Auxin-related gene families in abiotic stress response in Sorghum bicolor

Functional and Integrative Genomics

Volumn 10, Issue 4, 2010, Pages 533-546

  Wang, Suikang ^a   Bai, Youhuang ^a,b   Shen, Chenjia ^a   Wu, Yunrong ^a   Zhang, Saina ^a   Jiang, Dean ^a   Guilfoyle, Tom J ^c   Chen, Ming ^a,b   Qi, Yanhua ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c University of Missouri   (United States)

Author keywords

Abiotic stress; ARF; Aux IAA; GH3; LBD; Sorghum bicolor

Indexed keywords

AUXIN; AUXIN RESPONSE FACTOR; BRASSINOSTEROID; GRETCHEN HAGEN 3 PROTEIN; INDOLEACETIC ACID; LATERAL ORGAN BOUNDARIES PROTEIN; PLANT RNA; UNCLASSIFIED DRUG;

ABIOTIC STRESS; ARTICLE; AUXIN RESPONSE FACTOR GENE; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; DROUGHT STRESS; EXON; GENE DUPLICATION; GENE EXPRESSION PROFILING; GRETCHEN HAGEN 3 GENE; INDOLE 3 ACETIC ACID GENE; INTRON; LATERAL ORGAN BOUNDARIES GENE; MOLECULAR INTERACTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PLANT GENE; PLANT LEAF; PLANT ROOT; PRIORITY JOURNAL; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; SALT STRESS; SIGNAL TRANSDUCTION; SORGHUM; SORGHUM BICOLOR;

ANIMALS; CHROMOSOME MAPPING; GENES, PLANT; INDOLEACETIC ACIDS; PLANT GROWTH REGULATORS; PLANT PROTEINS; PROMOTER REGIONS, GENETIC; SORGHUM; STRESS, PHYSIOLOGICAL;

ARABIDOPSIS; SORGHUM BICOLOR;

EID: 78650524304     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-010-0174-3     Document Type: Article

References (90)

