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How can we exploit functional genomics approaches for understanding the nature of plant defences? Barley as a case study

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Abstract

The concept ‘functional genomics’ refers to the methods used for the functional characterisation of genomes. The methods utilised provide new opportunities for studying the nature and role of defence mechanisms in plants. Unlike Arabidopsis, poplar and rice, the full genomic sequence of barley is not available. In this case, the analysis of barley gene expression data plays a pivotal role for obtaining insight into the functional characterisation of individual gene products. Many genes are activated transcriptionally following attack by pathogens and these often contribute to the defence mechanisms which underlie disease resistance. The use of large-scale complementary DNA library constructions and genome-wide transcript profiles of plants exposed to biotic stress provide the data required to drive hypotheses concerning the function of newly identified genes. In this paper, we illustrate how publicly available gene expression data has proved valid for studies of plant defence responses; enabling a cost-effective workflow starting from isolated gene transcripts to elucidation of biological function upon biotic stress.

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  1. http://pgrc.ipk-gatersleben.de/etgi/publications/whitepaper_barley_physmap_and_sequence.pdf; http://www.ars.usda.gov/research/projects/projects.htm?ACCN_NO=411452

References

  • Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., & Tasaka, M. (1997). Genes involved in organ separation in Arabidopsis: An analysis of the cup-shaped cotyledon mutant. The Plant Cell, 9, 841–857.

    Article  PubMed  CAS  Google Scholar 

  • Boddu, J., Cho, S. G., Kruger, W. M., & Muehlbauer, G. J. (2006). Transcriptome analysis of the barley–Fusarium graminearum interaction. Molecular Plant–Microbe Interactions, 19, 407–417.

    Article  PubMed  CAS  Google Scholar 

  • Boguski, M. S., & Schuler, G. D. (1995). ESTablishing a human transcript map. Nature Genetics, 10, 369–371.

    Article  PubMed  CAS  Google Scholar 

  • Caldo, R. A., Nettleton, D., Peng, J., & Wise, R. P. (2006). Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. Molecular Plant–Microbe Interactions, 19, 939–947.

    Article  PubMed  CAS  Google Scholar 

  • Caldo, R. A., Nettleton, D., & Wise, R. P. (2004). Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. The Plant Cell, 16, 2514–2528.

    Article  PubMed  CAS  Google Scholar 

  • Christensen, A. B., Thordal-Christensen, H., Zimmermann, G., Gjetting, T., Lyngkjær, M. F., Dudler, R., et al. (2004). The germinlike protein GLP4 exhibits superoxide dismutase activity and is an important component of quantitative resistance in wheat and barley. Molecular Plant–Microbe Interactions, 17, 109–117.

    Article  PubMed  CAS  Google Scholar 

  • Close, T. J., Wanamaker, S. I., Caldo, R. A., Turner, S. M., Ashlock, D. A., Dickerson, J. A., et al. (2004). A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiology, 134, 960–968.

    Article  PubMed  CAS  Google Scholar 

  • Collinge, D. B., Gregersen, P. L., & Thordal-Christensen, H. (2002). The nature and role of defence response genes in cereals. In The powdery mildews: A comprehensive treatise (pp. 146–160). St. Paul: APS.

    Google Scholar 

  • Collinge, D. B., Lund O. S., Thordal-Christensen, H. (2008) What are the prospects for genetically engineered, disease resistant plants? European Journal of Plant Pathology, (in press).

  • Douchkov, D., Nowara, D., Zierold, U., & Schweizer, P. (2005). A high-throughput gene-silencing system for the functional assessment of defense-related genes in barley epidermal cells. Molecular Plant–Microbe Interactions, 18, 755–761.

    Article  PubMed  CAS  Google Scholar 

  • Eichmann, R., Biemelt, S., Schäfer, P., Scholz, U., Jansen, C., Felk, A., et al. (2006). Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis. Journal of Plant Physiology, 163, 657–670.

    Article  PubMed  CAS  Google Scholar 

  • Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America, 95, 14863–14868.

    Article  PubMed  CAS  Google Scholar 

  • Field, B., Jordan, F., & Osbourn, A. (2006). First encounters–Deployment of defence-related natural products by plants. New Phytologist, 172, 193–207.

    Article  PubMed  CAS  Google Scholar 

  • Gjetting, T., Hagedorn, P. H., Schweizer, P., Thordal-Christensen, H., Carver, T. L. W., & Lyngkjær, M. F. (2007). Single-cell transcript profiling of barley attacked by the powdery mildew fungus. Molecular Plant–Microbe Interactions, 20, 235–246.

    Article  PubMed  CAS  Google Scholar 

  • Glazebrook, J. (2005). Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annual Review of Phytopathology, 43, 205–227.

    Article  PubMed  CAS  Google Scholar 

  • Gregersen, P. L., & Collinge, D. B. (2001). Penetration attempts by the powdery mildew fungus into barley leaves are accompanied by increased gene transcript accumulation in the epidermal cell layer. Journal of Plant Pathology, 83, 257–260.

