Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice

Plant Signaling and Behavior

Volumn 7, Issue 8, 2012, Pages 951-956

  Garg, Rohini ^a   Tyagi, Akhilesh K ^a   Jain, Mukesh ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

Gene expression; Hormones; Microarray; Rice (oryza sativa); Transcriptional response

Indexed keywords

PHYTOHORMONE;

ARTICLE; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; PLANT GENE; RICE;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT GROWTH REGULATORS; TRANSCRIPTION, GENETIC;

EID: 85046982511     PISSN: 15592316     EISSN: 15592324     Source Type: Journal    
DOI: 10.4161/psb.20910     Document Type: Article

References (35)

1. Santner A, Estelle M. Recent ad vances and emerging trends in plant hormone signalling. Nature 2009; 459:1071-8. PMID:19553990; http://dx.doi.org/10.1038/nature08122.
2. Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP. Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics 2006; 6:47-59. PMID:16200395; http://dx.doi.org/10.1007/s10142-005-0005-0.
3. Jain M, Kaur N, Tyagi AK, Khurana JP. The auxin-responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genomics 2006; 6:36-46. PMID:15856348; http://dx.doi.org/10.1007/s10142-005-0142-5.
4. Jain M, Tyagi AK, Khurana JP. Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice (Oryza sativa). BMC Plant Biol 2006; 6:1. PMID:16472405; http://dx.doi.org/10.1186/1471-2229-6-1.
5. Goda H, Shimada Y, Asami T, Fujioka S, Yoshida S. Microarray analysis of brassinosteroid-regulated genes in Arabidopsis. Plant Physiol 2002; 130:1319-34. PMID:12427998; http://dx.doi.org/10.1104/pp.011254.
6. Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, et al. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J 2008; 55:526-42. PMID:18419781; http://dx.doi.org/10.1111/j.1365-313X.2008.03510.x.
7. Zhong GY, Burns JK. Profiling ethylene-regulated gene expression in Arabidopsis thaliana by microarray analysis. Plant Mol Biol 2003; 53:117-31. PMID:14756311; http://dx.doi.org/10.1023/B:PLAN.0000009270.81977.ef.
8. Jain M, Khurana JP. Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J 2009; 276:3148-62. PMID:19490115; http://dx.doi.org/10.1111/j.1742-4658.2009.07033.x.
9. Wang JR, Hu H, Wang GH, Li J, Chen JY, Wu P. Expression of PIN genes in rice (Oryza sativa L.): tissue specificity and regulation by hormones. Mol Plant 2009; 2:823-31. PMID:19825657; http://dx.doi.org/10.1093/mp/ssp023.
10. Garg R, Jhanwar S, Tyagi AK, Jain M. Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice. DNA Res 2010; 17:353-67. PMID:21044985; http://dx.doi.org/10.1093/dnares/dsq023.
11. Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, et al. Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol Genet Genomics 2012; 287:1-19. PMID:22102215; http://dx.doi.org/10.1007/s00438-011-0659-3.
12. Gazzarrini S, McCourt P. Cross-talk in plant hormone signalling: what Arabidopsis mutants are telling us. Ann Bot 2003; 91:605-12. PMID:12714359; http://dx.doi.org/10.1093/aob/mcg064.
13. Zhang S, Wei Y, Lu Y, Wang X. Mechanisms of brassinosteroids interacting with multiple hormones. Plant Signal Behav 2009; 4:1117-20. PMID:20514225; http://dx.doi.org/10.4161/psb.4.12.9903.
14. Jaillais Y, Chory J. Unraveling the paradoxes of plant hormone signaling integration. Nat Struct Mol Biol 2010; 17:642-5. PMID:20520656; http://dx.doi.org/10.1038/nsmb0610-642.
15. Depuydt S, Hardtke CS. Hormone signalling crosstalk in plant growth regulation. Curr Biol 2011; 21:R365-73. PMID:21549959; http://dx.doi.org/10.1016/j.cub.2011.03.013.
16. Nemhauser JL, Hong F, Chory J. Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell 2006; 126:467-75. PMID:16901781; http://dx.doi.org/10.1016/j.cell.2006.05.050.
17. Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, et al. Genomics approach to abscisic acid-and gibberellin-responsive genes in rice. DNA Res 2003; 10:249-61. PMID:15029956; http://dx.doi.org/10.1093/dnares/10.6.249.
18. Jan A, Komatsu S. Functional characterization of gibberellin-regulated genes in rice using microarray system. Genomics Proteomics Bioinformatics 2006; 4:137-44. PMID:17127211; http://dx.doi.org/10.1016/S1672-0229(06)60026-0.
19. Hirose N, Makita N, Kojima M, Kamada-Nobusada T, Sakakibara H. Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism. Plant Cell Physiol 2007; 48:523-39. PMID:17293362; http://dx.doi.org/10.1093/pcp/pcm022.
20. Cheong YH, Chang HS, Gupta R, Wang X, Zhu T, Luan S. Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis. Plant Physiol 2002; 129:661-77. PMID:12068110; http://dx.doi.org/10.1104/pp.002857.
21. O'Donnell PJ, Schmelz EA, Moussatche P, Lund ST, Jones JB, Klee HJ. Susceptible to intolerance--a range of hormonal actions in a susceptible Arabidopsis pathogen response. Plant J 2003; 33:245-57. PMID:12535339; http://dx.doi.org/10.1046/j.1365-313X.2003.01619.x.
22. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006; 312:436-9. PMID:16627744; http://dx.doi.org/10.1126/science.1126088.
23. Wang D, Pajerowska-Mukhtar K, Culler AH, Dong X. Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr Biol 2007; 17:1784-90. PMID:17919906; http://dx.doi.org/10.1016/j.cub.2007.09.025.
24. Ghanashyam C, Jain M. Role of auxin-responsive genes in biotic stress responses. Plant Signal Behav 2009; 4:846-8. PMID:19847104; http://dx.doi.org/10.4161/psb.4.9.9376.
25. An C, Mou Z. Salicylic acid and its function in plant immunity. J Integr Plant Biol 2011; 53:412-28. PMID:21535470; http://dx.doi.org/10.1111/j.1744-7909.2011.01043.x.
26. Hoffmann M, Hentrich M, Pollmann S. Auxin-oxylipin crosstalk: relationship of antagonists. J Integr Plant Biol 2011; 53:429-45. PMID:21658177; http://dx.doi.org/10.1111/j.1744-7909.2011.01053.x.
27. Tanaka M, Takei K, Kojima M, Sakakibara H, Mori H. Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance. Plant J 2006; 45:1028-36. PMID:16507092; http://dx.doi.org/10.1111/j.1365-313X.2006.02656.x.
28. Suzuki M, Kao CY, Cocciolone S, McCarty DR. Maize VP1 complements Arabidopsis abi3 and confers a novel ABA/auxin interaction in roots. Plant J 2001; 28:409-18. PMID:11737778; http://dx.doi.org/10.1046/j.1365-313X.2001.01165.x.
29. Brady SM, Sarkar SF, Bonetta D, McCourt P. The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis. Plant J 2003; 34:67-75. PMID:12662310; http://dx.doi.org/10.1046/j.1365-313X.2003.01707.x.
30. Gazzarrini S, McCourt P. Genetic interactions between ABA, ethylene and sugar signaling pathways. Curr Opin Plant Biol 2001; 4:387-91. PMID:11597495; http://dx.doi.org/10.1016/S1369-5266(00)00190-4.
31. Cary AJ, Liu W, Howell SH. Cytokinin action is coupled to ethylene in its effects on the inhibition of root and hypocotyl elongation in Arabidopsis thaliana seedlings. Plant Physiol 1995; 107:1075-82. PMID:7770519; http://dx.doi.org/10.1104/pp.107.4.1075.
32. Robert-Seilaniantz A, Grant M, Jones JD. Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annu Rev Phytopathol 2011; 49:317-43. PMID:21663438; http://dx.doi.org/10.1146/annurev-phyto-073009-114447.
33. Garg R, Sahoo A, Tyagi AK, Jain M. Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem Biophys Res Commun 2010; 396:283-8. PMID:20399753; http://dx.doi.org/10.1016/j.bbrc.2010.04.079.
34. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, et al. F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 2007; 143:1467-83. PMID:17293439; http://dx.doi.org/10.1104/pp.106.091900.
35. Zheng Q, Wang XJ. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 2008; 36(Web Server issue):W358-63. PMID:18487275; http://dx.doi.org/10.1093/nar/gkn276.