Rice Genetics IV - IRRI books - International Rice Research Institute

view of procedures, pitfalls, and necessary controls in microarray generation, hybridization,and analysis.Tissue-specific expression profilesOne useful application of microarray analysis is the determination of tissue- and cellspecificity.Figure 1 shows the intensity distribution for 2,400 ESTs (open circles)from Mesembryanthemum in stems of this plant and in epidermal bladder cells (EBC),which are modified trichomes that accumulate NaCl in this halophyte. Plotted areintensity data. Added to this array were 96 probes derived from a cDNA library generatedfrom isolated EBC (black squares). It is obvious that most EBC-derived ESTsare more highly represented in the target RNA derived from EBC. An inspection ofESTs that are more highly represented in EBC RNA indicated that these sequencesencode functions that can be considered epidermis-specific, for example, pathogenesis-induced(antifungal, antibacterial, wound-inducible) or lipid transfer proteins.Signal intensity (bladder cells)100,00080,00060,00040,00020,000010,000 30,000 50,000 70,000Signal intensity (side shoot cells)Fig. 1. Tissue- and cell-specific transcript abundance detected by microarrayanalysis. A microarray including in excess of 2,000 ESTs from various cDNAlibraries ( ) from the ice plant (Mesembryanthemum crystallinum) is shown.Additionally included were 96 ESTs derived from a cDNA library made fromisolated epidermal bladder cells (EBC) ( ). After hybridization with targetDNA (Cy3) from stems and EBC (Cy5), most EBC-derived ESTs are morehighly expressed in the EBC.Isolation of candidate genes for tolerance of abiotic stresses 355