Rao et al. 10.1073/pnas.0709059105.

Plant genotype and phenotype

Panicle length*

(cm ± SD)

Node numbers on central rachis (± SD)

Prb^† length (cm ± SD)

Node number on prb (± SD)

Srb^‡ length (cm ± SD)

Node Numbers on srb (± SD)

Spikelet^§ numbers on a panicle

(± SD)

Strong dsRNAiRFL

4.4 ± 0.32

2.4 ± 0.78

1.0 ± 0.99

2 ± 0.83

4.6 ± 3.8

Weak dsRNAiRFL

5.8 ± 0.92

5 ± 0.81

2.5 ± 0.93

4 ± 0.0

14 ± 2.71

Control plant

10.8 ± 1.2

5.8 ± 1.1

6.2 ± 1.32

5.58 ± 0.55

3.2 ± 0.64

2.9 ± 1.0

28.2 ± 4.2

Plant genotype and phenotype

Panicle length,* cm

Node no. on central rachis

Prb^† length, cm

Node no. on Prb

Srb^‡ length, cm

Node no. on Srb

Spikelet^§ no. on a panicle

Weak phenotype UbiRFL(AS)

8.011 ± 1.48

3.55 ± 1.01

3.921 ± 1.8

5.2 ± 0.93

0.6 ± 0.19

2 ± 0.53

14.2 ± 8.4

Moderate phenotype UbiRFL(AS)

6.8 ± 0.92

3.2 ± 0.89

3.2 ± 0.79

4.0 ± 1.0

-

-

10 ± 3.8

Strong phenotype UbiRFL(AS)

5.3 ± 1.6

3 ± 0.8

2.8 ± 0.4

2.1 ± 0.96

-

-

8 ± 4.1

Control plant

11.9 ± 2.0

5.66 ± 1.15

6.8 ± 1.48

6.62 ± 0.75

3.4 ± 0.54

3.2 ± 1.5

32.6 ± 5.8

Accession number*

Fold down- regulation in UbiRFL(AS)^†

Fold down- regulation in dsRNAiRFL^‡

Annotation^§

Functional category^¶

AK071306

2.3

1.5

Hydrolase, alpha

D

AK071703

2.515

1.5

Hydrolase, alpha/beta

D

AK109014

3.7

2.38

Expressed protein

I

AK073507

1.55

1.5

Senescence-induced receptor-like serine/threonine-protein kinase precursor

D

AK108249

3.9

2

Probable CCCH-type zinc-finger protein

A

AK105729

1.9

1.82

GASR1 mRNA for Gibberellin stimulated transcript related protein 1

B

AK067339

1.75

1.9

MAP kinase 1

B

AK107199

2.55

1.89

Putative DNA-binding protein ABF1

A

AK071303

1.6

1.75

Ras-related GTP-binding protein

B

AK069785

2.75

2.55

Serine carboxypeptidase S10 family protein

D

AK109702

2.1

2.6

Mitogen-activated protein kinase

C

AK109087

5.5

4.89

Unknown

I

AK107567

4.8

3.5

Anthranilate N-benzoyltransferase-like protein

D

AK061645

2.4

2.18

Probable MAP kinase

B

AK100389

2.15

2.75

Mitogen-activated protein kinase

C

AK107172

4.12

3.7

Unknown

I

AK109281

2.9

2.45

Short-chain dehydrogenase/reductase

D

AK107750

2.9

2

Unknown

I

AK070304

2.3

2.1

Putative oligopeptide transporter

F

AK106934

2.3

2.65

Unknown

I

AK067801

5.5

3.2

Phenylalanine ammonia-lyase

D

AK100844

1.2

2.5

Probable peptidylprolyl isomerase

D

AK070719

1.7

2

Glycosyl transferase family 29 protein

D

AK062781

1.8

2.75

Unknown

I

AK062295

2

3.3

Proline rich protein homolog

E

AK100278

1.7

2.3

probable phospholipase D

D

AK111124

1.5

1.8

unknown

I

AK108530

1.7

1.7

hypothetical protein AT4g30850 [imported]

