291 Sergey Shabala and Tracey Ann Cuin (eds.), Plant Salt Tolerance: Methods and Protocols, Methods in Molecular Biology, vol. 913, DOI 10.1007/978-1-61779-986-0_20, © Springer Science+Business Media, LLC 2012 Chapter 20 Transcriptome Analysis of Membrane Transporters in Response to Salinity Stress Prasad Senadheera and Frans J.M. Maathuis Abstract 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, cDNA 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. Key words: Microarray , Transcriptomics, Membrane transporter, Salinity Soil salinity is a global issue that challenges the food security of future generations and is likely to be aggravated by global warming (1). Virtually 40% of irrigated land worldwide is salt affected and about ten million ha of arable land is lost annually to salinization (2). Soil salinization is the result of an excessive presence of mineral nutrients such as Na + , Mg 2+ , Ca 2+ , Cl - , SO 4 2- and typically, saline soils show electrical conductivity >4 dS/m, with the most preva- lent ions being Na + , Cl - , and SO 4 2- (3). Most crop plants are glycophytes so are severely affected by salt stress (4). Yet crops differ in tolerance. For example, cereals include 1. Introduction