A primary component of seedling establishment is the photomorphogenic response as seedlings emerge from the soil. This process is characterized by a reduced growth rate in the hypocotyl, increased root growth, opening of the apical hook, and expansion of the cotyledons as photosynthetic organs. While fundamental to plant success, the photomorphogenic response can be highly variable. Additionally, studies of Arabidopsis thaliana are made difficult by subtle differences in growth rate between individuals. High-resolution imaging and computational processing have emerged as useful tools for quantification of such phenotypes. This study sought to: 1) develop an imaging methodology which could capture changes in growth rate as seedlings transition from darkness to blue light in real time, and 2) apply this methodology to single-QTL analysis using the Cvi x Ler RIL mapping population. Significant differences in the photomorphogenic response were observed between the parent lines and analysis of 158 RILs revealed a wide range of growth rate phenotypes. QTL analysis detected significant loci associated with dark growth rate on chromosome 5 and significant loci associated with light growth rate on chromosome 2. Candidate genes associated with these loci, such as the previously characterized ER locus, highlight the application of this approach for QTL analysis. Genetic analysis of Landsberg lines without the erecta mutation also supports a role for ER in modulating the photomorphogenic response, consistent with previous QTL analyses of this population. Strengths and limitations of this methodology are presented, as well as means of improvement.

Growth rate was determined by measuring hypocotyl length with ImageJ software. A calibration value of 35.509 pixels/mm was used for scale. Dark growth rate was determined based on the following formula: (Hypocotyl length (T1) - Hypocotyl length (T0))/3 hrs Light growth rate was determined based on the following formula: (Hypocotyl length (T2) - Hypocotyl length (T1))/5 hrs Percent Reduction in growth rate was determined based on the following formula: 1 - (light growth rate)/(dark growth rate)

Dark-grown 2d-old seedlings were imaged in darkness (T0), after 3 hrs of growth in the darkness (T1) and after 5 hrs of growth in 20 µM m-2 s-1 blue light (T2). Images have not been processed.