Review
Patterns of beauty – omics meets plant development

https://doi.org/10.1016/j.tplants.2007.05.002Get rights and content

Developmental biology aims to identify mechanisms that govern cell proliferation and differentiation in the body plan formation of multicellular organisms. In the past, developmental biologists described how anatomy and morphology are established during ontogenesis, and developmental geneticists identified many developmental regulators. In contrast to the traditional approaches that mostly focus on one or a few genes at a time, highly parallel profiling technologies have been developed for use in biological research over the past decade. Such parallel profiling technologies probe many genes, transcripts, proteins or metabolites at once. In this review, I discuss the growing impact of transcriptomics, proteomics, metabolomics and modelling on plant developmental biology. Novel profiling technologies will not make traditional gene-centred approaches obsolete but should instead complement forward developmental genetics.

Section snippets

Parallel investigations – functional genomics technologies

Plants come in many shapes and colours, and the beauty of plants has fascinated mankind for thousands of years. Long before Mendel discovered the laws of heritability and Darwin developed his theory on evolution, the affection for ornamental plants led people to select alleles that establish novel plant forms. Not surprisingly, people have been wondering how these elaborate forms arise. Developmental biology aims to identify mechanisms that govern the body plan formation of multicellular

Caught in the act – identifying targets of developmental regulators

Key genes for development often encode transcriptional regulators, but identifying the target genes of such regulators is not trivial. RNA profiling is often used. However, RNA profiling usually identifies both direct and indirect target genes. Chromatin immunoprecipitation (ChIP) is used as a gold-standard to test direct in vivo binding of transcriptional regulators to candidate target genes. In addition, in vitro DNA binding tests combined with in vivo analysis of mutated binding sites can

Profiling the transcriptome

Highly parallel technologies are used to establish reference maps and ‘parts lists’ for specific developmental stages 18, 19. Such maps attempt to catalogue all transcripts, proteins and metabolites present in any cell type at a given developmental stage and are expected to assist in defining the molecular differences of diverse cell fates. Eventually, this should enable us to find out what makes cells different from one another. Several studies have analysed the transcript populations during

Profiling proteome and metabolome

Proteome profiling of organs or developmental transitions is complementing transcriptome profiling data [41]. Because proteomics approaches cannot benefit from amplification protocols, usually far fewer proteins than transcripts can be detected. In addition, studies analysing specific cell types are rare, although attempts to couple LCM to 2D-PAGE and LC-MS/MS have been reported [42]. Because pollen can be isolated relatively easily, published organ-specific proteome reference maps are

Finding the connections – constructing networks of development

Profiling technologies easily generate data – but it is less clear how to use the data to construct or even model networks of development. Here, modelling specifically means mathematical models, in which plant development is described using mathematical formulae. Models of plant development are often: (i) descriptive simulation models, which aim to reconstruct empirical data, or (ii) mechanistic simulation models, which aim to show how different components of a system might work together and

What's next? Conclusions and outlook

Integration of molecular profiling technologies in plant developmental biology has just begun, and many exciting developments can be anticipated for the near future. First, the range of model species will expand. Because certain developmental processes, such as wood formation, bud dormancy and nodulation, are foreign to Arabidopsis, the importance of model species such as poplar and Medicago will further increase 57, 58, 59. Similarly, extensive work on various monocot species already exists

Acknowledgements

I thank my wife, Claudia Köhler, and Sacha Baginsky for critical reading of the manuscript and Wilhelm Gruissem for stimulating discussions. Work in my group is supported by SNF project 3100AO-116060, ETH project TH-16/05-2 and a grant from the Zürich-Basel Plant Science Center. I apologize for not citing all the relevant papers of my colleagues owing to space constraints.

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