Zea mays Transcriptome or Gene expression. Zea mays

Zea mays is a C4 plant that utilizes two distinct cell types, mesophyll (M) and bundle sheath (BS), to cooperatively fix carbon. Regulation of M and BS cell differentiation is poorly understood. Here, we explore the transcriptional networks of M and BS cells by microarray analysis. The maize mutant bundle sheath defective2 lacks the accumulation of Rubisco small and large subunits (Roth et al 1996; Brutnell et al 1999) and cannot perform the Calvin Cycle (Smith et al 1998). Therefore, this mutant provides an opportunity to study M and BS cell differentiation in a perturbed BS background, potentially revealing regulons important to cell identity. M and BS cells were independently isolated from mutant and wild-type siblings. Transcriptional profiling was then performed in a cell specific manner between mutant and wild-type. Overall design: Both M and BS cell experiments were performed using the Maize Oligonucleotide Array (University of Arizona). For each experiment, six biological replicates were conducted in a dye swap arrangement using the 900MPX Expression Array Detection Kit and company protocol (Genisphere). After scanning, feature intensity values were log-transformed, corrected for local background, and filtered to include only those that were at least 2x background. The data was then LOWESS normalized and corrected for dye-effect. Differentially expressed genes were identified by moderated-t test and the false discovery rate (q) was determined.