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

Physical and Molecular Responses of Pennycress (Thlaspi arvense L.) to Waterlogging


Andrea R. Gschwend1* (, Rachel Combs-Giroir1, Thiranya Lanka Wanigarathna1, John C. Sedbrook2


1The Ohio State University; 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.


Field pennycress (Thlaspi arvense L.) is a winter annual with extreme cold hardiness and seed oil properties desirable for sustainable aviation fuel production. Integration of pennycress as an off-season biofuel cash crop into Midwest corn and soybean rotations could lead to the production of 1 billion liters of seed oil annually, therefore boosting farmer revenue and offsetting carbon emissions. Pennycress fields are vulnerable to heavy spring precipitation events, which can lead to waterlogged soils where the root system is submerged under water. However, it is unknown if growth, development, or yield of pennycress is affected by waterlogging at the reproductive developmental stage, which occurs during April. This work aimed to characterize the morphological and transcriptomic responses of pennycress under 1 week of waterlogging during the reproductive stage. This was done with two core research pennycress lines: MN106 and SP32-10. One week of waterlogging at the reproductive stage under controlled conditions significantly impacted SP32-10 traits at harvest, including a reduction in shoot and root dry weight, total seed count, and total seed weight, whereas MN106 yield traits were not significantly affected. Therefore, natural phenotypic variation in waterlogging responses existed between these two pennycress accessions, so they were further investigated to determine the transcriptomic responses contributing to waterlogging tolerance. Twice as many genes were differentially expressed between waterlogged and control roots in MN106 (3,424 genes) compared to SP32-10 (1,767 genes) after 1 week of waterlogging at the reproductive stage. Functional enrichment analysis of upregulated differentially expressed genes in both lines revealed gene ontology (GO) terms associated with hypoxia and decreased oxygen, including genes involved in alcoholic fermentation and glycolysis. Compared to SP32-10,MN106 waterlogged roots exhibited stronger upregulation of genes involved in hypoxia and glycolysis, as well as strong downregulation of cell wall biogenesis genes. This indicates a better ability of MN106 to respond to the severe energy crisis invoked by waterlogging, possibly by strongly activating anaerobic responses and limiting growth to conserve energy. Lastly, to functionally tests the roles of HRE2 and SUS1 in waterlogging tolerance, which were highly expressed in waterlogged roots, EMS mutagenesis lines were waterlogged at the reproductive stage for 1 week. These two mutant lines were highly sensitive to waterlogging and had significantly reduced seed weight compared to controls, supporting the involvement of these genes in the response and adaptation to low-oxygen stress in pennycress. This research has identified phenotypic and transcriptomic variation in waterlogging responses in pennycress, leading to the identification of candidate genes and pathways involved in waterlogging tolerance. This work provides a foundation for understanding root waterlogging responses in pennycress, which will be useful for breeding climate-resilient pennycress varieties to improve yield following flood events and to grow pennycress on marginal lands.


Combs-Giroir, R., and A. R. Gschwend. 2024. “Physical and Molecular Responses to Flooding in Brassicaceae,” Environmental and Experimental Botany 216, 105664. DOI:10.1016/j.envexpbot.2024.105664.

Funding Information

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