Uncovering the genetic basis for variation in adaptive responses to water deficit in Arabidopsis thaliana roots
Plant Cell and Developmental Biology
Final Report Abstract
The group of Prof. Dinneny developed the GLO-Roots (Growth and Luminescence Observatory of Roots, U.S. patent application 13/970,960) system that enables the visualization of roots in soil using custom-made growth vessels, called rhizotrons, luminescent reporters, and a customdesign imaging platform. In this project, the GLO-Roots system was further developed and complemented by engineering an automated rhizotron-handling robot, called GLO-Bot. GLO-Bot enables daily imaging of growing plant roots from germination to senescence yielding novel insights in dynamic changes in root system architecture over time and upon induction of environmental stresses. Root system architecture is the overall shape of the root system. Certain “shapes” or idiotypes have been proposed to be beneficial for different environmental conditions like nutrient or water availability. For example, genetic modifications that yielded in steeper and/or deeper root growth resulted in rice, barley, and wheat plants that were more tolerant to water deficit. Working with cereal crops, however, is time consuming, requires elaborate biotechnology protocols and lacks genetic diversity due to domestication. Therefore, the use of the model species Arabidopsis thaliana with a comparably short generation time, established genetic tools and extensive natural variation could facilitate the characterization of genes and pathways that can later be tested in crop species in a more targeted approach. Independent of the plant model, the two major obstacles for studying changes in root system architecture upon environmental stresses are the visualization of roots in soil and the realistic simulation of stress conditions. Here, we used the GLO-Roots/GLO-Bot system to observe and define root traits shaping the root system architecture over time and identify responsible genes by making use of the genetic toolbox in Arabidopsis thaliana. First, a set of six accessions was analyzed to optimize GLO-Bot and the image processing pipelines. Interestingly, this set of six accessions already showed striking differences in root system architecture over time and will be further analyzed to identify involved genes. In addition, we used the large-scale phenotyping platform GLO-Bot to perform a genome-wide association study (GWAS). GWAS is a genetic screen of natural variation that statistically correlates phenotypic variation among diverse accessions with specific polymorphisms in the genome. We aimed to identify phenotypic variation of root traits and their underlying genetic variants that lead to specific root system architectures. We transformed 171 Arabidopsis accessions with the GLO-Roots reporter gene to make their roots “glow”. A subset of this population was grown in rhizotrons and imaged from day 14 to day 28 after sowing. Extensive image analysis using a specifically designed image analysis pipeline showed reproducible and statistically different aspects of root system architecture among the accessions. GWAS analysis of differences in average root angle at 28 days after sowing yielded significant genetic variants in various promoter and gene regions. These candidate genes will be characterized and tested for their involvement in setting specific root growth angles. In addition, GWAS analyses of several other root traits both over time and at specific time points will be performed to describe the genetic setup required to build specific root system architectures. We have shown that time-lapse imaging of the “hidden half” of plants using the GLO-Roots/GLO- Bot system produces reproducible and informative data that allows for the identification of relevant genetic variants that guide root system architecture. Importantly, we successfully described natural variation in root system architecture under well-watered conditions and identified underlying genetic variants. This data will serve as the foundation to identify genes involved in shaping beneficial root system architectures under water-deficit conditions and create possibilities to make future crops more stress-resilient in a changing climate.
Publications
- (2015) GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 2015;10.7554/eLife.07597
Rellán-Álvarez R, Lobet G, Lindner H, Pradier P-L, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager A, Haney C, Nieu R, Maloof J, Vogel JP, Dinneny JR
(See online at https://dx.doi.org/10.7554/eLife.07597.001) - (2016) Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses. The Plant Cell vol. 28 no. 8 1769-1782
Feng W, Lindner H, Robbins II N, Dinneny JR
(See online at https://doi.org/10.1105/tpc.16.00182)
