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

•The present study profiled and analyzed gene expression of the maize ear at four key developmental stages.•Several well-known genes were found with reported mutant analyses, such as ct2, zag1, bde, and si1.•MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development.•13 TFs from 10 TF families (B3, bZIP, ERF, HD-ZIP, LBD, MIKC, MYB, NAC, SBP, and TCP) were identified.•Antisense transcripts were widespread throughout all the four stages in maize ear development.

The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.