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Dynamic analysis of hypocotyl growth reveals novel Arabidopsis shade avoidance phenotypes


Most research aimed at understanding the molecular mechanism of growth and development uses measurements of molecules (RNA, Protein) that fluctuate on vastly different timescales than the phenotypes they are thought to control. One growth readout of particular interest is the hypocotyl system of Arabidopsis, for which a broad wealth of genetic and physiological data exist, yet very little is known about the growth dynamics of this seedling organ.

IGERT student Ben Cole has developed an imaging platform targeted to accurately measure hypocotyl growth in a dynamic assay which is better aligned with the speed at which most molecular events proceed. This platform consists of a high-resolution camera and macro lens housed in an LED chamber capable of manipulating red, far-red, and blue light intensities, and newly-developed software which can automatically measure hypocotyl lengths of the images acquired. Using this platform, Ben has shown that shade conditions (simulated by a high red/far-red light ratio) is capable of eliciting a hypocotyl growth response in as little as 45 minutes, is multi-phasic, and is regulated both by newly-synthesized auxin and by the phytochrome pathway in temporally distinct ways (Cole B. et al., Plant Journal 65: 991-1000 (2011)). He is presently characterizing other hormone pathways within this response, as well as the role of the circadian clock in gating hypocotyl growth within the context of shade. In the future, Ben hopes to ultimately build a dynamic model of how the shade signal is transduced, which can be tested and updated as new data comes to light.

Address Goals

Primary: The Arabidopsis hypocotyl, while a relatively simple organ, has been an intense focus of study for light signaling research. Studying shade avoidance in a dynamic way can give new perspectives on how the response is elicited, and may better elucidate the shade avoidance signaling pathway, with the long-term possibility of identifying points of agricultural intervention.Shade avoidance determines cropping density and is critical for crop yields.

Secondary: A computational tool was developed enabling dynamic studies of light-grown Arabidopsis hypocotyls, previously lacking in the field, and the utility was demonstrated by characterizing a novel phenotype of shade avoiding Arabidopsis hypocotyls.