ARABIDOPSIS MICROARRAYS TO STUDY PLANT-PATHOGEN INTERACTIONS

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Introduction

Plant diseases represent a major threat to the human food source globally. Efforts to curb such diseases have involved control measures such as using suppressive soils, alteration of farming practices, treating plants with chemical sprays and classical breeding to produce varieties with enhanced tolerance or resistance against the disease (Agrios, 1997). An integrative approach, which incorporates several methods of control, has been recognised as most successful in curbing disease incidence. Progress towards producing resistant or tolerant plant varieties has been accelerated by the availability of genomic tools; in particular, the adoption of Arabidopsis thaliana as a model plant.
Various plant pathogens are also virulent on Arabidopsis, providing a model to conduct pathogenicity tests. Such studies in Arabidopsis and other plant species have shown that plants have a sophisticated and complex immune system reminiscent of the animal immune system involving receptors, signalling pathways and the activation of antimicrobial and antifungal proteins for protection (reviewed in Jones and Dangl, 2006). It is expected that by elucidating these defences, genes involved in resistance or susceptibility can be identified. The long-term goal is that orthologues of these genes can be identified in the more important crop plants and targeted for genetic modification or in breeding programs for crop improvement.
The particular pathogen discussed in this study is the bacterial wilt bacterium Ralstonia solanacearum. The pathogen has a wide host range and as such presents a problem worldwide. This review focuses on the epidemiology, molecular and genetic characteristics of the pathogen and efforts towards determining resistance against the pathogen. The current knowledge regarding the plant defence response deemed most pertinent to this study is presented. Information on the application of microarray expression profiling and tools for data mining are also provided in this review.

Host Range and Epidemiology

R. solanacearum infects over 200 plant species representing more than 50 plant families. Hosts include solanaceous crops such as tobacco, tomato, potato and eggplant (Agrios, 1997), leguminous plants such as groundnut and French bean (Genin and Boucher, 2002), and in monocotyledonous plants, such as banana, the pathogen causes Moko disease. R. solanacearum also causes bacterial wilt disease on several shrub and tree species such as cashew, mulberry, olive (He et al., 1983; Shiomi et al., 1989) and Eucalyptus. Eucalyptus was initially reported as a host in Brazil and China but is currently also a host of the pathogen in Australia and Africa i.e. South African and Uganda (Hayward, 1991; Hayward et al., 1994; Coutinho et al., 2000; Roux et al., 2001).
The severity of the disease in Africa may be underestimated as a limited number of Eucalyptus plantations have been surveyed. There is a discrepancy in the distribution of bacterial wilt on specific hosts i.e. bacterial wilt may pose a problem on a certain host in one geographic location, and be absent from the same host in another location. This suggests that a combination of environmental factors conducive to disease incidence is necessary for R. solanacearum prevalence on a particular host (Hayward, 1991). R. solanacearum has the ability to survive in the soil in the absence of a host for extended periods as well as in the protected niche of a weed’s rhizosphere (Hayward, 1991).
High soil moisture in well-drained soils is conducive to R. solanacearum survival, however, its survival in the soil is temperature dependent. A high day temperature of 40o C maintained for more than four hours has been shown to reduce bacterial populations (van Elsas et al., 2000) although an increase in ambient temperature between 30-35o C has been correlated with an increase in disease incidence and rate of onset of bacterial wilt on hosts such as tomato (Hayward, 1991). Some soil types suppress the pathogen as the soil moisture determines the antagonistic population levels, which compete with R. solanacearum. Nematode infestation (Meloidogyne species) also contributes to spread of the disease. This is thought to be primarily a result of the increase in wounding of plants by the nematodes, which promotes bacterial infection, however, the nematode may also modify plant tissue making it suitable for bacterial invasion (Hayward, 1991).

TABLE OF CONTENTS :

• ACKNOWLEDGEMENTS
• PREFACE
• SUMMARY
• ABBREVIATIONS
• CHAPTER LITERATURE REVIEW
  • 1.1. INTRODUCTION
  • 1.2. RALSTONIA SOLANACEARUM
  • 1.3. ARABIDOPSIS THALIANA
  • 1.4. PLANT DEFENCE RESPONSE
  • 1.5. THE ARABIDOPSIS- RALSTONIA PLANT-PATHOGEN INTERACTION
  • 1.6. MICROARRAYS
  • 1.7. ARABIDOPSIS MICROARRAYS TO STUDY PLANT-PATHOGEN INTERACTIONS
  • 1.8. AIMS
  • 1.9. REFERENCES
• CHAPTER MICROARRAY EXPERIMENTS: CONSIDERATIONS FOR EXPERIMENTAL DESIGN
  • 2.1. ABSTRACT
  • 2.2. INTRODUCTION
  • 2.3. MICROARRAY PLATFORMS
  • 2.4. QUESTIONS ON DESIGN
  • 2.5. REPLICATION
  • 2.6. DESIGN TYPES
  • 2.7. FACTORIAL EXPERIMENTS
  • 2.8. TIME-COURSE EXPERIMENTS
  • 2.9. SAMPLE SIZE
  • 2.10. ANALYSIS
  • 2.11. REFERENCES
• CHAPTER MICROARRAY ANALYSIS OF THE ARABIDOPSIS THALIANA CIR (CONSTITUTIVELY INDUCED RESISTANCE 1) MUTANT REVEALS CANDIDATE DEFENCE RESPONSE GENES AGAINST PSEUDOMONAS SYRINGAE PV TOMATO DC
  • 3.1. ABSTRACT
  • 3.2. INTRODUCTION
  • 3.3. MATERIALS AND METHODS
  • 3.4. RESULTS
  • 3.5. DISCUSSION
  • 3.6. REFERENCES
• CHAPTER HOST TRANSCRIPT PROFILING IN ARABIDOPSIS THALIANA ECOTYPE COL DURING INFECTION WITH THE EUCALYPTUS ISOLATE OF RALSTONIA SOLANACEARUM, K (BCCF 401)
  • 4.1 ABSTRACT
  • 4.2 INTRODUCTION
  • 4.3 MATERIALS AND METHODS
  • 4.4 RESULTS
  • 4.4. DISCUSSION
  • 4.5. REFERENCES
• CHAPTER TRANSCRIPTOME ANALYSIS OF AN ARABIDOPSIS THALIANA ECOTYPE SHOWING RESISTANCE TO AN AFRICAN ISOLATE OF RALSTONIA SOLANACEARUM
  • 5.1 ABSTRACT
  • 5.2. INTRODUCTION
  • 5.3. MATERIALS AND METHODS
  • 5.4 RESULTS
  • 5.5 DISCUSSION
• CHAPTER

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Microarray expression studies in the model plant Arabidopsis thaliana infected with the bacterial pathogen Ralstonia solanacearum