Spatio-temporal transcriptional profiling of leaf development in rice

Rice leaves consist of three distinct regions along a proximal-distal axis, namely, the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, however,but the genetic programs underlying the development of each region are poorly understood. To capture the entire picture of rice leaf development and to discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. To obtain a comprehensive transcriptome of leaf development in rice, we sampled 12 leaf parts representing various stages and components along the longitudinal axis. Rice seedlings at the four-leaf stage were dissected into 12 parts: shoot apex containing the SAM and P1 and P2 leaf primordia; entire P3 leaf primordium; apical, middle, and proximal parts of P4 leaf blade; P4 leaf sheath; and the leaf blade, sheath, and boundary region of P5 and P6 leaves. Three biological replicates were prepared for each part, and their RNA was hybridized to a 44K rice microarray.