| Plants, as sessile photosynthetic organisms, have evolved photoreceptors that sense both light quantity and quality. Signals from these photoreceptors input into many key developmental pathways and play an integral role in optimizing plant growth and development. One family of photoreceptors, the phytochromes, are specialized sensors of both red and far-red wavelengths of light. Phytochromes exist in two photointerconvertible forms: a Pr form that absorbs red light and a Pfr form that absorbs far-red light. The ratio of Pr to Pfr phytochrome is therefore dependent on the ratio of red to far-red (R:FR) of ambient light.;By sensing changes in R:FR light, plants gain insight into the state of neighboring vegetation. Since plants absorb red light to use in photosynthesis, light that passes through, or reflects off of, green foliage is characterized by a low R:FR ratio. Phytochrome B (phyB) senses this change in light quality and elicits a suite of developmental changes called shade avoidance that include increased elongation of plant organs, increased leaf angle, and acceleration of flowering.;The goal of the work described in this thesis was to understand natural variation in phyB signaling and shade avoidance. The first study used a candidate gene mapping approach to confirm that the LIGHT2 QTL described in Borevitz et al. [3], was likely due to PHYB variation. The remaining two parts of this thesis describe genome-wide association studies (GWAS) designed to uncover allelic variation underlying phenotypic variation in shade avoidance responses. The first study focused on a well-understood response, hypocotyl elongation, while the second addressed a less studied response, leaf morphology changes. Although the associations between candidate genes and phenotypes identified in these two studies require additional verification and characterization, these results can be used to generate hypotheses about both the molecular mechanisms and evolution of phyB-mediated phenotypic plasticity. In conclusion, association studies, both using candidate genes and GWAS, were useful tools for uncovering natural variation in the phyB signaling pathway. |
