Genome-wide analysis of gene expression profiles during ear development of maize

In order to unravel the molecular mechanism of maize ear development, a microarray containing approximately 56,000 probes was used to monitor the gene expression profiles of ears at four developmental stages. The results showed that 2,794 genes, accounting for 5.0% of the total probes, changed significantly during ear development. Among the 2,794 genes, 1,844 genes differentially expressed during the spikelet differentiation phase, 836 genes during the floret primordium differentiation phase and 645 genes during the floret organ differentiation phase. Hierarchical clustering revealed that the differentially expressed genes had 9 major expression patterns. Based on Mips Functional Catalogue, 684 differentially expressed genes were grouped into at least one functional category, including metabolism (30.4%), protein related function (29.2%), biogenesis of cellular components (15.4%) and transcription (13.7%). The analysis revealed that the auxin signaling pathway play an important role in ear development. Moreover, regulation of some transcription factors may play a key role during ear development. RT-PCR and in situ hybridization for some selected genes validated our microarray data and supplied additional information on ear developmental processes.