Abstract
Plants, as any other organisms, possess evolutionary old mechanisms to cope with the various stresses they are exposed to day by day. The management of stresses and their consequences requires substantial energy, which is frequently subtracted from biomass (in crops: yield). Therefore, a deeper understanding of stress biology has been, is, and will be of paramount importance for plant breeding. One goal of plant stress research centers around the transcriptome, the entirety of transcripts from expressed genes, and aims at identifying major genes in the stress management of the inflicted plant. The development of appropriate technologies to quantitatively study the transcriptomes (indeed the various sub-transcriptomes) in stressed plants and to extract biological meaning from the massive data will be demonstrated here. In particular, reduced complexity sequencing techniques such as deepSuperSAGE and MACE (massive analysis of cDNA ends) and their potential in stress biology are portrayed.
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Abbreviations
- deepSuperSAGE:
-
Serial analysis of gene expression coupled to next-generation sequencing
- MACE:
-
Massive analysis of cDNA ends.
References
Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annual Rev Plant Biol 55:373–399
Batelli G, Verslues PE, Agius F, Qiu Q, Fujii H, Pan S, Schumaker KS, Grillo S, Zhu JK (2007) SOS2 promotes salt tolerance in part by interacting with the vacuolar H+-ATPase and up-regulating its transport activity. Mol Cell Biol 27:7781–7790
Boudsocq M, Lauriere C (2005) Osmotic signaling in plants: multiple pathways mediated by emerging kinase families. Plant Physiol 138:1185–1194
Cheng NH, Pittman JK, Zhu JK, Hirschi KD (2004) The protein kinase SOS2 activates the Arabidopsis H(+)/Ca(2+) antiporter CAX1 to integrate calcium transport and salt tolerance. J Biol Chem 279:2922–2926
Dat J, Vandenabeele S, Vranova E, Van Montagu M, Inze D, Van Breusegem F (2000) Dual action of the active oxygen species during plant stress responses. Cell Mol Life Sci 57:779–795
Gadjev I, Vanderauwera S, Gechev TS, Laloi C, Minkov IN, Shulaev V, Apel K, Inze D, Mittler R, Van Breusegem F (2006) Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiol 141:436–445
Garg R, Jain M (2011) Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea. Plant Signal Behav 11:1868–70
Gong Z, Koiwa H, Cushman MA, Ray A, Bufford D, Kore-eda S, Matsumoto TK, Zhu J, Cushman JC, Bressan RA, Hasegawa PM (2001) Genes that are uniquely stress regulated in salt overly sensitive (SOS) mutants. Plant Physiol 126:363–375
Gong D, Guo Y, Schumaker KS, Zhu JK (2004) The SOS3 family of calcium sensors and SOS2 family of protein kinases in Arabidopsis. Plant Physiol 134:919–926
Gurjar GS, Giri AP, Gupta VS (2012) Gene expression profiling during wilting in chickpea caused by Fusarium oxysporum F. sp. Ciceri. Am J Plant Sci 3:190–201
Kahl G, Molina Medina C, Winter P (2011) Functional genomics. Transcriptomics for Legumes: background, tools and insights. In: Genetics, genomics and breeding of cool season grain legumes, pp 237–284
Laloi C, Apel K, Danon A (2004) Reactive oxygen signalling: the latest news. Curr Opin Plant Biol 7:323–328
Lee HK, Braynen W, Keshav K, Pavlidis P (2005) ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinforma 6:269
Liu J, Ishitani M, Halfter U, Kim CS, Zhu JK (2000) The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. Proc Natl Acad Sci U S A 97:3730–3734
Mahajan S, Pandey GK, Tuteja N (2008) Calcium- and salt-stress signaling in plants: shedding light on SOS pathway. Arch Biochem Biophys 471:146–158
Mantri NL, Ford R, Coram TE, Pang EC (2007) Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought. BMC Genomics 8:303
Martinez-Atienza J, Jiang X, Garciadeblas B, Mendoza I, Zhu JK, Pardo JM, Quintero FJ (2007) Conservation of the SOS salt tolerance pathway in rice. Plant Physiol 143(2):1001–1012
Matsumura H, Bin Nasir KH, Yoshida K, Ito A, Kahl G, Kruger DH, Terauchi R (2006) SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Meth 3:469–474
Matsumura H, Kruger DH, Kahl G, Terauchi R (2008) SuperSAGE: a modern platform for genome-wide quantitative transcript profiling. Curr Pharmaceut Biotech 9:368–374
Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krüger DH, Kahl G, Schroth GP, Terauchi R (2010) High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing. PLoS One 5(8):e12010. doi:10.1371/journal.pone.0012010
Matsumura H, Yoshida K, Luo S, Krüger DH, Kahl G, Schroth GP, Terauchi R (2011) High-throughput SuperSAGE. Meth Mol Biol 687:135–146
Matsumura H, Terauchi R, Krüger DH, Rotter B, Winter P, Kahl G (2012) deepSuperSAGE: High-throughput transcriptome sequencing with now- and next-generation sequencing technologies. In: Harbers M, Kahl G (eds) Tag-based next generation sequencing. Wiley-Blackwell, New York, pp 3–21
Millan T, Clarke H, Siddique K, Buhariwalla H, Gaur P, Kumar J, Gil J, Kahl G, Winter P (2006) Chickpea molecular breeding: new tools and concepts. Euphytica 147:81–103
Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:553–581. doi:10.1186/1471-2164-9-553
Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon J-J, Winter P, Kahl G (2011) deepSuperSAGE: The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC Plant Biol 11:31. doi:10.1186/1471-2229-11-31
Moller IM (2001) Plant mitochondria and oxidative stress: electron transport, NADPH turnover, and metabolism of reactive oxygen species. Annu Rev Plant Physiol Plant Mol Biol 52:561–591
Qiu Q-S, Guo Y, Dietrich MA, Schumaker KS, Zhu J-K (2002) Regulation of SOS1, a plasma membrane Na+/H + exchanger in Arabidopsis thaliana, by SOS2 and SOS3. Proc Natl Acad Sci USA 99:8436–8441
Quan R, Lin H, Mendoza I, Zhang Y, Cao W, Yang Y, Shang M, Chen S, Pardo JM, Guo Y (2007) SCABP8/CBL10, a putative calcium sensor, interacts with the protein kinase SOS2 to protect Arabidopsis shoots from salt stress. Plant Cell 19:1415–1431
Roorkiwal M, Sharma PC (2012) Sequence similarity based identification of abiotic stress responsive genes in chickpea. Bioinformation 8:92–97
Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273
Acknowledgements
Research of the authors was supported by funds from Deutsche Forschungsgemeinschaft (DFG grant Ka 332/22-1), Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ, project 08.7860.3-001.00), and BMBF IGSTC IND09/514. GK appreciates an invitation to contribute to the International Conference on Plant Biotechnology for Food Security: New Frontiers” on February 21–24, 2012 (ICPBFS-2012) in New Delhi and gratefully remember the kind and warm hospitality of all Indian colleagues.
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Kahl, G., Molina, C., Rotter, B. et al. Reduced representation sequencing of plant stress transcriptomes. J. Plant Biochem. Biotechnol. 21 (Suppl 1), 119–127 (2012). https://doi.org/10.1007/s13562-012-0129-y
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DOI: https://doi.org/10.1007/s13562-012-0129-y