    Google Scholar 

  • Gregersen, P. L., Collinge, D. B., & Smedegaard-Petersen, V. (1990). Early induction of new mRNAs accompanies the resistance reaction of barley to the wheat pathogen, Erysiphe graminis f.sp. tritici. Physiological and Molecular Plant Pathology, 36, 471–481.

    Article  CAS  Google Scholar 

  • Gregersen, P. L., Thordal-Christensen, H., Forster, H., & Collinge, D. B. (1997). Differential gene transcript accumulation in barley leaf epidermis and mesophyll in response to attack by Blumeria graminis f.sp. hordei (syn. Erysiphe graminis f.sp. hordei). Physiological and Molecular Plant Pathology, 51, 85–97.

    Article  CAS  Google Scholar 

  • Hammerschmidt, R. (1999). Phytoalexins: What have we learned after 60 years? Annual Review of Phytopathology, 37, 285–306.

    Article  PubMed  CAS  Google Scholar 

  • Hein, I., Campbell, E. I., Woodhead, M., Hedley, P. E., Young, V., Morris, W., et al. (2004). Characterisation of early transcriptional changes involving multiple signalling pathways in the Mla13 barley interaction with powdery mildew (Blumeria graminis f.sp. hordei). Planta, 218, 803–813.

    Article  PubMed  CAS  Google Scholar 

  • Hein, I., Barciszewska-Pacak, M., Hrubikova, K., Williamson, S., Dinesen, M., Soenderby, I. E., et al. (2005). Virus-induced gene silencing-based functional characterization of genes associated with powdery mildew resistance in barley. Plant Physiology, 138, 2155–2164.

    Article  PubMed  CAS  Google Scholar 

  • Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., et al. (2006). Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proceedings of the National Academy of Sciences of the United States of America, 103, 12987–12992.

    Article  PubMed  CAS  Google Scholar 

  • Jabs, T., & Slusarenko, A. (2000). The hypersensitive response. In A. Slusarenko, R. S. S. Fraser, & L. C. Loon (Eds.) Mechanisms of resistance to plant diseases (pp. 279–323). Dordrecht: Kluwer.

    Google Scholar 

  • Jensen, M. K., Rung, J. H., Gregersen, P. L., Gjetting, T., Fuglsang, A. T., Hansen, M., et al. (2007). The HvNAC6 transcription factor: A positive regulator of penetration resistance in barley and Arabidopsis. Plant Molecular Biology, 65, 137–150.

    Article  PubMed  CAS  Google Scholar 

  • Jørgensen, J. H. (1992). Discovery, characterization and exploitation of Mlo powdery mildew resistance in barley. Euphytica, 63, 141–152.

    Article  Google Scholar 

  • Jørgensen, J. H. (1994). Genetics of powdery mildew resistance in barley. Critical Reviews in Plant Sciences, 13, 97–119.

    Article  Google Scholar 

  • Kølster, P., Munk, L., Stølen, O., & Løhde, J. (1986). Near-isogenic barley lines with genes for resistance to powdery mildew. Crop Science, 26, 903–907.

    Google Scholar 

  • Liang, P., & Pardee, A. B. (1997). Differential display. A general protocol. Methods Molecular Biology, 85, 3–11.

    CAS  Google Scholar 

  • Lindbo, J. A., & Dougherty, W. G. (2005). Plant pathology and RNAi: A brief history. Annual Review of Phytopathology, 43, 191–204.

    Article  PubMed  CAS  Google Scholar 

  • Lu, P. L., Chen, N. Z., An, R., Su, Z., Qi, B. S., Ren, F., et al. (2006). A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis. Plant Molecular Biology, 63, 289–305.

    Article  PubMed  CAS  Google Scholar 

  • MacDiarmid, R. (2005). RNA silencing in productive virus infections. Annual Review of Phytopathology, 43, 523–544.

    Article  PubMed  CAS  Google Scholar 

  • Manners, J. M., & Scott, K. J. (1985). Reduced translatable messenger RNA activities in leaves of barley infected with Erysiphe graminis f.sp. hordei. Physiological Plant Pathology, 26, 297–308.

    Article  CAS  Google Scholar 

  • Mejlhede, N., Kyjovska, Z., Backes, G., Burhenne, K., Rasmussen, S. K., & Jahoor, A. (2006). EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley. Plant Breeding, 125, 461–467.

    Article  CAS  Google Scholar 

  • Mörschbacher, B., & Mendgen, K. W. (2000). Structural aspects of defense. In A. J. Slusarenko, R. S. S. Fraser, & L. C. van Loon (Eds.) Mechanisms of resistance to plant diseases (pp. 231–227). Dordrecht: Kluwer.

    Google Scholar 

  • Panstruga, R., & Schulze-Lefert, P. (2002). Live and let live: Insights into powdery mildew disease and resistance. Molecular Plant Pathology, 3, 495–502.

    Article  CAS  Google Scholar 

  • Ramonell, K. M., & Somerville, S. (2002). The genomics parade of defense responses: To infinity and beyond. Current Opinion in Plant Biology, 5, 291–294.