1. F Abascal R Zardoya D Posada 2005 ProtTest: selection of best-fit models of protein evolution Bioinformatics 21 2104 2105 1:CAS:528:DC%2BD2MXjsl2ns7Y%3D 10.1093/bioinformatics/bti263 15647292 (Pubitemid 40668057)
2. S Abel A Theologis 1996 Early genes and auxin action Plant Physiol 111 9 17 1:CAS:528:DyaK28XivFektL4%3D 10.1104/pp.111.1.9 8685277
3. S Abel PW Oeller A Theologis 1994 Early auxin-induced genes encode short-lived nuclear proteins Proc Natl Acad Sci USA 91 326 330 1:CAS:528:DyaK2cXntlCruw%3D%3D 10.1073/pnas.91.1.326 8278386 (Pubitemid 24018697)
4. WM Ainley JC Walker RT Nagao JL Key 1988 Sequence and characterization of two auxin-regulated genes from soybean J Biol Chem 263 10658 10666 1:CAS:528:DyaL1MXhsVyqt7w%3D 2899079
5. E Bortiri G Chuck E Vollbrecht T Rocheford R Martienssen S Hake 2006 ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize Plant Cell 18 574 585 1:CAS:528:DC%2BD28XisFahtbs%3D 10.1105/tpc.105.039032 16399802 (Pubitemid 43956162)
6. JE Bowers BA Chapman J Rong AH Paterson 2003 Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events Nature 422 433 438 1:CAS:528:DC%2BD3sXitlGgtbk%3D 10.1038/nature01521 12660784 (Pubitemid 36411396)
7. A Chalfun-Junior J Franken JJ Mes N Marseh-Martinez A Pereira GC Angenent 2005 ASYMMETRIC LEAVES2-LIKEl gene, a member of the AS2/LOB family, controls proximal-distal patterning in Arabidopsis petals Plant Mol 57 559 575 1:CAS:528:DC%2BD2MXjtV2gs7w%3D 10.1007/s11103-005-0698-4 (Pubitemid 40588709)
8. EJ Chapman M Estelle 2009 Mechanism of auxin-regulated gene expression in plants Annu Rev Genet 43 265 285 1:CAS:528:DC%2BD1MXhsF2qtrnI 10.1146/annurev-genet-102108-134148 19686081
9. L Chen F Ren H Zhong Y Feng W Jiang X Li 2010 Identification and expression analysis of genes in response to high-salinity and drought stresses in Brassica napus Acta Biochim Biophys Sin (Shanghai) 42 154 164 1:CAS:528:DC%2BC3cXhsVSqu7o%3D 10.1093/abbs/gmp113
10. Davies PJ (1995) The plant hormones: their nature, occurrence and functions. In: Davies PJ (ed) Plant Hormones Physiology, Biochemistry and Molecular Biology. Kluwer Academic Publishers, Dordrecht, pp 1-12
11. CB Do MS Mahabhashyam M Brudno S Batzoglou 2005 ProbCons: probabilistic consistency-based multiple sequence alignment Genome Res 15 330 340 1:CAS:528:DC%2BD2MXhsVKgu7w%3D 10.1101/gr.2821705 15687296 (Pubitemid 40309398)
12. SR Eddy 1998 Profile hidden Markov models Bioinformatics 14 755 763 1:CAS:528:DyaK1MXktlCmtQ%3D%3D 10.1093/bioinformatics/14.9.755 9918945
13. RC Edgar 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucl Acids Res 32 1792 1797 1:CAS:528:DC%2BD2cXisF2ks7w%3D 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
14. Jagadeeswaran G, Raina S, Acharya BR, Maqbool SB, Mosher SL, Appel HM, Schultz JC, Klessig DF, Raina R (2007) Arabidopsis GH3-LIKE DEFENSE GENE 1 is required for accumulation of salicylic acid, activation of defense responses and resistance to Pseudomonas syringae. Plant J 51:234-246
15. MB Eisen PT Spellman PO Brown D Botstein 1998 Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 95 14863 14868 1:CAS:528:DyaK1cXotVGmurk%3D 10.1073/pnas.95.25.14863 9843981 (Pubitemid 29003722)
16. MM Evans 2007 The indeterminate gametophyte1 gene of maize encodes a LOB domain protein required for embryo sac and leaf development Plant Cell 19 46 62 1:CAS:528:DC%2BD2sXjtFynsbs%3D 10.1105/tpc.106.047506 17209126 (Pubitemid 46852700)
