Genes and pathways induced in early response to defoliation in rice seedlings

Current Issues in Molecular Biology

Volumn 11, Issue 2, 2009, Pages 81-100

  Chen, Shuangyan ^a   Li, Xiu Qing ^b   Zhao, Aiguo ^a,d   Wang, Lijuan ^a,d   Li, Xiaofeng ^a,d   Shi, Qingyun ^c   Chen, Ming ^c   Guo, Juan ^a,d   Zhang, Jichong ^a,d   Qi, Dongmei ^a   Liu, Gongshe ^a  

^a INSTITUTE OF BOTANY   (China)

^b FREDERICTON RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^c ZHEJIANG UNIVERSITY   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; STARCH SYNTHASE; SUCROSE; TRANSCRIPTION FACTOR;

ANAEROBIC METABOLISM; CARBOHYDRATE METABOLISM; CELL FUNCTION; CELL METABOLISM; CHEMICAL SINK; CONTROLLED STUDY; DEFOLIATION; ENERGY RESOURCE; EVOLUTIONARY ADAPTATION; GENE ACTIVITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GRAZING; HORMONAL REGULATION; MICROARRAY ANALYSIS; NONHUMAN; PLANT ANIMAL INTERACTION; PLANT DEFENSE; PLANT GENETICS; PLANT GENOME; PLANT GROWTH; PLANT METABOLISM; PLANT STRESS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RICE; SEEDLING; SIGNAL TRANSDUCTION;

BIOSYNTHETIC PATHWAYS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; ORYZA SATIVA; PLANT LEAVES; PLANT PROTEINS; SEEDLING;

EID: 70349191645     PISSN: 14673037     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (69)

