DNA microarray technology has become a powerful tool for systematic analysis of expression profiles of large numbers of genes in several plant species (3-8). It is currently being used to investigate a variety of physiological and developmental processes in plants. Expression profiles have been studied for responses to various stresses (9-11), environmental conditions, such as light (12), and day/night cycling (13), symbionts (14), pathogens (15-17), rehydration after dehydration (18), and various developmental processes (19).

Two types of microarrays are currently in use: cDNA microarrays (20) and oligonucleotide microarrays (21). The basic microarray analysis performed with both types of arrays is similar and based on the specific hybridization of a labeled target to the immobilized nucleic acids (probe) on the array. These two systems differ primarily in the nature of the DNA fixed to the solid support. A number of reviews are available on their uses and advantages (1, 2, 3, 7, 22, 23).

In this chapter, we summarize the methodology on gene expression profiling in plants using cDNA microarrays.

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