Fruit represent unique plant developmental systems and constitute important components of human and animal diets. Tomato (Solanum lycopersicum), an economically important crop, has emerged as the principal model for studies of fleshy fruit development, ripening, shelf life and nutritional quality. However, many fundamental questions related to key aspects of the development, physiology, quality traits and environmental responses of fleshy fruit remain unanswered.

In addition, most biochemical and molecular studies involving the extraction of transcripts or proteins from plant organs use a homogenized amalgam of tissues and cell types. This approach limits insights into cell specialization, and lower abundance molecules that are present only in certain cell types are often diluted below the level of detection. There is therefore a critical ‘information void’ when it comes to annotating and presenting gene expression data.

We are addressing these issues in the context of understanding the entirety of gene expression during tomato fruit development, by coupling RNA-seq analysis with laser capture microdissection (LCM), which allows the precise isolation of individual fruit cells/tissue types. In addition to resolving gene expression down to the level of cell/ tissue type, this approach has enabled: (i) the identification of previously unannotated genes, demonstrating the value of LCM as a tool for gene discovery; (ii) inferences regarding gene functions, based on the patterns of tissue- or cell type-related expression.