D

AK065941

2.3

1.9

bZIP transcription factor family protein

A

AK065435

2.35

1.8

kelch repeat-containing F-box family protein similar

G

AK107185

4.1

3.3

obtusifoliol 14-alpha demethylase CYP51

D

AK061818

2.2

2.1

late embryogenesis abundant protein,

I

AK071798

5

3.8

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase

D

AK059951

4.2

3.6

Soluble inorganic pyrophosphatase

D

AK101978

3.3

3.5

starch synthase

D

AK106282

5.2

4.3

WRKY family transcription factor

A

AK070731

3.3

2.4

probable AAA-type ATPase

B

AK071443

1.8

2

Allene oxide cyclase 3

A

AK068620

2.3

3.05

Cytochrome P450 74A1, chloroplast precursor

D

AK100103

3.5

2.5

unknown

I

AK111335

3.9

3.1

unknown

I

AK071507

3.5

2.6

Putative salt tolerance-like protein

A

AK103400

2.6

2.95

Remorin family protein contains

I

AK106228

3.3

2.99

Hypothetical protein

D

AK100808

5.7

4.7

Potassium channel KAT1

B

AK110587

2.6

2.3

Probable WRKY transcription factor 11

A

AK071310

1.5

1.5

Oligopeptide transporter

F

AK110695

2.2

1.6

Quinone reductase family protein

D

AK100153

1.5

1.7

plastocyanin-like domain-containing protein

I

AK066162

2

2.9

Putative serine/threonine-protein kinase

D

AK071121

2.7

1.6

Probable lipoxygenase

D

AK066971

1.7

1.5

hypothetical protein

I

AK098880

1.6

1.5

probable UDPglucose 6-dehydrogenase

D

AK072410

3.9

4

Gibberellin 20 oxidase 2

D

AK109228

2.3

2.89

unknown

I

AK105729

1.9

1.8

Gibberellin-stimulated transcript 1 like protein

B

AK106044

1.5

1.6

Lysine-specific histone demethylase 1

D

AK069389

1.5

1.54

expressed protein

I

AK067891

1.6

1.5

alternative oxidase, putative

D

AK073690

1.8

1.5

xyloglucan fucosyltransferase

D

AK061160

1.4

1.5

unknown

I

AK071989

1.4

2.1

hypothetical protein

I

AK072586

3

3.1

hypothetical protein

I

AK066397

1.9

2.6

probable protein kinase

D

AK109382

1.8

1.6

Probable NADP-dependent oxidoreductase

D

AK061440

1.58

1.5

Peroxisomal acyl-coenzyme A thioester hydrolase1

D

AK069366

1.2

1.5

basic helix-loop-helix (bHLH) family protein

A

AK106400

3.99

2.1

Putative Myb family transcription factor

A

AK108418

2

1.8

hypothetical protein At2g35930

I

AK070790

1.9

2.3

Multicopper oxidase

D

AK067667

1.6

1.7

probable peroxidase

D

AK105582

1.4

2.35

probable calcium-binding protein

B

AK058634

3.3

2.6

pectin acetylesterase

D

AK067339

1.7

1.9

mitogen-activated protein kinase 1 homolog

C

AK061443

1.7

2.1

probable membrane protein

B

AK062571

1.8

1.5

hypothetical protein

I

AK072029

1.8

1.6

unknown

I

AK065394

2.4

2

expressed protein

I

AK063782

2.7

1.5

expressed protein

I

AK107781

5.9

4.1

hypothetical protein

I

AK063727

3.3

1.5

unknown

I

AK105398

1.7

1.5

UDP-glucoronosyl/UDP-glucosyl transferase family

D

AK064054

2

3.4

Non-symbiotic hemoglobin 1

B

AK105769

1.7

1.7

4-coumarate-CoA ligase 1

D

AK101594

2.9

1.3

pyruvate decarboxylase

D

AK066587

1.6

1.2

very-long-chain fatty acid condensing enzyme CUT1

D

AK069807

1.45

1.5

hypothetical protein

I

AK106493

4.8

4

unknown

I

AK073426

1.5

1.5

Squalene monooxygenase

I

AK100934

2.6

2

hypothetical protein

I

AK069285

1.9

1.5

Fructose-2,6-bisphosphatase

D

AK073459

3.1

1.5

ATP-dependent protease

G

AK071397

4.6

2.9

hypothetical protein

D

AK108245

2

2.2

probable lipase

D

AK060309

2

2.1

ovate protein,

A

AK099727

1.5

1.5

probable endosomal protein

B

AK067755

1.5

1.55

glyceraldehyde-3-phosphate dehydrogenase (NADP)

