Rice as a model for comparative genomics of plants

Annual Review of Plant Biology

Volumn 53, Issue , 2002, Pages 399-419

  Shimamoto, Ko ^a   Kyozuka, Junko ^a  

^a NONE

Author keywords

Defense; Evolution; Gene function; Reproductive development

Indexed keywords

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0037002267     PISSN: 15435008     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.arplant.53.092401.134447     Document Type: Review

References (119)

1. Ambrose BA, Lerner DR, Ciceri P, Padilla CM, Yanofsky M, Schmidt RJ. 2000. Molecular and genetic analysis of the SilkyI gene reveal conservation in floral organ specification between eudicots and monocots. Mol. Cell 5:569-79
2. Alvarez J, Guli CL, Yu X-H, Smyth DR. 1992. Terminal flower: a gene affecting inflorescence development in Arabidopsis thaliana. Plant J. 2:103-16
3. Araki T. 2000. Transition from vegetative to reproductive phase. Curr. Opin. Plant Biol. 4:63-68
4. Ashikari M, Wu J, Yano M, Sasaki T, Yoshimura A. 1999. Rice gibberellin-insensitive dwarf mutant gene Dwarf I encodes the alpha-subunit of GTP-binding protein. Proc. Natl. Acad. Sci. USA 96:10284-89
5. Bell AD. 1991. Plant Form. New York: Oxford Univ. Press
6. Bradley D, Carpenter R, Copsey L, Vincent C, Rothstein R, Coen E. 1996. Control of inflorescence architecture in Antirrhinum. Nature 379:791-97
7. Bradley D, Ratcliffe O, Vincent C, Carpenter R, Coen E. 1997. Inflorescence commitment and architecture in Arabidopsis. Science 275:80-83
8. Blumwald E, Aharon GS, Lamb C-H. 1998. Early signal transduction pathways in plant-pathogen interactions. Trends Plant Sci. 3:342-46
9. Bryan GT, Wu K-S, Farrall L, Jia Y, Hershey HP, et al. 2000. A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033-45
10. Cao H, Glazebrook J, Clarke J, Volko S, Dong X. 1997. The Arabidopsis nprI gene that controls systemic aquired resistance encodes a novel protein containing ankyrin repeats. Cell 88:57-63
11. Cao H, Li X, Dong X. 1998. Generation of broad-spectrum disease resistance by overexpression of an essential regulatory gene in systemic acquired resistance. Proc. Natl. Acad. Sci. USA 95:6531-36
12. Chern M-S, Fitzgerald HA, Yadav RC, Canlas PE, Dong X, et al. 2001. Evidence for a disease-resistance pathway in rice similar to the NPRI-mediated signaling pathway in Arabidopsis. Plant J. 27:101-13
13. Chern M-S, Canlas PE, Fitzgerald HA, Yadav RC, Dong X, et al. 2001. Components of a rice disease resistance pathway similar to the NPRI-mediated pathway in Arabidopsis. Int. Congr. Mol. Plant-Microbe Interact., 10th, Abstr. 299
14. Chin HG, Choe MS, Lee SH, Park SH, Koo JC, et al. 1999. Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. Plant J. 19:615-23
15. Chuc G, Meeley RB, Hake S. 1998. The control of maize spikelet meristem fate by the Apetala2-like gene indeterminate spikelet1. Genes Dev. 12:1145-54
16. Chung Y-Y, Kim S-R, Finkel D, Yanofsky M, An G. 1994. Early flowering and reduced apical dominance result from ectopic expression of a rice MADS box gene. Plant Mol. Biol. 26:657-65
17. Chung YY, Kim SR, Kang HG, Noh YS, Park MC, et al. 1995. Characterization of two rice MADS box genes homologous to GLOBOSA. Plant Sci. 109:45-56
18. Coen ES, Nugent JM. 1994. Evolution of flowers and inflorescences. Development Suppl.:107-16
19. Coen ES, Romero JM, Doyle S, Elliott R, Murphy G, Carpenter R. 1990. Floricaula: a homeotic gene required for flower development in Antirrhinum majus. Cell 63:1311-22
20. Dangl JL, Jones JDG. 2001. Plant pathogens and integrated defence responses to infection. Nature 411:826-33
21. Dong X. 2001. Genetic dissection of systemic acquired resistance. Curr. Opin. Plant Biol. 4:309-14
22. Enoki H, Izawa T, Kawahara M, Komatsu M, Koh S, et al. 1999. Ac as a tool for functional genomics of rice. Plant J. 19:605-13