17. Khan S, Stone JM (2007) Arabidopsis thaliana GH3.9 influences primary root growth. Planta 226:21-34
18. AR Franco MA Gee TJ Guilfoyle 1990 Induction and superinduction of auxin-responsive messenger-RNAs with auxin and protein-synthesis inhibitors J Biol Chem 265 15845 15849 1:CAS:528:DyaK3cXls12jtbY%3D 2394751
19. H Fukaki Y Nakao Y Okushima A Theologis M Tasaka 2005 Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14 alters lateral root development in Arabidopsis Plant J 44 382 395 1:CAS:528:DC%2BD2MXht1alsbnO 10.1111/j.1365-313X. 2005.02537.x 16236149
20. C Ghanashyam M Jain 2009 Role of auxin-responsive genes in biotic stress responses Plant Signal Behav 4 846 848 1:CAS:528:DC%2BC3cXkt1Sis7w%3D 10.4161/psb.4.9.9376 19847104
21. Guilfoyle TJ (1999) Auxin-regulated genes and promoters. In: Hooykaas PJJ, Hall MA, Libbenga KR (eds) Biochemistry and molecular biology of plant hormones. Elsevier, Amsterdam, pp 423-459
22. TJ Guilfoyle G Hagen 2001 Auxin response factors: recent advances in auxin biology J Plant Growth Regul 10 281 291 10.1007/s003440010026 (Pubitemid 34088623)
23. TJ Guilfoyle G Hagen 2007 Auxin response factors Curr Opin Plant Biol 10 453 460 1:CAS:528:DC%2BD2sXhtFekurvE 10.1016/j.pbi.2007.08.014 17900969 (Pubitemid 47505406)
24. TJ Guilfoyle T Ulmasov G Hagen 1998 The ARF family of transcription factors and their role in plant hormone-responsive transcription Cell Mol Life Sci 54 619 627 1:CAS:528:DyaK1cXkvFKgs70%3D 10.1007/s000180050190 9711229 (Pubitemid 28379665)
25. AY Guo QH Zhu X Chen JC Luo 2007 GSDS: a gene structure display server Yi Chuan 29 1023 1026 1:CAS:528:DC%2BD1cXpvVGjs7s%3D 17681935
26. WM Gray S Kepinski D Rouse O Leyser M Estelle 2001 Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins Nature 414 271 276 1:CAS:528:DC%2BD3MXovFaqtb4%3D 10.1038/35104500 11713520 (Pubitemid 33097797)
27. G Rubin T Tohge F Matsuda K Saito W-R Scheible 2009 Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis Plant Cell 21 11 3567 3584 10.1105/tpc.109.067041 1:CAS:528:DC%2BC3cXovVWqsQ%3D%3D 10.1105/tpc.109.067041 19933203
28. G Hagen TJ Guilfoyle 2002 Auxin-responsive gene expression: genes, promoters and regulatory factors Plant Mol Biol 49 373 385 1:CAS:528: DC%2BD38XktlSqt7g%3D 10.1023/A:1015207114117 12036261 (Pubitemid 34519755)
29. T Hamann E Benkova I Baurle M Kientz G Jürgens 2004 The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS- mediated embryo patterning Gene Dev 16 1610 1615 10.1101/gad.229402
30. CS Hardtke W Ckurshumova DP Vidaurre SA Singh G Stamatiou SB Tiwari G Hagen TJ Guilfoyle T Berleth 2004 Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4 Development 131 1089 1100 1:CAS:528:DC%2BD2cXis1emsro%3D 10.1242/dev.00925 14973283 (Pubitemid 38380462)
31. T Heinekamp A Strathmann M Kuhlmann M Froissard A Müller C Perrot-Rechenmann W Dröge-Laser 2004 The tobacco bZIP transcription factor BZI-1 binds the GH3 promoter in vivo and modulates auxin-induced transcription Plant J 38 298 309 1:CAS:528:DC%2BD2cXkt1Kks7g%3D 10.1111/j.1365-313X.2004. 02043.x 15078332 (Pubitemid 38503730)
32. A Husbands EM Bell B Shuai HM Smith PS Springer 2007 LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins Nucleic Acids Res 35 6663 6671 1:CAS:528:DC%2BD2sXht1yktbrP 10.1093/nar/gkm775 17913740 (Pubitemid 350111630)
