Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice

Plant Molecular Biology

Volumn 63, Issue 3, 2007, Pages 337-349

  Su, Ning ^a,b   He, Kun ^a,b   Jiao, Yuling ^b   Chen, Chen ^c,d   Zhou, Junli ^b   Li, Lei ^b   Bai, Sulan ^a,b   Li, Xueyong ^b   Deng, Xing Wang ^a,b  

^a PEKING UNIVERSITY   (China)

^b YALE UNIVERSITY   (United States)

^c Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^d ZHEJIANG UNIVERSITY   (China)

Author keywords

Development; Oligo chip; Organogenesis; Rice; Transcriptome

Indexed keywords

GENES; PLANT CELL CULTURE; PLANTS (BOTANY);

MONOCOT PLANTS; OLIGO CHIPS; ORGANOGENESIS; TRANSCRIPTOMES;

CROPS;

ARTICLE; CELL CULTURE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT; PLANT ROOT; PRENATAL DEVELOPMENT; RICE;

CELLS, CULTURED; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT ROOTS; PLANT SHOOTS; TRANSCRIPTION, GENETIC;

CELLS; FARM CROPS; GENES; PLANTS;

ORYZA SATIVA;

EID: 33846833829     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-006-9092-0     Document Type: Article

References (68)

1. Aida M, Ishida T, Fukaki H, Fujisawa H, Tasaka M (1997) Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9:841-857
2. Bennett MJ, Marchant A, Green HG, May ST, Ward SP, Millner PA, Walker AR, Schulz B, Feldmann KA (1996) Arabidopsis AUX1 gene: a permiase-like regulator of root gravitropism. Science 273:948-950
3. Boerjan W, Cervera MT, Delarue M, Beeckman T, Dewitte W, Bellini C, Caboche M, Onckelen HV, Montagu MV, Inze D (1995) Superroot, a recessive mutation in Arabidopsis, confers auxin overproduction. Plant Cell 7:1405-1419
4. Casimiro I, Marchant A, Bhalerao RP, Beeckman T, Dhooge S, Swarup R, Graham N, Inzé N, Sandberg G, Casero PJ, Bennett M (2001) Auxin transport promote Arabidopsis lateral root initiation. Plant cell 13:843-852
5. Celenza JL, Grisafi PL, Fink GR (1995) A pathway for lateral root formation in Arabidopsis thaliana. Genes Dev 9:2131-2142
6. Che P, Gingerich DJ, Lall S, Howell SH (2002) Global and hormone-induced gene expression changes during shoot development in Arabidopsis. Plant cell 14:2771-2785
7. Christianson ML, Warnick DA (1983) Competence and determination in the process of in vitro shoot organogenesis. Dev Biol 95:288-289
8. Chu CC, Wang CC, Sun CS, Hus C, Yin KC, Chu CY (1975) Establishment of an efficient medium for anther culture of rice through comparative experiments on the nitrogen sources. Sci Sin 18:659-668
9. Clark SE, Running MP, Meyerowitz EM (1993) CLAVATA1, a regulator of meristem and flower development in Arabidopsis. Development 119:397-418
10. Clark SE, Running MP, Meyerowitz EM (1995) CLAVATA3 is a specific regulator of shoot and floral meristem development affecting the same processes as CLAVATA1. Development 121:2057-2067
11. Fletcher JC, Brand U, Running MP, Simon R, Meyerowitz EM (1999) Communication of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science 283:1911-1914
12. Friml J, Benkova E, Blilou I, Wisniewska J, Hamann T, Ljung K, Woody S, Sandberg G, Scheres B, Jürgens G, Palme K (2002a) AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis. Cell 108:661-673
13. Friml J, Wisniewska J, Benkova E, Mendgen K, Palme K (2002b) Lateral relocation of auxin efflux regulator PIN3 mediates tropism in Arabidopsis. Nature 415:806-809
14. Fukaki H, Tameda S, Masuda H, Tasaka M (2002) Lateral root formation is blocked by a gain-of-function mutation in the SOLITARY-ROOT/IAA14 gene of Arabidopsis. Plant J 29:153-168
15. Gälweiler L, Guan C, Muller A, Wisman E, Mendgen K, Yephremov A, Palme K (1998) Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue. Science 282:2226-2230
16. Geldner N, Friml J, Stierhof YD, Jurgens G, Palme K (2001) Auxin transport inhibitors block PIN1 cycling and vesicle trafficking. Nature 413:425-428