D

AK070391

3.4

1.8

probable coproporphyrinogen oxidase

D

AK059063

3

1.5

Alanine transaminase

D

AK065551

1.5

1.8

ubiquitin carboxyl-terminal hydrolase

D

AK106404

1.5

2

probable cytochrome P450

D

AK109321

2.6

4.1

ubiquitin carboxyl-terminal hydrolase

D

AK111665

2.2

1.5

disease resistance protein RPM1

B

AK070793

1.6

1.8

hypothetical protein

I

AK103655

2

1.5

unknown

I

AK069919

2.5

1.7

unknown

I

AK072460

1.6

1.5

acetyl-CoA C-acyltransferase,

D

AK107635

2.3

1.5

glycosyl transferase

D

AK072288

2.8

3.3

nodulin-like protein

D

AK108440

2.6

2.4

unknown

I

AK107743

3.4

2.5

unknown

I

AK072734

1.5

1.5

expressed protein

I

AK101309

5

5.15

conserved hypothetical protein

I

AK110990

1.5

1.5

unknown

I

AK067258

1.5

1.5

probable ankyrin

B

AK068343

1.9

1.5

Hexose carrier protein HEX6

F

AK067795

1.7

1.5

hypothetical protein

I

AK103834

2.8

3.3

iron-deficiency-responsive protein

B

AK072272

1.5

1.5

MLO-like protein 10

B

AK111104

1.5

1.6

pathogenesis-related protein

I

AK105773

1.5

1.5

cytochrome P450

D

AK069456

2.7

2.6

Peroxidase 52 precursor

D

AK061977

1.5

1.5

Glutamate decarboxylase

D

AK061602

2.5

2.6

unknown

I

AK064287

2.5

2.3

probable cytochrome P450

D

AK064287

2.6

2.4

probable cytochrome P450

D

AK106901

1.5

1.5

unknown

I

AK059860

1.5

1.6

Phytosulfokines 5 precursor

D

AK072984

2.6

1.5

Vegetatable incompatibility protein

I

AK073770

3

1.5

fructose-bisphosphate aldolase

D

AK070707

3.8

2.2

hypothetical protein

I

AK108426

4.35

5.8

transport protein homolog

F

AK109339

1.7

6.5

2'-hydroxyisoflavone reductase

D

AK107156

2

2.9

Anthocyanidin 5,3-O-glucosyltransferase

D

AK064944

1.6

1.7

deoxyxylulose synthase

D

AK060147

1.7

1.5

dolichyl-phosphate beta-glucosyltransferase

D

AK103295

1.5

3.3

acidic endochitinase

D

AK061884

1.5

1.6

nucellin-like protein,

D

AK060487

1.5

1.5

Cytochrome P450 51

D

AK069330

3.2

1.8

alcohol dehydrogenase

D

AK102799

6

3.5

alcohol dehydrogenase

D

AK071051

4.7

2.35

abscisic acid-induced protein

B

AK108017

4

2.3

probable glutaredoxin

D

AK108705

1.5

1.9

unknown

I

AK110798

2.8

2.2

invertase/pectin methylesterase

D

AK071816

4.5

3.7

Phosphoribosylamine-glycine ligase,

D

AK109146

1.5

2.1

hypothetical protein

I

AK069870

1.5

1.5

adenylate kinase

D

AK109056

1.5

1.7

unknown

I

AK105051

2.6

1.5

Thioredoxin-like

D

AK101860

2.4

3.2

COBRA protein precursor

A

AK061478

1.9

1.8

hypothetical protein

I

AK102726

1.7

1.5

unknown

I

AK069789

2.1

2.6

expressed protein

I

AK061072

2.3

1.9

29 kDa ribonucleoprotein

H

AK111249

3.8

1.7

unknown

I

AK062850

1.6

1.5

calcium-binding protein

B

AK073731

1.8

1.8

xyloglucan:xyloglucosyl transferase,

I

AK073667

3.1

1.7

no apical meristem (NAM) family OsNAC3

A

AK063639

2.2

1.5

plastocyanin-like domain-containing protein

D

AK066585

1.5

1.8

hypothetical protein

D

AK062882

2

2.4

Ethylene-responsive transcription factor 4

A

AK099939

1.5

2.5

diphosphate-fructose-6-phosphate 1-phosphotransferase

D

AK073487

5.3

2.5

alpha-amylase

D

AK103896

5.4

3.6

kelch repeat-containing protein

B

AK098912

3.4

1.8

early-responsive to dehydration stress protein (ERD4

B

AK068504

1.8

1.7

Serine/threonine-protein kinase BRI1-like 1 precursor

D

AK107120

2

1.5

hydrolase

D

AK060806

2.45

1.6

ethylene-insensitive 3-like1 (EIL1)

