Table 1 Differentially expressed proteins in shoot tissues of pokkali w.r.t IR64

 Oxygen-evolving enhancer protein 1, chloroplast

70

60

8.5507

0.0022

LOC_Os01g31690.1

PS.lightreaction.photosystem II.PSII polypeptide subunits’

 PsbP

73.6

48

6.0813

0.01

LOC_Os07g04840.1

PS.lightreaction.photosystem II.PSII polypeptide subunits’

 Inorganic pyrophosphatase, putative

61.5

26

2.421

0.0041

LOC_Os02g52940.2

‘nucleotide metabolism.phosphotransfer and pyrophosphatases.misc’

 Salt stress root protein RS1

76.5

19

6.6069

0.0013

LOC_Os01g13210.2

‘stress.abiotic.drought/salt’

 Expressed protein

71.5

13

1.4588

0.0226

LOC_Os10g18340.2

‘not assigned.unknown’

 Thioredoxin, putative

41.3

22

6.1376

0.0349

LOC_Os12g08730.1

‘redox.thioredoxin’

 Superoxide dismutase [Cu-Zn]

62.6

19

99.0832

0.0032

LOC_Os08g44770.1

‘redox.dismutases and catalases’

 Peptidyl-prolyl cis-trans isomerase

46.4

10

5.1051

0.0327

LOC_Os05g01270.1

‘cell.cycle.peptidylprolyl isomerase’

 Thylakoid lumenal protein, putative

54.7

8

1.3932

0.0174

LOC_Os10g35810.1

biological process

 NAD dependent epimerase/dehydratase

45.9

7

16.4437

0.0008

LOC_Os05g01970.5

‘protein.degradation’

 ATP-dependent Clp protease ATP-binding subunit

14.5

6

3.8019

0.0046

LOC_Os04g32560.1

‘protein.degradation.serine protease’

 Peptidyl-prolyl cis-trans isomerase

31.7

5

20.3236

0.0225

LOC_Os06g45340.1

‘protein.folding’

 RAD23 DNA repair protein, putative

24.9

4

99.0832

0.0265

LOC_Os06g15360.1

‘DNA.repair’

 Thylakoid lumenal 16.5 kDa protein

19.3

5

1.0666

0.0043

LOC_Os06g49160.1

Biological process

 Calvin cycle protein CP12, putative,

44.4

5

7.8705

0.0334

LOC_Os01g19740.1

‘PS.calvin cycle’

 Elongation factor protein

38.9

8

10.2802

0.0371

LOC_Os07g42300.1

‘protein.synthesis.elongation’

 70 kDa heat shock protein

31.1

14

2.5351

0.0029

LOC_Os12g14070.1

‘stress.abiotic.heat’

 Remorin, putative, expressed

38.4

3

1.6596

0.0182

LOC_Os04g45070.1

‘RNA.regulation of transcription.putative transcription regulator’

 Proteasome subunit alpha type

31.7

3

3.0479

0.0444

LOC_Os11g40140.1

‘protein.degradation.ubiquitin.proteasom’

 Oryzain alpha

10.3

4

1.4588

0.0025

LOC_Os04g55650.1

‘protein.degradation.cysteine protease’

 acyl CoA binding protein, putative

79.1

5

1.1588

0.0204

LOC_Os06g02490.1

‘lipid metabolism.FA synthesis and FA elongation.acyl-CoA binding protein’

 Lipid transfer protein-like

14.5

3

13.9316

0.033

LOC_Os08g42040.1

‘lipid metabolism.lipid transfer proteins etc’

 Uridylyltransferase-related

23.9

3

1.2942

0.0067

LOC_Os08g14440.2

‘amino acid metabolism’

 Nucleoside diphosphate kinase 1

34.2

2

99.0832

0.0265

LOC_Os07g30970.1

‘nucleotide metabolism.phosphotransfer and pyrophosphatases.nucleoside diphosphate kinase’

