Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

A Temporal Atlas and Response to Nitrate Availability of 3D Root System Architecture in Diverse Pennycress (Thlaspi arvense L.) Accessions


Marcus Griffiths1* ([email protected]), Alexander E. Liu1, Shayla L. Gunn1, Nida M. Mutan1, Elisa Y. Morales1, Vannessica Jawahir1, Dmitri Nusinow1, Christopher Topp1, and John C. Sedbrook2


1Donald Danforth Plant Science Center; and 2Illinois State University



This project employs evolutionary and computational genomic approaches to identify key genetic variants that have enabled Thlaspi arvense L. (Field Pennycress; pennycress) to locally adapt and colonize all temperate regions of the world. This, combined with knowledge of metabolic and cellular networks derived from first principles, guides precise laboratory efforts to create and select high-resilience lines, both from arrays of random mutagenesis and by employing cutting-edge CRISPR genome editing techniques. This project will deliver speed-breeding methods and high-resilience mutants inspired by natural adaptations and newly formulated biological principles into a wide range of commercial pennycress varieties to precisely adapt them to the desired local environments.


Roots have a central role in plant resource capture and are the interface between the plant and the soil affecting multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich oil seeds amenable as a biofuel (30-35% oil) or high-protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand adaptive responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Using a root imaging and analysis pipeline 4D pennycress root system architecture was characterized under four nitrate treatments across time. Significant nitrate condition response and genotype interaction was identified for many root traits with a greater impact on lateral root traits. In trace nitrate conditions a greater lateral root count, length, interbranch density, and a steeper lateral root angle was observed compared to high nitrate conditions. Genotype by nitrate condition interaction were observed for root width, width depth ratio, mean lateral root length, and lateral root density. Further, a large format mesocosm system has been developed and used to visualize root system architecture of mature plants with neighbors. Using this system, researchers are assessing how variation in pennycress root system architecture can affect ecosystem service and abiotic stress tolerance scaling from single plant to canopy level traits. These results illustrate root trait variance available in pennycress accessions and useful targets for breeding of improved nitrate responsive cover crops for greater productivity, resilience, and ecosystem service.


Griffiths, M., et al. 2022. “Optimisation of Root Traits to provide Enhanced Ecosystem Services in Agricultural Systems: A focus on cover crops.” Plant, Cell & Environment. DOI:

Griffiths, M., et al. 2023. “A Temporal Atlas and Response to Nitrate Availability of 3D Root System Architecture in Diverse Pennycress (Thlaspi arvense) Accessions.” bioRxiv. DOI:

Funding Information

This research is supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science program grant no. DE-SC0021286.