Measuring Hypocotyl Length in Arabidopsis

Circadian clocks allow organisms to synchronize growth to occur at the most optimal time of the day. In plants, the circadian clock controls the timing of hypocotyl (seedling stem) elongation. The activity of the circadian clock subsequently results in hypocotyl elongation being restricted to a small window around dawn and the early morning. Measuring hypocotyl elongation has provided circadian biologists a quick and non-intensive experimental tool to understand the effect of a circadian mutation on plant growth. Furthermore, hypocotyl elongation is also independently regulated by light, temperature, and hormone signaling pathways. Thus, hypocotyl assays can be expanded to investigate the crosstalk between the circadian clock and other extrinsic and intrinsic signaling pathways in controlling plant development. In this chapter we describe the resources and methods required to set up and analyze hypocotyl elongation in Arabidopsis.