protein
Auxin biosynthesis
Auxin signaling
Bna39187786
Ethylene response sensor
7.74
2.03E-04
Bna39242827
EIN3-Binding F BOX Protein 2, EBF2
3.34
6.64E-13
Bna38894261
Ethylene-responsive transcription factor ERF069
0.72
1.70E-05
Bna44672452
Ethylene-responsive transcription factor ERF060
0.45
4.78E-06
Bna25414333
Ethylene-responsive transcription factor ERF023
0.44
2.16E-09
Bna39240712
CYP83B1
3.48
3.99E-13
Bna25486014
Nitrilase-like protein
0.34
0
Bna39240426
Nitrilase activity
0.21
5.02E-14
Bna39242071
Aldehyde oxidase
0.87
1.73E-07
Bna39233668
Auxin response factor 8, ARF
1.18
1.61E-05
Bna38920344
Auxin responsive protein IAA
8.43
1.06E-06
Bna39296834
Auxin reponsive protein
4.63
6.57E-05
Bna37279562
Auxin responsive protein
3.86
6.57E-05
Bna53139981
Auxin responsive protein
2.07
1.77E-06
Bna39163068
Auxin responsive protein
0.39
7.07E-15
Bna39166254
SAUR; Auxin-induced protein-like
0.09
1.28E-29
Bna39166442
SAUR-like; Auxin-responsive protein
0.39
1.63E-59
Bna39201713
Dormancy/Auxin associated protein
4.50
6.57E-05
Bna39224187
Dormancy/Auxin associated protein
1.61
7.62E-11
Bna38997093
Auxin-induced atb2-like protein
0.12
1.5E-04
ABA biosynthesis
Bna46922371
Zeaxanthin epoxidase, ZEP
0.30
1.36E-15
Bna39227479
NCED4, 9-cis-epoxycarotenoid dioxygenase 4
0.34
5.06E-21
Bna39126794
NCED3, 9-cis-epoxycarotenoid dioxygenase 3
0.11
5.41E-09
Bna44680032
Short-chain dehydrogenase/reductase family
3.53
3.95E-05
1.89
1.91E-05
1.75
1.11E-13
protein, SDR
Bna38903535
Short-chain dehydrogenase/reductase family
protein
Bna25429379
Short-chain dehydrogenase/reductase family
protein
ABA catabolism
ABA signaling
Bna39242071
Aldehyde oxidase, AAO
0.87
1.73E-07
Bna39181541
(+)-abscisic acid 8'-hydroxylase
2.89
1.27E-04
Bna39208628
(+)-abscisic acid 8'-hydroxylase
0.09
1.82E-19
Bna38999997
Abscisic acid receptor PYL5; ABI1-binding
10.26
0
3.70
6.57E-05
protein 3
Bna39003260
Abscisic acid receptor PYL4; ABI1-binding
protein 2
Bna25461271
Abscisic acid receptor PYL7
3.32
1.28E-13
Bna39003811
Abscisic acid receptor PYL8
2.09
0
Bna32888989
Protein phosphatase 2C, PP2C
1.80
1.26E-06
Bna38993743
Phosphatase 2C family protein, PP2C
1.38
2.29E-09
Bna52593230
Serine/threonine phosphatases family 2C, PP2C
1.14
2.02E-06
Bna38971261
Phosphatase 2C, PP2C
0.74
8.38E-08
Bna39185822
Protein phosphatase 2C 41; PP2C41
0.58
4.71E-06
Bna39280151
Protein phosphatase 2C 16; PP2C16
0.34
1.19E-15
Bna37268194
SnRK; SNF1 related protein kinase
0.37
3.31E-208
Bna39211698
AFP3; ABI 5 Binding Protein 3
0.46
7.15E-11
Bna39202750
ABA-induced-like protein
0.12
1.87E-06
Bna39003448
ABA-responsive protein (GRAM domain)
3.41
3.95E-05
Bna39283498
hb-6-like protein
0.52
7.44E-32
Table S4 DEGs related to G protein signaling, Ca2+ signaling, and ubiquitination signaling in transgenic T-4 rapeseed
G protein signaling
Ca2+ signaling
Gene ID
Description
Fold change
P-Value
Bna39005343
Ran-binding protein 1-a
7.84
1.05E-04
Bna37281287
GTP binding protein
3.22
6.78E-05
Bna44678152
Ras-related protein RABA1b
2.48
1.80E-05
