Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray

Molecules and Cells

Volumn 26, Issue 6, 2008, Pages 595-605

  Lee, Sang Choon ^a   Lim, Myung Ho ^a   Kim, Jin A ^a   Lee, Soo In ^a   Kim, Jung Sun ^a   Jin, Mina ^a   Kwon, Soo Jin ^a   Mun, Jeong Hwan ^a   Kim, Yeon Ki ^b   Kim, Hyun Uk ^a   Hur, Yoonkang ^c   Park, Beom Seok ^a  

^a National Institute of Animal Science   (South Korea)

^b Genomics Genetics Institute   (South Korea)

^c Chungnam National University   (South Korea)

Author keywords

Abiotic stress; Brassica rapa; Microarray; Transcriptome

Indexed keywords

OLIGONUCLEOTIDE; SODIUM CHLORIDE; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ABIOTIC STRESS; ARTICLE; COLD; CONTROLLED STUDY; DROUGHT; GENE CONSTRUCT; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN MICROARRAY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; TURNIP; UNINDEXED SEQUENCE;

BRASSICA RAPA; COLD TEMPERATURE; DROUGHTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SODIUM CHLORIDE; STRESS, PHYSIOLOGICAL;

BRASSICA; BRASSICA RAPA;

EID: 63449139874     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (57)