 DnaK family protein

16.5

3

3.767

0.0049

LOC_Os02g53420.1

‘stress.abiotic.heat’

 Hydroxyacylglutathione hydrolase

14.3

2

99.0832

0.019

OC_Os03g21460.1

‘Biodegradation of Xenobiotics.hydroxyacylglutathione hydrolase’

 H0801D08.11 protein

14.3

2

87.9023

0.0185

LOC_Os04g58240.1

transport

 Kinase, pfkB family,

22

2

2.884

0.0377

LOC_Os08g02120.1

‘major CHO metabolism.degradation.sucrose.fructokinase’

 Histone H2B

16.5

2

1.1803

0.0033

LOC_Os05g49860.1

‘DNA.synthesis/chromatin structure.histone’

 Putative group 3 LEA protein

32

2

1.7701

0.0191

LOC_Os05g46480.1

reproduction, post-embryonic development, embryo development

 Putative Ras-GTPase-activating protein binding protein 1

6.5

2

87.0964

0.0182

LOC_Os02g29480.1

‘protein.targeting.nucleus’

 Coproporphyrinogen III oxidase, chloroplast

16.8

1

87.9023

0.0189

LOC_Os04g52130.1

‘tetrapyrrole synthesis.coproporphyrinogen III oxidase’

 OsAPx6 - Stromal Ascorbate Peroxidase

25.6

5

8.091

0.0366

LOC_Os12g07820.1

‘redox.ascorbate and glutathione.ascorbate’

 Peptidyl-prolyl cis-trans isomerase

26.8

1

99.0832

0.0192

LOC_Os02g52290.1

‘protein.folding’

 Methionyl-tRNA synthetase, putative

23

1

87.9023

0.0185

LOC_Os04g23820.1

‘protein.aa activation’

 Dihydroorotate dihydrogenase protein

9.4

1

1.0965

0.027

LOC_Os02g50350.1

‘nucleotide metabolism.degradation.pyrimidine.dihydrouracil dehydrogenase’

 Thylakoid lumenal protein

24.6

4

1.1482

0.0409

LOC_Os02g42960.1

Biological process

 cDNA clone:001–039-F07

24.5

3

2.9648

0.0454

LOC_Os12g02370.2

‘secondary metabolism.flavonoids.chalcones’

 Putative uncharacterized protein

23.8

3

31.0456

0.0009

LOC_Os01g34700.1

biological_process/metabolic process

 Non-specific lipid-transfer protein

27.1

3

64.8634

0.0186

LOC_Os11g02369.1

LTPL7 - Protease inhibitor/seed storage/LTP family protein precursor

 EF hand family protein

27.9

3

2.0137

0.0175

LOC_Os03g29770.1

‘signalling.calcium’

 Os05g0291700 protein

25.8

2

2.2491

0.0411

LOC_Os05g22614.4

metabolic process/biological process

 ATP synthase subunit alpha

15.3

2

1.4997

0.0367

LOC_Os09g08910.1

‘mitochondrial electron transport / ATP synthesis.F1-ATPase’

 High mobility group protein

17.8

2

99.0832

0.0172

LOC_Os06g51220.4

cellular component organization

 stress responsive protein

8.3

2

1.2474

0.0481

LOC_Os03g21040.2

Biological process

 phytocyanin-related protein Pn14

10.4

2

87.9023

0.0188

LOC_Os08g17160.1

‘misc.plastocyanin-like’

 Putative uncharacterized protein/aminotransferase

3.9

2

87.9023

0.0182

LOC_Os04g52440.1

‘amino acid metabolism.synthesis.central amino acid metabolism.GABA.GABA transaminase’

 PREDICTED: DNA-binding protein MNB1B

43.4

3

8.0168

0.0009

LOC_Os02g26440.1

protein metabolic process

 xyloglucan endotransglycosylase/hydrolase protein 8

15.9

2

6.5464

0.0388

LOC_Os08g13920.1

‘cell wall.modification’

 ribosomal protein/LOC_Os02g33140.1

20.2

1

99.0832

0.0188

LOC_Os02g33140.1

‘protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S14’