33. Y Inukai T Sakamoto M Ueguchi-Tanaka Y Shibata K Gomi I Umemura Y Hasegawa M Ashikari H Kitano M Matsuoka 2005 Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling Plant Cell 17 1387 1396 1:CAS:528:DC%2BD2MXksVKksrY%3D 10.1105/tpc.105.030981 15829602 (Pubitemid 43138192)
34. H Iwakawa Y Ueno E Semiarti H Onouchi S Kojima H Tsukaya M Hasebe T Soma M Ikezaki C Machida Y Machida 2002 The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper Plant Cell Physiol 43 467 478 1:CAS:528:DC%2BD38XktFWgtrY%3D 10.1093/pcp/pcf077 12040093
35. M Jain JP Khurana 2009 Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice FEBS J 276 3148 3162 1:CAS:528:DC%2BD1MXmslaqsrY%3D 10.1111/j.1742-4658. 2009.07033.x 19490115
36. K Katoh K Misawa K Kuma T Miyata 2002 MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucl Acids Res 30 3059 3066 1:CAS:528:DC%2BD38XlslOqu7s%3D 10.1093/nar/gkf436 12136088
37. J Kim K Harter A Theologis 1997 Protein-protein interactions among the Aux/IAA proteins Proc Natl Acad Sci USA 94 11786 11791 1:CAS:528: DyaK2sXntFSnu7w%3D 10.1073/pnas.94.22.11786 9342315 (Pubitemid 27467795)
38. H Kim PJ Park HJ Hwang SY Lee MH Oh SG Kim 2006 Brassinosteroid signals control expression of the AXR3/IAA17 gene in the cross-talk point with auxin in root development Biosci Biotechnol Biochem 70 768 773 1:CAS:528: DC%2BD28Xks1Sgsr4%3D 10.1271/bbb.70.768 16636440
39. S Kumar J Dudley M Nei K Tamura 2008 MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences Brief Bioinform 9 299 306 1:CAS:528:DC%2BD1cXpt1artrg%3D 10.1093/bib/bbn017 18417537 (Pubitemid 351890826)
40. ML Lang YX Zhang TY Chai 2005 Identification of genes up regulated in response to Cd exposure in Brassica juncea L Gene 363 151 158 1:CAS:528:DC%2BD2MXht1Klu7%2FO 10.1016/j.gene.2005.07.037 (Pubitemid 41691903)
41. HW Lee NY Kim DJ Lee J Kim 2009 LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis Plant Physiol 151 1377 1389 1:CAS:528:DC%2BD1MXhsVCjsbnN 10.1104/pp.109.143685 19717544
42. A Li Y Zhang X Wu W Tang R Wu Z Dai G Liu H Zhang C Wu G Chen X Pan 2008 DH1, a LOB domain-like protein required for glume formation in rice Plant Mol Biol 66 491 502 1:CAS:528:DC%2BD1cXitVWrtLk%3D 10.1007/s11103-007-9283-3 18180880
43. ZB Liu T Ulmasov X Shi G Hagen TJ Guilfoyle 1994 Soybean GH3 promoter contains multiple auxin-inducible elements Plant Cell 6 645 657 1:CAS:528:DyaK2cXmvFChtb0%3D 10.1105/tpc.6.5.645 8038604 (Pubitemid 2103507)
44. H Liu S Wang X Yu J Yu X He S Zhang H Shou P Wu 2005a ARL1, a LOB-domain protein required for adventitious root formation in rice Plant J 43 47 56 10.1111/j.1365-313X.2005.02434.x (Pubitemid 40962734)
45. KD Liu BC Kang H Jiang 2005b A GH3-like gene, CcGH3, isolated from Capsicum chinense L. fruit is regulated by auxin and ethylene Plant Mol Biol 58 447 464 1:CAS:528:DC%2BD2MXmt1Wns7o%3D 10.1007/s11103-005-6505-4 (Pubitemid 41125978)
46. A Matsui J Ishida T Morosawa Y Mochizuki E Kaminuma TA Endo M Okamoto E Nambara M Nakajima M Kawashima M Satou JM Kim N Kobayashi T Toyoda K Shinozaki M Seki 2008 Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array Plant Cell Physiol 49 1135 49 1:CAS:528:DC%2BD1cXhtFSrsbnN 10.1093/pcp/pcn101 18625610
47. BA McClure T Guilfoyle 1989 Rapid redistribution of auxin-regulated RNAs during gravitropism Science 243 91 93 1:CAS:528:DyaL1MXhtlagtLs%3D 10.1126/science.11540631 11540631
