Imaging of biophotons from leaves has been used as a method for assaying R gene responses. These genes and their associated proteins are responsible for pathogen recognition and activation of defense signaling networks leading to the hypersensitive response, which is one of the mechanisms of the resistance of plants to pathogen infection. It involves the generation of reactive oxygen species (ROS), which have crucial roles in signal transduction or as toxic agents leading to cell death.
Biophotons have been also observed in the roots of stressed plants. In healthy cells, the concentration of ROS is minimized by a system of biological antioxidants. However, heat shock and other stresses changes the equilibrium between oxidative stress and antioxidant activity, for example, the rapid rise in temperature induces biophoton emission by ROS.