Trends in Plant Science
ReviewPatterns of beauty – omics meets plant development
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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2013, Trends in BiotechnologyCitation Excerpt :For instance, the metabolic compositions of Chlamydomonas reinhardtii under mixotrophic and autotrophic conditions were used to specify the condition-specific biomass functions which can in turn be used as objectives maximized by this unicellular organism [37]. Recent studies making use of this knowledge have shed light on resource allocation during seedling establishment [38–41], aromatic and flavor associated traits of fruits [42,43], as well as on developmental processes [44]. Although knowledge-based networks capture substrate–product relationships, they neglect the concerted regulation characteristic of cell metabolism.
MS based proteomic approaches for analysis of barley malt
2012, Journal of Cereal ScienceCitation Excerpt :Proteomics not only allows the determination of global changes in plant gene expression, but also the level and the complexity of proteins and the resultant metabolite profile. The number of publications related to plant proteomics has increased steeply (Fig. 2) (Bolwell et al., 2004; Cánovas et al., 2004; Figeys, 2003; Hennig, 2007) including studies of the relationships between proteins and plant development, seed maturation, responses to biotic and abiotic stresses and human allergies (e.g. Chen and Harmon, 2006; Hossain et al., 2012; Komatsu et al., 2012; Kosová et al., 2011; Sergeant and Renaut, 2010; Takáč et al., 2011; Timperio et al., 2008; Zhang et al., 2012). Many plants have been studied including A. thaliana, tobacco, vegetables, fruits and cereals.
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Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum
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