Bna38993100
GTP binding / GTPase
2.74
2.60E-13
Bna44687568
RabGTPase-like protein A5B
2.37
3.08E-07
Bna39240837
GTP-binding protein; Ran3E-1
1.99
4.11E-13
Bna39126676
RabGTPase Homolog A4B
1.65
6.59E-07
Bna39162467
GTP-binding protein subunit beta-like protein
1.49
2.91E-13
Bna39064011
Ran-binding protein 1 domain-containing protein
1.46
0
Bna39167534
Rac-like GTP-binding protein ARAC4
1.37
1.52E-05
Bna39164803
GTP-binding protein
1.19
1.83E-05
Bna39237762
RabGTPase Homolog A2C
1.14
3.07E-13
Bna52602738
Ras-related small GTP-binding family protein
1.10
2.05E-13
Bna38998453
GTP-binding family protein
0.94
6.34E-08
Bna38993578
RabGTPase homolog G3d
0.52
2.68E-21
Bna39170190
GTP-binding protein
0.41
8.55E-05
Other G protein signaling
Bna36047404
Rho-GTPase-activating protein
5.34
6.64E-13
components
Bna38891812
GTPase-activating protein, GAP
2.15
6.44E-06
Bna39163118
Ras-GTPase-activating protein
1.27
0
Bna38997321
Regulator of G protein signaling, RGS
3.67
2.29E-05
Bna39003001
G protein-coupled receptor, GPCR
2.12
3.00E-09
Bna39278860
Extracellular ligand-gated ion channel
0.12
3.48E-05
Bna25424071
Extracellular ligand-gated ion channel
0.12
8.06E-06
G protein, GTP-binding protein
Generation of ‘ Ca2+ signature’
Ca2+
sensors
Bna38969315
Metal transport protein
3.61
3.95E-05
Bna39279444
Ion transmembrane transporter
2.00
6.67E-07
Bna39244563
Ion transmembrane transporter
1.18
1.61E-13
Bna39189656
Ca2+-transporting ATPase like protein
8.43
1.06E-06
Bna38958555
Ca2+-transporting ATPase
0.38
8.35E-05
Bna38956719
H+
2.44
4.08E-06
Bna39201211
H+-transporting
1.77
3.97E-14
Bna39197711
H+-transporting ATP
0.57
4.59E-41
Bna39179237
Calcium-binding EF-hand protein
4.29
7.59E-14
Bna39244053
Calcium-binding EF-hand protein
3.30
4.29E-08
Bna39244947
Calcium-binding EF hand family protein
2.81
7.14E-06
Bna25488162
Calcium-binding protein
1.85
1.86E-12
Bna37278469
Calcineurin B-like protein, CBL
1.22
2.60E-06
Bna39250210
Calmodulin, CaMs
2.33
5.95E-07
Bna44681667
Calmodulin
2.18
4.78E-06
Bna39248612
Calmodulin-
2.1
0
Bna39204571
Calmodulin
1.75
3.37E-13
Bna39237836
Calmodulin
1.52
1.84E-12
Bna39187620
Calmodulin
1.01
8.63E-05
Bna39212315
Calmodulin
0.52
3.12E-07
Bna38992493
Calmodulin-binding protein
2.38
5.80E-09
Bna25485403
Calmodulin-binding protein
1.52
1.97E-13
Bna38909508
Calmodulin-binding protein
1.41
6.30E-07
Bna39244829
Calmodulin-binding protein
1.27
9.02E-05
Bna39184517
Calmodulin-binding protein
1.23
1.18E-06
Bna39004149
Calmodulin-binding family protein
0.75
1.28E-27
transporting ATP synthase
two-sector ATPase
synthase
ubiquitination signaling
Ub
Bna37296759
Ubiquitin-like proteins, Ub
0.90
0
SUMO
Bna39229781
Small ubiquitin-related modifier 3
3.04
1.29E-05
E2
Bna39076839
Ubiquitin-conjugating enzyme E2
2.49
4.73E-13
Bna39189083
Ubiquitin-conjugating enzyme E2
1.39
2.90E-12
Bna52585743
Ubiquitin-conjugating enzyme E2
0.78
1.72E-07
UCH
Bna38992999
Ubiquitin carboxyl-terminal hydrolase-related protein
1.65
6.59E-07
E3
Bna25416785
Cullin-RING ubiquitin ligase complex
2.38
