A floral induction system for the study of early Arabidopsis flower development

Postembryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root Organs

Postembryonic organogenesis is a critical component in plant root and shoot development and its adaptation to the environment. Decades of scientific analyses have yielded a wealth of experimental data about the cellular and molecular processes orchestrating the postembryonic formation of new shoot and root organs. Among these, distribution and signaling of the plant hormone auxin play a prominent role. Systems biology approaches are now particularly interesting to study the emerging properties of such complex and dynamic regulatory networks. To fully explore the precise kinetics of these organogenesis processes, efficient protocols for the synchronized induction of shoot and root organogenesis are extremely valuable. Two protocols for shoot and root organ induction are detailed.

Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis

Assessing molecular changes that occur through altering a gene's activity is often hampered by difficulties that arise due to the typically static nature of the introduced perturbation. This is especially problematic when investigating molecular events at specific stages and/or in certain tissues or organs during Arabidopsis development. To circumvent these issues, we have employed chemically inducible artificial microRNAs (amiRNAs) for the specific knockdown of developmental regulators. For our own research, we have combined this gene perturbation approach with a floral induction system, which allows the simultaneous induction of a large number of flowers on the inflorescence of a single plant, and the ability to knock down a gene's activity at any given stage of development. To enable the plant community to avail of the full benefits of these systems, we describe, in this chapter, strategies for amiRNA-mediated gene perturbations and address some common problems that can be encountered when generating inducible amiRNA constructs, growing these plants, and collecting floral buds for analysis.

Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

Background

The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation.

Results

Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.

Conclusions

Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users.