Loc No a

Transcription, Translation, ReplicationbZIP transcription factor Os11g0234300 9.02 0.00 10.38 0.00Histone H3 (Lys9) methyltransferase Os12g0198700 5.71 0.00 4.31 0.00Leucine rich repeat Os12g0493900 5.08 0.00 5.78 0.00histone-lysine N-methyltransferase Os02g0621100 4.08 0.00 5.79 0.00PHD Zn-finger proteins (PHD Zn-finger) Os11g0234200 3.25 0.01 3.43 0.00AP2 transcription factor Os10g0166600 3.19 0.00 3.98 0.00

Cellular processesThioredoxin Os08g0140700 7.11 0.00 7.41 0.00Cdc2-related protein kinase Os07g0535100 5.62 0.00 4.15 0.00Multitransmembrane protein Os09g0566500 5.17 0.00 4.66 0.00Jacalin Os11g0550100 5.10 0.00 4.75 0.00Ankyrin repeat Os11g0265900 5.01 0.00 5.49 0.00Ferroportin1 Os06g0560000 5.00 0.00 6.47 0.00Translational repressor MPT5/PUF4 Os02g0774100 4.53 0.00 7.82 0.00Iron transporter (Iron Transporter) Os09g0343200 4.23 0.00 4.87 0.00Serine/threonine protein kinase Os09g0548400 4.08 0.00 5.14 0.00Tyrosine kinase Os11g0260100 3.56 0.00 5.57 0.002-keto-3-deoxy-6-phosphogluconate aldolase Os10g0429400 3.20 0.00 3.81 0.00

MetabolismAmino acid transporters Os01g0795200 4.88 0.00 4.54 0.00Apoptotic ATPase Os10g0419400 4.24 0.01 3.86 0.01Phosphoglucomutase Os05g0555600 4.09 0.00 3.94 0.00Flavin-containing monooxygenase Os01g0260100 4.00 0.03 3.37 0.03Amino acid/polyamine transporter Os01g0945300 3.38 0.01 4.52 0.00Iron/ascorbate oxidoreductases Os02g0299300 3.38 0.00 3.55 0.002-oxoglutarate (2OG) - Fe(II) oxygenase Os08g0480200 3.13 0.00 8.37 0.00Glutamate synthase (Glutameate synthase) Os07g0518500 3.05 0.01 3.03 0.00Soluble epoxide hydrolase Os06g0476200 3.03 0.00 4.25 0.00

Pooly characterizedKinesin Os03g0629800 12.58 0.00 12.49 0.00Sulfotransferase Os12g0428300 7.95 0.00 8.32 0.00DUF151 Os01g0702000 5.37 0.00 6.52 0.00Drf_FH1 Os04g0397800 4.79 0.02 5.17 0.01Cytochrome P450 Os11g0547000 4.13 0.00 4.54 0.00Ca-binding EF-hand Os01g0845900 4.12 0.00 5.55 0.00SAM dependent carboxyl methyltransferase Os02g0163500 3.77 0.00 4.43 0.00MtN3 (transmembrane) Os05g0214300 3.52 0.03 4.53 0.01SGNH_plant_lipase Os10g0140300 3.32 0.00 3.90 0.00Subtilisin N-terminal Region Os06g0329900 3.08 0.03 5.13 0.00double-stranded beta-helix domain Os11g0162900 3.06 0.00 4.26 0.00

AP37 and AP59

Gene Name(IRGSP) Maen b

AP37

P val cP val c Maen b

AP59

Supplemental Table S1. Up-regulated Genes in OsCc1:AP37 and OsCc1:AP59 Plants in Comparison to Nontransgenic Controls.

