Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics. (10th December 2018)

• Record Type: Journal Article
• Authors: Chopra, Ratan; Johnson, Evan B.; Daniels, Erin; McGinn, Michaela; Dorn, Kevin M.; Esfahanian, Maliheh; Folstad, Nicole; Amundson, Kirk; Altendorf, Kayla; Betts, Kevin; Frels, Katherine; Anderson, James A.; Wyse, Donald L.; Sedbrook, John C.; David Marks, M.
• Is Part Of: Plant journal. Volume 96:Number 6(2018)
• Page Start: 1093
• Page End: 1105
• Publication Date: 2018-12-10
• Subjects: pennycress -- forward genetics -- reverse genetics -- model plant -- transparent testa -- trichome -- gene index -- mutagenesis -- whole‐genome sequencing; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14147
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: 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. Significance statement: The domestication of pennycress has the potential to create a new oilseed cash/cover crop that can be grown during the fallow period between traditional summer crops, such as between the >80 million acres undergoing corn/soybean rotation in the Upper Midwest of the USA. This report demonstrates that translational genomics using Arabidopsis can serve as a tool to help greatly speed up the domestication process.