17. Gisel A, Barella S, Hempel FD, Zambryski PC (1999) Temporal and spatial regulation of symplastic trafficking during development in Arabidopsis thaliana apices. Development 126:1879-1889
18. Goldberg RB, De Paiva G, Yadegari R (1994) Plant embryogenesis: zygote to seed. Science 266:605-614
19. Gray WM, del Pozo JC, Walker L, Hobbie L, Risseeuw E, Banks T, Crosby WL, Yang M, Ma H, Estelle M (1999) Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana. Genes Dev 13:1678-1691
20. Haberer G, Kieber JJ (2002) Cytokinins. New insights into a classic phytohormone. Plant Physiol 128:354-362
21. Hattori T, Terada T, Hamasuna S (1995) Regulation of the osem gene by abscisic and the transcriptional activator VP1: analysis of cis-acting promoter elements required for regulation by abscisic acid and VP1. Plant J 7:913-925
22. Himanen K, Vuylsteke M, Vanneste S, Vercruysse S, Boucheron E, Alard P, Chriqui D, Van Montagu M, Inze D, Beechman T (2004) Transcript profiling of early lateral root initiation. PNAS 101(14):5146-5151
23. Hobbie L, Estelle M (1995) The axr4 auxin-resistant mutants of Arabidopsis thaliana define a gene important for root gravitropism and lateral root initiation. Plant J 7:211-220
24. Howell SH, Lall S, Che P (2003) Cytokinins and shoot development. Trends Plant Sci 8:453-459
25. Hwang I, Sheen J (2001) Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413:383-289
26. Hwang I, Chen HC, Sheen J (2002) Two-component signal transduction pathways in Arabidopsis. Plant Physiol 129:500-515
27. Ingram GC, Boisnard-Lorig, Dumas C, Rogowsky PM (2000) Expression patterns of genes encoding HD-ZipIV homeo domain proteins define specific domains in maize embryos and meristems. Plant J 22:401-414
28. Inoue T, Higuchi M, Hashimoto Y, Seki M, Kobayashi M, Kato T, Tabata S, Shinozaki K, Kakimoto T (2001) Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature 409:1060-1063
29. Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW (2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17(6):1641-1657
30. Kakimoto T (1996) CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science 274:982-985
31. Kayes JM, Clark SE (1998) CLAVATA2, a regulator of meristem and organ development in Arabidopsis. Development 125:3843-3851
32. King JJ, Stimart DP, Fisher RH, Bleecker AB (1995) A mutation altering auxin homeostasis and plant morphology in Arabidopsis. Plant Cell 7:2023-2037
33. Laskowski MJ, Williams ME, Nusbaum HC, Sussex IM (1995) Formation of lateral root meristems is a two-stage process. Development 121:3303-3310
34. Laux T, Mayer KFX, Berger J, Jürgens G (1996) The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development 122:87-96
35. Leyser HMO, Furner IJ (1992) Characterization of three shoot apical meristem mutants of Arabidopsis thaliana. Development 116:397-403
36. Leyser HMO, Pickett FB, Dharmasiri S, Estelle M (1996) Mutations in the AXR3 gene of Arabidopsis result in altered auxin response including ectopic expression from the SAUR-AC1 promoter. Plant J 10:403-413
37. Long JA, Moan EI, Medford JI, Barton MK (1996) A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 379:66-69
38. Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GKS, Wang J, Deng XW, Wang J (2005) A microarray analysis of the transcriptome and its comparison to Arabidopsis. Genome Res 15(9):1274-1283
39. Malamy JE, Benfey PN (1997) Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124:33-44
40. Mayer KF, Schoof H, Haecker A, Lenhard M, Jürgens G, Laux T (1998) Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95:805-815
41. Mok DWS, Martin RC (1994) Cytokinin metabolic enzymes. In: Mok DWS, Mok MC (eds) Cytokinins: Chemistry, activity and function, chap. 24, CRC Press, pp 129-138
42. Moussian B, Schoof H, Haecker A, Jurgens G, Laux T (1998) Role of the ZWILLE gene in the regulation of the central shoot meristem cell fate during Arabidopsis embryogenesis. Plant J 17:1799-1809