Loc No a

Transcription, Translation, ReplicationLeucine rich repeat Os12g0517100 3.50 0.00 2.43 0.01tRNA splicing endonuclease SEN2 Os11g0602400 3.15 0.00 2.98 0.01

MetabolismCytochrome P450 Os09g0275400 4.60 0.00 2.24 0.03UDP-glucosyl transferase Os04g0206500 3.53 0.00 2.10 0.02Terpene cyclases Os04g0340300 3.16 0.00 2.27 0.02Isocitrate lyase (Isocitrate lyase) Os07g0529000 3.08 0.00 1.39 0.06Chitinase Os11g0462100 3.01 0.00 1.65 0.13

Poorly characterizedDUF584 (Duf584) Os05g0531100 4.10 0.00 1.24 0.32Integrase Os11g0224300 3.36 0.00 -1.18 0.42Extensin_2 Os07g0561200 3.29 0.00 2.56 0.04

Transcription, Translation, ReplicationMyb Os11g0700500 2.84 0.00 4.09 0.00HORMA domain Os01g0165800 2.05 0.01 3.69 0.00Valyl-tRNA synthetase Os10g0506200 2.97 0.00 3.32 0.00GATA-4/5/6 transcription factors Os02g0618200 2.39 0.00 3.30 0.00Mismatch repair ATPase MSH4 Os07g0486000 2.50 0.00 3.22 0.00Zn-finger Os06g0687200 1.00 1.00 3.19 0.01RNA polymerase Os03g0845700 2.38 0.01 3.11 0.02RNA Methylase Os03g0100500 1.95 0.01 3.06 0.01

Cellular processesSulfurtransferase (sulfurtransferase) Os04g0249600 2.83 0.00 8.19 0.00Glutathione S-transferase Os12g0123200 1.90 0.00 3.81 0.00Defense-related protein Os01g0382000 2.31 0.01 3.70 0.01E3 ubiquitin ligase (E3 ubiquitin ligase) Os10g0445400 2.86 0.00 3.70 0.00Serine/Threonine protein kinases Os09g0339000 2.64 0.00 3.42 0.00Apoptotic ATPase Os06g0693100 2.68 0.00 3.36 0.00SAM-dependent methyltransferases Os04g0175600 2.05 0.00 3.34 0.00Secretory peroxidases Os08g0113000 1.39 0.03 3.33 0.00DnaJ Os01g0606900 2.54 0.00 3.33 0.00RbcX (RbcX) Os08g0425200 2.94 0.00 3.59 0.00Tyrosine kinase Os10g0136500 1.42 0.05 3.02 0.00

MetabolismMethyltransferases Os06g0152400 2.30 0.01 3.77 0.01Beta-glucosidase Os06g0320200 2.38 0.00 3.62 0.00UDP-glucuronosyltransferase Os10g0178500 -2.28 0.00 3.62 0.00Transporter Os02g0574100 2.52 0.00 3.59 0.00NADH:flavin oxidoreductase Os02g0559400 2.61 0.00 3.49 0.01drug/metabolite transporter Os01g0803300 2.15 0.00 3.46 0.00H+/oligopeptide symporter Os10g0111700 2.37 0.00 3.40 0.00Iron/ascorbate oxidoreductases Os01g0351800 1.74 0.02 3.34 0.00Alpha-L-arabinofuranosidase Os03g0320100 2.02 0.01 3.30 0.01Fructose-2,6-bisphosphatase Os01g0660900 2.24 0.00 3.22 0.00Glycogen synthase Os06g0133000 2.38 0.00 3.14 0.00Flavin-containing monooxygenase Os07g0437000 1.56 0.01 3.13 0.00Glycine cleavage system H protein Os02g0120400 1.96 0.00 3.12 0.00Glycolate oxidase Os04g0623600 2.80 0.00 3.02 0.00

Poorly characterizedCytochrome P450 Os09g0530300 2.29 0.00 3.13 0.01DUF952 Os03g0564200 2.28 0.01 3.53 0.01Chalcone and stilbene synthases Os04g0116800 2.87 0.00 3.40 0.00NB-ARC domain Os11g0161700 2.97 0.00 3.22 0.00Acetamidase/Formamidase Os01g0764900 2.47 0.00 3.04 0.00

AP37

AP59

Gene NameAP37 AP59

(IRGSP) Maen b Maen bP val c P val c

Supplemental Table S1. (Continued)

Supplemental Table S2. Agronomic Traits of the OsCc1:AP37 and OsCc1:AP59 Transgenic Rice Plants under Normal Growth and Drought Stress Conditions in the field.

