Far-red Fraction: An Improved Metric for Characterizing Phytochrome Effects on Morphology

Phytochrome, a well-studied photoreceptor in plants, primarily absorbs in the red (R) and far-red (FR) regions and is responsible for the perception of shade and subsequent morphological responses. Experiments performed in controlled environments have widely used the R:FR ratio to simulate the natural environment and used phytochrome photoequilibrium (PPE) to simulate the activity of phytochrome. We review why PPE may be an unreliable metric, including differences in weighting factors, multiple phytochromes, nonphotochemical reversions, intermediates, variations in the total pool of phytochrome, and screening by other pigments. We suggest that environmental signals based on R and FR photon fluxes are a better predictor of plant shape than the more complex PPE model. However, the R:FR ratio is nonintuitive and can approach infinity under electric lights, which makes it difficult to extrapolate from studies in controlled environments to the field. Here we describe an improved metric: the FR fraction (FR/R+FR) with a range from 0 to 1. This is a more intuitive metric both under electric lights and in the field compared with other ratios because it is positively correlated with phytochrome-mediated morphological responses. We demonstrate the reliability of this new metric by reanalyzing previously published data.

Automated summary

Phytochrome in plants primarily absorbs in the red and far-red regions to perceive shade and induce morphological responses. However, the traditional phytochrome photoequilibrium may not be a reliable metric, and using R and FR photon fluxes as environmental signals may be a better predictor of plant shape. Introducing the FR fraction metric improves intuitive understanding and reliability in both electric lights and field conditions.