A

AK107137

3

1.8

CBL-interacting protein kinase 1

B

AK058819

1.5

1.5

CBL-interacting protein kinase 10

B

AK058749

3.4

2.9

unknown

I

AK105513

1.9

1.5

xyloglucan endotransglycosylase

D

AK107208

2.8

3.2

IAA-Ala hydrolase

D

AK072606

2

1.5

expressed protein

I

AK070963

1.9

1.5

basic helix-loop-helix (bHLH) family protein

A

AK069499

2.9

2.1

hypothetical protein

I

AK058579

2.3

1.9

unknown

I

AK067003

1.9

2

unknown

I

AK069266

2.1

1.6

scarecrow-like protein

A

AK107947

4

2

probable alcohol dehydrogenase

D

AK107166

4.5

3.6

wall-associated serine/threonine kinase

E

AK109104

1.8

1.7

zinc finger (C3HC4-type RING finger) family protein

A

AK109549

2.6

1.9

MutT/nudix family protein similar to SP|Q58549 ADP-ribose

D

AK068834

2.1

1.5

hypothetical protein

I

AK106533

3.8

2.4

calcineurin-like phosphoesterase

D

AK101709

1.5

1.5

hypothetical protein

D

AK108154

2.2

2.3

phytoene synthase

D

AK058296

3.1

3

1-aminocyclopropane-1-carboxylate oxidase

D

AK108361

2.5

1.5

zinc finger (C3HC4-type RING finger) family protein

A

AK065265

1.5

1.5

WRKY family transcription factor AR411

A

AK073913

2.4

3

unknown

I

AK063300

1.7

1.6

phosphatidylinositol-3-phosphate 5-kinase

D

AK100778

2.7

2

Disease resistance protein RPM1

B

AK063923

4

3.3

hypothetical protein

D

AK073267

2

2.1

chitinase

D

AK065259

2.2

2.2

cellulose synthase

D

AK060654

2.1

1.7

xyloglucan:xyloglucosyl transferase

D

AK110630

1.5

1.7

senescence-associated protein,

D

AK109868

1.5

2.2

receptor lectin kinase-like protein

D

AK067628

1.5

1.5

expressed protein contains

I

AK073244

3.9

2.3

expressed protein

I

AK067229

1.5

1.5

alkaline alpha galactosidase,

D

AK061187

2.5

3.2

receptor protein kinase-like protein

B

AK100858

3.3

1.5

probable ABC transporter

F

AK106955

5.5

4.4

probable protein kinase

H

AK073978

1.6

2.3

probable peroxidase

D

AK111034

2.6

2.5

unknown

I

AK066972

2.2

18

hydrolase,

D

AK060738

3.2

2.3

calcium-dependent protein kinase family protein

B

AK110813

3

1.8

ankyrin-related protein

C

AK108494

4

2.7

U-box domain-containing protein

H

AK072610

2.3

1.5

Nudix hydrolase

D

AK108718

1.6

2.4

FAD-binding domain-containing protein

D

AK072697

2.8

3.2

flavonol synthase

D

AK108113

1.8

1.5

unknown

I

AK063042

1.9

1.7

senescence-associated protein

D

AK106415

2.2

1.6

expressed protein

I

AK059759

3.2

3.6

oxidoreductase

D

AK106743

2.5

1.5

Late embryogenesis abundant protein

D

AK064127

1.5

1.6

vacuolar proton ATPase

D

AK071016

3.1

2

expressed protein

I

AK063618

2.4

1.8

unknown

I

AK108435

2.3

4.3

hypothetical protein

I

AK072204

3.1

2.3

calcium-dependent protein kinase

B

AK073842

1.5

1.8

hypothetical protein

I

AK069091

5

3.8

Probable WRKY transcription factor 57

A

AK071234

2.7

2.7

permease

D

AK063832

3

2.9

unknown

I

AK061174

3.7

3.6

hin1 protein homolog - rice

H

AK107006

1.5

2

pectin esterase

D

AK101504

3

3

putative (PIN3) similar to auxin transport protein

F

AK059894

3

2.1

unknown

I

AK071045

1.8

1.8

myosin heavy chain

E

AK110957

2.4

1.6

aspartyl protease family protein

D

AK070670

2.2

1.6

phosphatidic acid phosphatase

D

AK107370

2.4

2.3

Epidermis-specific secreted glycoprotein

E

AK108522

2.9

2.1

WRKY family transcription factor DNA-binding protein,

A

AK062377

1.5

1.5

unknown

I

AK058550

4.5

3.6

hypothetical protein

I

AK107118

5.9

4.1

hairpin-induced protein-related / HIN1-related

H

AK103552

2.1

3.2

expressed protein

I

AK102472

6

4.8

1-aminocyclopropane-1-carboxylate oxidase

D

AK108910

2

1.5

probable protein kinase

D

AK073812

1.6

1.5

ethylene-responsive element-binding protein 1 (ERF1)

A

AK059448

4.7

3

myb family transcription factor

A

AK059349

2.2

3

unknown

I

AK103774

1.9

1.8

Multidrug resistance protein

I

AK073663

3

3.5

probable beta-1,3-glucanase

D

AK105639

2.5

1.5

hypothetical protein

I

AK107146

2.9

4

AP2 domain-containing transcription factor

A

AK110418

2

1.7

hypothetical protein

I

AK111339

1.95

2.8

phototropic-responsive NPH3 family protein

B

AK068885

1.7

1.5

anthranilate phosphoribosyltransferase-like protein

H

AK060261

1.5

2.2

Saccharum officinarum SoDip22 mRNA for drought inducible 22 kD protein

I

AK111118

3.2

3

unknown

I

AK064487

2.3

3.6

leucine-rich repeat family protein

B

AK108312

1.5

1.5

proton-dependent oligopeptide transport

F

AK072239

1.9

1.5

hypothetical protein

I

AK100501

5.6

3.8

pyruvate decarboxylase

D

AK110441

1.9

2.4

proton-dependent oligopeptide transport

F

AK067992

2.9

1.9

early-responsive to dehydration protein-related / ERD protein-related similar to ERD4 protein

B

AK070825

3.8

2.7

serine carboxypeptidase

D

AK105683

2.9

4

leucine-rich repeat transmembrane protein kinase

B

AK071155

4

1.5

unknown

I

AK069074

2.5

1.5

ERD protein-related

B

AK100678

6.6

6.6

pyruvate decarboxylase

D

AK107134

6.6

5.5

Myb family transcription factor

A

AK103599

3.6

3.7

unknown

I

AK107235

2.65

2.7

ATPase E1-E2 type family protein

B

AK102763

1.5

1.5

amino acid permease 6 (AAP6)

D

AK110639

4.2

5.8

unknown

I

AK059502

3.3

2.3

unknown

I

AK105449

2.3

2.2

alpha-glucosidase 1

D

AK110453

2.1

3.4

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

B

AK063382

3.7

3.4

Cationic amino acid transporter-4

F

AK063624

3.4

1.5

unknown

I

AK058704

2

2.2

phosphate-responsive protein,

B

AK106234

1.5

2.5

unknown

I

AK111076

1.6

3.2

unknown

I

AK058604

1.7

1.9

acid phosphatase

D

AK071556

5.3

3.7

glutamate decarboxylase

D

AK072119

5.6

4.9

Peptide transporter PTR2

F

AK068968

2.3

1.7

probable beta-amylase

D

AK105400

1.5

2

Gibberellin 20 oxidase 1

D

AK059150

3.2

2

unknown

I

AK109470

1.5

1.5

Calcium-binding protein

B

AK108265

2.2

3.2

unknown

I

AK109161

4.1

3

Spotted leaf protein 11

I

AK058242

2.4

2.2

omega-3 fatty acid desaturase

I

AK071011

1.5

1.5

1-aminocyclopropane-1-carboxylate synthase

D

AK063584

3.6

2.7

elicitor-responsive gene 3 (OsERG3)