 Putative Photosystem I reaction center subunit IV

12.8

1

8.0168

0.0191

LOC_Os07g25430.1

‘PS.lightreaction.photosystem I.PSI polypeptide subunits’

 Actin-1

15.9

1

99.0832

0.019

LOC_Os03g50885.1

cellular component organization

 Putative peptidyl-prolycis-trans isomerase protein

6.7

1

1.6904

0.0385

LOC_Os07g37830.1

‘cell.cycle.peptidylprolyl isomerase’

 HMG protein

31.8

1

87.9023

0.0179

LOC_Os04g47690.2

Biological process (DNA binding)

 Putative uncharacterized protein

5.3

1

9.3756

0.0384

LOC_Os12g15470.2

‘protein.degradation.serine protease’

 ferredoxin-dependent glutamate synthase,

2.1

1

64.2688

0.0187

LOC_Os07g46460.1

‘N-metabolism.ammonia metabolism.glutamate synthase’

 Os07g0585000 protein

8.1

1

87.9023

0.0183

LOC_Os07g39620.2

‘stress.abiotic.cold’

 putative CR9/Light-regulated protein

22.7

1

99.0832

0.0182

LOC_Os01g01340.1

vacuolar transport

 GDP-mannose 3,5-epimerase 1

5.6

1

99.0832

0.0187

LOC_Os10g28200.1

‘redox.ascorbate and glutathione.ascorbate.GME’

 Lipid transfer protein-like

4.8

1

99.0832

0.0181

LOC_Os07g09970.1

‘misc.protease inhibitor/seed storage/lipid transfer protein (LTP) family protein’

 TA9 protein-like

1.5

1

99.0832

0.0181

LOC_Os01g47430.2

DUF1296 domain containing protein

 Os01g0763650 protein

7.9

1

99.0832

0.0188

LOC_Os01g0763700

lipid metabolic process

 dirigent protein 22

6.3

1

99.0832

0.0189

LOC_Os11g07670.1

‘stress.biotic.PR-proteins’

 KE2 family protein

5.4

1

99.0832

0.0186

LOC_Os12g30060.2

protein metabolic process

 Glucan endo-1,3-beta-glucosidase 5

5.5

1

99.0832

0.0198

LOC_Os11g36940.1

‘misc.beta 1,3 glucan hydrolases.glucan endo-1,3-beta-glucosidase’

 Os08g0459300 protein

5.8

1

85.5067

0.019

LOC_Os08g35710.1

‘PS.lightreaction.other electron carrier (ox/red).ferredoxin’

 LOC_Os03g45340.1/hsp20/alpha crystallin family protein

15.6

1

25.3513

0.019

LOC_Os03g45340.1

response to abiotic stimulus

 Os08g0530200/Putative ribosomal protein L17

15.8

2

6.3096

0.0441

LOC_Os08g41810.1

‘protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L17’

 HIPL1 protein, putative

6.1

1

15.1356

0.0188

LOC_Os12g44230.1

‘cell.organisation’

 T-complex protein, putative,

48.3

29

0.1585

0

LOC_Os12g17910.1

‘protein.folding’

 ATP synthase subunit beta

46.4

18

0.4786

0.026

LOC_Os10g21266.1

‘mitochondrial electron transport / ATP synthesis.F1-ATPase’

 Putative transketolase

28

10

0.0692

0.0002

LOC_Os06g04270.1

‘PS.calvin cycle.transketolase’

 Dehydroascorbate reductase

65.3

9

0.0929

0.0485

LOC_Os05g02530.1

‘redox.ascorbate and glutathione.ascorbate’

 Peptidyl-prolyl cis-trans isomerase

61.1

10

0.092

0.0103

LOC_Os02g02890.1

‘cell.cycle.peptidylprolyl isomerase’

