Clark, Randy2013-09-162018-08-202013-08-19bibid: 8267471https://hdl.handle.net/1813/34347Plant root systems and associated symbiotic organisms act as critical links between the growing shoot and the rhizosphere, providing both vital nutrients and water to sustain growth. Many tools have been developed to study plant root systems; however, the efficient quantification of root traits remains a key bottleneck to effectively utilizing expanding collections of genomic and germplasm resources during the study of root system development and function. This dissertation presents results from root system phenotyping research where root phenotyping platforms were developed and used to investigate the genetic components of root system architecture and development in crop plants. It begins with a review chapter that discusses the importance of root system architecture (RSA) during resource acquisition and provides an overview of established root growth and measurement techniques while highlighting modern root phenotyping approaches that have been developed for genetic mapping studies. Subsequently, two distinct and complementary phenotyping platforms are described that were designed to improve the flexibility and throughput for root system phenotyping using digital imaging and software analysis tools to quantify root systems in 2-dimensions (2D) and 3-dimensions (3D). The use of the 3D phenotyping platform is then discussed where global root system traits were captured and quantitative trait loci (QTL) and genome wide association (GWA) mapping studies were performed in order to investigate the genetic components of RSA development in rice (Oryza sativa). Finally, future research directions are outlined and include additional phenotyping platform development as well as new strategies to mine the RSA mapping results to identify candidate genes involved in root development and verify the functional relevance of the measured root traits and detected loci for nutrient and water acquisition.en-USRoot PhenotypingRoot System ArchitectureRice (Oryza sativa) and Maize (Zea mays)dissertation or thesis