1. Agarwal, S., and Grover, A. (2006) Molecular biology, biotechnology and genomics of flooding-associated low O2 stress response in plants. Crit. Rev. Plant Sci. 25, 1-21.
2. Belesky, D. P., and Hill, N. S. (1997) Defoliation and leaf age influence on ergot alkaloids in tall fescue. Ann. Bot. 79, 259-264.
3. Brueland, B. A., Harmoney, K. R., Moore, K. J., George, J. R., and Brummer, E. C. (2003) Forage and grazing lands: Developmental morphology of smooth bromegrass growth following spring grazing. Crop Sci. 43, 1789-1796.
4. Cheong, Y. H., Chang, H.-S., Gupta, R., Wang, X., Zhu, T., and Luan, S. (2002) Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis. Plant Physiol. 129, 661-677.
5. Cosgrove, D. J., Li, L. C., Cho, H. T., Hoffmann-Benning, S., Moore, R. C., and Blecker, D. (2002) The growing world of expansins. Plant Cell Physiol. 43, 1436-1444.
6. Crawley, M. J. (1990) Rabbit grazing, plant competition and seedling recruitment in acid grassland. J. Appl. Ecol. 27, 803-820.
7. Davletova, S., Schlauch, K., Coutu, J., and Mittler, R. (2005) The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol. 139, 847-856.
8. De Vos, M., Van Oosten, V. R., Van Poecke, R. M. P., Van Pelt, J. A., Pozo, M. J., Mueller, M. J., Buchala, A. J., Métraux, J. P., Van Loon, L. C., Dicke, M., and Pieterse, C. M. J. (2005) Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol. Plant-Microbe Interact. 18, 923-937.
9. Del-Val, E., and Crawley, M. J. (2005) Are grazing increaser species better tolerators than decreasers? An experimental assessment of defoliation tolerance in eight British grassland species. J. Ecol. 93, 1005-1016.
10. Detling, J. K., Dyer, M. I., and Winn, D. T. (1979) Net photosynthesis, root respiration, and regrowth of Bouteloua gracilis following simulated grazing. Oecologia 41, 127-134.
11. Donaghy, D. J., and Fulkerson, W. J. (2002) The impact of defoliation frequency and nitrogen fertilizer application in spring on summer survival of perennial ryegrass under grazing in subtropical Australia. Grass Forage Sci. 57, 351-359.
12. Ecker, J. R. (1995) The ethylene signal transduction pathway in plants. Science 268, 667-675.
13. Eulgem, T., Rushton, P. J., Robatzek, S., and Somssich, I. E. (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5, 199-206.
14. Felton, G. W., Bi, J. L., Mathews, M. C., Murphy, J. B., Korth, K., Wesley, S. V., Lamb, C., and Dixon, R. A. (1999) Cross-talk between the signal pathways for pathogen-induced systemic acquired resistance and grazing-induced insect resistance. In Novartis Foundation Symposium, Vol 223, pp 166-174.
15. Gibson, G. (2002) Microarrays in ecology and evolution: a preview. Mol. Ecol. 11, 17-24.
16. Givan, C. V. (1999) Evolving concepts in plant glycolysis: Two centuries of progress. Biol. Rev. Camb. Phil. Soc. 74, 277-309.
17. Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison. D., Martin. C., Katagiri. F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W.L., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean, R., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J., Macalma, T., Oliphant, A., and Briggs, S. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100.
18. Goffard, N., and Weiller, G. (2007) GeneBins: A database for classifying gene expression data, with application to plant genome arrays. BMC Bioinfo. 8, 87.
19. Gold, W. G., and Caldwell, M. M. (1990) The effects of the spatial pattern of defoliation on regrowth of a tussock grass - III. Photosynthesis, canopy structure and light interception. Oecologia 82, 12-17.
20. Guan, Y., and Nothnagel, E. A. (2004) Binding of Arabinogalactan Proteins by Yariv Phenylglycoside Triggers Wound-Like Responses in Arabidopsis Cell Cultures. Plant Physiol. 135, 1346-1366.
21. Hagen, G., and Guilfoyle, T. (2002) Auxin-responsive gene expression: Genes, promoters and regulatory factors. Plant Mol. Biol. 49, 373-385.
22. Heitz, T., Geoffroy, P., Fritig, B., and Legrand, M. (1991) Two apoplastic α-amylases are induced in tobacco by virus infection. Plant Physiol. 97, 651-656.
23. Hill, C. S., and Treisman, R. (1995) Transcriptional regulation by extracellular signals: Mechanisms and specificity. Cell 80, 199-211.