I

AK105289

1.8

1.6

probable serine/threonine-specific protein kinase

D

AK100415

4.1

3.4

Calcium-transporting ATPase 2

B

AK110902

1.6

2.3

unknown

I

AK102285

1.9

1.9

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

B

AK099545

1.5

1.5

ABA-responsive protein homolog

B

AK063676

3.4

1.8

unknown

D

AK107879

1.6

1.65

anthranilate synthase

D

AK111866

3.3

2.7

probable glucosyltransferase

D

AK070734

3.7

3.3

xyloglucan endo-1,4-beta-D-glucanase

D

AK071148

1.5

1.5

hypothetical protein

I

AK059661

1.5

1.5

peroxidase,

D

AK107440

1.6

1.6

unknown

I

AK106001

1.5

1.6

cytochrome P450

D

AK071033

1.5

1.6

probable cytochrome P450

D

AK065014

1.6

1.5

hypothetical protein

I

AK059734

3.2

1.5

Two-component response regulator ARR6

B

AK073360

1.5

2.2

peroxidase 12

D

AK058755

2.1

1.5

unknown

I

AK103558

2.15

4.72

peroxidase 12

D

AK066799

2.7

1.5

ubiquitin-conjugating enzyme

G

AK107276

2.7

1.5

unknown

D

AK110485

2.9

2.3

protease inhibitor/seed storage/lipid transfer protein

F

AK058573

2.4

5.2

arginine decarboxylase 1

D

AK068961

1.5

2

unknown

I

AK105832

5.4

3.4

Early nodulin 93

D

AK065261

2

3

GDSL-motif lipase/hydrolase family protein similar to family II lipases

D

AK063497

1.7

1.5

xyloglucan:xyloglucosyl transferase

D

AK067955

2.4

2.2

P51104) Dihydroflavonol-4-reductase

D

AK070508

2.7

2.5

cysteine synthase

D

AK073833

1.9

2.15

peroxidase

D

AK105402

2.5

2

MATE efflux family protein similar to ripening regulated protein

F

AK109806

2.5

2.3

Cytokinin-N-glucosyltransferase

D

AK065891

2.1

2.4

amino acid transport protein AAP1

F

AK110619

3.8

3.6

basic helix-loop-helix (bHLH) family protein

A

AK109568

5.9

6.2

Probable WRKY transcription factor 28

A

AK069648

2.6

2

unknown

I

AK105208

2.1

2.3

protease inhibitor/seed storage/lipid transfer protein

F

AK065008

1.7

2.1

AP2 domain transcription factor

A

AK060078

2.8

1.5

universal stress protein (USP) family protein similar to ER6 protein

G

AK108308

1.5

4

fasciclin-like arabinogalactan-protein

E

AK070467

3

6

trypsin inhibitor

H

AK067516

2.7

1.5

hypothetical protein

I

AK107136

1.6

1.5

expressed protein

I

AK066406

1.7

2.6

AMP-dependent synthetase

D

AK102146

2.9

1.5

pyrophosphate-energized vacuolar membrane proton pump

B

AK108780

4

3.8

C2 domain-containing protein low similarity to splicing coactivator

I

AK068993

1.9

1.5

phenylalanine ammonia-lyase 1

D

AK099886

1.7

1.9

peroxidase

D

AK067907

4.7

3.7

beta-ketoacyl-CoA synthase

D

AK108630

1.6

1.5

unknown

I

AK072692

1.7

2.1

Nucleoside-triphosphatase

H

AK071917

2.1

2.8

bifunctional nuclease

H

AK067319

1.6

1.5

hypothetical protein

I

AK068628

3.4

1.8

calmodulin-binding protein

B

AK109785

1.6

1.9

unknown

I

AK071623

3.4

2.2

amino acid permease

D

AK107199

2.4

1.7

WRKY family transcription factor

A

AK058473

2.1

2.1

Beta,beta-carotene 9',10'-dioxygenase

D

AK061224

4.6

2.5

raffinose synthase family protein

D

AK068181

1.7

2.1

glycosyl transferase family

D

AK073549

2.5

1.85

probable aminotransferase

D

AK103139

5.5

3.8

Eukaryotic translation initiation factor 6

H

AK069298

1.6

1.5

hypothetical protein

I

AK108464

1.5

2.2

unknown

I

AK066556

2.3

1.75

probable phospholipase D

D

AK058518

2.6

2.5

Mitogen-activated protein kinase kinase kinase 1

C

AK070254

2.3

1.8

leucine-rich repeat transmembrane protein kinase,

B

AK065515

1.5

2.1

caffeoyl-CoA O-methyltransferase

D

AK109553

3.4

3.85

hsr201 protein, hypersensitivity-related

D

AK108491

1.5

1.55

zinc finger (C3HC4-type RING finger) family protein

A

AK111734

1.9

2.3

receptor protein kinase-like protein

B

AK100909

3.4

1.8

Probable 1-deoxy-D-xylulose-5-phosphate synthase

D

AK071716

1.5

1.6

galactinol synthase,

D

AK062503

1.7

3.85

unknown

I

AK107152

6.3

3.3

universal stress protein (USP) family protein similar to ER6

G

AK111957

1.95

4

hypothetical protein

D

AK102113

1.7

1.5

Putative disease resistance protein RGA3

G

AK104810

3.5

1.8

RING finger and CHY zinc finger domain containing protein 1

A

AK063244

1.6

1.5

peptidoglycan-binding LysM domain-containing protein

I

AK067013

2.8

1.7

zinc finger (C3HC4-type RING finger)

