Lay summary
Developmental and physiological processes occur within the context of complex tissues and organs. However, relevant events often occur in only a subset of cells or in a single cell type. For instance, gametogenesis and embryogenesis are initiated in a single cell, gas exchange is controlled by the specialized guard cells, and interactions with pathogenic fungi such as powdery mildew occur by colonization of individual epidermal cells. Over the last decade new approaches have been developed that allow the genome-wide survey of transcriptional changes (transcriptomics) during developmental processes or in response to endogenous and exogenous factors, for example stress or pathogen attack. These methods usually rely on significant quantities of tissue and have usually been performed on whole organisms, organs or, at best, tissues. It is clear, however, that an understanding of the underlying molecular mechanisms will often require the monitoring of events in single cell types. Microgenomics, the combination of Laser Assisted Microdissection (LAM) with transcript profiling offers this possibility. LAM allows the isolation of individual cells from sectioned specimens such that a focus on the relevant cell type is possible. After RNA extraction and amplification, the transcripts expressed by this cell type can be analyzed using a variety of transcript profiling methods. Thus, microgenomics allows the determination of cell type-specific transcriptomes or the analysis of molecular changes occurring in a cell under specific conditions, for instance biotic or abiotic stress. Over the last few years, we have adapted and optimized methods for laser-assisted micro-dissection to plant tissues and have successfully developed protocols that allow us to perform transcript profiling with starting material consisting of only 200-400 cells. However, up to now, we had to perform laser assisted microdissection experiments at other institutes with the disadvantages that i) the instruments were frequently unavailable, and ii) that samples suffered during transport, which led to a lower quality of results. Thanks to funding by the Swiss National Fund, we are now able to buy a Laser Capture Microscope (LCM) for the Institute of Plant Biology, as well as an automated in situ hybridization system, which together with the automated embedding station that we acquired earlier will allow us to identify, confirm and test the candidate genes identified through microgenomics in a high-throughput fashion.