23. Ferrandiz C, Gu Q, Martinssen R, Yanofsky MF. 2000. Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1, and CAULIFLOWER. Development 127:725-34
24. Fujisawa Y, Kato T, Iwasaki Y. 2001. Structure and function of heterotrimeric G proteins in plants. Plant Cell Physiol. 42:789-94
25. Fujisawa Y, Kato T, Ohki S, Ishikawa A, Kitano H, et al. 1999. Suppression of the heterotrimeric G protein causes abnormal morphology, including dwarfism in rice. Proc. Natl. Acad. Sci. USA 96:7575-80
26. Gocal GFW, King RW, Blundell CA, Schwartz OM, Andersen CH, Weigel D. 2001. Evolution of floral meristem identity genes. Analysis of Lolium temulentum genes related to APETALA1 and LEAFY of Arabidopsis. Plant Physiol. 125:1788-801
27. Goff SA. 1999. Rice as a model for cereal genomics. Curr. Opin. Plant Biol. 2:86-89
28. Gomez-Gomez L, Bauer Z, Boller T. 2001. Both the extracellular leucine-rich repeat domain and the kinase activity of FSL2 are required for flagellin binding and signaling in Arabidopsis. Plant Cell 13:1155-63
29. Gomez-Gomez L, Boller T. 2000. FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol. Cell 5:1003-11
30. Goto K, Kyozuka J, Bowman JL. 2001. Turning floral organs into leaves, leaves into flowers. Curr. Opin. Genet. Dev. 11:449-56
31. Greco R, Ouwerkerk PBF, Sallaud C, Kohli A, Colombo L, et al. 2001. Transposon insertional mutagenesis in rice. Plant Physiol. 125:1175-77
32. Greco R, Ouwerkerk PBF, Taal AJ, Favalli C, Beguiristain T, et al. 2001. Early and multiple Ac transposition in rice suitable for efficient insertional mutagenesis. Plant Mol. Biol. 46:215-27
33. Hamm HE. 1998. The many faces of G protein signaling. J. Biol. Chem. 273:669-72
34. He Z, Wang ZY, Li J, Zhu O, Lamb C, et al. 2000. Perception of brassinosteroids by the extracellular domain of the receptor kinase BRI1. Science 288:2360-63
35. He Z, Zhu Q, Dabi T, Li D, Weigel D, Lamb C. 2000. Transformation of rice with the Arabidopsis floral regulator LEAFY causes early beading. Transgenic Res. 9:223-27
36. Hiei Y, Ohta S, Komari T, Kumashiro T. 1994. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 6:271-82
37. Himi S, Sano R, Nishiyama T, Tanahashi T, Kato M, et al. 2001. Evolution of MADS-box gene induction by FLO/LFY genes. J. Mol. Evol. 53:387-93
38. Hirochika H, Sugimoto K, Ohtsuki Y, Tsugawa H, Kanda M. 1996. Retrotransposon office involved in mutation induced by tissue culture. Proc. Natl. Acad. Sci. USA 93:7783-88
39. Hirochika H. 2001. Contribution of the Tos17 retrotransposon to rice functional genomics. Curr. Opin. Plant Biol. 4:118-22
40. Izawa T, Miyazaki C, Yamamoto M, Terada R, Iida S, et al. 1991. Introduction and transposition of the maize transposable element Ac in rice (Oryza sativa L.). Mol. Gen. Genet. 227:391-96
41. Izawa T, Ohnishi T, Nakano T, Ishida N, Enoki H, et al. 1997. Transposon tagging in rice. Plant Mol. Biol. 35:219-29
42. Izawa T, Oikawa T, Tokutomi S, Okuno K, Shimamoto K. 2000. Phytochromes confer the photoperiodic control of flowering in rice (a short-day plant). Plant J. 22:391-99
43. Izawa T, Shimamoto K. 1996. Becoming a model plant: the importance of rice to plant science. Trends Plant Sci. 1:95-99
44. Jensen CS, Salchert K, Nielsen KK. 2001. A TERMINAL FLOWERI - like gene from perennial ryegrass involved in floral transition and axillary meristem identity. Plant Physiol. 125:1517-28
45. Jeon J, An G. 2001. Gene tagging in rice: a high throughput system for functional genomics. Plant Sci. 161:211-19
46. Jeon JS, Jang S, Nam J, Kim C, Lee S-H, et al. 2000. Leafy hull sterile 1 is a homeotic mutation in a rice MADS box gene affecting rice flower development. Plant Cell 12:871-84
47. Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, et al. 2000. T-DNA insertional mutagenesis for functional genomics of rice. Plant J. 22:561-70
48. Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B. 2000. Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J. 19:4004-14
