To fully understand how animals develop, it is often necessary to remove the function of a particular gene in a specific cell type or subset of cells. InDrosophila melanogaster, mosaic animals have been widely utilized to study cell fate, growth and patterning, and restriction of cell fate. This chapter describes using FLP recombinase to generate mosaicDrosophila, discussing the chromosomes and cross scheme, how to induce the clones, how to properly identify the appropriate progeny, and how to prepare and analyze the tissues, clones, and phenotypes. It then presents three examples, applying this technique to study Hedgehog signaling. The first example describes moderate-sizedcostalclones in imaginal discs, using green fluorescent protein (GFP) as a marker anddppLacZand Engrailed expression as phenotypic reporters. The second describes filling the adult eye withroadkillmutant clones, usingwhiteas a marker and scoring morphology. The third describes clonal misexpression of a truncated form of Smoothened, using GFP andyellowas markers.
