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

Reduced Environmental Plasticity in Pennycress Improves Responses to Competition and Climate Change


Vanessica Jawahir1* (, Bhabhesh Borphukan2, Zhaslan Akhmetov2, Salma Adams1, Marcus Griffiths1, David Marks3, Pubudu Handakumbura4, Dan Jacobson5, Karen A. Sanguinet2, Dmitri A. Nusinow1, John Sedbrook6


1Donald Danforth Plant Science Center; 2Department of Crop and Soil Sciences, Washington State University–Pullman; 3College of Biological Sciences, University of Minnesota–Minneapolis; 4Pacific Northwest National Laboratory; 5Oak Ridge National Laboratory; 6School of Biological Sciences, Illinois State University



IPReP: 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.


Pennycress (Thlaspi arvense), an emergent winter annual bioenergy oilseed cover crop, is under development to be grown in the Midwest during typical fallow periods. Pennycress varieties can yield over 1,680 kg ha-1 (1,500 lb ac-1) of seeds, producing 600 liters ha-1 (65 gal ac-1) of oil annually without competing with food crops. However, crucial work remains to domesticate and optimize pennycress for incorporation into present cropping systems and its resilience to climate change. For example, interseeding into standing fields in late fall leads to shade-induced responses in pennycress. Similarly, higher temperatures during fall planting cause seedlings to elongate, resulting in poor stand establishment. Researchers have established that pennycress is shade and heat-intolerant and elongates in response to these stresses. Excessive elongation creates a cyclical dilemma in which the elongated plants increasingly shade their neighbors, further inducing retaliatory elongation responses to outgrow neighboring plants. These adaptive morphogenic changes are undesirable in cropping systems as elongated plants establish poorly, are more prone to lodging, and reduce yields. Researchers are using the knowledge base from Arabidopsis thaliana to manipulate genes in the phytochrome signaling pathway to improve resilience to shade present during interseeding and increasing winter and spring temperatures. Evaluation of CRISPR and EMS alleles of PHYTOCHROME INTERACTING FACTOR 7 show that pif7 mutants have reduced organ elongation and retain a compact rosette when exposed to shade, elevated temperature, and combined stresses while maintaining yield and desirable phenotypes such as earlier flowering in stress conditions. By lowering elongation responses to shade and elevated temperature, researchers aim to increase pennycress ground cover when grown at high densities, reduce shade-induced responses when interseeded into standing crops, and elongation in response to higher temperatures. In addition to light responses, researchers are addressing the freezing tolerance of pennycress by examining the role of fatty acid modifications on winter survival and in response to chilling and freezing stress. Furthermore, researchers have used CRISPR and gene editing to target CAMTA and CBF family genes and RNAseq, metabolomics, and fatty acid analysis to examine global changes to low temperatures. Future work will determine if these changes to shade and temperature responses improve the performance, productivity, and resilience of pennycress in the field.

Funding Information

This research is supported by the U.S. DOE, Office of Science, BER Program, GSP grant no. DE-SC0021286.