Thlaspi arvense (field pennycress) is a cold tolerant oilseed species that is being domesticated as a new rapid cycling, winter annual cover crop and feedstock for biodiesel production. Pennycress is related to Arabidopsis thaliana, a model species that has provided an in-depth understanding of many basic developmental and physiological plant processes, which will provide vital information for the rapid domestication of a wild species into a new crop. By targeting key pennycress traits for improvement, such as reducing seed dormancy, increasing rates of spring flowering and maturity, increasing yield, and modifying seed oil composition, we are poised to develop a new winter cash crop that can fit within the corn/soybean rotation. To enable a mutation breeding approach that utilizes the massive amount of Arabidopsis-based knowledge, genomic resources are needed to identify target genes believed to influence key traits. In this dissertation, the first comprehensive annotated transcriptome assembly and comparative analyses are presented, along with the first draft genome sequence for pennycress. In these analyses, target assembled transcripts and corresponding DNA sequences are identified and compared to Arabidopsis homologs and enable the forward and reverse genetic screening of large scale mutant populations. An analysis of winter and spring annual pennycress accessions is also presented, which identified several wild alleles of the pennycress FLOWERING LOCUS C homolog which was found to be responsible for differentiating between spring and winter annual phenotypes. The resources presented herein will provide an unprecedented set of tools to enable the rapid domestication of a new crop species.