24. Ho, S. L., Chao, Y. C., Tong, W. F., and Yu, S. M. (2001) Sugar coordinately and differentially regulates growth- and stress-related gene expression via a complex signal transduction network and multiple control mechanisms. Plant Physiol. 125, 877-890.
25. Hua, H., Lu, Q., Cai, M., Xu, C., Zhou, D. X., Li, X., and Zhang, Q. (2007) Analysis of rice genes induced by striped stemborer (Chilo suppressalis) attack identified a promoter fragment highly specifically responsive to insect feeding. Plant Mol. Biol. 65, 519-530.
26. Hunter, T., and Karin, M. (1992) The regulation of transcription by phosphorylation. Cell 70, 375-387.
27. Jacobsen, J. V., Hanson, A. D., and Chandler, P. C. (1986) Water stress enhances expression of an a-amylase gene in barley leaves. Plant Physiol. 80, 350-359.
28. Jauregui, B. M., Celaya, R., Garcia, U., and Osoro, K. (2007) Vegetation dynamics in burnt heather-gorse shrublands under different grazing management with sheep and goats. Agroforest. Sys. 70, 103-111.
29. Jones-Rhoades, M. W., and Bartel, D. P. (2004) Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787-799.
30. Kato-Noguchi, H., Ohashi, C., and Sasaki, R. (2003) Metabolic adaptation to flooding stress in upland and lowland rice seedlings. Acta Physiol. Plant. 25, 257-261.
31. Kim, K. M., Cho, S. K., Shin, S. H., Kim, G. T., Lee, J. H., Oh, B. J., Kang, K. H., Hong, J. C., Choi, J. Y., Shin, J. S., and Chung, Y. S. (2005) Analysis of differentially expressed transcripts of fungal elicitor- and wound-treated wild rice (Oryza grandiglumis). J. Plant Res. 118, 347-354.
32. Koizuka, N., Tanaka, Y., and Morohashi, Y. (1995) Expression of alpha-amylase in response to wounding in mung bean. Planta 195, 530-534.
33. Kursteiner, O., Dupuis, I., and Kuhlemeier, C. (2003) The Pyruvate decarboxylase1 gene of Arabidopsis is required during anoxia but not other environmental stresses. Plant Physiol. 132, 968-978.
34. Lan, L., Li, M., Lai, Y., Xu, W., Kong, Z., Ying, K., Han, B., and Xue, Y. (2005) Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.). Plant Mol. Biol. 59, 151-164.
35. Li, C., and Wong, W. H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. U. S. A. 98, 31-36.
36. Li, C., and Wong, W. H. (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome biol. 2
37. Liscum, E., and Reed, J. W. (2002) Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol. Biol. 49, 387-400.
38. Maleck, K., Levine, A., Eulgem, T., Morgan, A., Schmid, J., Lawton, K. A., Dangl, J. L., and Dietrich, R. A. (2000) The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat. Genet. 26, 403-410.
39. McConn, M., Creelman, R. A., Bell, E., Mullet, J. E., and Browse, J. (1997) Jasmonate is essential for insect defense in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 94, 5473-5477.
40. McPherson, K., and Williams, K. (1998) The role of carbohydrate reserves in the growth, resilience, and persistence of cabbage palm seedlings (Sabal palmetto). Oecologia 117, 460-468.
41. Meers, T., and Adams, R. (2003) The impact of grazing by Eastern Grey Kangaroos (Macropus giganteus) on vegetation recovery after fire at Reef Hills Regional Park, Victoria. Ecol. Manage. Rest. 4, 126-132.
42. Moran, P. J., Cheng, Y., Cassell, J. L., and Thompson, G. A. (2002) Gene expression profiling of Arabidopsis thaliana in compatible plant-aphid interactions. Arch. Insect Biochem. Physiol. 51, 182-203.
43. Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., Voinnet, O., and Jones, J. D. G. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312, 436-439.
44. Nowak, R. S., and Caldwell, M. M. (1984) A test of compensatory photosynthesis in the field: Implications for herbivory tolerance. Oecologia 61, 311-318.
45. Orodho, A. B., and Trlica, M. J. (1990) Clipping and long-term grazing effects on biomass and carbohydrate reserves of Indian ricegrass. J. Range Manage. 43, 52-57.
46. Pecetti, L., and Piano, E. (2002) Penetrance of creeping-rootedness in clonal progenies of lucerne and observations on underground morphology of plants differing for this character. Euphytica 128, 35-45.
