Abstract
Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner.
Highlights
Over the past two decades, flower development has attracted widespread attention as an excellent model system for studying organogenesis in plants at a molecular level [1]
The vast majority of the floral regulatory genes identified to date encode transcription factors or other proteins involved in the regulation of gene expression, indicating the existence of a complex gene regulatory network that underlies flower development (Figure 1)
In addition to a rapid activation of GA4, we found an up-regulation of a gene encoding a GA2oxidase, which is involved in the degradation of gibberellic acid (GA) and counteracts GA4 activity
Summary
Over the past two decades, flower development has attracted widespread attention as an excellent model system for studying organogenesis in plants at a molecular level [1]. Global Analysis of Stage-Specific Gene Expression We used the 35S:AP1-GR ap cal floral induction system to analyze gene expression during early flower development on a genome-wide scale (Figure 3) To this end, we treated inflorescences with dexamethasone and collected tissue immediately after the treatment, as well as at 1-d intervals for the following 5 d. Several closely related members of the plant-specific family of B3 domain proteins were detected as induced at different time points after AP1-GR activation, suggesting that they might have distinct expression patterns during early flower development. As the floral homeotic genes were rapidly activated after the synchronized induction of flower development (Figure 4B), we expected to find their known target genes among the genes that showed significant expression changes in our experiment Most of these genes were present in our dataset (Table S5). The floral homeotic factors might either have a limited number of target genes during early flower development, or they might be able to bind to sites other, or less conserved, than the CArG box consensus sequence we have screened for in our analysis
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