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Executive Summary

DEEPER is an integrated platform of phenomic, genomic, and in silico technologies to generate maize lines with deeper roots. DEEPER is:

1.  LEADER, to nondestructively quantify root depth in the field using the plant itself as a sensor. LEADER uses available equipment but requires protocol development. Our technical goal is to quantify the root depth of mature maize plants in any field in 2 minutes.

2.  RootRobot/DIRT3D, to automatically phenotype root architecture in any field, combining RootRobot, a mechatronics platform to excavate, clean, section, and image mature root crowns, with DIRT3D, software to quantify architectural traits in 3D. Our technical goals are to: 

    • Quantify between 20-30 architectural traits in the field at the rate of 2 minutes per plot
    • Extrapolate 3D root architecture from 2D optical and 3D terahertz imaging
    • Discover and validate novel architectural traits regulating root depth in maize.

3.  Anatomics, a high-throughput platform to phenotype root anatomy, combining LAT 2.0, a technology for 3D imaging of root anatomy and composition, with RootScan3D, software to automatically extract 3D anatomical and cell wall composition metrics from LAT 2.0 output. Our technical goals are to:

    • Improve precision and speed of LAT by 2-3x
    • Extract 3D anatomy and cell wall composition phenotypes from LAT 2.0 output
    • Discover and validate novel anatomical traits regulating root depth in maize.

4.  SimRoot/deep, software to simulate root interaction with hard subsoils. SimRoot/deep will be linked to BORG, a platform for multiobjective genetic optimization modeling, to identify combinations of root traits to maximize root depth in specific soils. SimRoot/deep will be synergistic with other DEEPER technologies and will guide trait and gene discovery. Our technical goal is to simulate and predict how root traits regulate penetration of hard subsoils.

5.  DeepGenes, a toolkit of genes, parent lines, and genomic selection strategies to enable breeding hybrids with deeper roots. Hybrids will be evaluated with LEADER, RootRobot/DIRT3D, and Anatomics across environments and stresses, providing a substrate for gene discovery and genetic model development. Our technical goal is to predict hybrids with desirable root traits through phenotypic and genetic information.

DEEPER will deliver validated ideotypes for deeper-rooted maize; novel technologies to rapidly assess root depth, root architecture and anatomy in field-grown plants; novel software tools for root modeling and 3D image analysis of root architecture and anatomy; and validated genes and genomic selection models to deploy traits for deeper rooting in maize breeding. DEEPER will also be a community platform to test and deploy new phenotyping tools and technologies. Each DEEPER technology would be transformative in its own right, and would exceed existing technologies, many of which were created by our team, in speed, cost, and capabilities. They are mutually synergistic, deployable for field-grown plants, and would be ready for application in the span of this project. The phenotyping and modeling technologies are readily applicable to many crops, and genetic leads in maize may have utility in other grasses. Taken as a whole they represent a transformative platform to develop deeper-rooted crops.