1.51E-09
Bna44669387
Cullin-RING ubiquitin ligase complex
2.08
2.01E-10
Bna38908200
Ubiquitin-protein ligase
8.03
2.82E-05
Bna32880464
Ubiquitin-protein ligase
3.29
7.70E-10
Bna38909755
Ubiquitin-protein ligase
2.12
2.02E-12
Bna39292037
Ubiquitin-protein ligase
1.87
8.97E-10
Bna38909176
Ubiquitin-protein ligase
2.01
2.26E-13
Bna44672740
Ubiquitin-protein ligase
0.40
4.85E-05
Bna39171470
Kelch repeat-containing F-box family protein
2.15
2.22E-15
Bna39267303
F-box family protein
2.09
2.66E-11
Bna38978210
F-box family protein
1.89
1.91E-05
Bna39238218
F-box/kelch-repeat protein
1.77
5.55E-13
Bna39167932
F-box family protein
0.26
8.17E-194
Bna25485650
F-box protein
0.26
0
Bna39209444
U-box domain-containing protein
2.05
0
Bna52607229
RING/U-box domain-containing protein
1.57
1.69E-11
Bna39203619
PUB18,,Plant U-BOX 18
0.34
4.00E-17
F-box protein
U-box protein
Table S5 DEGs related to protein kinases in transgenic T-4 rapeseed
Gene ID
Description
Fold change
P-value
Calcium dependent protein kinase, CDPK
Bna39171028
Calcium-dependent protein kinase 9
0.96
1.14E-05
Mitogen activated protein kinase , MAPK
Bna51749245
MAP kinase 4
2.48
1.13E-12
Bna52602272
MAP kinase 6
1.09
1.42E-04
Bna39182231
MAP kinase 9
0.58
4.90E-53
Bna39278589
MAP kinase 19
0.68
1.19E-34
Bna39185837
MKK9, MAP KINASE KINASE 9
2.15
9.10E-08
Bna25477586
MAPKKK beta 1 protein kinase
1.46
7.74E-10
Bna37215836
Feronia receptor-like kinase
3.79
3.95E-05
Bna39298115
Cysteine-rich receptor-like protein kinase 8
0.34
8.98E-11
Bna39179688
Wall-associated receptor kinase-like 10
0.27
3.81E-08
Bna39249379
Leucine-rich repeat receptor-like protein kinase
7.84
1.05E-04
Bna39004716
Leucine-rich repeat receptor-like protein kinase
1.35
3.78E-10
Bna39189036
Leucine-rich repeat receptor-like protein kinase
0.12
1.67E-05
Bna39162161
CBL-interacting protein kinase 1
3.97
2.29E-05
Bna39227495
CBL-interacting protein kinase 14
0.40
4.85E-05
Bna39232261
CBL-interacting protein kinase 25
0.27
4.04E-34
Bna32887901
Shaggy-related protein kinase
8.03
2.82E-05
Bna39004145
D6 protein kinase like 1
3.36
2.00E-10
Bna39238716
Sel1-like repeat-containing protein kinase
2.86
3.88E-06
Bna39078506
Leucine-rich repeat like serine/threonine protein kinase
2.59
1.18E-04
Bna39126918
LRR receptor-like serine/threonine protein kinase
1.15
1.29E-06
Bna32880127
CKI1, casein kinase I
1.56
3.29E-06
Receptor like protein kinase, RLK
Leucine-rich repeat receptor-like protein kinase, LRR-PLK
Serine/threonine protein kinase, STK
Other protein kinase
Bna39232167
Serine/threonine protein kinase-like protein
2.26
6.27E-07
Bna25486250
Serine/threonine kinase BNK1
2.01
2.15E-07
Bna39290547
Serine/threonine protein kinase ATPK10
1.65
1.55E-05
Bna53140005
Serine/threonine protein kinase family protein
1.59
3.50E-05
Bna39198824
Serine/threonine-protein kinase
0.62
1.60E-39
Bna32882415
Histidine kinase
7.84
1.05E-04
Bna39249952
Histidine kinase
3.58
7.13E-06
Bna39247965
Protein tyrosine kinase
1.86
1.08E-13
Bna39254452
Protein tyrosine kinase
1.38
1.82E-07
