Table 2 Functions and fold changes of selected seed dormany/germination-related DEGs during MD and PD release

i0_LQ_SeedM_c3069/f1p14/781

AtGIM2

GA biosynthesis

1.85

i1_HQ_SeedM_c1802/f5p2/1957

AtNPF3.1

GA transport

−1.76

2.63

i0_LQ_SeedM_c1919/f2p0/830

AtSLY1

GA signaling

−2.23

i3_LQ_SeedM_c33971/f1p0/3810

AtSPY

GA signaling

−3.75

3.98

i4_LQ_SeedM_c21157/f1p3/4409

AtSPY

GA signaling

2.66

−1.96

i1_HQ_SeedM_c1756/f2p5/1840

AtGID1c

GA signaling

−1.53

2.46

i2_LQ_SeedM_c18534/f1p7/2257

AtRGI3

GA signaling

−1.47

i2_HQ_SeedM_c14207/f11p9/2283

AtGAI

GA signaling

−2.8

i0_LQ_SeedM_c8549/f1p3/650

AtGASA6

GA signaling

−7.4

i1_LQ_SeedM_c9540/f1p1/1818

AtCYP707A1

ABA catabolism

3.28

−5.32

i1_LQ_SeedM_c24968/f1p3/1093

AtPYL8

ABA signaling

1.46

i0_LQ_SeedM_c8831/f1p3/976

AtPYR1

ABA signaling

−2.4

i3_LQ_SeedM_c18408/f1p3/3496

AtS2P

ABA signaling

3.3

−2.78

i2_LQ_SeedM_c46616/f3p4/2678

AtHAB1

ABA signaling

−1.67

1.43

i1_LQ_SeedM_c3858/f2p106/1553

AtHON

ABA signaling

−2.52

3.13

i2_LQ_SeedM_c25671/f1p3/2973

AtAFP3

ABA signaling

−2.4

1.94

i1_LQ_SeedM_c5687/f1p17/2029

AtPP2CA

ABA signaling

2.62

i1_LQ_SeedM_c9533/f1p0/1988

AtPP2C5

ABA signaling

−1.81

i3_LQ_SeedM_c20125/f1p4/3251

AtSnRK2.6

ABA signaling

−2.63

i0_LQ_SeedM_c10659/f1p0/461

AtSnRK3.6

ABA signaling

−2.7

i5_LQ_SeedM_c2274/f1p2/5125

AtPP2CE

EGR2 phosphatase

−3.34

2.56

i1_LQ_SeedM_c6124/f1p7/1511

AtHAI3

ABA signaling

−1.75

2.01

i4_LQ_SeedM_c21538/f1p0/4527

AtABF4

ABA signaling

2.9

i1_LQ_SeedM_c8820/f1p3/1489

AtWRKY41

regulator of ABI3 expression

−2.5

i2_LQ_SeedM_c36664/f1p0/2863

AtABI3

ABA signaling

−6.26

i1_LQ_SeedM_c22586/f1p9/1509

AtABI5

ABA signaling

−1.89

i3_HQ_SeedM_c17466/f2p2/3841

AtARF2

Auxin signaling

−5.55

7.14

i3_LQ_SeedM_c7465/f1p21/3129

AtARF2

Auxin signaling

2.21

−4.07

i0_HQ_SeedM_c12179/f2p3/788

AtIAA8

Auxin signaling

−1.83