48. A Nakamura K Higuchi H Goda MT Fujiwara S Sawa T Koshiba Y Shimada S Yoshida 2003 Brassinolide induces IAA5, IAA19 and DR5, a synthetic auxin response element in Arabidopsis, implying a cross talk point of brassinosteriod and auxin signaling Plant Physiol 133 1843 1853 1:CAS:528:DC%2BD2cXhvFGm 10.1104/pp.103.030031 14605219 (Pubitemid 38047313)
49. L Navarro P Dunoyer F Jay B Arnold N Dharmasiri M Estelle O Voinnet JDG Jones 2006 A plant miRNA contributes to antibacterial resistance by repressing auxin signaling Science 312 436 439 1:CAS:528:DC%2BD28XjslSktbw%3D 10.1126/science.1126088 16627744
50. JL Nemhauser TC Mockler J Chory 2004 Interdependency of brassinosteroid and auxin signaling in Arabidopsis PLoS Biol 2 1460 1471 1:CAS:528: DC%2BD2cXns1Gku74%3D 10.1371/journal.pbio.0020258 (Pubitemid 39245253)
51. C Notredame DG Higgins J Heringa 2000 T-coffee: a novel method for fast and accurate multiple sequence alignment J Mol Biol 302 205 217 1:CAS:528:DC%2BD3cXmtVGntr8%3D 10.1006/jmbi.2000.4042 10964570
52. Y Okushima PJ Overvoorde K Arima JM Alonso A Chan C Chang JR Ecker B Hughes A Lui D Nguyen C Onodera H Quach A Smith G Yu A Theologis 2005 Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19 Plant Cell 17 444 463 1:CAS:528:DC%2BD2MXhsFKqsro%3D 10.1105/tpc.104.028316 15659631 (Pubitemid 41672967)
53. Okushima Y, Fukaki H, Onoda M, Theologis A, Tasaka M (2007) ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell 19:118-130
54. N Ori Y Eshed G Chuck JL Bowman S Hake 2000 Mechanisms that control knox gene expression in the Arabidopsis shoot Development 127 5523 5532 1:CAS:528:DC%2BD3MXltFWkug%3D%3D 11076771
55. IA Paponov M Paponov W Teale M Menges S Chakrabortee JA Murray K Palme 2008 Comprehensive transcriptome analysis of auxin responses in Arabidopsis Mol Plant 1 321 337 1:CAS:528:DC%2BD1cXoslyks7c%3D 10.1093/mp/ssm021 19825543
56. JE Park JY Park YS Kim PE Staswick J Jeon J Yun SY Kim J Kim YH Lee CM Park 2007 GH3-mediated auxin homeostasis links growth regulation with stress adaptation response in Arabidopsis J Biol Chem 282 10036 10046 1:CAS:528:DC%2BD2sXjtlCisLg%3D 10.1074/jbc.M610524200 17276977 (Pubitemid 47104632)
57. AH Paterson JE Bowers BA Chapman 2004 Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics Proc Natl Acad Sci USA 101 9903 9908 1:CAS:528:DC%2BD2cXlvVahtbY%3D 10.1073/pnas.0307901101 15161969 (Pubitemid 38869334)
58. AH Paterson JE Bowers R Bruggmann I Dubchak J Grimwood H Gundlach G Haberer U Hellsten T Mitros A Poliakov J Schmutz M Spannagl H Tang X Wang T Wicker AK Bharti J Chapman FA Feltus U Gowik IV Grigoriev E Lyons CA Maher M Martis A Narechania RP Otillar BW Penning AA Salamov Y Wang L Zhang NC Carpita M Freeling AR Gingle CT Hash B Keller P Klein S Kresovich MC McCann R Ming DG Peterson Mehboob-ur-Rahman D Ware P Westhoff KF Mayer J Messing DS Rokhsar 2009 The Sorghum bicolor genome and the diversification of grasses Nature 457 551 556 1:CAS:528:DC%2BD1MXhtFOmsb4%3D 10.1038/nature07723 19189423
59. M Riemann M Riemann M Takano M Riemann M Riemann M Takano 2008 Rice JASM0NATE RESISTANT 1 is involved in phytochrome and iasmonate signaling Plant Cell Environ 31 783 792 1:CAS:528:DC%2BD1cXnvVOmtbs%3D 10.1111/j.1365-3040.2008. 01790.x 18266905 (Pubitemid 351667677)
60. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425 1:STN:280: DyaL1c7ovFSjsA%3D%3D 3447015
61. AJ Saldanha 2004 Java Treeview-extensible visualization of microarray data Bioinformatics 20 3246 3248 1:CAS:528:DC%2BD2cXhtVSrur%2FO 10.1093/bioinformatics/bth349 15180930 (Pubitemid 39619217)