43. Müller A, Guan C, Gälweiler L, Tänzler P, Huijser P, Marchant A, Parry G, Bennett M, Wisman E, Palme K (1998) AtPIN2 defines a locus of Arabidopsis for root gravitropism control. EMBO J 17:6903-6911
44. Müller AJ, Grafe R (1978) Isolation and characterization of cell lines of Nicotiana tabacum lacking nitrate reductase. Mol Gen Genet 161:67-76
45. Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453-460
46. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiol Plant 15:473-497
47. Ohira K, Ojima K, Fijiwara A (1973) Studies on the nutrition of rice cell culture. Plant Cell Physiol 14:1113-1121
48. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M (2003) The transcriptional activity of human chromosome 22. Genes Dev 17:529-540
49. Rinne PLH, Schoot C (1998) Symplastic fields in the tunica of the shoot apical meristem coordinate morphogenetic events. Development 125:1477-1485
50. Rogg LE, Lasswell J, Bartel B (2001) A gain-of-function mutation in IAA28 suppresses lateral root development. Plant Cell 13:465-480
51. Ruegger M, Dewey E, Gray WM, Hobbie L, Turner J, Estelle M (1998) The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast Grr1p. Genes Dev 12:198-207
52. Rupp HM, Frank M, Werner T, Strnad M, Schmuelling T (1999) Increased steady state mRNA levels of the STM and KNAT1 homeobox genes in cytokinin overproducing Arabidopsis thaliana indicate a role for cytokinins in the shoot apical meristem. Plant J 18:557-563
53. Sakai H, Honma T, Aoyama T, Sato S, Kato T, Tabata S, Oka A (2001) ARR1, a transcription factor for genes immediately responsive to cytokinins. Science 294:1519-1521
54. Schoot C, Rinne P (1999) Networks for shoot design. Trends Plant Sci 4:31-37
55. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3(1): [Article 3]
56. Skoog F, Miller CO (1957) Chemical regulation of growth and organ formation in plant tissues cultured in vitro. Symp Soc Exp Biol 11:118-131
57. Steeves T, Sussex I (1989) Patterns in plant development, 2nd edn. Cambridge University Press, Cambridge, NY
58. Suzuki T, Sakurai K, Imamura A, Nakamura A, Ueguchi C, Mizuno T (2000) Compilation and characterization of histindine-containing phosphotransmitters implicated in His-to Asp phosphorelay in plants: AHP signal transducers of Arabidopsis thaliana. Biosci Biotechnol Biochem 64:2486-2489
59. Takada S, Hibara K, Ishida T, Tasaka M (2001) The CUPSHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development 128:1127-1135
60. Teo W, Kumar PP, Goh CJ, Swarup S (2001) The expression of Brostm, a KNOTTED1-like gene, marks the cell type and timing of in vitro shoot induction in Brassica oleracea. Plant Mol Biol 46:567-580
61. Tian Q, Reed JW (1999) Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene. Development 126:711-721
62. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25-29
63. Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, Meinke D (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135:1206-1220
64. Ueguchi C, Koizumi H, Suzuki T, Mizuno T (2001a) Novel family of sensor histidine kinase genes in Arabidopsis thaliana. Plant Cell Physiol 42:231-235
65. Ueguchi C, Sato S, Kato T, Tabata T (2001b) The AHK4 gene involved in the cytokinin-signaling pathway as a direct receptor molecule in Arabidopsis thaliana. Plant Cell Physiol 42:751-755
66. Vollbrecht E, Veit B, Sinha N, Hake S (1991) The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature 350:241-243
67. William B, Tsang A (1991) A maize gene expressed during embryogenesis is abscisic acid- inducible and highly conserved. Plant Mol Biol 16:919-923
68. Zhang SP (1995) Efficient plant regeneration from Indica (group1) rice protoplasts of one advanced breeding line and three varieties. Plant Cell Rep 15:68-71