i2_LQ_SeedM_c3798/f1p9/2925

AtAUX1

auxin transport

4.36

−3.19

i3_LQ_SeedM_c14993/f1p0/3065

AtAUX1

auxin transport

−3.58

3.13

i2_LQ_SeedM_c41269/f1p5/2679

AtLAX

auxin transport

2.13

−3.86

i4_LQ_SeedM_c20675/f1p4/4170

AtABCB1/PGP1

auxin transport

2.49

−5.04

i4_LQ_SeedM_c4985/f1p0/4218

AtABCB1/PGP1

auxin transport

−4.58

3

i4_LQ_SeedM_c3741/f1p0/4833

AtABCB19/PGP19

auxin transport

2.77

−2.41

i4_LQ_SeedM_c18157/f1p5/4494

AtABCG36

auxin transport

−3.28

6.15

i2_HQ_SeedM_c17187/f5p6/2691

AtPIN1

auxin transport

−1.61

2.1

i2_LQ_SeedM_c11796/f1p4/2422

AtPIN1

auxin transport

4.76

−6.81

i2_LQ_SeedM_c37994/f1p3/2426

AtPIN1

auxin transport

−2.99

i2_LQ_SeedM_c41403/f1p2/2390

AtPIN2

auxin transport

−2.9

i2_LQ_SeedM_c56557/f1p2/2726

AtPIN3

auxin transport

1.85

i2_LQ_SeedM_c60075/f1p3/2081

AtPIN4

auxin transport

−5.78

i1_HQ_SeedM_c2547/f4p0/2003

AtNRT1.1

auxin transport

5.38

− 4.32

i2_LQ_SeedM_c37693/f1p22/2372

AtBIN2

BR signaling

−2.05

2.97

i1_LQ_SeedM_c20577/f1p2/1956

AtBIN2

BR signaling

5.57

i3_HQ_SeedM_c11682/f2p0/3684

AtBRI1

BR signaling

−6.27

5.35

i3_LQ_SeedM_c5302/f1p0/3667

AtBRI1

BR signaling

5.44

−6.97

i1_LQ_SeedM_c10003/f1p34/1668

AtMYC2

JA signaling

−1.92

i2_LQ_SeedM_c56779/f1p3/2496

AtAKIN10

Energy sensor

−2.81

2.76

i2_HQ_SeedM_c26414/f2p8/2462

AtCOI1

ubiquitin-dependent protein degradation

1.22

i0_LQ_SeedM_c9980/f1p0/847

AtASK2

ubiquitin-dependent protein degradation

−2.8

2.15

i0_LQ_SeedM_c3002/f1p6/571

AtRHA2b

ubiquitin-dependent protein degradation

−2.56

i3_HQ_SeedM_c7511/f2p11/3746

AtUBP26

ubiquitin-dependent protein degradation

2.92

−2.44

i2_LQ_SeedM_c48471/f2p3/2487

AtATE2

protein degradation

−1.91

i4_HQ_SeedM_c15243/f2p0/4126

AtCOP10

ubiquitin-conjugating enzyme E2

−1.58

i3_LQ_SeedM_c15448/f1p3/3019

AtDWA

substrate receptor for cullin-RING ubiquitin ligase 4 complexes for protein degradation