1. Ashraf, M., and McNeilly, T. (1990). Responses of four Brassica species to sodium chloride. Environ. Exp. Bot. 30, 475-487.
2. Breton, G., Danyluk, J., Charron, J.B., and Sarhan, F. (2003). Expression profiling and bioinformatic analyses of a novel stress-regulated multispanning transmembrane protein family from cereals and Arabidopsis. Plant Physiol. 132, 64-74.
3. Capel, J., Jarillo, J.A., Salinas, J., and Martínez-Zapater, J.M. (1997). Two homologous low-temperature-inducible genes from Arabidopsis encode highly hydrophobic proteins. Plant Physiol. 115, 569-576.
4. Carlsson, J., Lagercrantz, U., Sundstrom, J., Teixeira, R., Wellmer, F., Meyerowitz, E.M., and Glimelius, K. (2007). Microarray analysis reveals altered expression of a large number of nuclear genes in developing cytoplasmic male sterile Brassica napus flowers. Plant J. 49, 452-462.
5. Doyle, M.R., Davis, S.J., Bastow, R.M., McWatters, H.G., Kozma-Bognar, L., Nagy, F., Millar, A.J., and Amasino, R.M. (2002). The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419, 74-77.
6. Eguchi, T., Matsumura, T., and Koyama, T. (1963). The effect of low temperature on flower and seed formation in Japanese radish and Chinese cabbage. Proc. Am. Soc. Hort. Sci. 82, 322-331.
7. Fahey, J.W., and Talalay, P. (1995). The role of crucifers in cancer chemoprotection. In Phytochemicals and Health, D.L. Gustin and H.E. Flores, eds. (Rockville, USA: American Society of Plant Physiologists), pp. 87-93.
8. Fei, H., Tsang, E., and Cutler, A.J. (2007). Gene expression during seed maturation in Brassica napus in relation to the induction of secondary dormancy. Genomics 89, 419-428.
9. Francois, L.E. (1994). Growth, seed yield and oil content of canola grown under saline conditions. Argon. J. 86, 233-237.
10. Fujita, M., Fujita, Y., Maruyama, K., Seki, M., Hiratsu, K., Ohme-Takagi, M., Tran, L.S., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2004). A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J. 39, 863-876.
11. Gao, M.J., Allard, G., Byass, L., Flanagan, A.M., and Singh, J. (2002). Regulation and characterization of four CBF transcription factors from Brassica napus. Plant Mol. Biol. 49, 459-471.
12. Gomez-Campo, C., and Prakash, S. (1999). Origin and domestication. In Biology of Brassica Coenospecies, C. Gomez-Campo, ed. (Amsterdam: Elsevier), pp. 33-58.
13. Hegedus, D., Yu, M., Baldwin, D., Gruber, M., Sharpe, A., Parkin, I., Whitwill, S., and Lydiate, D. (2003). Molecular characterization of Brassica napus NAC domain transcriptional activators induced in response to biotic and abiotic stress. Plant Mol. Biol. 53, 383-397.
14. Heintzen, C., Melzer, S., Fischer, R., Kappeler, S., Apel, K., and Staiger, D. (1994). A light- and temperature-entrained circadian clock controls expression of transcripts encoding nuclear proteins with homology to RNA-binding proteins in meristematic tissue. Plant J. 5, 799-813.
15. Heintzen, C., Nater, M., Apel, K., and Staiger, D. (1997). AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 94, 8515-8520.
16. Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., and Xiong, L. (2006). Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc. Natl. Acad. Sci. USA 103, 12987-12992.
17. Ingram, J., and Bartels, D. (1996). The molecular basis of dehydration tolerance in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 277-403.
18. IPCC (Intergovernmental Panel on Climate Change) (2007). Climate change 2007: climate change impacts, adaptation and vulnerability. In Summary for Policymakers. IPCC Working Group II, ed. pp. 1-22.
19. Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15.
20. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and Harter, K. (2007). The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50, 347-363.
21. Kim, S.J., Moon, J., Lee, I., Maeng, J., and Kim, S.R. (2003). Molecular cloning and expression analysis of a CONSTANS homologue, PnCOL1, from Pharbitis nil. J. Exp. Bot. 54, 1879-1887.
22. Kimura, M., Yamamoto, Y.Y., Seki, M., Sakurai, T., Sato, M., Abe, T., Yoshida, S., Manabe, K., Shinozaki, K., and Matsui, M. (2003). Identification of Arabidopsis genes regulated by high light-stress using cDNA microarray. Photochem. Photobiol. 77, 226-233.
23. Lee, S., and Yun, S.C. (2006). The ozone stress transcriptome of pepper (Capsicum annuum L.). Mol. Cells 21, 197-205.
24. Li, F., Wu, X., Tsang, E., and Cutler, A.J. (2005). Transcriptional profiling of imbibed Brassica napus seed. Genomics 86, 718-730.
25. Merlot, S., Gosti, F., Guerrier, D., Vavasseur, A., and Giraudat, J. (2001). The ABI1 and ABI2 protein phosphatases 2C act in a negative feedback regulatory loop of the abscisic acid signalling pathway. Plant J. 25, 295-303.
26. Morinaga, T. (1933). Interspecific hybridisation in Brassica. 5. The cytology of F1 hybrid of B. carinata and B. alboglabra. Jpn. J. Bot. 6, 467-475.
27. Morinaga, T. (1934). Interspecific hybridisation in Brassica: 6. The cytology of B. carinata and B. alboglabra Cytologia 6, 62-67.
28. Munshi, S.K., Bhatia, N., Dhillon, K.S., and Sukhija, P.S. (1986). Effect of moisture and salt stress on oil filling in Brassica napus seeds. Proc. Indian Natl. Sci. Acad. B52, 755-759.
29. Nakashima, K., Tran, L.S., Van Nguyen, D., Fujita, M., Maruyama, K., Todaka, D., Ito, Y., Hayashi, N., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007). Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J. 51, 617-630.