Bna39248161
Pyruvate kinase
2.13
1.17E-08
Bna39239811
Pyruvate kinase
1.36
2.18E-13
Bna39186063
Adenylate kinase family protein
2.20
9.55E-14
Bna34328859
Aspartate/glutamate/uridylate kinase family protein
2.19
1.72E-07
Bna39167637
Nucloside diphosphate kinase 2
2.10
5.15E-08
Bna39245257
S-methyl-5-thiribose kinase
1.93
1.16E-13
Bna53140005
Protein kinase family protein
1.59
3.50E-05
Bna39162792
Diacylglycerol kinase 1
0.40
7.84E-11
Table S6 DEGs related to transcription factors in transgenic T-4 rapeseed
MYB transcription factor
AP2/EREBP transcription factor
Gene ID
Description
Log2Ratio
P-value
Bna29940217
MYB family transcription factor
10.38
0
Bna39004392
MYB-like transcription factor
2.08
9.99E-15
Bna39088037
MYB family transcription factor
0.54
1.52E-04
Bna37267028
MYB-related transcription factor
0.61
6.51E-05
Bna37216008
R2R3-MYB transcription factor
0.47
3.22E-23
Bna25462218
MYB domain protein 95
0.49
3.97E-30
Bna37277406
C-MYC binding protein
0.30
1.80E-06
Bna39244115
CCA1 (circadian clock associated 1) transcription factor
0.11
1.01E-07
Bna39248644
APL (Altered phloem development) transcription factor
1.34
0
Bna39188380
GCC box of the ethylene response element (ERE)
9.49
2.89E-13
Bna39093151
AP2/ERF transcription factor
7.94
5.44E-05
Bna39238487
AP2/ERF and B3 domain-containing transcription factor RAV2
2.54
4.08E-13
Bna37279577
AP2 transcription factor
1.13
2.98E-12
Bna39241287
AP2 domain containing protein RAP2.7
0.44
7.60E-19
Bna25484966
DREB2-19
0.43
1.25E-47
Bna39182169
ERF2 transcription factor
1.35
1.01E-04
Bna25414333
Ethylene-responsive transcription factor ERF023
0.44
2.16E-09
Bna44672452
Ethylene-responsive transcription factor ERF060
0.45
4.78E-06
Bna38894261
Ethylene-responsive transcription factor ERF069
0.72
1.70E-05
Bna39140511
VAM3; SNAP receptor
1.5
1.15E-04
Bna38995243
TINY transcription factor
8.79
2.05E-08
Bna39004503
TINY transcription factor
2.16
3.81E-07
Bna34817726
Baby boom interacting protein 2
1.83
1.04E-12
NAC-domain protein
bZIP transcription factor
Zinc finger protein
Bna39006051
NAC domain-containing protein 5
4.61
1.08E-04
Bna25479726
NAC-domain protein 5-8
2.95
0
Bna39288059
NAC domain-containing protein
2.08
0
Bna25478767
NAC-domain protein 14
1.47
8.62E-09
Bna25479707
NAC-domain protein 5-11
0.84
2.32E-28
Bna25479785
NAC-domain protein 1-1
0.8
1.78E-06
Bna39180164
NAM/CUC2-like protein
0.43
4.81E-05
Bna35033058
NAC domain containing protein 47
0.32
1.99E-37
Bna39249308
NAC-domain protein 3
0.12
8.06E-06
Bna39168304
bHLH32 ( Basic helix-loop-helix 32) transcription factor
2.52
1.59E-05
Bna38996261
bHLH148 transcription factor
2.42
1.60E-07
Bna36045964
bHLH family protein
2.35
3.77E-12
Bna39169220
bHLH60 transcription factor
2.24
4.08E-13
Bna39293241
bHLH transcription factor
1.59
3.50E-05
Bna25418073
bHLH transcription factor like protein
1.20
3.61E-06
Bna39162682
bHLH64 transcription factor
0.25
4.72E-40
Bna48316871
bHLH DNA-binding domain transcription factor
0.60
1.47E-04
Bna39164403
bHLH93 transcription factor
0.66