−2.11

1.95

i0_LQ_SeedM_c5286/f1p0/992

AtCathB3

Cysteine proteinase

4

−4.3

i3_LQ_SeedM_c32927/f1p20/3736

AtSIZ1

protein sumoylation

3.27

−4.75

i3_LQ_SeedM_c22466/f1p6/3768

AtSIZ1

protein sumoylation

−1.89

2.66

i2_LQ_SeedM_c11836/f4p3/2198

AtKAPP

kinase-associated protein phosphatase

3.34

−4.77

i2_LQ_SeedM_c56819/f1p3/2379

AtKAPP

kinase-associated protein phosphatase

−4.31

3.14

i1_LQ_SeedM_c7267/f1p11/1962

AtDjA3

Chaperone protein

−3.28

2.05

i2_LQ_SeedM_c66006/f1p10/2500

AtDjA3

Chaperone protein

2.34

−2.54

i0_LQ_SeedM_c17946/f1p1/823

AtCAM7

calcium signaling

1.76

−3.25

i4_LQ_SeedM_c16211/f1p0/4095

AtCAM7

calcium signaling

−4.25

3.63

i1_LQ_SeedM_c15573/f1p3/1075

AtCML39

calcium signaling

−4.27

i4_LQ_SeedM_c16133/f1p0/4048

AtCAMTA6

calmodulin-binding TF

3.78

i3_LQ_SeedM_c4760/f1p1/3504

AtCAMTA6

calmodulin-binding TF

−2.51

i2_LQ_SeedM_c52294/f1p1/2157

AtIQM4

Ca2 + −independent CaM-binding protein

1.69

i2_LQ_SeedM_c59734/f2p3/2262

AtCPK6

Calcium-dependent protein kinase

4.13

−3.16

i3_LQ_SeedM_c18100/f1p6/3246

AtGLR3.5

ionotropic glutamate receptor

−1.9

i1_LQ_SeedM_c21031/f1p0/1778

AtCAT1

catalase

4.88

−7.79

i1_LQ_SeedM_c5525/f1p5/1792

AtTFIIS

transcript elongation factor

−1.59

i2_HQ_SeedM_c3213/f3p5/2849

AtCBC80

RNA metabolism

−3.02

i2_LQ_SeedM_c13505/f1p1/2439

AtCFM9

RNA metabolism

−1.82

i6_LQ_SeedM_c1081/f1p4/6064

AtDCL1

RNA metabolism

2.82

−2.07

i2_LQ_SeedM_c23333/f1p14/2786

AtSE

RNA metabolism

−2.41

2.59

i2_LQ_SeedM_c27773/f1p0/2851

AtNG1

RNA metabolism

2.71

i0_LQ_SeedM_c2368/f1p9/737

AtGRP7

RNA metabolism

−4

3.68

i4_HQ_SeedM_c3551/f2p0/4808

AtSUA

RNA metabolism

−6.6

5.58

i3_LQ_SeedM_c23460/f1p11/3454

AtSUA

RNA metabolism

6.77

−6.94

i2_LQ_SeedM_c23171/f1p11/2948

AtFY

mRNA processing

2.17

−2.07

i3_LQ_SeedM_c20086/f1p0/3799

AtFY

mRNA processing

−4.59

4.24

i3_LQ_SeedM_c30639/f1p0/3050

AtSF1

mRNA processing

6.59

−7.57

i3_LQ_SeedM_c9329/f1p0/3408

AtSF1

mRNA processing

6.55

i1_LQ_SeedM_c4043/f1p9/1960

AtRRP41L

mRNA degradation

1.74

i3_LQ_SeedM_c9561/f1p61/3436

AtXRN4

mRNA degradation

4.36

−6.43

i5_LQ_SeedM_c4155/f1p1/5195

AtXRN4

mRNA degradation

5.44

i4_LQ_SeedM_c2767/f1p0/4467

AtVCS

mRNA degradation

−3.54

2.82

i3_LQ_SeedM_c9026/f1p0/3591

AtVCS

mRNA degradation

1.95

−2.55

i2_LQ_SeedM_c10778/f1p19/2311

AtTudor2

mRNA degradation

−1.55

1.58

i1_LQ_SeedM_c2372/f1p11/1714

AtCHO1

AP2/ERF-AP2 TF

−2.13

i2_LQ_SeedM_c29982/f1p4/2011

AtASG1

DNA helicase

−1.93

i2_LQ_SeedM_c4618/f1p3/2576

AtASG1

DNA helicase

2.39

i4_LQ_SeedM_c25313/f1p14/4107

AtEMF1

histone methylation

−2.76

2.38

i5_LQ_SeedM_c10657/f1p1/5263

AtCHR12

chromatin modification

3.6

−3.5

i3_LQ_SeedM_c6562/f1p0/3365

AtCLF

chromatin modification

−1.98

2.68

i6_LQ_SeedM_c990/f1p0/6104

AtEFS

chromatin modification

−3.15

i5_HQ_SeedM_c466/f6p0/6094

AtHAC1

chromatin modification

−2.19

1.83

i4_LQ_SeedM_c1879/f1p8/5031

AtHAC1

chromatin modification

2.98

−2.54

i5_LQ_SeedM_c8676/f1p0/5895

AtPKL

chromatin modification

−8.64

7.42