30. O'Neill, C.M., and Bancroft, I. (2000). Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J. 23, 233-243.
31. Orr, W., lu, B., White, T.C., Robert, L.S., and Singh, J. (1992). Complementary DNA sequence of a low temperature-induced Brassica napus gene with homology to the Arabidopsis thaliana kinlgene. Plant Physiol. 98, 1532-1534.
32. Rabbani, M.A., Maruyama, K., Abe, H., Khan, M.A., Katsura, K., Ito, Y., Yoshiwara, K., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2003). Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol. 133, 1755-1767.
33. Rana, D., van den Boogaart, T., O'Neill, C.M., Hynes, L., Bent, E., Macpherson, L., Park, J.Y., Lim, Y.P., and Bancroft, I. (2004). Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J. 40, 725-733.
34. RDA (Rural Development Administration) (2007). Culture plan of principal horticultural crops (Suwon, South Korea: RDA).
35. Rensink, W.A., Iobst, S., Hart, A., Stegalkina, S., Liu, J., and Buell, C.R. (2005). Gene expression profiling of potato responses to cold, heat, and salt stress. Funct. Integr. Genomics 5, 201-207.
36. Schultz, T.F., Kiyosue, T., Yanovsky, M., Wada, M., and Kay, S.A. (2001). A role for LKP2 in the circadian clock of Arabidopsis. Plant Cell 13, 2659-2670.
37. Seki, M., Narusaka, M., Ishida, J., Nanjo, T., Fujita, M., Oono, Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., et al. (2002). Monitoring the expression profiles of 7000 Arabidopsus genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J. 31, 279-292.
38. Shin, D.H., In, J.G., Lim, Y.P., Hasunuma, K., and Choi, K.S. (2004). Molecular cloning and characterization of nucleoside diphosphate (NDP) kinases from Chinese cabbage Brassica campestris. Mol. Cells 17, 86-94.
39. Shinozaki, K., Yamaguchi-Shinozaki, K., and Seki, M. (2003). Regulatory network of gene expression in the drought and cold stress responses. Curr. Opin. Plant Biol. 6, 410-417.
40. Söderman, E., Mattsson, J., and Engström, P. (1996). The Arabidopsis homeobox gene ATHB-7 is induced by water deficit and by abscisic acid. Plant J. 10, 375-381.
41. Soeda, Y., Konings, M.C., Vorst, O., van Houwelingen, A.M., Stoopen, G.M., Maliepaard, C.A., Kodde, J., Bino, R.J., Groot, S.P., and van der Geest, A.H. (2005). Gene expression programs during Brassica oleracea seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level. Plant Physiol. 137, 354-368.
42. Takeuchi, T., Watanabe, Y., Takano-Shimizu, T., and Kondo, S. (2006). Roles of jumonji and jumonji family genes in chromatin regulation and development. Dev. Dyn. 235, 2449-2459.
43. Talamè, V., Oztuk, N.Z., Bohnert, H.J., and Tuberosa, R. (2006). Barley transcript profiles under dehydration shock and drought stress treatments: a comparative analysis. J. Exp. Bot. 58, 229-240.
44. Tang, D., Qian, H., Yu, S., Cao, Y., Liao, Z., Zhao, L., Sun, X., Huang, D., and Tang, K. (2004). cDNA cloning and characterization of a new stress-responsive gene BoRS1 from Brassica oleracea var. Physiol. Planta 121, 578-585.
45. Thomashow, M.F. (1999). Plant cold acclimation: Freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50, 571-599.
46. Tran, L.S., Nakashima, K., Sakuma, Y., Simpson, S.D., Fujita, Y., Maruyama, K., Fujita, M., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2004). Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16, 2481-2498.
47. U, N. (1935). Genomic analysis of Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot. 7, 389-452.
48. Weretilnyk, E., Orr, W., White, T.C., Iu, B., and Singh, J. (1993). Characterization of three related low-temperature-regulated cDNAs from winter Brassica napus. Plant Physiol. 101, 171-177.
49. Workman, C., Jensen, L.J., Jarmer, H., Berka, R., Gautier, L., Nielser, H.B., Saxild, H.H., Nielsen, C., Brunak, S., and Knudsen, S. (2002). A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol. 3, research0048.1-0048.16.
50. Xiong, L., Schumaker, K.S., and Zhu, J.K. (2002). Cell signaling during cold, drought, and salt stress. Plant Cell 14, Suppl S165-183.
51. Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006). Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu. Rev. Plant Biol. 57, 781-803.
52. Yang, K.A., Lim, C.J., Hong, J.K., Jin, Z.L., Hong, J.C., Yun, D.J., Chung, W.S., Lee, S.Y., Cho, M.J., and Lim, C.O. (2005). Identification of Chinese cabbage genes up-regulated by prolonged cold by using microarray analysis. Plant Sci. 169, 959-966.
53. Yang, T.J., Kim, J.S., Kwon, S.J., Lim, K.B., Choi, B.S., Kim, J.A., Jin, M., Park, J.Y., Lim, M.H., Kim, H.I., et al. (2006). Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica napus. Plant Cell 18, 1339-1347.
54. Yin, H., Li, S., Zhao, X., Du, Y., and Ma, X. (2006). cDNA microarray analysis of gene expression in Brassica napus treated with oligochitosan elicitor. Plant Physiol. Biochem. 44, 910-916.
55. + antiporters in the salt stress response. Plant J. 30, 529-539.
56. Yu, L.X., and Setter, T.L. (2003). Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit. Plant Physiol. 131, 568-582.
57. Zhao, T.J., Sun, S., Liu, Y., Liu, J.M., Liu, Q., Yan, Y.B., and Zhou, H.M. (2006). Regulating the drought-responsive element (DRE)-mediated signaling pathway by synergic functions of trans-active and trans-inactive DRE binding factors in Brassica napus. J. Biol. Chem. 281, 10752-10759.