4.93E-06
Bna39240049
bHLH family protein 47
0.76
1.56E-04
Bna38996145
bHLH family protein
0.85
9.60E-05
Bna38993093
bZIP transcription factor-like protein
2.57
4.57E-14
Bna39002380
bZIP transcription factor-like protein
2.26
1.16E-13
Bna25470935
Homeobox leucine zipper protein HAT4
0.44
5.67E-254
Bna38972292
Cox19-like CHCH family protein
2.03
8.46E-06
Bna37220088
Coiled-coil-helix-coiled-coil-helix domain containing protein
2.48
1.80E-05
Bna39231727
Constans-like 1 protein
8.36
2.04E-06
Bna25465836
CSL zinc finger domain-containing protein
8.84
1.06E-08
Bna39234598
CSL zinc finger domain-containing protein
2.58
1.41E-13
Bna39264037
B-box type Zinc finger family protein
8.20
7.59E-06
Bna39225597
B-box type Zinc finger family protein
8.03
2.82E-05
Bna39264828
B-box type Zinc finger family protein
0.44
2.68E-05
Bna52586232
Zim17-type zincfingerprotein
2.51
1.56E-13
Bna37215566
Zim17-type zincfingerprotein
0.95
3.84E-06
Bna39166435
C3HC4-type RING finger family protein
2.44
4.08E-06
Bna37610386
C3HC4 type family protein,
1.18
2.89E-05
Bna39201747
C3HC4-type RING finger family protein
0.88
2.18E-113
Bna39072927
C2H2-like zinc finger protein
2.31
5.12E-05
Bna52594307
C2H2-type zincfingerprotein
1.12
3.70E-05
Bna39272387
C2H2-like zinc finger protein
0.46
7.83E-05
Bna25459686
C2H2 zinc finger protein 1
0.61
3.47E-05
Bna39179208
Dof-type zinc finger domain-containing protein
2.23
3.24E-07
Bna39241433
Dof-zinc finger protein
0.09
2.27E-21
Bna39245449
Dof zinc finger protein
0.35
2.21E-88
Bna39284837
CCCH-type zinc finger family protein
1.58
1.81E-11
Bna39240170
CCCH-type zinc finger family protein
1.42
8.64E-05
Bna36047913
CCCH-type zinc finger family protein
0.50
2.08E-05
Bna38995502
BTB and TAZ domain protein 1
3.53
1.13E-12
Bna38994782
BTB and TAZ domain protein 5
2.23
1.80E-13
Bna39170153
BTB/POZ domain-containing protein
3.13
0
Bna38999342
BTB-POZ and math domain 1
1.79
7.02E-05
Bna38992332
RING-H2 type zinc finger protein-related
1.87
2.11E-12
Bna39130810
Vascular plant one zinc finger protein 2
1.83
7.65E-06
WRKY transcription factor
Cupin domain protein
Bna44666214
RING-H2 zinc finger protein-like
1.81
0
Bna39292590
Zinc finger helicase family protein
1.80
2.38E-08
Bna39223553
RING/U-box protein with C6HC-type zinc finger
1.75
3.47E-08
Bna25470625
AN1-like Zinc finger family protein
1.21
3.15E-13
Bna32878817
Iron-binding zinc finger CDGSH type domain-containing protein
0.17
3.78E-211
Bna38895002
LZF1, Light-regulated zinc finger protein1
0.25
5.91E-18
Bna39163520
GATA type zinc finger family protein
0.59
1.77E-07
Bna37292167
GATA transcription factor 1
1.68
0
Bna39222792
C3H4 type zincfingerprotein
0.96
7.34E-05
Bna39273016
Zinc finger family protein
7.84
1.05E-04
Bna36047585
Zinc finger protein
2.53
1.13E-08
Bna38944840
Zinc finger family protein
2.35
5.80E-09
Bna32883654
Zinc finger family protein
2.04
7.12E-12
Bna39224430
Zinc finger family protein
1.94
0
Bna39288231
Zinc finger family protein
1.70
2.63E-05
Bna39005516
Zinc finger family protein
1.29
0
Bna53140263