49. Jofuku KD, den Boer BG, Van Montagu M, Van Montagu Okamuro. 1994. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6:1211-25
50. Kang HG, Jeon J-S, Lee S, An G. 1998. Identification of class B and class C organ identity genes from rice plants. Plant Mol. Biol. 38:1021-29
51. Kang HG, Noh YS, Chung YY, Costa M, An K, An G. 1995. Phenotypic alterations of petals and sepals by ectopic expression of a rice MADS box gene in tobacco. Plant Mol. Biol. 29:1-10
52. Kawasaki T, Henmi K, Ono E, Hatakeyama S, Iwano M, et al. The small GTP-binding protein Rac is a regulator of cell death in plants. Proc. Natl. Acad. Sci. USA 96:10922-26
53. Kempin SA, Savidge B, Yanofsky MF. 1995. Molecular basis of the cauliflower phenotype in Arabidopsis. Science 267:522-25
54. 1) in relation to penetration and growth of Pyricularia oryzae. Can. J. Bot. 72:1463-77
55. Komari T, Hiei Y, Ishida Y, Kumashiro T, Kubo T. 1998. Advances in cereal gene transfer. Curr. Opin. Plant Biol. 1:161-65
56. Komatsu M, Maekawa M, Shimamoto K, Kyozuka J. 2001. The LAXI and FRIZZY PANICLE2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development. Dev. Biol. 231:364-73
57. Kyozuka J, Kobayashi T, Morita M, Shimamoto K. 2000. Spatially and temporally regulated expression of rice MADS box genes with similarity to Arabidopsis class A, B, C genes. Plant Cell Physiol. 41:710-18
58. Kyozuka J, Konishi S, Nemoto K, Izawa T, Shimamoto K. 1998. Down-regulation of RFL, the FLO/LFY homolog of rice, accompanied with panicle branch initiation. Proc. Natl. Acad. Sci. USA 95:1979-82
59. Lawton-Rauh AL, Alvarez-Buylla ER, Purugganan MD. 2000. Molecular evolution of flower development. Trends Ecol. Evol. 15:144-49
60. Liljegren S, Gustafson-Brown C, Pinyopich A, Ditta GS, Yanofsky MF. 1999. Interactions among APETALA1, LEAFY, and TERMINAL FLOWER1 specify meristem fate. Plant Cell 11:1007-18
61. Lim J, Moon YH, An G, Jang SK. 2000. Two rice MADS domain proteins interact with OsMADS1. Plant Mol. Biol. 44:513-27
62. Ma H. 1998. To be, or not to be, a flower - control of floral meristem identity. Trends Genet. 14:26-32
63. Mandel MA, Bowman JL, Kempin SA, Ma H, Meyerowitz EM, Yanofsky MF. 1992. Manipulation of flower structure in transgenic tobacco. Cell 71:133-43
64. Mandel MA, Gustafson-Brown C, Savidge B, Yanofsky MF. 1992. Molecular characterization of the Arabidopsis floral hopmeotic gene APETALA1. Nature 360:273-77
65. Matsumoto T, Wu J, Baba T, Katayose Y, Yamamoto K, et al. 2001. Rice genomics: current status of genome sequencing. Novartis Found. Symp. 236:28-36
66. McSteen P, Laudencia-Chingcuanco D, Colasanti J. 2000. A floret by any other name: control of meristem identity in maize. Trends Plant Sci. 5:61-66
67. Mena M, Ambrose BA, Meeley RB, Briggs SP, Yanofsky M, Schmidt RJ. 1996. Diversification of C-function activity in maize flower development. Science 274:1537-40
68. Mena M, Mandel MA, Lerner DR, Yanofsky MF, Schmidt RJ. 1995. A characterization of the MADS-box gene family in maize. Plant J. 8:845-54
69. Midoh N, Iwata M. 1997. Cloning and characterization of a probenazole-inducible gene for an intracellular pathogenesis-related protein in rice. Plant Cell Physiol. 37:9-18
70. Mizukami Y, Ma H. 1992. Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity. Cell 71:119-31
71. Molinero-Rosales N, Jamilena M, Zurita S, Gomez P, Capel J, Lozano R. 1999. FALSIFLORA, the tomato orthologue of FLORICAULA and LEAFY, controls flowering time and floral meristem identity. Plant J. 20:685-93
72. Moon YH, Jung JY, Kang HG, An G. 1999. Identification of a rice APETALA3 homologue by yeast two-hybrid screening. Plant Mol. Biol. 40:167-77
73. Moon YH, Kang HG, Jung JY, Jeon JS, Sung SK, An G. 1999. Determination of the motif responsible for interaction between the rice APETALA1/AGAMOUS-like nine family proteins using yeast two-hybrid system. Plant Physiol. 120:1193-204