i4_LQ_SeedM_c13881/f1p0/4335

AtPKL

chromatin modification

1.98

−2.06

i3_LQ_SeedM_c14311/f1p0/3164

AtSUVH5

chromatin modification

−4.1

i3_LQ_SeedM_c6655/f1p1/3369

AtHDA9

chromatin modification

4.93

i2_LQ_SeedM_c6979/f1p2/2448

AtHDA15

chromatin modification

−1.56

i4_LQ_SeedM_c18037/f1p21/4801

AtPWR

chromatin modification

1.93

−2.1

i2_LQ_SeedM_c27191/f1p4/2756

AtCRY1

light signaling

3.66

−3.76

i2_HQ_SeedM_c35624/f2p2/2375

AtCRY2

light signaling

−2.16

3.56

i3_LQ_SeedM_c33308/f1p0/3596

AtPHYA

light signaling

2.9

−4.08

i2_LQ_SeedM_c36242/f1p4/2456

AtPIF3

light and GA signaling

−5.16

4.2

i2_LQ_SeedM_c21496/f1p3/2439

AtPIF3

light and GA signaling

−2.43

i1_LQ_SeedM_c17359/f1p1/1778

AtCIPK3

CBL-interacting protein kinase

−2.74

2.91

i3_LQ_SeedM_c21126/f1p9/3152

AtPRR9

circadian rhythm

−7.9

6.9

i2_LQ_SeedM_c52693/f1p0/2189

AtTOC1

circadian rhythm

1.7

i2_LQ_SeedM_c48681/f1p5/2590

AtMED25

light and JA signaling

1.98

−1.94

i1_LQ_SeedM_c10304/f1p0/1883

AtCYCD1;1

cell cycle protein

−2.59

i2_LQ_SeedM_c66356/f1p3/2916

AtSAUR62

Cell-elongated related genes

2.01

i1_HQ_SeedM_c2317/f3p4/1843

AtWRKY2

WRKY TF

3.07

−10.19

i2_LQ_SeedM_c69494/f1p7/2362

AtWRKY2

WRKY TF

−2.1

3.34

i2_LQ_SeedM_c59966/f1p0/2048

AtWRKY6

WRKY TF

4.72

i2_LQ_SeedM_c50026/f1p2/2377

AtWRKY40

WRKY TF

−2.47

i3_LQ_SeedM_c23462/f1p0/3258

AtGBF1

bZIP TF

2.1

i2_LQ_SeedM_c36125/f1p5/3079

AtLUG

transcriptional corepressor

2.2

−5.54

i3_LQ_SeedM_c29344/f1p0/3137

AtLUG

transcriptional corepressor

−3.02

3.29

i2_LQ_SeedM_c21274/f1p0/2367

AtNIA1

nitrate assimilation

6.39

−7.04

i3_LQ_SeedM_c30611/f1p0/3119

AtGCN2

amino acid metabolism

−7.11

6.39

i1_LQ_SeedM_c17195/f2p0/1544

AtGln1;1

amino acid metabolism

1.47

−1.53

i3_LQ_SeedM_c12339/f1p3/3098

AtTPS5

trehalose biosynthesis

−1.89

i1_LQ_SeedM_c20939/f1p0/1223

AtGOLS1

galactinol synthase

4.59

i2_HQ_SeedM_c62143/f13p14/2507

AtMFP2

Fatty acid degradation

3.92

−4.32

i2_LQ_SeedM_c18604/f1p14/2485

AtMFP2

Fatty acid degradation

3.99

i1_LQ_SeedM_c11103/f1p4/1439

AtLIP1

lipid metabolism

2.62

−1.9

i3_LQ_SeedM_c26493/f1p7/3651

AtKPNB1

protein transport

−1.58

i3_LQ_SeedM_c30926/f1p0/3119

AtPHO1

phosphate ion transport

−4.63

i2_LQ_SeedM_c20018/f1p30/2524

AtCER9

cuticular wax biosynthesis

−3.68

i1_LQ_SeedM_c5889/f1p2/1648

AtPGIP2

cell wall metabolism

−1.6

i1_LQ_SeedM_c8885/f1p0/1852

AtPLY

cell wall metabolism

2.57

−5.77

i1_LQ_SeedM_c22277/f1p18/1916

AtPME58

cell wall metabolism

5.59

i1_LQ_SeedM_c20327/f1p9/1915

AtMAN2

cell wall metabolism

−8.51

i2_LQ_SeedM_c17702/f1p2/2902

AtMAN7

cell wall metabolism

3.28

−4.5

i1_LQ_SeedM_c15435/f1p3/1132

AtEXPA4

cell wall metabolism

1.58

−3.82

i1_LQ_SeedM_c2665/f1p0/2002

AtNEK6

cortical microtubule organization

−1.92

i2_LQ_SeedM_c6535/f2p1/2253

AtDREB2C

DREB TF

1.73

i2_LQ_SeedM_c3709/f1p3/2689

AtERD15

dehydration-induced protein

−3.37

1.92

i1_LQ_SeedM_c22084/f1p0/1316

AtLEA31

Seed maturation protein

4.12

i4_LQ_SeedM_c19775/f1p33/4207

AtGSO1

peptide hormone signaling

−2.57