Table 1

Selected genes for expression analysis by RT-qPCR in response to auxin

TIGR Id

FC

Annotation

BBMH Arabidopsis

Annotation

References


UPIC (up-regulated in crl1 relative to WT)


Os05g43820

11,11

ras-related protein

At4g28950

ROP9 (RHO-RELATED PROTEIN FROM PLANTS 9)

[54]


Os08g02490

8,64

AT hook motif domain containing protein

At4g12080

DNA-binding family protein


O

Os02g24740

8,14

OsSAUR9 - Auxin-responsive SAUR gene family member

At4g34760

auxin-responsive family protein

[55,56]


Os03g51580

6,89

helix-loop-helix DNA-binding domain containing protein

At2g22750

basic helix-loop-helix (bHLH) family protein


O

Os07g22534

5,78

WD domainG-beta repeat domain containing protein

At3g49180

RID3 (ROOT INITIATION DEFECTIVE 3); nucleotide binding

[40,41]


Os02g02600

5,06

serine/threonine-protein kinase Cx32chloroplast precursor

At2g17220

protein kinase


O

Os12g41900

4,94

SET domain containing protein

At5g42400

SDG25 (SET DOMAIN PROTEIN 25)/ATXR7/MDH9

[46]


O

Os02g45810

4,72

WD domainG-beta repeat domain containing protein

At5g24520

TTG1 (TRANSPARENT TESTA GLABRA 1)

[57]


O

Os03g20720

3,85

GTPase-activating protein

At1g08680

ZIGA4 (ARF GAP-like zinc finger-containing protein ZiGA4)

[58]


O

Os08g40560

3,32

ZOS8-11 - C2H2 zinc finger protein

At2g27100

SERRATE (SE)

[44]


O

Os06g05350

2,96

whirly transcription factor domain containing protein

At2g02740

WHY3 (WHIRLY 3); DNA binding; PTAC11

[59]


O

Os01g62760

2,88

protein phosphatase 2C

At5g59220

protein phosphatase 2CA

[73,74]


O

Os05g14550

2,86

Phosphatidylinositol kinase and FAT containing domain protein

At1g50030

TOR (TARGET OF RAPAMYCIN)

[60]


O

Os12g06610

2,54

nucleolar complex protein 2

At3g55510

RBL (REBELOTE)

[45]


O

Os12g01140

2,39

ACG kinases include homologs to PKAPKG and PKC

At3g45780

PHOT1 (PHOTOTROPIN 1); protein serine/threonine kinase

[72]


Os01g49160

2,33

MYB family transcription factor


O

Os05g41070

2,31

bZIP transcription factor

At3g56850

AREB3 (ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3)

[33]


A O

Os07g08460

2,30

OsIAA24 - Auxin-responsive Aux/IAA gene family member

[20,61]


O

Os03g43890

2,24

WD domain G-beta repeat domain containing protein

At5g58230

MSI1 (MULTICOPY SUPRESSOR OF IRA1)

[62]


Os01g69850

2,13

OsMADS65 - MADS-box family gene with MIKC type-box


Os06g49510

2,06

zinc knuckle family protein

At4g19190

zinc knuckle (CCHC-type) family protein

[63]


Os07g47820

2,05

acyl-CoA dehydrogenase family member 10

At3g06810

IBR3 (IBA-RESPONSE 3)

[64]


O

Os03g43400

2,05

OsIAA11 - Auxin-responsive Aux/IAA gene family member

[20,61]


O

Os03g42750

2,02

roothairless 1

At1g47550

AtSec3a (Exocyst complex)


DOIC (down-regulated in crl1 relative to WT)


Os03g24930

25,48

tyrosine protein kinase domain containing protein

At1g61590

protein kinase

[65]


Os03g18810

15,00

ll-Diaminopimelate Aminotransferase

At4g33680

AGD2 (ABERRANT GROWTH AND DEATH 2); aminotransferase

[66]


Os11g11790

8,16

NBS-LRR type disease resistance protein


A O

Os03g55890

8,14

ternary complex factor MIP1

At5g66600

unknown protein

[26]


Os03g07450

4,24

HOX21 homeobox associated leucine zipper

At1g69780

ATHB13

[67]


A O

Os09g36220

3,60

OsPRR95 - response regulator receiver domain containing protein

At5g24470

APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5)

[68]


Os08g41340

3,10

ras-related protein

At2g31680

AtRABA5d (Arabidopsis Rab GTPase homolog A5d)


Os09g38980

2,81

T-complex protein

At5g18820

EMB3007 (embryo defective 3007)


A O

Os09g09370

2,64

BTBN18 - BTB domain with non-phototropic hypocotyl 3 domain

At5g47800

BTB - NPH3 domain


Os04g55560

2,62

AP2 domain containing protein

At4g36920

PLETHORA-like transcription factor


CA O

Os01g67100

2,61

OsFSM, expressed protein

At1g65470

FAS1 (FASCIATA 1)

[48,50]


CA

Os08g40620

2,59

rabGAP/TBC domain-containing protein

At4g29950

microtubule-associated protein


A O

Os03g58350

2,40

OsIAA14 - Auxin-responsive Aux/IAA gene family member

[20]


Os02g08310

2,31

Tubby-like protein 4

At1g16070

AtTLP8 (TUBBY LIKE PROTEIN 8)

[69]


O

Os06g03860

2,28

uncharacterized membrane protein

At4g22990

SPX (SYG1/Pho81/XPR1) domain-containing protein

[29]


Os01g07630

2,18

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase

At1g60800

NIK3 (NSP-INTERACTING KINASE 3)


Os07g04700

2,16

MYB family transcription factor

At3g18100

MYB4R1 (myb domain protein 4R1)


O

Os12g37780

2,13

tetratricopeptide repeat domain containing protein

At2g43040

NPG1 (no pollen germination 1); calmodulin binding

[70]


CA

Os02g15220

2,13

bromodomain containing protein, expressed

At1g06230

GTE4 (GLOBAL TRANSCRIPTION FACTOR GROUP E 4)

[51]


Os04g26850

2,10

SAD2

[71]


Os10g37640

2,04

HIT zinc finger domain containing protein

At5g63830

unknown protein


O

Os02g52990

2,04

OsSAUR12 - Auxin-responsive SAUR gene family member

[20,61]


O

Os10g23220

2,14

GIL1

At2g45260

unknown protein


"O" a gene mentioned in Figure 3. "A" indicates a CRL1-independent auxin responsive gene. "CA" indicates a CRL1-dependent auxin responsive gene. ID; identifier. BBMH; Best Blast Mutual Hit. TIGR; Rice Genome Annotation Resource [52-74].

Coudert et al. BMC Genomics 2011 12:387   doi:10.1186/1471-2164-12-387

Open Data