Genes regulated by R:FR ratio and the circadian clock in Arabidopsis thaliana

The shade avoidance response is of major adaptive significance to plants. Angiosperms in particular have developed a wide range of strategies to avoid shade. In canopy shade conditions, the ratio of red to far-red light wavelengths decreases (low R:FR ratio) this acts as a signal to instruct plants that they are in the proximity of neighbouring flora. A decrease in R:FR ratio is perceived through the phytochrome system, which results in onset of several developmental responses; such as elongation growth; that help promote escape from shade. Although much is known of the role phytochromes play in light perception and the concomitant physiological responses triggered by a decrease in the R:FR ratio, little is known of the downstream molecular components that bring about these changes. This study focuses on a small number of genes (DIN2, ENDO1 and XTH15) that whilst known to be R:FR ratio regulated, have as yet unknown roles during shade avoidance. This work demonstrates that all three genes respond with extreme rapidity and reversibility to changes in light quality conditions. The role phytochromes play in regulation of these genes is investigated. In addition a number of light regulated transcription factors, downstream of the phytochromes, are identified as intermediate regulators of these genes. As it has recently come to light that a number of R:FR ratio regulated genes are also under the control of the circadian clock the ability of this signalling pathway to influence expression of these genes was also investigated. Molecular analysis revealed that the circadian clock modulates two of the three genes examined within this study. Finally, systematic physiological characterisation of mutant and over-expressing lines was performed with an aim to determine the biological function of these genes during shade avoidance. Additionally, this study reveals that one of the genes studied; XTH15; not only exhibits R:FR ratio regulation of expression, but also blue light mediated transcriptional responses. This raises the possibility that R:FR ratio and blue light signaling pathways converge. Preliminary data suggests that XTH15 could represent a point of cross over with the phytochromes and the cryptochromes. This work, which characterises the response and potential role of three R:FR regulated genes downstream of the phytochromes, provides important and novel contributions to our understanding of the environmental regulation of plant development.