47. Reymond, P., Bodenhausen, N., Van Poecke, R. M. P., Krishnamurthy, V., Dicke, M., and Farmer, E. E. (2004) A conserved transcript pattern in response to a specialist and a generalist herbivore. Plant Cell 16, 3132-3147.
48. Reymond, P., Weber, H., Damond, M., and Farmer, E. E. (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12, 707-719.
49. Rushton, P. J., Torres, J. T., Parniske, M., Wernert, P., Hahlbrock, K., and Somssich, I. E. (1996) Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J. 15, 5690-5700.
50. Schenk, P. M., Kazan, K., Wilson, I., Anderson, J. P., Richmond, T., Somerville, S. C., and Manners, J. M. (2000) Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc. Natl. Acad. Sci. U. S. A. 97, 11655-11660.
51. Sowokinos, J. R. (2001) Biochemical and molecular control of cold-induced sweetening in potatoes. Am. J. Potato Res. 78, 221-236.
52. Stintzi, A., Weber, H., Reymond, P., Browse, J., and Farmer, E. E. (2001) Plant defense in the absence of jasmonic acid: The role of cyclopentenones. Proc. Natl. Acad. Sci. U. S. A. 98, 12837-12842.
53. Stotz, H. U., Koch, T., Biedermann, A., Weniger, K., Boland, W., and Mitchell-Olds, T. (2002) Evidence for regulation of resistance in Arabidopsis to Egyptian cotton worm by salicylic and jasmonic acid signaling pathways. Planta 214, 648-652.
54. Sunkar, R., and Zhu, J. K. (2004) Novel and stress regulated microRNAs and other small RNAs from Arabidopsis w inside box sign. Plant Cell 16, 2001-2019.
55. Takatsuji, H. (1999) Zinc-finger proteins: The classical zinc finger emerges in contemporary plant science. Plant Mol. Biol. 39, 1073-1078.
56. Thornburg, R. W., and Li, X. (1991) Wounding Nicotiana tabacum leaves causes a decline in endogenous indole-3-acetic acid. Plant Physiol. 96, 802-805.
57. Tognolli, M., Penel, C., Greppin, H., and Simon, P. (2002) Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana. Gene 288, 129-138.
58. Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 98, 5116-5121.
59. Van Poecke, R. M. P., and Dicke, M. (2004) Indirect defence of plants against herbivores: Using Arabidopsis thaliana as a model plant. Plant Biol. 6, 387-401.
60. Voelckel, C., Weisser, W. W., and Baldwin, I. T. (2004) An analysis of plant-aphid interactions by different microarray hybridization strategies. Mol. Ecol. 13, 3187-3195.
61. Vogel, J. T., Zarka, D. G., Van Buskirk, H. A., Fowler, S. G., and Thomashow, M. F. (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J. 41, 195-211.
62. Vourch', G., Russell, J., and Martin, J. L. (2002) Linking deer browsing and terpene production among genetic identities in Chamaecyparis nootkatensis and Thuja plicata (Cupressaceae). Journal of Heredity 93(5), 370-376.
63. Winkel-Shirley, B. (2002) Biosynthesis of flavonoids and effects of stress. Curr. Opin. Plant Biol. 5, 218-223.
64. Yang, D. H., Chung, B. Y., Kim, J. S., Kim, J. H., Yun, P. Y., Lee, Y. K., Lim, Y. P., and Lee, M. C. (2005) cDNA cloning and sequence analysis of the rice cinnamate-4-hydroxylase gene, a cytochrome P450-dependent monooxygenase involved in the general phenylpropanoid pathway. J. Plant Biol. 48, 311-318.
65. Yang, Z., Zhang, F., Zhu, L., and He, G. (2006) Identification of differentially expressed genes in brown planthopper Nilaparvata lugens (Hemiptera: Delphacidae) responding to host plant resistance. Bull. Entomol. Res. 96, 53-59.
66. Yuan, H., Chen, X., Zhu, L., and He, G. (2005) Identification of genes responsive to brown planthopper Nilaparvata lugens Stål (Homoptera: Delphacidae) feeding in rice. Planta 221, 105-112.
67. Yuan, J. S., Köllner, T. G., Wiggins, G., Grant, J., Degenhardt, J., and Chen, F. (2008) Molecular and genomic basis of volatile-mediated indirect defense against insects in rice. Plant J. 55, 491-503.
68. Zhang, Y., Fan, W., Kinkema, M., Li, X., and Dong, X. (1999) Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene. Proc. Natl. Acad. Sci. U. S. A. 96, 6523-6528.
69. Zhou, J. M., Trifa, Y., Silva, H., Pontier, D., Lam, E., Shah, J., and Klessig, D. F. (2000) NPR1 differentially interacts with members of the TGA/OBF family of transcription factors that bind an element of the PR-1 gene required for induction by salicylic acid. Mol. Plant-Microbe Interact. 13, 191-202.