Microarray analyses to study plant defence and rhizosphere-microbe interactions.

Plant defence responses are mediated by key regulatory proteins that affect expression of thousands of genes. Over the last decade, microarrays have played a pivotal role to elucidate the underlying networks of gene regulation that lead to a wide variety of defence responses. Undoubtedly, they provided a valuable tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. The usefulness of this reverse genetics approach has been demonstrated by numerous discoveries of key regulatory genes important for defence signalling as well as valuable end-point genes whose products display direct action against pests and diseases. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides, some of which are synthesized directly on the underlying substrate. The frequent use of microarrays has enabled the creation of powerful microarray databases that allow researchers a rapid retrieval of gene expression profiles from various treatments and tissues. While physiological pathways are in parts positively or negatively linked, the discovery of a regulatory defence signalling network by microarrays has demonstrated that ultimately genes and their products, and not pathways are controlled by regulation. Future research should focus on simultaneous time-course analyses of host cells and pathogens to fully understand the biology of disease progression. In addition, most research on plant defence responses has focused on single pathogens, pests and/or signalling compounds. However, plants in nature grow under the influence of multiple environmental stresses while interacting immensely with other organisms. Recent studies of plant-microbe interactions have revealed transcriptional responses of plants to multiple organisms. New technology has enabled a metatranscriptomics approach that will allow the analysis of plants interacting with entire microbial communities, such as those present in the rhizosphere.