Table 1 Selected genes for expression analysis by RT-qPCR in response to auxin

ras-related protein

ROP9 (RHO-RELATED PROTEIN FROM PLANTS 9)

[54]

AT hook motif domain containing protein

DNA-binding family protein

OsSAUR9 - Auxin-responsive SAUR gene family member

auxin-responsive family protein

[55, 56]

helix-loop-helix DNA-binding domain containing protein

basic helix-loop-helix (bHLH) family protein

WD domainG-beta repeat domain containing protein

RID3 (ROOT INITIATION DEFECTIVE 3); nucleotide binding

[40, 41]

serine/threonine-protein kinase Cx32chloroplast precursor

protein kinase

SET domain containing protein

SDG25 (SET DOMAIN PROTEIN 25)/ATXR7/MDH9

[46]

WD domainG-beta repeat domain containing protein

TTG1 (TRANSPARENT TESTA GLABRA 1)

[57]

GTPase-activating protein

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

[58]

ZOS8-11 - C2H2 zinc finger protein

SERRATE (SE)

[44]

whirly transcription factor domain containing protein

WHY3 (WHIRLY 3); DNA binding; PTAC11

[59]

protein phosphatase 2C

protein phosphatase 2CA

[73, 74]

Phosphatidylinositol kinase and FAT containing domain protein

TOR (TARGET OF RAPAMYCIN)

[60]

nucleolar complex protein 2

RBL (REBELOTE)

[45]

ACG kinases include homologs to PKAPKG and PKC

PHOT1 (PHOTOTROPIN 1); protein serine/threonine kinase

[72]

MYB family transcription factor

bZIP transcription factor

AREB3 (ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3)

[33]

OsIAA24 - Auxin-responsive Aux/IAA gene family member

[20, 61]

WD domain G-beta repeat domain containing protein

MSI1 (MULTICOPY SUPRESSOR OF IRA1)

[62]

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

zinc knuckle family protein

zinc knuckle (CCHC-type) family protein

[63]

acyl-CoA dehydrogenase family member 10

IBR3 (IBA-RESPONSE 3)

[64]

OsIAA11 - Auxin-responsive Aux/IAA gene family member

[20, 61]

roothairless 1

AtSec3a (Exocyst complex)

DOIC (down-regulated in crl1 relative to WT)

tyrosine protein kinase domain containing protein

protein kinase

[65]

ll-Diaminopimelate Aminotransferase

AGD2 (ABERRANT GROWTH AND DEATH 2); aminotransferase

[66]

NBS-LRR type disease resistance protein

ternary complex factor MIP1

unknown protein

[26]

HOX21 homeobox associated leucine zipper

ATHB13

[67]

OsPRR95 - response regulator receiver domain containing protein

APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5)

[68]

ras-related protein

AtRABA5d (Arabidopsis Rab GTPase homolog A5d)

T-complex protein

EMB3007 (embryo defective 3007)

BTBN18 - BTB domain with non-phototropic hypocotyl 3 domain

BTB - NPH3 domain

AP2 domain containing protein

PLETHORA-like transcription factor

OsFSM, expressed protein

FAS1 (FASCIATA 1)

[48, 50]

rabGAP/TBC domain-containing protein

microtubule-associated protein

OsIAA14 - Auxin-responsive Aux/IAA gene family member

[20]

Tubby-like protein 4

AtTLP8 (TUBBY LIKE PROTEIN 8)

[69]

uncharacterized membrane protein

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

[29]

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase

NIK3 (NSP-INTERACTING KINASE 3)

MYB family transcription factor

MYB4R1 (myb domain protein 4R1)

tetratricopeptide repeat domain containing protein

NPG1 (no pollen germination 1); calmodulin binding

[70]

bromodomain containing protein, expressed

GTE4 (GLOBAL TRANSCRIPTION FACTOR GROUP E 4)

[51]

SAD2

[71]

HIT zinc finger domain containing protein

unknown protein

OsSAUR12 - Auxin-responsive SAUR gene family member

[20, 61]

GIL1

unknown protein