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

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.

Genetic Diversity of Field Pennycress (Thlaspi arvense) Reveals Untapped Variability and Paths Toward Selection for Domestication

“…Thlaspi arvense L., also known as field pennycress, is a promising species for domestication as a cash cover crop that produces a biofuel feedstock [1][2][3]. As a winter annual, it can be integrated into the fallow periods of traditional cropping systems in the U.S. Midwest [4,5].…”

Progress toward the identification and stacking of crucial domestication traits in pennycress

“…Like Arabidopsis, pennycress is self-fertile and has a relatively small non-repetitive diploid genome. Genome sequencing and analyses revealed a mostly one-to-one functional correspondence between single Arabidopsis genes and single pennycress ortholog genes (Chopra et al 2018b, Dorn et al 2013, Dorn et al 2015). Importantly and directly related to the domestication of pennycress, recessive Arabidopsis mutants have been described that eliminate weedy and other agronomically undesirable traits (Provart et al 2015, Sedbrook , et al 2014).…”

Ta Ta for now: Thlapsi arvense (pennycress), an emerging model for genetic analyses

“…Several modifications to plant architecture, oil content and quality will be needed to domesticate pennycress (reviewed by Sedbrook et al ., ). In the highlighted paper (Chopra et al ., ), the Marks and Sedbrook labs present tools that will help in these domestication efforts. A companion paper (McGinn et al ., ) presents other desirable tools for using pennycress as a complementary model to Arabidopsis, i.e.…”

“…As the schematic in Figure shows, Chopra et al . () focused on mutagenizing seed, then screened the M2 populations for obvious phenotypes and carried out whole genome sequencing of selected lines. The Marks lab had previously generated a draft genome and transcriptomics resources for pennycress (Dorn et al ., ).…”

“…In Chopra et al . () they aligned the draft pennycress genome to the Arabidopsis genome and showed that synteny was substantial, thus hypothesizing that the Arabidopsis genome could be used as a guide for identifying causal mutations in the pennycress mutant populations. Their Data S5 lists over 16 000 pennycress genes with mutations as well as the closest Arabidopsis homolog for each.…”