 Glyoxalase

26.5

9

0.1472

0.0436

LOC_Os08g09250.2

amino acid metabolism.degradation.aspartate family.threonine’

 peroxiredoxin, putative

35.6

4

0.038

0.0465

LOC_Os02g09940.1

‘redox.peroxiredoxin’

 T-complex protein, putative

14.3

4

0.3373

0.0418

LOC_Os06g02380.2

‘protein.folding’

 Carbonic anhydrase

32.7

5

0.5395

0.0208

LOC_Os01g45274.1

‘TCA / org. Transformation.carbonic anhydrases’

 glycine-rich protein 2, putative

47.2

3

0.138

0.014

LOC_Os01g36570.1

‘stress.abiotic.cold’

 plasminogen activator inhibitor 1 RNA-binding protein

30.5

4

0.5445

0.0414

LOC_Os05g45660.2

‘RNA.RNA binding’

 NAD dependent epimerase/dehydratase

8.4

1

0.278

0.0448

LOC_Os07g11110.1

‘RNA.regulation of transcription.unclassified’

 60 kDa chaperonin alpha subunit

39.8

17

0.0871

0.0445

LOC_Os11g47970.1

AAA-type ATPase family protein

 Ribulose bisphosphate carboxylase small chain

57.7

14

0.1169

0.0039

LOC_Os12g17600.1

ribulose bisphosphate carboxylase small chain

 Putative uncharacterized protein

34.9

3

0.1614

0.0324

LOC_Os03g08800.1

CutA, chloroplast precursor, putative

 Protein CutA, chloroplast,

20.4

1

0.9204

0.043

LOC_Os04g50110.1

RNA recognition motif containing protein,

 Putative uncharacterized protein

8.3

2

0.0111

0.0444

LOC_Os03g20630.2

histidine triad family protein,

 Oxygen-evolving enhancer protein 1, chloroplast

58

43

15.7036

0.0028

LOC_Os01g31690.1

PS.lightreaction.photosystem II.PSII polypeptide subunits’

 Ribulose bisphosphate carboxylase large chain 1

53.5

41

5.4954

0.0126

LOC_Os10g21268.1

‘PS.calvin cycle.rubisco large subunit’

 PsbP

71.3

32

19.0546

0.0129

LOC_Os07g04840.1

PS.lightreaction.photosystem II.PSII polypeptide subunits’

 Putative inorganic pyrophosphatase

65.4

22

4.7424

0.0126

LOC_Os02g52940.2

‘nucleotide metabolism.phosphotransfer and pyrophosphatases.misc’

 Catalase

36.2

16

3.2509

0.0041

LOC_Os02g02400.1

‘redox.dismutases and catalases’

 protein|ribosome recycling factor, putative

49.6

18

3.1623

0.0001

LOC_Os07g38300.1

‘cell.division’

 Phosphoribulokinase

45.2

16

2.5119

0.0214

LOC_Os02g47020.1

‘PS.calvin cycle.PRK’

 protein|salt stress root protein RS1

71.6

13

7.5858

0.0005

LOC_Os01g13210.2

‘stress.abiotic.drought/salt’

 Carbonic anhydrase

53.3

16

8.1658

0.0016

LOC_Os01g45274.1

‘TCA / org. Transformation.carbonic anhydrases’

 RNA recognition motif containing protein

49

12

5.4954

0.002

LOC_Os09g10760.1

‘RNA.RNA binding’

 ABA/WDS induced protein,

58

10

4.8306

0.0302

LOC_Os11g06720.1

abscisic stress-ripening

 protein|expressed protein

60.6

8

1.9409

0.0023

LOC_Os10g18340.2

‘not assigned.unknown’

 30S ribosomal protein S1, chloroplast

23.7

6

2.0893

0.0321

LOC_Os03g20100.1

‘protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.30S subunit.S1’