A

AK100739

5.1

2.8

potassium channel protein KAT1

B

AK073030

2.5

1.55

probable nuclear transport factor 2

F

AK101022

2.4

1.55

cytokinin oxidase family

D

AK101524

3

2.9

acyl-[acyl-carrier-protein] desaturase

D

AK102590

2

1.7

probable diacylglycerol kinase [imported] - Arabidopsis thaliana

D

AK100351

1.5

2.6

subtilisin-like serine proteinase

D

AK065697

3.8

1.55

probable heat shock protein EMB1

G

AK069125

3.1

4.4

Acyl-protein thioesterase 2

D

AK101962

3.3

1.5

pectin methylesterase-like protein

D

AK059325

2.9

2.4

amino acid permease 2

D

AK064298

2

3.3

probable flavonol glucosyltransferase

D

AK111571

2.15

2.2

Myb family transcription factor

A

AK071274

4

2.6

no apical meristem

A

AK060734

3.6

2.75

expressed protein

I

AK063282

2.5

1.5

hypothetical protein

I

AK108555

2.3

2.5

Probable WRKY transcription factor 51

A

AK103608

2.5

2.1

early-responsive to dehydration protein-related

I

AK067269

2.9

1.5

speckle-type POZ protein-related contains Pfam PF00651

A

AK061290

1.6

1.5

formin homology 2 domain-containing protein

B

AK108127

1.7

1.5

Putative glucan endo-1,3-beta-glucosidase 1 precursor

D

AK065307

2

1.9

E3 ubiquitin ligase PUB14

G

AK112030

2.1

1.7

ubiquitin-conjugating enzyme 13

G

AK111782

2

1.9

Myb family transcription factor (MYB4)

A

AK104148

1.7

1.7

ubiquitin-conjugating enzyme 13

G

AK059805

2.1

1.5

triose-phosphate isomerase

D

AK105791

1.5

2.75

glycosyl hydrolase family 3 protein

D

AK099496

1.5

1.7

zinc finger (C3HC4-type RING finger) family protein

A

AK108311

2.7

2.6

zinc finger (C3HC4-type RING finger) family protein

A

AK071289

2.98

2.3

unknown

I

AK059087

1.6

3.8

senescence/dehydration-associated protein-related

I

AK064257

2.9

2

hypothetical protein

I

AK061128

2.9

4.1

cytochrome P450

D

AK062404

2

1.75

unknown

I

AK106157

2.4

1.5

hypothetical protein

I

AK107168

1.5

1.6

NPK1-related protein kinase homolog

C

AK062919

2

1.6

unknown

I

AK108553

1.5

2.9

bZIP transcription factor family

A

AK060804

1.5

1.5

unknown

I

AK110833

2.75

2

basic helix-loop-helix (bHLH) family protein

A

AK072727

1.5

1.7

tetratricopeptide repeat (TPR)-containing protein

I

AK071248

2

3.4

UTP-glucose-1-phosphate uridylyltransferase

D

AK064401

6.6

2.8

cinnamoyl-CoA reductase

D

AK111294

1.5

1.5

senescence-associated protein-related similar to senescence-

I

AK070746

3.4

1.9

cinnamoyl-CoA reductase

D

AK106847

1.5

4.25

unknown

I

AK058773

2.9

3.3

DNA-binding protein ABF2 - wild oat

A

AK070197

1.5

1.5

protein flavonol sulfotransferase

D

AK073398

1.9

3.1

unknown

I

AK073462

1.85

1.7

unknown

I

AK101655

1.5

2.7

phosphate-responsive protein, putative (EXO)

I

AK065150

1.7

1.8

expressed protein

I

AK069842

2.8

1.7

major intrinsic protein - rice

F

AK111348

2.1

3.55

defense-related protein

D

AK103832

3.9

2.4

Anthocyanin 5-aromatic acyltransferase

D

AK105563

1.6

1.5

probable flavonol glucosyltransferase

D

AK071523

2.1

1.9

phosphatidic acid phosphatase-related

D

AK066636

1.5

1.51

pectate lyase-like protein

D

AK071303

1.6

1.74

Ras-related protein Rab11C

B

AK058693

2.4

1.8

expressed protein

I

AK061145

2

1.7

expressed protein

I

AK071060

1.7

1.5

unknown

I

AK111775

2.8

2.3

AP2 domain-containing transcription factor,

A

AK102492

1.6

1.7

unknown

I

AK063719

1.5

1.7

unknown

I

AK101598

1.5

1.8

expressed protein

I

AK107997

2.9

1.5

unknown

I

AK100308

1.5

1.8

Hypothetical GMC-type oxidoreductase

D

AK070415

6

5.9

Jasmonate O-methyltransferase

D

AK104991

2.14

2.4

expressed protein

I

AK073848

4.3

2.3

OsNAC6 protein

A

AK073320

1.5

1.7

probable serine carboxypeptidase II

D

AK071737

1.9

1.7

hypothetical protein

I

AK068337

2.5

1.5

WRKY family transcription factor

A

AK107918

1.5

1.6

hypothetical protein YY1 - rice

I

AK109236

2.3

1.5

unknown

I

AK073281

2.4

3.3

hypothetical protein

I

AK064644

4.4

2.7

calcium-binding EF hand family

B

AK070024

2.6

2

probable protein kinase

G

AK073894

1.5

1.5

glutamate receptor family protein

B

AK103316

4.7

2.4

glutathione S-transferase

D

AK108607

2.2

2.4

probable bZIP transcription factor

A

AK068380

1.5

2.25

disease resistance protein - rice

I

AK109098

1.7

1.66

unknown

I

AK064121

1.5

1.7

Putative disease resistance protein RGA4

G

AK063578

3

1.99

ABA-responsive protein

I

AK103409

2.6

1.5

calcium-binding EF hand family protein

B

AK063572

1.5

1.8

actin 7 (ACT7) / actin 2 identical to SP

E

AK071225

4.2

2.5

COBRA protein precursor (Cell expansion protein)

I

AK109037

3

2.7

calcium-transporting ATPase,

F

AK072826

1.6

1.56

actin 2 identical to SP

E

AK061576

2.9

1.8

proline-rich protein GPP1

I

AK067303

1.8

1.9

unknown

I

AK100652

2.1

2.25

Potassium transporter 7 (OsHAK7)

