Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics

Ratan Chopra, Evan B. Johnson, Erin Daniels, Michaela Mcginn, Kevin M. Dorn, Maliheh Esfahanian, Nicole Folstad, Kirk Amundson, Kayla Altendorf, Kevin Betts, Katherine Frels, James A. Anderson, Donald L. Wyse, John C. Sedbrook, M. David Marks

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Thlaspi arvense (pennycress) has the potential for domestication as a new oilseed crop. Information from an extensive body of research on the related plant species Arabidopsis can be used to greatly speed this process. Genome-scale comparisons in this paper documented that pennycress and Arabidopsis share similar gene duplication. This finding led to the hypothesis that it should be possible to isolate Arabidopsis-like mutants in pennycress. This proved to be true, as forward genetic screens identified floral and vegetative pennycress mutants that were similar to mutants found in Arabidopsis. Extending this approach, it was shown that most of the pennycress genes responsible for the formation of oxidized tannins could be rapidly identified. The causative mutations in the pennycress mutants could be identified either by PCR amplification of candidate genes or through whole-genome sequencing (WGS) analysis. In all, WGS was used to characterize 95 ethyl methane sulfonate mutants, which revealed a mutation rate of 4.09 mutations per megabase. A sufficient number of non-synonymous mutations were identified to create a mutant gene index that could be used for reverse genetic approaches to identify pennycress mutants of interest. As proof of concept, a Ta-max3-like dwarf mutant and Ta-kcs5/cer60-like wax mutants deficient in the biosynthesis of long chain fatty acids were identified. Overall, these studies demonstrate that translational genomics can be used to promote the domestication of pennycress. Furthermore, the ease with which important findings could be made in pennycress makes this species a new potential model plant.

Original languageEnglish (US)
Pages (from-to)1093-1105
Number of pages13
JournalThe Plant Journal
Volume96
Issue number6
DOIs
StatePublished - Dec 2018

Keywords

  • forward genetics
  • gene index
  • model plant
  • mutagenesis
  • pennycress
  • reverse genetics
  • transparent testa
  • trichome
  • whole-genome sequencing

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

Fingerprint Dive into the research topics of 'Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics'. Together they form a unique fingerprint.

  • Cite this

    Chopra, R., Johnson, E. B., Daniels, E., Mcginn, M., Dorn, K. M., Esfahanian, M., Folstad, N., Amundson, K., Altendorf, K., Betts, K., Frels, K., Anderson, J. A., Wyse, D. L., Sedbrook, J. C., & David Marks, M. (2018). Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics. The Plant Journal, 96(6), 1093-1105. https://doi.org/10.1111/tpj.14147