Date of flowering

NT Aug. 26 78.27 ± 4.90 12.70 ± 1.55 20.46 ± 0.53

AP37-4 Aug. 26 72.03 ± 12.97 13.50 ± 2.21 20.78 ± 1.71

%Δ -7.98 6.30 1.54

P value

AP37-5 Aug. 27 76.33 ± 3.08 12.55 ± 1.32 21.69 ± 0.87

%Δ -2.48 -1.18 6.01

P value

AP37-9 Aut. 26 71.18 ± 3.73 14.50 ± 2.48 20.85 ± 0.78

%Δ -9.06 14.17 1.89

P value

NT Aug. 26 79.95 ± 2.87 13.50 ± 2.21 20.86 ± 0.52

AP59-1 Aug. 28 76.72 ± 3.39 14.00 ± 1.91 19.78 ± 2.77

%Δ -4.03 3.73 -5.13

P value

AP59-2 Aug. 27 73.07 ± 4.08 14.50 ± 2.72 21.99 ± 0.99

%Δ -8.59 7.40 5.43

P value

AP59-6 Aug. 26 78.35 ± 2.20 13.05 ± 1.76 21.30 ± 0.79

%Δ -2.00 -3.33 2.14

P value

(g)

0.009

0.031

0.000

(A) Normal Growth Conditions (n=20)

ConstructsCulm length No. of panicles 1,000 grain weight

(cm) (per hill)

0.002 0.472

0.120

0.199 0.359

0.003 0.005 0.261

0.404 0.809 0.001

0.152 0.024

0.517 0.371

Date of flowering

NT Sep. 07 72.00 ± 5.47 16.00 ± 7.87 16.68 ± 3.18

AP37-4 Sep.06 72.80 ± 5.35 16.20 ± 8.04 17.47 ± 1.70

%Δ 1.11 1.25 4.73

P val

AP37-5 Sep.05 76.00 ± 3.37 18.50 ± 1.29 18.92 ± 0.28

%Δ 5.55 15.65 13.38

P val

AP37-9 Sep. 06 66.00 ± 4.55 17.25 ± 2.87 16.59 ± 0.66

%Δ -8.33 7.81 -0.50

P val

NT Sep. 07 71.25 ± 5.50 16.50 ± 7.04 16.19 ± 4.15

AP59-1 Sep. 09 68.50 ± 3.00 17.50 ± 3.70 12.80 ± 4.10

%Δ -3.85 6.06 -20.95

P val

AP59-2 Sep. 06 75.87 ± 2.78 14.00 ± 6.97 17.47 ± 2.43

%Δ 6.49 -15.15 7.90

P val

AP59-6 Sep. 06 73.33 ± 3.51 18.67 ± 2.52 16.57 ± 2.04

%Δ 2.92 13.13 2.34

P val

(B) Drought stress Conditions

0.808 0.961 0.531

(cm)

ConstructsCulm length No. of panicles 1,000 grain weight

(g)

0.543 0.608

0.187

0.101 0.774 0.945

0.261

(per hill)

0.624 0.8890.497

0.8060.338

0.568 0.108

0.120

Supplemental Table S3. Primers Used for RT-PCR.

Acc. No

AP37 AK061380 5'- TGCACGTCCAGCAACGCATC -3' 5'- TGCCGCCTTGTTCGCCGTAA -3'

AP59 AK073812 5'- TTCCTCCTCGTCGTCGTCTT -3' 5'- TAGCTCACCAGCTGCTGGAT -3'

Iron transporter Os09g0343200 5'- GCCATACCAGGAGGTTACAA -3' 5'- AACTGAAGGCCAGGAGTAGA -3'

PHD Zn-finger Os11g0234200 5'- ACCACCTATTCCGTGACATC -3' 5'- TCAACCTGGTCAGCTAGTTC -3'

Glutamate synthase Os07g0518500 5'- CCTGCTCGATTCGAGAACAA -3' 5'- GCATCTCGGCTCCAGTTCAA -3'

DUF584 Os05g0531100 5'- ATTCCAAGAGGCTGACATCC -3' 5'- TCGTTGGTCTGGTCGAACAT -3'

Isocitrate lyase Os07g0529000 5'- GCGCCAACTTCTACGACAGG -3' 5'- CTTGGCTGAAGTCCAGAGTG -3'