Zinc finger family protein
1.21
1.49E-05
Bna38993118
Zinc finger family protein
1.13
5.64E-06
Bna39029510
Zinc finger family protein
1.03
5.52E-05
Bna39261055
Zinc finger family protein
0.12
3.88E-06
Bna39017485
Zinc finger family protein
0.91
5.26E-05
Bna38961641
WRKY DNA-binding protein 21
1.83
2.22E-15
Bna52434848
WRKY70-1 transcription factor
1.47
2.36E-06
Bna52434864
WRKY26-1 transcription factor
0.72
2.74E-20
Bna39167495
Cupin domain-containing protein
1.67
5.06E-09
Bna39167830
Cupin domain-containing protein
0.55
1.10E-227
Ankyrin repeat protein
WD repeat protein
Pentatricopeptide repeat-containing protein, PPRs
Nuclear transport factor, NTF
G-box binding factor
MADS-box protein
Bna39252971
Cupin superfamily protein
1.04
2.91E-13
Bna32887604
Cupin, RmlC-type protein
2.89
1.29E-05
Bna38957218
Cupin, RmlC-type protein
8.12
1.46E-05
Bna52584676
Ankyrin repeat family protein
8.43
1.06E-06
Bna39238666
Ankyrin repeat family protein
2.19
2.22E-15
Bna25462898
Ankyrin repeat family protein
1.14
5.07E-13
Bna39068259
Ankyrin repeat family protein
0.92
6.64E-11
Bna52594010
Ankyrin repeat family protein
0.87
5.66E-05
Bna39255739
WD-repeat protein
4.74
0.000107518
Bna38901381
WD40 domain-containing protein
1.51
3.59E-13
Bna37294233
Notchless protein-like protein
0.60
9.67E-07
Bna39164037
Pentatricopeptide repeat-containing protein
2.28
0
Bna38889670
Pentatricopeptide repeat-containing protein
1.54
7.77E-05
Bna39242797
Pentatricopeptide repeat-containing protein
1.39
8.15E-14
Bna39242741
Pentatricopeptide repeat-containing protein
1.35
8.34E-08
Bna38967185
Pentatricopeptide repeat-containing protein
0.71
7.66E-14
Bna39211712
Pentatricopeptide repeat-containing protein
0.45
8.39E-20
Bna39285860
Pentatricopeptide repeat-containing protein
0.46
1.56E-06
Bna38886972
Nuclear transport factor 2 superfamily
1.20
3.13E-09
Bna39220246
Nuclear transport factor 2A
1.17
3.87E-06
Bna39173773
Nuclear transport factor 2 family protein
0.54
0
Bna39163779
Nuclear transport factor 2 family protein
0.54
4.40E-17
Bna25500472
G-box binding factor 2A
2.25
1.13E-12
Bna39283027
G-BOX Binding factor 6
0.10
2.18E-14
Bna39162581
G-BOX Binding factor 6
0.42
2.76E-05
Bna25499168
MADS-box protein
2.59
0.000118035
CCAAT-box binding transcription factor
High mobility group protein
Homeo-box transcription factor
Armadillo/beta-catenin repeat protein
AT hook motif-containing protein
PAK-box/P21-Rho-binding protein
Proton-dependent oligopeptide transport protein, POT
C2 domain-containing protein
Bna25485472
MADS-box protein
0.62
3.89E-13
Bna39174956
CCAAT-box binding transcription factor subunit B (NF-YB) family
7.95
5.44E-05
Bna38956976
CCAAT-binding transcription factor family protein
0.90
3.80E-14
Bna39019364
High mobility group family protein
2.25
2.00E-10
Bna39237481
High mobility group family protein
1.20
1.63E-13
Bna37278549
High mobility group
1.07
3.39E-13
Bna52590617
Homeo-demain glabrous 2 transcription factor
1.09
7.69E-08
Bna35033044
Homeo-box transcription factor 12
0.24
2.18E-32
Bna39237404
