Abstract
Among the open-ended techniques for identifying differentially expressed genes in response to stress, the PCR-based suppression subtraction hybridization (SSH) is widely used. The popularity of this technique stems from the ease of conducting this procedure in any laboratory set up for basic molecular biology research. Further, the availability of a comprehensive kit for conducting suppression subtractions from BD Biosciences has made this technique easy to adapt and adopt to any biological system. In this chapter we describe in detail the SSH procedure and explain the subtle changes that have been incorporated to make this technique adaptable for identifying stress-responsive genes in plants.
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References
Agarwal, P.K., Agarwal, P., Reddy, M.K., and Sopory, S.K. (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25, 1263–1274.
Chen, W.J., and Zhu, T. (2004) Networks of transcription factors with roles in environmental stress response. Trends Plant Sci 9, 591–596.
Chinnusamy, V., Schumaker, K., and Zhu, J.K. (2004) Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J Exp Bot 55, 225–236.
Umezawa, T., Fujita, M., Fujita, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotechnol 17, 113–122.
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.
Green, C.D., Simons, J.F., Taillon, B.E., and Lewin, D.A. (2001) Open systems: panoramic views of gene expression. J Immunol Methods 250, 67–79.
Liang, P., and Pardee, A.B. (1992) Differential Display of Eukaryotic Messenger-RNA by Means of the Polymerase Chain Reaction. Science 257, 967–971.
Gabriels, S.H., Takken, F.L., Vossen JH, et al. (2006) CDNA-AFLP combined with functional analysis reveals novel genes involved in the hypersensitive response. Mol Plant Microbe Interact 19, 567–576.
Velculescu, V.E., Zhang, L., Vogelstein, B., Kinzler, K.W. (1995) Serial Analysis of Gene-Expression. Science 270, 484–487.
Brenner, S., Johnson, M., Bridgham, J., et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotech 18, 630–634.
Hara, E., Kato, T., Nakada, S., Sekiya, S., and Oda, K. (1991) Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells. Nucleic Acids Res. 19, 7097–7104.
Hedrick, S.M., Cohen, D.I., Nielsen, E.A., Davis, M.M. (1984) Isolation of cDNA clones encoding T cell-specific membrane-associated proteins. Nature 308, 149–153.
Sargent, T.D., and Dawid, I.B. (1983) Differential gene expression in the gastrula of Xenopus laevis. Science 222, 135–139.
Diatchenko, L., Lau, Y.F.C., Campbell. A.P, et al. (1996) Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA, 93, 6025–6030.
Gurskaya, N.G., Diatchenko, L., Chenchik, A., et al. (1996) Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: Cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal Biochem 240, 90–97.
Mahalingam, R., Gomez-Buitrago, A., Eckardt, N, et al. (2003) Characterizing the stress/defense transcriptome of Arabidopsis. Genome Biol 4, R20.
Puckette, M., Peal, L., Steele, J., Tang, Y., and Mahalingam, R. (2009) Ozone responsive genes in Medicago truncatula: Analysis by suppression subtraction hybridization. J Plant Physiol. 166, 1284–1295.
Tomkins, J. P., Mahalingam, R., Smith, H., Goicoechea., J. L., Knap, H. T., and Wing R. A. (1999) A bacterial artificial chromosome library for soybean PI 437654 and identification of clones associated with cyst nematode resistance. Plant Mol Biol. 41, 25–32.
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This work was partially supported by the Oklahoma Agricultural Experiment Station (Project No. 2528).
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Peal, L., Puckette, M., Mahalingam, R. (2010). Identification of Stress-Responsive Genes in Plants Using Suppression Subtraction Hybridization: Ozone Stress as an Example. In: Sunkar, R. (eds) Plant Stress Tolerance. Methods in Molecular Biology, vol 639. Humana Press. https://doi.org/10.1007/978-1-60761-702-0_9
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DOI: https://doi.org/10.1007/978-1-60761-702-0_9
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