    Article  PubMed  CAS  Google Scholar 

  • Rostoks, N., Borewitz, J., Hedley, P. E., Russell, J., Mudie, S., Morris, J., et al. (2005). Single-feature polymorphism discovery in the barley transcriptome. Genome Biology, 6, R54.

    Article  PubMed  CAS  Google Scholar 

  • Schweizer, P., Pokorny, J., Schulze-Lefert, P., & Dudler, R. (2000). Double-stranded RNA interferes with gene function at the single-cell level in cereals. The Plant Journal, 24, 895–903.

    Article  PubMed  CAS  Google Scholar 

  • Shen, L. H., Gong, J., Caldo, R. A., Nettleton, D., Cook, D., Wise, R. P., et al. (2005). BarleyBase–An expression profiling database for plant genomics. Nucleic Acids Research, 33, D614–D618.

    Article  PubMed  CAS  Google Scholar 

  • Shen, Q. H., Saijo, Y., Mauch, S., Biskup, C., Bieri, S., Keller, B., et al. (2007). Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. Science, 315, 1098–1103.

    Article  PubMed  CAS  Google Scholar 

  • Shirasu, K., Nielsen, K., Piffanelli, P., Oliver, R., & Schulze-Lefert, P. (1999). Cell-autonomous complementation of mlo resistance using a biolistic transient expression system. The Plant Journal, 17, 293–299.

    Article  CAS  Google Scholar 

  • Souer, E., van Houwelingen, A., Kloos, D., Mol, J., & Koes, R. (1996). The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell, 85, 159–170.

    Article  PubMed  CAS  Google Scholar 

  • Svensson, J. T., Crosatti, C., Campoli, C., Bassi, R., Stanca, A. M., Close, T. J., et al. (2006). Transcriptome analysis of cold acclimation in barley albina and xantha mutants. Plant Physiology, 141, 257–270.

    Article  PubMed  CAS  Google Scholar 

  • Takken, F. L. W., Tameling, W. I. L., & Joosten, M. H. A. J. (2008). Molecular basis of plant disease/resistance and disease resistance proteins. European Journal of Plant Pathology, (in press).

  • Trujillo, M., Troeger, M., Niks, R. E., Kogel, K.-H., & Hückelhoven, R. (2004). Mechanistic and genetic overlap of barley host and non-host resistance to Blumeria graminis. Molecular Plant Pathology, 5, 389–396.

    Article  CAS  Google Scholar 

  • van den Berg, N., Crampton, B. G., Hein, I., Birch, P. R. J., & Berger, D. K. (2004). High-throughput screening of suppression subtractive hybridization cDNA libraries using DNA microarray analysis. Biotechniques, 37, 818–824.

    PubMed  Google Scholar 

  • van Loon, L. C., Rep, M., & Pieterse, C. M. J. (2006). Significance of inducible defense-related proteins in infected plants. Annual Review of Phytopathology, 44, 135–162.

    Article  PubMed  CAS  Google Scholar 

  • Waterhouse, P. M., Wang, M. B., & Lough, T. (2001). Gene silencing as an adaptive defence against viruses. Nature, 411, 834–842.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, H. N., Sreenivasulu, N., Weschke, W., Stein, N., Rudd, S., Radchuk, V., et al. (2004). Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant Journal, 40, 276–290.

    Article  PubMed  Google Scholar 

  • Zierold, U., Scholz, U., & Schweizer, P. (2005). Transcriptome analysis of mlo-mediated resistance in the epidermis of barley. Molecular Plant Pathology, 6, 139–151.

    Article  CAS  Google Scholar 

  • Zimmerli, L., Stein, M., Lipka, V., Schulze-Lefert, P., & Somerville, S. (2004). Host and non-host pathogens elicit different jasmonate/ethylene responses in Arabidopsis. Plant Journal, 40, 633–646.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

Authors would like to thank Drs. Patrick Schweizer for fruitful discussions and access to data. MKJ was supported by a Ph.D. scholarship from the University of Copenhagen, Faculty of Life Sciences (formerly the Royal Veterinary and Agricultural University) and research financed by a Danish Research Council grant ‘Cell specific analysis of host plant responses to pathogens using a functional genomic approach’ SJVF 23-03-0167 (to MFL and DBC). This paper is based on two oral contributions held at the EFPP conference held in Copenhagen in August 2006.

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Authors and Affiliations

  1. Department of Plant Biology, Faculty of Life Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark

    David B. Collinge, Michael K. Jensen & Jesper Rung

  2. Biosystems Department, Risoe National Laboratory, Technical University of Denmark, 4000 Roskilde, Denmark

    Michael F. Lyngkjaer

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  1. David B. Collinge
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  2. Michael K. Jensen
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Correspondence to David B. Collinge.

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Collinge, D.B., Jensen, M.K., Lyngkjaer, M.F. et al. How can we exploit functional genomics approaches for understanding the nature of plant defences? Barley as a case study. Eur J Plant Pathol 121, 257–266 (2008). https://doi.org/10.1007/s10658-008-9271-8

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