F

AK069101

2.6

2.66

unknown

I

AK072220

4.15

3.31

probable cytochrome P450

D

AK069685

1.5

1.7

leaf development protein Argonaute / Zwille protein

H

AK100306

2.6

1.5

Sucrose synthase 3

D

AK073356

4.5

2.25

hypothetical protein

I

AK105369

1.9

2.5

unknown

I

AK063204

5.4

5.2

unknown

I

AK065224

1.75

1.5

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

G

AK106081

6

3.4

cytochrome P450 family protein

D

AK108527

4

3.3

unknown

I

AK101616

4.5

2.8

Putative serine/threonine-protein kinase

G

AK072505

3.2

3

hypothetical protein

I

AK106668

2.5

1.6

hypothetical protein

I

AK107730

4

2

calcium-binding EF hand family protein

B

AK109708

2.6

1.7

glycosyl transferase family 20 protein

D

AK108225

1.5

1.8

CBL-interacting protein kinase 6

B

AK102363

2.4

1.8

nitrate reductase

D

AK072477

2.4

2.8

unknown

I

AK064081

1.9

2.3

unknown

I

AK058651

2.5

2.9

pectinesterase-like protein

D

AK058358

1.9

2.4

probable protein gypsy/Ty3 element polyprotein

I

AK063640

2.2

1.66

endonuclease/exonuclease/phosphatase

D

AK069153

1.5

1.6

unknown

I

AK069322

4.9

3.7

kelch repeat-containing protein

B

AK063041

4.9

2.4

blue copper-binding protein II

D

AK108206

2.5

5.5

unknown

I

AK070738

1.5

1.7

Potassium transporter 2

F

AK103465

3

2

pyruvate kinase

D

AK107951

2.4

2

unknown

I

AK102303

1.6

1.6

WWE domain-containing protein

B

AK111568

1.5

1.5

senescence-related protein

I

AK101290

1.6

1.5

hypothetical protein

I

AK069070

1.7

2.4

aspartyl protease family protein

D

AK068610

2.1

1.5

serine proteinase-like protein

I

AK100314

1.6

1.8

Auxin-responsive protein IAA26

A

AK102504

1.5

1.8

Carboxy-terminal domain RNA polymerase

H

AK067076

2.5

2.6

branched-chain amino acid aminotransferase

D

AK066468

1.7

1.8

sodium/calcium exchanger family protein

B

AK060710

1.5

2

cytochrome P450 homolog

D

AK060256

3.2

2.5

unknown

I

AK071240

1.5

2

class II heat shock protein

G

AK108924

1.6

2.5

RING-H2 finger protein ATL4L

A

AK070609

3.2

3.8

hypothetical protein

I

AK066680

3.1

1.5

cytochrome P450

D

AK065840

1.8

2.7

Peptide transporter PTR2

F

AK064058

3.4

2.2

unknown

I

AK062531

3

1.5

unknown

I

AK066682

2

5.1

jacalin lectin family protein similar to agglutinin

I

AK066940

1.5

1.5

hydroxymethylglutaryl-CoA lyase

D

AK109504

1.7

1.5

cytochrome P450

D

AK073422

1.7

2.4

hypothetical protein

I

AK064745

1.5

1.9

probable acid phosphatase

D

AK073044

2.3

2.6

auxin-responsive protein / indoleacetic acid-induced protein 3

A

AK058453

2.5

2.9

Polygalacturonase

D

AK072588

3.95

4.1

trans-cinnamate 4-monooxygenase

D

AK070444

3.5

2

unknown

I

AK109337

1.5

2

Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase A

D

LFY-Activated gene* (1, 2)

Rice homolog^†

Status of rice homolog in dsRNAiRFL^‡

At1g01600

Os04g0560100

AK106001 down-regulated

CYP86A4

(AK106001)

At1g63710

Os02g0666500

Not affected

CYP86A7

(AK069029)

At4g39950

Os04g0171800

Not affected

Os04g0174100

(AK121124)

At1g26310

Not identified

-

CAL (AGL10)

At1g11580

Os01g0880300

AK101962 down-regulated

Pectin methyl esterase

(AK101962)

At1g11850

Os07g0688700

Not affected

Unknown protein

At1g13680

Os03g0415200

Not affected

Phospholipase C

At1g19180

Not identified

-

Jasmonate-Zim-domain protein 1

At1g58430

Not identified

-

Anther-specific proline-rich protein

At1g65500

Not identified

-

Unknown protein

At1g69180

Not identified

-

CRC

At1g70700

Not identified

-

Jasmonate-Zim-domain protein 9

At1g76790

Not identified

-

O-methyltransferase family 2 protein

At2g04570

Os06g0636700

Not affected

GDSL-motif lipase/hydrolase protein

(AK058562)

At2g36590

Not identified

-

Proline transporter

At2g42990

Os02g0189300

Not affected

(AK060691)

GDSL-motif lipase/hydrolase family protein

Os06g0636700

(AK058562)

At2g46650

Not identified

-

Member of cytochromes b₅

At3g09260

Not identified

-

b-Glucosidase phosphate starvation-response 3.1

At3g10570

Not identified

-

Cytochrome P450 CYP77A

At3g13662

Not identified

-

Disease resistance-responsive protein

At3g14060

Not identified

-

Unknown protein

At3g28220

Not identified

-

Meprin and TRAF domain-protein

At3g45140

Os08g39850

Not affected

Chloroplast lipoxygenase

At3g48460

Os03g0844600

Not affected

GDSL-motif lipase/hydrolase family protein

(AK059168)