 30S ribosomal protein S31, chloroplast precursor,

37.3

5

3.1046

0.001

LOC_Os05g09400.3

translation

 Putative group 3 LEA protein

31.5

3

5.445

0.001

LOC_Os05g46480.1

reproduction, post-embryonic development, embryo development

 Ankyrin repeat domain protein 2,

15.1

3

1.5136

0.0012

LOC_Os03g63480.1

‘RNA.regulation of transcription.AtSR Transcription Factor family’

 protein|OsCML7 - Calmodulin-related calcium sensor protein

32.4

3

1.6596

0.0248

LOC_Os08g02420.1

‘signalling.calcium’

 Class III peroxidase 125

13.1

3

6.2517

0.0012

LOC_Os10g02040.1

‘misc.peroxidases’

 linker histone H1 and H5 family protein

20.2

1

52.9663

0.0181

LOC_Os08g33190.1

‘DNA.synthesis/chromatin structure.histone’

 Lipid transfer protein-like

9.5

2

83.1764

0.0179

LOC_Os08g42040.1

‘lipid metabolism.lipid transfer proteins etc’

 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase protein

26.3

1

1.028

0.0176

LOC_Os03g06620.1

‘metal handling.regulation’

 oxygen evolving enhancer protein 3

66.8

47

11.1686

0.01

LOC_Os07g36080.1

‘PS.lightreaction.photosystem II.PSII polypeptide subunits’

 Ribulose bisphosphate carboxylase/oxygenase activase,

57.2

38

3.4995

0.0003

LOC_Os11g47970.1

‘PS.calvin cycle.rubisco interacting’

 ferredoxin-dependent glutamate synthase,

13

9

2.6546

0.0018

LOC_Os07g46460.1

‘N-metabolism.ammonia metabolism.glutamate synthase’

 Putative uncharacterized protein

40.5

9

9.3756

0.0202

XP_015634836.1

probable peroxisomal membrane protein PEX13

 Os01g0326000 protein/peroxidase 1

19.9

5

2.0137

0.0473

LOC_Os01g22230.1

‘misc.peroxidases’

 CDGSH iron-sulfur domain-containing protein NEET

52.3

4

10.3753

0.0159

LOC_Os07g28400.1

biological_process

 Os04g0445200 protein

56.5

3

3.4995

0.0045

LOC_Os04g36760.1

NO

 Q8LQN2|Q8LQN2_ORYSJ

24.6

5

1.3932

0.0463

LOC_Os01g57570.1

NADPH-dependent FMN reductase domain containing protein

 BBTI7 - Bowman-Birk type bran trypsin inhibitor precursor

15.1

2

2.2491

0.0023

LOC_Os01g03390.1

BBTI7 - Bowman-Birk type bran trypsin inhibitor precursor

 OSJNBa0086O06.22 protein/31 kDa ribonucleoprotein

10.7

3

1.9588

0.0013

LOC_Os04g50110.1

‘RNA.RNA binding’

 Os06g0671900 protein/Q0DA75|Q0DA75_ORYSJ

13.6

2

1.2246

0.0378

LOC_Os06g46000.1

tubulin/FtsZ domain containing protein

 LTPL52 - Protease inhibitor/seed storage

21.8

2

2.3768

0.0009

LOC_Os03g26820.1

transport

 Putative SHOOT1 protein

18.8

1

5.2966

0.0319

LOC_Os07g07540.1

response to stress

 Glutamate dehydrogenase

7.8

1

99.0832

0.019

LOC_Os03g58040.2

‘N-metabolism.N-degradation.glutamate dehydrogenase’

 Alpha-tubulin

9.1

1

42.0727

0.0184

LOC_Os11g14220.1

cell.organisation’/response to abiotic stimulus

 enolase, putative

37.1

9

0.4742

0.0065

LOC_Os10g08550.1

‘glycolysis.cytosolic branch.enolase’

 ubiquitin fusion protein, putative

61.2

13

0.3311

0.0313

LOC_Os09g39500.1

‘protein.degradation.ubiquitin.ubiquitin’

 Glyoxalase

33.7

10

0.2754

0.0121

LOC_Os08g09250.2

amino acid metabolism.degradation.aspartate family.threonine’