Sulfurtransferase Os04g0249600 5'- TACTTGGACGTCAGGACAGA -3' 5'- TGCTATGAGATCGGCAGATG -3'

E3 ubiquitin ligase Os10g0445400 5'- CAGCATCAGGCAATTCTACG -3' 5'- TCCAATCCTCGAAGCATCTC -3'

RbcX Os08g0425200 5'- GGATCTTGGAGGTCCGATCT -3' 5'- AGCTGTGTATCCGTGGAAGG -3'

Dip1 AY587109 5'- TCTCCAAGCTGCACCGATCC -3' 5'- GACCACCTCGCCGTTGTCAT -3'

OsUbi X76064 5'- GAATCGCCTTCTCAAGATGC -3' 5'- AATGGTGTCCGAGGACTCAA -3'

GENE

FORWORD REVERS

Primer sequence

Nucleotide Substitutions (x100)0

639.1

100200300400500600

OsDREB1AOs08g0545500

Os09g0522100Os08g0545400

OsDREB1BOs02g0677300Os09g0522000

Os06g0127100Os01g0968800

Os04g0550200Os02g0657000

Os02g0656600Os04g0549700

Os10g0560700Os01g0200600Os06g0166400

Os04g0648900Os03g0263000

Os08g0408500Os09g0369000

Os02g0752800Os06g0222400

Os03g0191900Os04g0529100

Os05g0572000OsDREB2A

Os05g0346200Os03g0174400

Os08g0565200Os01g0752500

Os08g0521600Os07g0227600Os03g0815800

Os01g0131600Os09g0309700

Os01g0224100Os01g0657400

Os05g0316800Os03g0150200

Os09g0457900Os08g0474000

Os02g0764700Os05g0497200

Os02g0594300Os04g0547600Os02g0655200

Os10g0562900Os04g0257500

Os02g0638400Os12g0582900

Os04g0399800Os07g0410700

Os07g0410300Os03g0860100

AP59Os04g0546800

Os04g0669200Os02g0189600

Os06g0691100Os02g0158000Os05g0497300AP37

Os04g0610400Os12g0168100

Os06g0635700Os07g0669500

Os02g0546600Os01g0868000

Os05g0437100Os04g0398000Os11g0168500

Os02g0782700Os06g0194000

Os09g0434500Os01g0313300

Os03g0183000Os07g0674800

Os07g0617000Os03g0341000

Os05g0361700Os06g0604000

Os02g0202000

Os06g0181700Os02g0797100

Os09g0287000

Os09g0286600

Os10g0390800Os03g0183300

Os03g0183200Os08g0537900

Subgroup V

Subgroup III

Subgroup VI

Subgroup II

Subgroup I

Subgroup IV

Supplemental Figure S1. Phylogenic Relationship of Rice AP2 Family.A phylogenic dendrogram was derived from an alignment of the deduced amino acid sequences of 90 rice AP2 factors using the CLUSTAL W program. Of 139 AP2 factors predicted from the rice genome, we selected 90 that have EST information from NCBI database search using the tBLAST N program. Forty two stress-inducible factors were indicated by boxes. Our subgroups I to VI shown in Table I are marked by circles.

Duf584

RbcX

98

7

6

5

4

3

2

1

0

5

4

3

2

1

0

E3 ubiquitin ligase

109876543210

8

7

6

5

4

3

2

1

0

Control Drought Salinity Low temperature

30

20

12

9

6

3

0

NTOsCc1:AP37OsCc1:AP59

Sulfurtransferase

Isocitrate lyase

Supplemental Figure S2. Up-Regulation of Five Target Genes in OsCc1:AP37 and OsCc1:AP59 Plants in Comparison to Nontransgenic Controls. Homozygous T4 lines of OsCc1:AP37, OsCc1:AP59, and nontransgenic (NT) control rice plants were grown in a greenhouse for 14 d. Transgenic and NT plants were then treated with various stress conditions as described in the legends of Fig. 2. Transcript levels of five target genes listed in Supplemental Table S1 online were determined by qRT-PCR (using primers listed in Supplemental Table S3 online).