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

From: Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice

  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  
  1. "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 [5274].