 Glyceraldehyde-3-phosphate dehydrogenase

37.1

10

0.3221

0.0005

LOC_Os04g40950.1

‘glycolysis.cytosolic branch.glyceraldehyde 3-phosphate dehydrogenase (GAP-DH)’

 Malate dehydrogenase

37.4

7

0.3048

0.0326

LOC_Os10g33800.1

‘TCA / org. Transformation.other organic acid transformaitons.cyt MDH’

 Nucleoside diphosphate kinase

48.3

5

0.2051

0.0283

LOC_Os10g41410.2

‘nucleotide metabolism.phosphotransfer and pyrophosphatases.nucleoside diphosphate kinase’

 Stress responsive protein

20.3

3

0.1644

0.0276

LOC_Os01g01450.1

Stress responsive protein

 L11 domain containing ribosomal protein

31.3

3

0.0316

0.0081

LOC_Os02g47140.1

‘protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L12’

 Class III peroxidase 65

21.6

6

0.1905

0.0181

LOC_Os05g04380.1

‘misc.peroxidases’

 RNase S-like protein

30.2

3

0.0119

0.0067

LOC_Os09g36680.1

‘RNA.processing.ribonucleases’

 Phenylalanine ammonia-lyase

13

3

0.7727

0.0162

LOC_Os02g41630.2

‘secondary metabolism.phenylpropanoids.lignin biosynthesis.PAL’

 Probable aldo-keto reductase 2

19.1

2

0.0938

0.016

LOC_Os04g26910.1

‘hormone metabolism.auxin.induced-regulated-responsive-activated’

 ranBP1 domain containing protein

5.7

2

0.0316

0.0075

LOC_Os05g28190.1

‘signalling.G-proteins’

 Putative Ras-GTPase-activating protein binding protein 1

13.1

1

0.2014

0.0451

LOC_Os02g29480.1

‘protein.targeting.nucleus’

 Fructose-bisphosphate aldolase

30.2

8

0.0296

0.0041

LOC_Os01g67860.1

‘PS.calvin cycle.aldolase’

 enoyl-acyl-carrier-protein reductase NADH

22.6

5

0.6982

0.0133

LOC_Os08g23810.1

‘lipid metabolism.FA synthesis and FA elongation.enoyl ACP reductase’

 dehydrogenase, putative

27.2

3

0.912

0.0169

LOC_Os08g29170.1

‘misc.oxidases - copper, flavone etc.’

 SOR/SNZ family protein

22.7

4

0.6138

0.0257

LOC_Os10g01080.1

‘Co-factor and vitamine metabolism’

 ketol-acid reductoisomerase

10.3

3

0.9376

0.0359

LOC_Os05g49800.1

‘amino acid metabolism.synthesis.branched chain group.common’

 NAD dependent epimerase/dehydratase family

10.6

3

0.0283

0.0056

LOC_Os03g16980.1

‘cell wall.precursor synthesis.UXS’

 erythronate-4-phosphate dehydrogenase domain containing

22.6

3

0.053

0.0119

LOC_Os06g29180.1

‘C1-metabolism’

 transaldolase

12.3

2

0.1019

0.0146

LOC_Os01g70170.1

‘OPP.non-reductive PP.transaldolase’

 peptidase, T1 family

11.5

2

0.0313

0.04

LOC_Os02g42320.2

‘protein.degradation.ubiquitin.proteasom’

 actin, putative

21

2

0.4966

0.048

LOC_Os11g06390.4

‘cell.organisation’

 RNA recognition motif containing protein

41.3

3

0.5058

0.0222

LOC_Os01g68790.2

‘RNA.RNA binding’

 osmotin, putative

11.6

2

0.5012

0.0451

LOC_Os12g38170.1

‘stress.abiotic’

 NADPH-dependent FMN reductase domain containing protein

19.2

3

0.0121

0.0492

LOC_Os08g04460.1

‘lipid metabolism.“exotics” (steroids, squalene etc)’