DEEPER: An Integrated Phenotyping Platform for Deeper Roots

Front left: Christopher Black, Hannah Schneider, Paul Heinemann, Xiaomeng Shi, Middle left: Kathleen Brown, Molly Hanlon, Catherine Hoover, Miranda Niemiec, Dauen Choi, Bob Snyder; Top left: Ricardo Fusi, Jonathan Lynch

Front left: Christopher Black, Hannah Schneider, Paul Heinemann, Xiaomeng Shi, Middle left: Kathleen Brown, Molly Hanlon, Catherine Hoover, Miranda Niemiec, Dauen Choi, Bob Snyder; Top left: Ricardo Fusi, Jonathan Lynch


Kathleen Brown, Penn State University

Dauen Choi, Penn State University

Paul Heinemann, Penn State University

Jonathan Lynch, Penn State University


Chris Black, Penn State University

Molly Hanlon, Penn State University

Hannah Schneider, Penn State University

Xiaomeng Shi, Penn State University


Ricardo Fusi, University of Nottingham

Catherine Hoover, Penn State University

Miranda Niemiec, Penn State University

Critical Need: 

Plants capture atmospheric carbon dioxide (CO2) using photosynthesis, and transfer the carbon to the soil through their roots. Soil organic matter, which is primarily composed of carbon, is a key determinant of soil's overall quality. Even though crop productivity has increased significantly over the past century, soil quality and levels of topsoil have declined during this period. Low levels of soil organic matter affect a plant's productivity, leading to increased fertilizer and water use. Automated tools and methods to accelerate the process of measuring root and soil characteristics and the creation of advanced algorithms for analyzing data can accelerate the development of field crops with deeper and more extensive root systems. Crops with these root systems could increase the amount of carbon stored in soils, leading to improved soil structure, fertilizer use efficiency, water productivity, and crop yield, as well as reduced topsoil erosion. If deployed at scale, these improved crops could passively sequester significant quantities of CO2 from the atmosphere that otherwise cannot be economically captured.

Project Innovation + Advantages: 

Pennsylvania State University (PSU) will develop DEEPER, a platform for identifying the traits of deeper-rooted crops that integrates breakthroughs in nondestructive field phenotyping of rooting depth, root modeling, high-throughput 3D imaging of root architecture and anatomy, gene discovery, and genomic selection modeling. The platform will be deployed to observe maize (corn) in the field under drought, nitrogen stress, and non-stressed conditions. Their key sensor innovation is to measure leaf elemental composition with x-ray fluorescence, and use it as a proxy for rooting depth. This above-ground, high throughput measurement for root depth will enable plant breeders to screen large populations and develop deep rooted commercial varieties. The team will also develop an automated imaging system for excavated roots that, with associated computer vision software, will identify architectural traits of roots. Lastly, they will greatly enhance a laser-based imaging platform to determine root anatomy. The combination of these technology platforms with advanced computational models developed for this program will allow PSU to determine the depth of plant roots, enabling better quantification of root biomass. As a full system platform, they aim to enable the breeding of maize with deeper roots that sequester more carbon and are more efficient in their utilization of nitrogen and water. The team will also contribute data to a nationwide dataset that seeks to study the interactions between genes and the environment. The dataset will include extensive plant data across multiple environments, a breeding toolkit of major genes regulating root depth, and genomic selection models for root depth, drought tolerance, and nitrogen use efficiency.

Potential Impact: 

If successful, developments from the ROOTS program will produce crops that will greatly increase carbon uptake in soil, helping to remove CO2 from the atmosphere, decrease nitrous oxide (N2O) emissions, and improve agricultural productivity.


America's soils are a strategic asset critical to national food and energy security. Improving the quality of soil in America's cropland will enable increased and more efficient production of feedstocks for food, feed, and fuel.


Increased organic matter in soil will help reduce fertilizer use, increase water productivity, reduce emissions of nitrous oxide, and passively sequester carbon dioxide from the atmosphere.


Healthy soil is foundational to the American economy and global trade. Increasing crop productivity will make American farmers more competitive and contribute to U.S. leadership in an emerging bio-economy.