At3g53980

Os01g0849000

AK105208 down-regulated

Protease inhibitor/seed storage/lipid transfer protein (LTP) family protein

(AK105208)

At4g04830

Os03g0360700

Not affected

Methionine sulfoxide reductase domain protein

(AK068764)

At4g11190

Not identified

-

Disease resistance-responsive family protein

At4g15210

Os03g0141200

AK068968 down-regulated

Cytosolic beta-amylase

(AK068968)

At4g23600

Not identified

-

Cystine lyase

At4g23680

Not identified

-

Major latex protein

At4g24130

Not identified

-

Unknown protein

At4g39940

Not identified

-

Adenosine-5'-phosphosulfate-kinase

At5g17220

Os09g0367700

AK103316 down-regulated

Glutathione transferase

(AK103316)

At5g28020

Os06g0564700

AK070508 down-regulated

Cysteine synthase AtcysD2

(AK070508)

At5g33370

Not identified

--

GDSL-motif lipase/hydrolase family protein

At5g48540

Os03g0277600

Not affected

(AK061425)

Secretory protein-related; similar to receptor protein kinase-related

Os03g0277700

(AK061148)

At5g55720

Os01g0546800

AK066636 down-regulated

Pectate lyase family protein

(AK066636)

At5g57720

Not identified

-

B3 domain

At3g04960

Not identified

-

Unknown protein

At3g17010

Not identified

-

B3 family transcription factor

At4g21590

Not identified

-

Endonuclease 3

At1g69230

Os12g0502000

Not affected

SPIRAL1-LIKE2

(AK060063)

At2g19800

Not identified

-

At2g44460

Not identified

-

Glycosyl hydrolase

At5g22430

Os02g0535000

Not affected

Unknown

At5g24910

Not identified

-

CYP714A1

At1g69120

Os07g0108900

Not affected

AP1

(AF345911)

At3g54340

Os06g0712700

Not affected

AP3

(AK069317)

At4g18960

AG

Os05g0203800

Not affected

OsMADS58

AK111723

At5g20240

Os01g0883100

Not affected

PI

AY551924

At5g15800

Not identified

-

SEP1 (AGL2)

At3g02310

Not identified

-

SEP2 (AGL4)

AT1G24260

SEP3

Os09g0507200

Not affected

OsMADS7

OsMADS8

AK072867

At5g60630

Not identified

-

Hydroxyproline-rich glycoprotein

At5g49770

Os01g0816600

Not affected

Leucine-rich repeat transmembrane protein kinase

At5g03790

Not identified

-

Homeodomain leucine zipper class I Late meristem identity1

At3g61250

Not identified

-

Myb domain protein 17

At1g16070

Not identified

-

Tubby like protein 8

At4g14090

Not identified

-

Anthocyanidin 5-O-glucosyltransferase

At5g03230

Not identified

-

Unknown protein

At4g22780

Not identified

-

ACT domain protein

At3g43190

Not identified

-

Protein with sucrose synthase activity

At3g52470

Not identified

-

Harpin-induced protein

At3g47340

Os03g18130

Not affected

Glutamine-dependent asparagine synthetase

At1g61830

Not identified

-

CHP-rich zinc finger protein

At2g44450

Os05g30390

Not affected

Glycosyl hydrolase family 1 protein

At3g19390

Not identified

-

Cysteine proteinase

At1g68880

Not identified

-

Basic leucine-zipper8

GENE/Annotated gene

Accession number

Forward primer (5'-3')

Reverse primer (5'-3')

Amplicon size (bp)

AK061988

ACCACTTTCGAACCGCCACTACT

ACGCCTAAGCCTGCCTGGTT

69

AF065992

GTTGTCCGAGGAGCATGAC

CCTCGCCGGGCTCCGTCACC

280

AB115668

ATGCTGGAGCAGGCCATCCA

GTTCAGCTCAAGGGCCAGA

154

AB003328

GACCGTAACATCAACACCAC

GAGATCCAGCTTATTCCTGG

154

AB062676

TGACCTAGATTCAAAGTCTAATCCTT

TGCCGGCCATGTCAAATTAATAAC

80

AB052942

GCTCACTATCATCATCCAGCATG

CCTTGCTCAGCTATTTAATTGCATAA

110

AB103120 

AGATGGTCGCCGGCTTCT

ATGGAGAGTAGGAGTCGGAG

140

AK243046

GTGAGTGAGCAATCGCAATC

CTAGGACTCTCCTGCCATGG

110

AK069685

GTCCAGGCACAGTAGTTGATAC

CGTAGTAAACAGGAGGTGGA

250

AK107405

TCGCCGGACCGCTCATCGC

ATCAGGTTGTGTGGCAGATG

200

AK101504

ATCCTGAGCACAGCGGTAAT

CAATGTCCGACAACAGGCTA

205

AK101022

CGTCATAGTGCACGCAAAGAAA

GATCAAGAACACCATGAACACCAA

70

AK060806

CGGAGTTCAGGTTCAGTTCA

GAACTAGGGGTGGTGATTCT

150

AK105729

ACAATGAAGCTCAACACCAC

TCGCAGAAATCTGATCCA

100

AK070963

CCAAGGTACCCAACACCAAC

TCTTCCTCGTTAGTGCCAGA

110

AK065008

ACAAGCTGCTCTTCATCGAC

GCATTGCCTCTTCAGTAGGA

200

b-ketoacyl-CoA synthase

AK064127

CTGGAAGGCGCTCAGGAC

GCTTATTCCGGTCGTACGTG

183