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Identification and stacking of crucial traits required for the domestication of pennycress

Nature Food volume 1, pages 84–91 (2020)Cite this article

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Abstract

The oilseed species Thlaspi arvense (pennycress)—a weed that was only recently removed from the wild—has the potential to provide new sources of food and bioproducts when grown as a winter cover crop. Domestication of wild species has historically taken hundreds to thousands of years, but by making use of large-scale high-throughput comparative gene and phenotype analyses, along with recently developed technological tools, it has been possible to greatly accelerate this process. By taking advantage of extensive gene and phenotype knowledge in the related plant Arabidopsis, mutations for early maturity, reduced pod shatter, reduced seed glucosinolates and improved fatty acid composition were identified. Progress has been made to rapidly stack these traits in order to domesticate the plant, allowing it to fit within current crop cycles and to have improved seed harvestability and nutritional content. Pennycress, domesticated as a winter cover crop, may provide new sources of food, animal feed and bioproducts—and solutions to food security.

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Fig. 1: Early-flowering pennycress mutant.
Fig. 2: Isolation and characterization of pennycress seedpod mutants.
Fig. 3: Comparison of glucosinolates in the wild type and Nutty (Ta-aop2-1) mutant pennycress.
Fig. 4: Comparison of wild-type fatty acid profiles with those of the pennycress Ta-fae1 and Ta-rod1 mutant lines.
Fig. 5: Comparison of the fatty acid profiles of wild-type pennycress and the Ta-fae1-1 Ta-rod1-1 double mutant with that of canola oil.

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Data availability

All sequence information described in this study is contained within the Supplementary Information. All plant materials described in this report are available upon completion of material transfer agreements.

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Acknowledgements

We acknowledge the hard work of many undergraduates and others who contributed to this study, including K. Nord, C. Branch, L. Sullivan, L. Aldrich, G. Rockstad and many others. We thank M. Cook and T. Nazarenus for help with tissue embedding, sectioning, microscopy and seed oil analyses, respectively. This material is based on work that is supported by the National Institute of Food and Agriculture, US Department of Agriculture, under award numbers 2014-67009-22305 and 2018-67009-27374 to M.D.M., J.C.S. and W.B.P. Funding for research conducted in the laboratory of E.B.C. was provided by the US Department of Energy, Office of Science, OBER (DOE-BER SC0012459) and NSF Plant Genome Program (13-39385). Additional funds were provided by the Minnesota Department of Agriculture and University of Minnesota Forever Green Initiative to J.A.A. and B.I., and by the Walton Family Foundation, PepsiCo, University of Minnesota Grand Challenges Fund and General Mills to D.L.W.

Author information

Author notes

  1. Evan B. Johnson

    Present address: Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, USA

  2. Ryan Emenecker

    Present address: Department of Biology, Washington University, Saint Louis, MO, USA

  3. Erin Daniels

    Present address: Salk Institute for Biological Studies, La Jolla, CA, USA

  4. Kevin M. Dorn

    Present address: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA

Authors and Affiliations

  1. Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA

    Ratan Chopra, Evan B. Johnson, Ryan Emenecker, Erin Daniels, Kevin M. Dorn, Nicole Folstad & M. David Marks

  2. Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, USA

    Edgar B. Cahoon

  3. Covercress, Saint Louis, MO, USA

    Joe Lyons & Tim Ulmasov

  4. Department of Plant Sciences, University of California, Davis, Davis, CA, USA

    Daniel J. Kliebenstein

  5. School of Biological Sciences, Illinois State University, Normal, IL, USA

    Maliheh Esfahanian, Michaela McGinn, Alexandra Berroyer & John C. Sedbrook

  6. Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA

    Katherine Frels, Matthew Ott, Kayla Altendorf, James A. Anderson & Donald L. Wyse

  7. Food Science and Nutrition, University of Minnesota, Saint Paul, MN, USA

    Cynthia Gallaher & Baraem Ismail

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Contributions

M.D.M. and J.C.S. conceived the study, designed the experiments, supervised and organized the coworkers, created the mutagenized populations, isolated the mutants, helped characterize the mutants, identified the candidate genes and co-wrote the manuscript. R.C. characterized the fatty acid profiles along with E.B.C., C.G. and B.I. K.M.D. performed the WGS analyses as well as independently performing extensive data analyses and helping to write the first draft of the manuscript. J.L., D.J.K. and T.U. were responsible for the wet lab glucosinolate analyses. E.B.J., E.D., N.F., R.E., M.E., M.M., A.B. and K.A. isolated mutants and helped to characterize the candidate genes. M.O. helped to evaluate FLC expression and the seed yield of the elf6 mutant. J.A.A. and K.A. helped with the initial NIRS set-up. K.M.D., K.F. and R.C. helped to characterize the elf6 mutant. A.B. generated and imaged the wild-type and ind-3 seedpod sections. D.L.W. isolated the wild-type line MN106 used in the study, and aided in planning.

Corresponding author

Correspondence to M. David Marks.

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Competing interests

The authors declare potential competing interests as intellectual property applications have been submitted on portions of the reported research (patent application no. US 2019/0225977 A1 to T.U., J.C.S., M.D.M., M.M., R.C.; US 2019/0053458 A1 to M.D.M., J.C.S., R.C., M.E.; US 2019/0053457 A1 to M.D.M; WO 2018/140782 A1 to M.D.M., J.C.S., K.M.D., D.L.W.; WO 2019/157504 A1 to M.D.M., R.C., N.F., J.C.S., D.L.W.).

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Supplementary information

Supplementary Information

Supplementary Figs. 1–5, Tables 1–7 and Data 1–3.

Reporting Summary

Supplementary Data 4

Summary of homozygous mutations identified in the mutant lines.

Source data

Source Data Fig. 1

Data used for generating box plots for figure 1d and 1e

Source Data Fig. 2

Data used for generating box plots for figure 2e

Source Data Fig. 3

Data used for generating box plots for figure 3a

Source Data Fig. 4

Data used for bar charts for figure 4a and 4b

Source Data Fig. 5

Data used for bar charts plots for figure 5

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Chopra, R., Johnson, E.B., Emenecker, R. et al. Identification and stacking of crucial traits required for the domestication of pennycress. Nat Food 1, 84–91 (2020). https://doi.org/10.1038/s43016-019-0007-z

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