74. Muramoto T, Kohchi T, Yokota A, Hwang I, Goodman HM. 1999. The Arabidopsis photomorphogenic mutant hy1 is deficient in phytochrome chromophore biosynthesis as a result of a mutation in a plastid heme oxygenase. Plant Cell 11:335-47
75. Nakagawa Y, Machida C, Machida Y, Toriyama K. 2000. Frequency and pattern of transposition of the maize transposable element Ds in transgenic rice plants. Plant Cell Physiol. 41:733-42
76. Ng M, Yanofsky MF. 2001. Function and evolution of the plant MADS-box gene family. Nat. Rev. 2:186-95
77. Okamoto H, Matsui M, Deng XW. 2001. Overexpression of the heterotrimeric G-protein α-subunit enhances phytochrome-mediated inhibition of hypocotyls elongation in Arabidopsis. Plant Cell 13:1639-51
78. Ono E, Wong H-L, Kawasaki T, Hasegawa M, Kodama O, et al. 2001. Essential role of the small GTPase Rac in disease resistance of rice. Proc. Natl. Acad. Sci. USA 98:759-64
79. Park J, Choi HJ, Lee S, Lee T, Yang Z, et al. 2000. Rac-related GTP-binding protein in elicitor-induced reactive oxygen generation by suspension-cultured soybean cells. Plant Physiol. 124:725-32
80. Pidkowich MS, Klenz JE, Haughn GW, 1999. The making of a flower: control of floral meristem identity in Arabidopsis. Trends Plant Sci. 4:64-70
81. Potikha TS, Collins CC, Johnson DI, Delmer DP, Levine A. 1999. The involvement of hydrogen peroxide in the differentiation of secondary walls in cotton fibers. Plant Physiol. 119:849-58
82. Putterill J, Robson F, Lee K, Simon R, Coupland G. 1995. The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zincfinger transcription factors. Cell 80:847-57
83. Ratcliff F, Martin-Hernandez AM, Baulcombe DC. 2001. Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J. 25:237-45
84. Ratcliffe OJ, Amaya I, Vincent CA, Rothstein S, Carpenter R, et al. 1998. A common mechanism controls the life cycle and architecture of plants. Development 124:1609-15
85. Ronald PC. 1997. The molecular basis of disease resistance in rice. Plant Mol. Biol. 35:179-86
86. Schiene K, Puhler A, Niehaus K. 2000. Transgenic tobacco plants that express an antisense construct derived from a Medicago sativa cDNA encoding a Rac-related small GTP-binding protein fail to develop necrotic lesions upon elicitor infiltration. Mol. Gen. Genet. 263:761-70
87. Schmidt RJ, Ambrose BA. 1998. The blooming of glass flower development. Curr. Opin. Plant Biol. 1:60-67
88. Schmidt RJ, Veit B, Mandel MA, Mena M, Hake S, Yanofsky M. 1993. Identification and molecular characterization of ZAGI, the maize homolog of the Arabidopsis floral homeotic gene AGAMOUS. Plant Cell 5:729-37
89. Schweizer P, Schlagenhauf E, Schaffrath U, Dudler R. 1999. Different patterns of host genes are induced in rice by Pseudomonas syringae, a biological inducer of resistance, and the chemical inducer benzothiadiazole (BTH). Eur. J. Plant Pathol. 105:659-65
90. Shannon S, Meeks-Wagner R. 1991. A mutation in the Arabidopsis TFLI gene affects inflorescence meristem development. Plant Cell 3:877-92
91. Shimamoto K, Miyazaki C, Hashimoto H, Izawa T, Itoh K, et al. 1993. Transactivation and stable integration of the maize transposable element Ds cotransfected with the Ac transposase gene in transgenic rice plants. Mol. Gen. Genet. 239:354-60
92. Shinozuka Y, Kojima S, Shomura A, Ichimura H, Yano M, et al. 1999. Isolation and characterization of rice MADS box gene homologues and their RFLP mapping. DNA Res. 6:123-29
93. Silverman P, Seskar M, Kanter D, Schweizer P, Metraux J-P. 1995. Salicylic acid in rice: biosynthesis, conjugation, and possible role. Plant Physiol. 108:633-39
94. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, et al. 1995. A receptor-kinase - like protein encoded by the rice disease resistance gene Xa21. Science 270:1804-6
95. Souer E, van der Krol A, Kloos A, Bliek M, Mol J, Koes R. 1998. Genetic control of branching pattern and floral identity during Petunia inflorescence development. Development 125:733-42
