ARS | Publication request: High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development

Submitted to: Plant Cell and Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 6, 2012
Publication Date: February 3, 2013
Citation: Clark, R., Famoso, A., Zhao, K., Shaff, J., Bustamante, C., Mccouch, S., Aneshansley, D., Kochian, L.V. 2013. High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell and Environment. 36(2):454-466.

Interpretive Summary: There is a growing understanding about how important root systems are to crop traits such as nutrient and water acquisition and utilization, and tolerance to toxic metals in the soil. For example, with regards to tolerance to low phosphorous (P) in the soil, it is now known that root system architecture (RSA), or where the plant places different roots in the soil within the entire root system, plays a key role in the ability for the plant to efficiently acquire P from low P environments. Therefore, we developed a novel system to digitally acquire images of the entire root system of plants in a rapid manner, and then quantitatively analyze these images to determine different root system traits such as total root growth, the total volume the root system explores, and root angle. We then went on to use this system to study different genetic populations in rice and maize, in order to set the stage for genetic mapping of RSA in relation to important crop traits in maize, sorghum and rice, such as more efficient utilization of limiting nutrients such as water, N and P. This system will enable us to begin to gather the basic information about RSA that will then enable plant breeders to develop higher yielding cereal varieties based on superior root.

Technical Abstract: High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyze these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminum (Al) tolerance were analyzed on the parents of the maize nested association mapping (NAM) population.