62. PJ Seo CM Park 2009 Auxin homeostasis during lateral root development under drought condition Plant Signal Behav 4 1002 1004 1:CAS:528: DC%2BC3cXms1aju7g%3D 10.4161/psb.4.10.9716 19826230
63. E Semiarti Y Ueno H Tsukaya H Iwakawa C Machida Y Machida 2001 The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves Development 128 1771 1783 1:CAS:528: DC%2BD3MXktFyjt7c%3D 11311158
64. K Shibasaki M Uemura S Tsurumi A Rahman 2009 Auxin response in Arabidopsis under cold stress: underlying molecular mechanisms Plant Cell 21 3823 3838 1:CAS:528:DC%2BC3cXhvFSisr4%3D 10.1105/tpc.109.069906 20040541
65. B Shuai CG Reynaga-Pena PS Springer 2002 The lateral organ boundaries gene defines a novel, plant-specific gene family Plant Physiol 129 747 761 1:CAS:528:DC%2BD38XkvV2jt70%3D 10.1104/pp.010926 12068116 (Pubitemid 34695944)
66. C Soderlund W Nelson A Shoemaker A Paterson 2006 SyMAP: a system for discovering and viewing syntenic regions of FPC maps Genome Res 16 1159 1168 1:CAS:528:DC%2BD28XpsFels78%3D 10.1101/gr.5396706 16951135 (Pubitemid 44320403)
67. T Soyano S Thitamadee Y Machida NH Chua 2008 ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis Plant Cell 20 3359 3373 1:CAS:528:DC%2BD1MXitVarurg%3D 10.1105/tpc.108.061796 19088331
68. A Stamatakis P Hoover J Rougemont 2008 A rapid bootstrap algorithm for the RAxML web servers Syst Biol 75 758 771 10.1080/10635150802429642
69. PE Staswick B Serban M Rowe I Tiryaki MT Maldonado MC Maldonado W Suza 2005 Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid Plant Cell 17 616 627 1:CAS:528: DC%2BD2MXhsFKqs7g%3D 10.1105/tpc.104.026690 15659623 (Pubitemid 41672979)
70. H Szemenyei M Hannon JA Long 2008 TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis Science 319 1384 1386 1:CAS:528:DC%2BD1cXislSktrc%3D 10.1126/science.1151461 18258861 (Pubitemid 351354872)
71. T Takase M Nakazawa A Ishikawa M Kawashima T Ichikawa N Takahashi H Shimada K Manabe M Matsui 2004 ydk1-D, an auxin-responsive GH3 mutant that is involved in hypocotyl and root elongation Plant J 37 471 483 1:CAS:528:DC%2BD2cXisVWhs7k%3D 10.1046/j.1365-313X.2003.01973.x 14756757 (Pubitemid 38258769)
72. S Tanaka N Mochizuki A Nagatani 2002 Expression of the AtGH3a gene, an Arabidopsis homologue of the soybean GH3 gene, is regulated by phytochrome B Plant Cell Physiol 43 281 289 1:CAS:528:DC%2BD38XisFOhtbw%3D 10.1093/pcp/pcf033 11917082
73. K Tatematsu S Kumagai H Muto A Sato MK Watahiki RM Harper E Liscum KT Yamamoto 2004 MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that functions together with the transcriptional activator NPH4/ARF7 to regulate differential growth responses of hypocotyl and formation of lateral roots in Arabidopsis thaliana Plant Cell 16 379 393 1:CAS:528:DC%2BD2cXhsFKis70%3D 10.1105/tpc.018630 14729917 (Pubitemid 38192697)
74. WD Teale IA Paponov K Palme 2006 Auxin in action: signalling, transport and the control of plant growth and development Nat Rev Mol Cell Biol 7 847 859 1:CAS:528:DC%2BD28XhtFSms77M 10.1038/nrm2020 16990790 (Pubitemid 44627478)
75. JM Tepperman T Zhu HS Chang X Wang PH Quail 2001 Multiple transcription-factor genes are early targets of phytochrome a signaling Proc Natl Acad Sci USA 98 9437 9442 1:CAS:528:DC%2BD3MXlvFSrtrg%3D 10.1073/pnas.161300998 11481498 (Pubitemid 32743935)
76. A Theologis TV Huynh RW Davis 1985 Rapid induction of specific mRNAs by auxin in pea epicotyl tissue J Mol Biol 183 53 68 1:CAS:528:DyaL2MXktlaqtLg%3D 10.1016/0022-2836(85)90280-3 4009721
