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Exposure to high ambient levels of NaCl affects plant water relations and creates ionic stress. To a large extent, responses to such stress depend on the action of membrane transporters, particularly those that move cations such as Na
+
and K
+
. A genomics approach can greatly help with the identification of important membrane transporter genes. This can be done by comparing transcriptomes of salinized and non-salinized plants, by comparing tolerant and non-tolerant species, or by using intraspecies variation. This chapter describes a protocol using oligo-microarrays to compare salinity treated (50 mM NaCl) and non-treated rice roots, presenting protocols for growth, RNA isolation, c
DNA
synthesis and labeling, and a summary of data collection, analysis, and interpretation. Although focused on rice root tissue, the described procedures can be applied to many different treatments, tissues, and plant species.
