PROGRAM IN PLANT BIOLOGY AND CONSERVATION

MS Projects for Prospective Students

Jeremie Fant

• Pitcher’s thistle (Cirsium pitcheri) is a federally threatened plant endemic to the western Great Lakes that is listed as endangered in Illinois and Indiana, threatened in Michigan and Wisconsin. Recent long-term studies have indicated that successional advancement is causing the decline of Pitcher’s thistle at blowouts but that populations are thriving on perched dune bluffs and large dune landscapes. To augment declining populations, we mixed seed sources from throughout the range to create genetically diverse and more viable populations. We are looking for a student to work with us to better understand and improve augmentation and restoration programs. We propose a series of studies to address efficacy of these methods for Pitcher’s thistle conservation. Previous genetic variation analysis (Fant et al. 2013-2014 and Sefton 2020) at these Great Lakes parks provides a unique opportunity to monitor temporal change in these populations and quantify the effectiveness of augmentation and reintroduction on generating genetically diverse populations, as well as examine impacts of weevil infestation on the genetics of this species. One goal is to quantify the effectiveness of population management.  One site has improved diversity and connectivity between subpopulations through the use of temporal monitoring of genetic variation and the use of paternity analysis to look at seed and pollen movement. This project will require a combination of both field and lab work.

Hector Ortiz

• Traditional knowledge of ancestral plants, building meaningful relationships with community partners, a community work framework beyond academia. 

Becky Barak

• The rethinking lawns project (rethinkinglawns.com) is setting up an experiment this summer testing establishment of native plants directly into turfgrass lawns. This study will consist of 5-6 native plant species planted into turfgrass from seed and plug, and under 2 mowing regimes, and will take place at two sites within the Chicago Park District. We are interested in how plants will establish in turfgrass, as well as whether they will flower under regular mowing. 

Suzy Strickler

Open to other project ideas that align with student's interests.

Aconitum Project

• The genus Aconitum comprises approximately 250 species of herbaceous perennials distributed throughout temperate montane regions of the Northern Hemisphere. These striking plants are key components of alpine and subalpine meadow ecosystems, where their nectar, pollen, and foliage support diverse insect communities ranging from butterflies to bumblebees. Aconitum species have long attracted human interest due to their potent alkaloid compounds—collectively known as aconite—extracted from leaves and rhizomes. These exceptionally bioactive molecules have been documented since early Greek and Roman pharmacopeia and remain integral to traditional European, Ayurvedic, and Chinese medicine. Root and rhizome extracts have also been historically used as arrow poisons for hunting and warfare across regions, including India, Tibet, Japan, and Alaska. However, unsustainable harvesting of wild populations for medicinal purposes and changing environmental factors have rendered many species threatened or endangered. Of the six Aconitum species native to North America, one—Aconitum noveboracense—is federally listed as threatened, with only a few small populations persisting across four U.S. states, including New York.
• To elucidate the taxonomy, population structure, and evolutionary diversification of alkaloid biosynthetic pathways in Aconitum, we are generating a high-quality draft reference genome for A. noveboracense. This genomic resource will serve as the foundation for integrative comparative genomic, transcriptomic, and metabolomic analyses aimed at (1) resolving the biogeography and population dynamics of North American species, (2) characterizing patterns of genetic diversity and gene flow to inform conservation strategies, and (3) identifying the genetic basis and chemical diversity of key medicinal metabolites across species.

Asimina Project

• Acetogenins are bioactive polyketides from the Annonaceae with potent cytotoxic, antiparasitic, and pesticidal activities (Ferreira et al. 2011; Jacobo-Herrera et al. 2019). Extracts from Annona crassiflora inhibit liver cancer cell proliferation (Justino et al. 2021), and A. triloba extracts are toxic to parasitic trematodes (Ferreira et al. 2011), which cause major global health and livestock losses. However, the acetogenin annonacin also induces cortical neuron death and has been linked to atypical Parkinsonism in humans (Lannuzel et al. 2003; Potts et al. 2012). These dual roles highlight both the therapeutic promise and toxicity of pawpaw (A. triloba) metabolites. Understanding the genetic and regulatory basis of acetogenin biosynthesis is therefore essential for both developing safer fruit varieties and harnessing these compounds as novel antiparasitic or anticancer agents.

1. Association mapping of acetogenin phenotypes in pawpaw seedling and parental populations to identify genomic loci linked to metabolite diversity.
2. Co-expression network analysis from RNA-seq data of high- and low-acetogenin genotypes under control and stress conditions to reveal co-regulated biosynthetic genes.
3. Comparative and evolutionary genomics across ten Asimina species to detect conserved pathway genes under purifying selection.

Together, these analyses will yield candidate biosynthetic genes, insights into pathway regulation, and evolutionary context for acetogenin metabolism—providing genomic resources to guide breeding and bioengineering efforts aimed at balancing safety with bioactivity.