The primary aerial surfaces of all land plants are coated by a lipidic cuticle, which restricts non-stomatal water loss and protects the plant from pathogens, herbivores, and ultraviolet radiation. The cuticle is made up of two components: cutin, a polymer of hydroxy- and epoxy- long-chain fatty acid derivatives and glycerol, and cuticular waxes, which are derivatives of very-long-chain fatty acids. While chemical analysis of cutin can be a lengthy and technically challenging task, analysis of cuticular waxes is relatively simple, and can be routinely used to characterize different plant species, adaptations of a given species to environmental conditions, or mutant phenotypes. Here, we present a protocol tailored for the analysis of cuticular waxes on the surface of the model organism Arabidopsis thaliana. Because cuticular waxes are found on the outermost surface of the plant, the wax extraction process is very simple, and sample processing can be completed in less than one day. Chemical analysis involves quantitation of wax monomers by gas chromatography coupled with flame ionization detection (GC/FID), and identification of wax monomers by either mass spectrometry or comparison of retention times of individual wax components to those of known standards.
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