Armadillo/beta-catenin-like repeat-containing protein
8.85
1.06E-08
Bna39237334
Armadillo/beta-catenin-like repeat-containing protein
2.64
8.58E-05
Bna38909465
Armadillo/beta-catenin repeat family protein
0.68
2.78E-14
Bna39189331
Armadillo/beta-catenin repeat family protein
0.13
0.000149854
Bna38977058
Armadillo/beta-catenin-like repeat-containing protein
0.10
6.30E-17
Bna38957858
AT hook motif-containing protein
1.75
8.33E-08
Bna38883405
AT hook motif DNA-binding family protein
0.52
1.86E-08
Bna38993870
PAK-box/P21-Rho-binding family protein
2.52
1.59E-05
Bna38992151
PAK-box/P21-Rho-binding family protein
1.64
4.14E-07
Bna39280883
POT family protein
2.80
1.11E-06
Bna39177881
POT family domain containing protein
1.72
4.57E-14
Bna36045813
POT family domain containing protein
1.15
8.38E-06
Bna52601200
POT family domain containing protein
0.80
2.11E-11
Bna39240634
C2 domain-containing protein
1.98
2.26E-06
Bna38885765
C2 domain-containing protein
1.20
1.94E-13
Bna37280278
C2 domain-containing protein
1.13
1.06E-12
Bna39196965
C2 domain-containing protein
0.42
4.65E-107
Bna38993229
C2 domain-containing protein
0.41
2.02E-13
B1
14-3-3 protein
Other transcription factors
Bna44681878
14-3-3-like protein GF14 Lambda
3.25
3.95E-05
Bna32888478
14-3-3-like protein GF14 omega
1.05
1.20E-06
Bna35033086
CDF1, Cell Growth Defect Factor 1
9.25
2.88E-11
Bna39231727
Constan-like 1 protein
8.36
2.04E-06
Bna39063491
6B-interacting protein 1-like 1
2.69
2.53E-05
Bna37282085
WW domain containing protein
2.63
1.35E-05
Bna52612004
SWP, struwwelpeter
2.34
7.70E-10
Bna25477613
BURP domain-containing protein
0.81
8.73E-211
Bna53130419
HYH, HY5-Homolog
0.59
9.30E-05
Bna38959385
VQ motif-containing protein
0.52
9.91E-06
Bna39242837
Transcription factor LHY
0.13
3.48E-05
Bna53140101
Early-phytochrome-responsive1, EPR1
0.11
1.56E-11
Table S7 PCR primers used in real-time RT-PCR analysis
Gene ID
Target Gene
Oligonucleotides primers
Bna39005120
Actin
F: 5'- GCTGACCGTATGAGCAAAGA
R: 5'- GCTGAGGGATGCCAAGATG
Bna39208628
(+)-Abscisic acid 8'-hydroxylase
F: 5'-AAGGTTACAATTCGATGCCAGTG
R: 5'- GATTATGTTGTCGGCGATCTGTT
Bna37279562
Auxin-responsive family protein
F: 5'- AGCTGTTACTCCTCCAACCATAA
R: 5'- GCTTGCGTAGTCTTGATCTCCTA
Bna43236380
Proline dehydrogenase
Bna39264037
Zinc finger family protein
F: 5'- CGCATTATCTTCCTCTTGTCTC
R: 5'- CGCTGATGATGTTGGTGGT
F: 5'- TCCATCATCACCCTTCT
R: 5'- TGTCCCACTTGACCTCT
Bna38995424
Putative peptide chain release factor
F: 5'- GACAGGCAGTAGGCGTAGGT
R: 5'- CCCGTCGGAGTGTATGAGT
Bna39189036
Leucine-rich repeat receptor-like protein kinase
F: 5'- GGCGGAGTTGGAGATGTATGGTG
R: 5'- CCCGTTCGTGGCCTGGAGAAGAT
Bna52591370
Transcription factor
F: 5'- TAGTGATGGAAGTGACGGGAATA
R: 5'- TGACTGAGAAACAGACCGAAATG
Bna25485078
Lipoxygenase
Bna42607382
Long chain acyl-CoA synthetase1
F: 5'- AAGGATGGTGGAGTGAAGTGAGG
R: 5'- GTGGTTGGTCGGTTGGGAAAGTA
F: 5'- AGGACGGGAAGGTCTTTGAGAAG
R: 5'- AAGCAGCCCTGTAACGCAATAAA
Bna25494861
Myrosinase-associated protein
F: 5'- CCGATGGTTCTGCTCAACAAGCT
R: 5'- TCACGATAGGAAAGCAACCCAGT