77. JK Thakur AK Tyagi JP Khurana 2001 OsIAA1, an Aux/IAA cDNA from rice, and changes in its expression as influenced by auxin and light DNA Res 8 193 203 1:CAS:528:DC%2BD3MXotlCgu7g%3D 10.1093/dnares/8.5.193 11759839
78. G Taramino M Sauer JL Stauffer D Multani X Niu H Sakai F Hochholdinger 2007 The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shoot-borne root initiation Plant J 50 649 659 1:CAS:528:DC%2BD2sXmt1CjtbY%3D 10.1111/j.1365-313X.2007.03075.x 17425722 (Pubitemid 46733753)
79. J Terol C Domingo M Talon 2006 The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis Gene 371 279 290 1:CAS:528:DC%2BD28XjsFeitbs%3D 10.1016/j.gene.2005.12.014 16488558
80. CE Tian H Muto K Higuchi T Matamura K Tatematsu T Koshiba KT Yamamoto 2004 Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyls elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition Plant J 40 333 343 1:CAS:528:DC%2BD2cXhtVShurjF 10.1111/j.1365-313X.2004.02220.x 15469491 (Pubitemid 39415615)
81. T Uehara Y Okushima T Mimura M Tasaka H Fukaki 2008 Domain II mutations in CRANE/IAA18 suppress lateral root formation and affect shoot development in Arabidopsis thaliana Plant Cell Physiol 49 1025 1038 1:CAS:528: DC%2BD1cXpvVOnsbk%3D 10.1093/pcp/pcn079 18505759 (Pubitemid 351989690)
82. T Ulmasov G Hagen TJ Guilfoyle 1997 ARF1, a transcription factor that binds to auxin response elements Science 276 1865 1868 1:CAS:528: DyaK2sXksVCnu7k%3D 10.1126/science.276.5320.1865 9188533 (Pubitemid 27443664)
83. S Vanneste J Friml 2009 Auxin: a trigger for change in plant development Cell 136 1005 1016 1:CAS:528:DC%2BD1MXltFSntro%3D 10.1016/j.cell.2009.03.001 19303845
84. X Wang U Gowik H Tang JE Bowers P Westhoff AH Paterson 2009 Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses Genome Biol 10 6 R68 10.1186/gb-2009-10-6-r68 10.1186/gb-2009-10-6-r68 19549309
85. AM Waterhouse JB Procter DMA Martin M Clamp GJ Barton 2009 Jalview Version 2-a multiple sequence alignment editor and analysis workbench Bioinformatics 25 1189 1191 1:CAS:528:DC%2BD1MXltFWis7Y%3D 10.1093/ bioinformatics/btp033 19151095
86. D Weijers E Benkova KE Jäger A Schlereth T Hamann M Kientz JC Wilmoth JW Reed G Jürgens 2005 Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators EMBO J 24 1874 1885 1:CAS:528:DC%2BD2MXkt1Smtr8%3D 10.1038/sj.emboj.7600659 15889151 (Pubitemid 40769506)
87. L Xu Y Xu A Dong Y Sun L Pi Y Xu H Huang 2003 Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity Development 130 4097 4107 1:CAS:528:DC%2BD3sXntFejs78%3D 10.1242/dev.00622 12874130 (Pubitemid 37063427)
88. KT Yamamoto H Mori H Imaseki 1992 cDNA cloning of indole-3-acetic acid regulated genes: Aux22 and SAUR from mung bean (Vigna radiata) hypocotyls tissue Plant Cell Physiol 33 93 97 1:CAS:528:DyaK3sXhslCl
89. Y Yang X Yu P Wu 2006 Comparison and evolution analysis of two rice subspecies LATERAL ORGAN BOUNDARIES domain gene family and their evolutionary characterization from Arabidopsis Mol Phylogenet Evol 39 248 262 1:CAS:528:DC%2BD28XisF2hsbg%3D 10.1016/j.ympev.2005.09.016 16290186
90. Z Zhang Q Li Z Li PE Staswick M Wang Y Zhu Z He 2007 Dual regulation role of GH3.5 in salicylic acid and auxin signaling during Arabidopsis-Pseudomonas syringae interaction Plant Physiol 145 450 464 1:CAS:528:DC%2BD2sXht1SjsLrI 10.1104/pp.107.106021 17704230 (Pubitemid 47575143)