96. Sugano S, Andronis C, Ong MS, Green RM, Tobin M. 1999. The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis. Proc. Natl. Acad. Sci. USA 96:12362-66
97. Takahashi A, Kawasaki T, Henmi K, Shii K, Kodama O, et al. 1999. Lesion-mimic mutants of rice with alterations in early signaling events of defense. Plant J. 17:535-45
98. Takahashi Y, Shomura A, Sasaki T, Yano M. 2001. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the subunit of protein kinase CK2. Proc. Natl. Acad. Sci. USA 98:7922-27
99. Ueguchi-Tanaka M, Fujisawa Y, Kobayahi M, Ashikari M, Iwasaki Y, et al. 2000. Rice dwarf mutant d1, which is defective in the alpha subunit of the heterotrimeric G protein, affects gibberellin signal transduction. Proc. Natl. Acad. Sci. USA 97:11638-43
100. Ullah H, Chen J-G, Young JC, Im K-H, Sussman MR, et al. 2001. Modulation of cell proliferation by heterotrimeric G protein in Arabidopsis. Science 292:2066-69
101. Valster AH, Hepler PK, Chernoff J. 2000. Plant GTPases: the Rhos in bloom. Trends Cell Biol. 10:141-46
102. Wang G-L, Leung H. 2000. Molecular biology of host-pathogen interactions in rice disease. In Molecular Biology of Rice, ed. K Shimamoto, pp. 201-32. Tokyo, Japan: Springer-Verlag
103. Wang X-Q, Ullah H, Jones AM, Assmann SM. 2001. G protein regulation of ion channels and abscisic acid signaling in Arabidopsis guard cells. Science 292:2070-72
104. Wang Z-X, Yano M, Yamanouchi U., Iwamoto M, Monna L, et al. 1999. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J. 19:55-64
105. Wang ZY, Tobin EM. 1998. Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED I (CCAI) gene disrupts circadian rhythms and suppresses its own expression. Cell 93:1207-17
106. Webering F. 1989. Morphology of Flowers and Inflorescences. New York: Cambridge Univ. Press. 405 pp.
107. Weigel D. 1995. The genetics of flower development: from floral induction to ovule morphogenesis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 29:19-39
108. Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM. 1992. LEAFY controls floral meristem identity in Arabidopsis. Cell 69:843-59
109. Weigel D, Nilsson O. 1995. A developmental switch sufficient for flower initiaiton in diverse plants. Nature 377:495-500
110. Winge P, Brembu T, Kristensen R, Bones AM. 2000. Genetic structure and evolution of RAC-GTPases in Arabidopsis thaliana. Genetics 156:1959-71
111. Yang Y, Qi M. 2001. Anti-oxidative role of salicylic acid in rice plants. Int. Congr. Mol. Plant-Microbe Interact., 10th, Abstr. 195
112. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, et al. 2000. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473-83
113. Yanofsky MF. 1995. Floral meristems to floral organs: genes controlling early events in Arabidopsis flower development. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:167-88
114. Yanofsky MF, Bowman JL, Drews G, Feldmann K, Meyerowitz EM. 1990. The protein encoded by the Arabidopsis homeotic gene AGAMOUS resembles transcription factors. Nature 346:35-39
115. Yazaki J, Kishimoto N, Nakamura K, Fujii F, Shimbo K, et al. 2000. Embarking on rice functional genomics via cDNA microarray: use of 3′ UTR probes for specific gene expression analysis. DNA Res. 7:367-70
116. Yin Z, Chen J, Zeng L, Goh L, Leung H, et al. 2000. Characterizing rice lesion mimic mutants and identifying a mutant with a broad-spectrum resistance to rice blast and bacterial blight. Mol. Plant-Microbe Interact. 13:869-76
117. Yokoo M, Okuno K. 1993. Genetic analysis of earliness mutations induced in rice cultivar Norin 8. Jpn. J. Breed. 43:1-11
118. Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, et al. 1998. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc. Natl. Acad. Sci. USA 95:1663-68
119. Zhu T, Wang X. 2000. Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol. 124:1472-76