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

532 Genomes Reveal Natural Variation and Local Adaptation History in Pennycress


Xing Wu1, Sebastian E. Toro Arana1,2* (, Lucas Czech1, Shannon Hateley1, Jason Thomas1, Ratan Chopra3, M. David Marks3, John C. Sedbrook4, and Moises Exposito-Alonso1,2


1Carnegie Institution for Science, Stanford, CA; 2Stanford University; 3University of Minnesota; and 4Illinois 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.


Pennycress is under development as an annual winter oilseed cover crop for the 80 million acre U.S. Midwest Corn Belt and other temperate regions including the Pacific Northwest. It has demonstrated unique attributes such as extreme cold resilience, rapid spring growth, and adaptation to various environments. Identifying genomic loci contributing to its resilience and local adaptation will significantly benefit its breeding programs and shed light on other Brassicaceae bioenergy crops for climate adaptation. Here is presented an analysis of 532 high-quality whole-genome resequenced wild pennycress accessions collected from their natural Eurasia and North American range (Pennycress Genome Portal, Nunn et al. 2022, Geng et al. 2021). The team comprehensively identified 6.3 million single nucleotide polymorphisms (SNPs) using the grenepipe variant calling pipeline (Czech, L. and Exposito-Alonso, M. 2022). In-depth analyses of population structure and demography indicate multiple recent migrations of the North American accessions from Europe with similar extensive genetic variation structured latitudinally. Preliminary admixture results suggest that introgression may play an important role in the local adaptation of pennycress. Genome-wide scans of selection signals and climate GWAS provide candidate genomic regions responsible for local adaptation and cold tolerance. In conclusion, this study offers valuable genomic resources for pennycress breeding and helps elucidate the history of migration and local adaptation in pennycress.


Pennycress – A solution for global food security, renewable energy and ecosystem benefits. [].

Nunn, A., et al. 2022. “Chromosome-Level Thlaspi arvense Genome Provides New Tools for Translational Research and for a Newly Domesticated Cash Cover Crop of the Cooler Climates,” Plant Biotechnol. J. 20, 944–63.

Geng, Y., et al. 2021. “Genomic Analysis of Field Pennycress (Thlaspi arvense) Provides Insights into Mechanisms of Adaptation to High Elevation,” BMC Biol. 19, 143.

Czech, L. and Exposito-Alonso, M. 2022. Grenepipe: A Flexible, Scalable and Reproducible Pipeline to Automate Variant Calling from Sequence Reads,” Bioinformatics 38, 4809–11.

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