Characterization of genetically effective cells and EMS mutagenesis on the novel winter oil seed Pennycress (Thlaspi arvense).

We investigated the impact of Ethyl methanesulfonate (EMS) on genetically effective cells (GECs) to characterize the intra-individual genetic variation of EMS mutagenesis in the novel intermediate crop pennycress (Thlaspi arvense L.). We identified that pennycress contains at least 4 GECs which, when treated with EMS, create unique mutations across different branches within the same individual plant. However, we also found that branches were not completely distinct with 3.83-34.2% of the observed mutations being shared between at least 2 branches. We then propagated the M2 plants for whole genome sequencing, providing extensive characterization of the EMS mutation profile and developing a gene index as a resource for future reverse genetic screenings. The gene index was then validated through identification of two traits. We identified 5 mutations in transparent testa (TT) family of genes which resulted in lighter seed coat coloration, and two mutations in the indehiscent (IND) gene which resulted in increased shatter resistance of the pennycress seed pod. These two investigations demonstrate the viability of the gene index as a resource for further reverse genetic screenings.