To determine day length, one first needs to know what time it is, specifically how long it has been since the sun came up, and then whether it is light or dark outside. Plants, like all organisms, have an internal circadian clock. Circadian clocks are biochemical mechanisms that oscillate with a 24-hour period and are coordinated with the day–night cycle. Phytochrome is the photoreceptor responsible for synchronizing the plant’s internal oscillator with the first light of dawn. The circadian clock tells the plant how long it has been since the sun came up, while phytochrome tells the plant whether it is light or dark during a specific phase of the circadian cycle.

The actual mechanism used by plants to determine day length relies on the fact that the plant’s circadian clock affects the transcription of many genes. For example, in Arabidopsis thaliana, a long-day plant, a gene whose protein product is critical for triggering flowering is transcribed at increasingly higher rates throughout the day, peaking ~16 hours after dawn. After that, the rate of transcription declines. The protein product of this gene is targeted for rapid degradation unless light is present. Thus, whether the protein builds up to a level sufficient to trigger flowering depends on day length. During long days, the protein reaches levels needed to trigger flowering because peak production occurs during daylight, when the protein is not targeted for destruction. During short days, the protein product does not reach levels needed to trigger flowering because the gene is transcribed at high rates only after the sun has gone down, so the protein is rapidly degraded.

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This mechanism explains why interrupting the dark period with a brief exposure to light alters the flowering response. In an early set of experiments, both short-day plants and long-day plants were grown under a photoperiod that would normally cause the short-day plants to flower and the long-day plants to produce only leaves. A brief exposure to light during the dark period reversed this result. The short-day plants no longer produced flowers, but the long-day plants did. Furthermore, the night interruption was effective only when the light contained red wavelengths, and the effects of red light could be reversed if exposure to far-red light immediately followed. These results indicate that the light is detected by phytochrome. We now understand that the night interruption acts like a switch that converts phytochrome into its active form. In that form, phytochrome can then affect the stability of proteins whose synthesis follows a circadian rhythm.

Other experiments demonstrated that day length is sensed by the leaves and not by the buds where the flowers will form. When conditions are right for flowering, the protein florigen is synthesized in leaves and transported through the phloem to the growing points of a plant. In this way, florigen is a chemical signal or hormone that converts shoot meristems into floral meristems.