Submitted to: The Plant Cell
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/20/2005
Publication Date: 11/1/2005
Citation: Alba, R., Payton, P.R., Fei, Z., Mcquinn, R.P., Debbie, P., Martin, G., Tanksley, S., Giovannoni, J.J. 2005. Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. The Plant Cell. 17(11):2954-2965. Interpretive Summary: Microarray technology affords expanded opportunities to dissect the molecular basis of biochemistry, physiology, and development through analysis of large collections of genes representing a substantial portion of the target organism's genome. The combination of these emerging tools with time-course analyses has been particularly informative. This approach - for the first time ever - makes it possible to correlate transitions in biochemistry, physiology, and development with global changes in the mRNA populations that underlie these biological phenomena. Understanding the molecular basis of plant biological processes will allow the regulatory networks that govern them to be elucidated. As regulatory networks are defined sufficiently in crop plants, it will become possible to more intelligently manipulate desirable components of plant physiology and development (e.g., nutritional quality, stress tolerance, yield) while minimizing or at minimum identifying, potential adverse effects on plant performance. For these and other reasons, a number of useful microarray resources for tomato have been developed and are presented here in the context of their use for analysis of the tomato transcriptome during fruit development and ripening.
Technical Abstract: Genomics resources for analysis of global gene expression have been developed and are used here to elucidate the molecular basis of fruit development and ripening. These resources include: a publicly available tomato microarray containing approximately 12,000 cDNA elements, a large collection of EST annotations based on the terminology developed by the Gene Ontology Consortium, and two integrated public databases for storage, retrieval, and analysis of tomato microarray data. An experimental design that allows the identification of statistically significant differences in gene expression is presented as an alternative to the frequently employed setting of arbitrary limits on levels of differential expression warranting further consideration (e.g. 2-fold). Gene expression profiling is often employed as a tool to identify groups of genes associated with a biological process and to be pursued in total or as subsets for further functional characterization. As such, robust statistical approaches that result in capturing the maximum number of genes with meaningful differential expression is imperative to the utility of gene expression profiling in defining molecular mechanisms. Here we report a comprehensive time-course analysis of the tomato transcriptome during fruit development with an emphasis on ripening. We have identified and annotated more than 500 loci that are differentially expressed at least once during the ten stages of fruit development investigated. Evidence of extensive coordinated gene expression during fruit development and ripening is presented in addition to two databases for data storage and analysis.