From cacao stewardship to climate resilience– these are just a few of the diverse graduate student projects recently funded through the Schmittau-Novak Small Grants Program. Supported by a bequest from the estate of Jean Schmittau in honor of Joseph Novak, Plant Biology Professor Emeritus, the Schmittau-Novak Small Grants Program is designed to provide graduate students in the School of Integrative Plant Science with the opportunity to experience the process of writing and reviewing proposals, and implementing a research plan of their own design. Ten proposals were selected for Spring 2025 funding. The program is directed by Dan Buckley and Teresa Pawlowska.
Gene Conversion–Driven Erosion of Wild Tomato Introgressions: Building Genomic Resources to Advance Crop Improvement and Evolutionary Insight
Lance “Teo” Courtney, Plant Biology PhD candidate, BTI/USDA, Giovannoni lab. His thesis work spans fruit genetics, agroecology, and the integration of research, education, and outreach. A non-traditional veteran student and part-time Air National Guard member, he owns and operates a farm locally with his family.
Alien introgressions are important drivers of evolution in nature and crop improvement; however, we believe that gene conversion events erode these donor sequences. Further, the rate of erosion is likely heterogenous across the genome and set by the divergence between the donor and background sequence. Our objectives are threefold: (1) to create a comprehensive and accessible wild tomato introgression database for high-resolution trait mapping; (2) leverage this resource to re-analyze extensive extant trait data; and (3) test our gene conversion-driven erosion model. We will construct high-resolution genotype maps and line-specific references for over 1000 introgression lines. This will include compiling existing data and generating population-scale genomic resources for two recently developed populations associate with S. neorickii and S. sitiens. These resources will be used for QTL and GWAS to reveal a diverse array of fruit trait associated loci. All data will be developed into a tomato introgression open-access database within the Sol Genomic Network (SGN) for use by the tomato breeding community. Finally, donor sequences will be evaluated for enrichment of background alleles, especially in association with putative conversion sites. We aim to test whether gene conversion erodes donor sequence and if this a function of divergence. This project will impact breeding programs and provide insight into how introgressions evolve in natural populations.
Indigenous Stewardship and Biodiversity: Preserving Cacao Genetic Diversity Through Agroforestry in Southeastern Costa Rica
Emma Herrighty is a Plant Breeding and Genetics PhD student in the EQUAL Lab under the direction of Hale Tufan. Her research focuses on the collection, characterization, and cultural documentation of heritage (“Criollo”) cacao in Costa Rica.
In southeastern Costa Rica, along the Caribbean coast, cacao is produced under various growing systems, including agroforestry. This method is widely practiced in the Indigenous Bribri and Cabécar communities of Talamanca, where 95% of all cacao in the country is produced. Despite this regional importance, the genetic diversity of cacao in Talamanca remains largely understudied. To address this gap, my research explores how Indigenous women, operating within traditional agroforestry systems, have shaped and preserved cacao diversity through their cultural values, preferences, and knowledge systems. Given the long-term management of these agroforestry systems – and that cacao is a long-lived perennial crop with individual trees often passed down through matrilineal land inheritance – I hypothesize that rare, ancient cacao germplasm (i.e. “Criollo” cacao) exists only under the stewardship of Indigenous producers. Using a mixed methods approach that integrates ethnographic fieldwork, morphological trait analysis, and genetic characterization, this study will document the extent and significance of cacao diversity maintained by Bribri and Cabécar communities. This heritage Criollo germplasm could contribute significantly to the production of fine flavor cacao, supporting the development of a regional designation unique to Costa Rica. Such production could enhance the market value of Costa Rican cacao and generate resources to support biodiversity conservation rooted in Indigenous agroforestry traditions.
Assessing the Impacts of Shading in an Agrivoltaic System on Weed Morphology and Community Differentiation
Dana Russell is a first-year MS student in Toni DiTommaso’s Weed Ecology and Management lab. Her research is focused on understanding how weed growth and community composition are affected in agrivoltaic cropping systems.
Agrivoltaic systems integrate solar energy generation with agricultural production and are emerging as a promising solution to the growing global demand for food and electricity. Light availability in these systems is lower than in conventional agricultural systems, which may impact weed and crop growth and competition dynamics. Effective weed management is essential for the economic viability of agrivoltaic systems, however, no published research has investigated how weed growth and community composition are affected in these systems. This project will investigate the morphological shade responses of a variety of weed species. Seeds will be collected from weeds growing within and outside of an operational solar array and subsequently grown under full sun and simulated shade in a greenhouse. We aim to characterize species-specific shade tolerance and assess the potential for heritable changes in weed populations exposed to long-term shading. Characterizing morphological shade responses of weed species will help predict their long-term fitness and how weed communities may shift as agrivoltaic systems mature. Morphological changes also affect the efficacy of weed control, as changes in height, canopy structure, or biomass allocation can alter the outcomes of tillage or herbicide application. By identifying species-specific responses to reduced light, we aim to predict weed-crop interactions and inform cropping system design and weed management in agrivoltaic systems. Ultimately, we hope that these insights will improve adoption and long-term viability of agrivoltaic cropping systems.
Deciphering Tissue-Specific Resin Glycoside Biosynthesis for Enhanced Sweet Potato Resistance and Breeding
Bhaswati Sarmah is a second year PhD student in Plant Breeding and Genetics working under the guidance of Gaurav Moghe. She studies the metabolic and molecular mechanisms underlying biotic and abiotic stress resistance in sweet potato, focusing on resin glycosides and arbuscular mycorrhizal fungi.
Richie Ragas is a third-year PhD candidate in Plant Biology under the supervision of Mike Scanlon. His work focuses on understanding the role of WOX3 genes in maize leaf development, specifically investigating the molecular, genetic, and biomechanical mechanisms that regulate the robust patterning of maize leaf sheath margins.
Resin glycosides (RGs) are a chemically diverse class of defense-related metabolites found in sweet potato (Ipomoea batatas) and other members of the Convolvulaceae family. These compounds have been associated with resistance to a wide range of pests and pathogens, yet the precise tissues and cell types responsible for their biosynthesis remain unknown. In this study, we aim to characterize the spatial localization of RGs in sweet potato roots and identify the biosynthetic genes involved in their production. Preliminary analyses across four cultivars—Beauregard, Tuskegee, Purple Japanese, and Murasaki—revealed striking differences in RG abundance across peel layers, with the highest levels concentrated in outer periderm tissues. Anatomical staining and confocal microscopy will be used to define tissue composition, while Liquid Chromatography-Mass Spectrometry (LC-MS) will quantify RG distribution across layers. We hypothesize that epidermal and subepidermal layers are key biosynthetic sites, and that cultivar-specific anatomical features such as periderm thickness and suberization may influence in RG accumulation. To identify the underlying genetic drivers, we will employ laser microdissection followed by cell-type specific RNA sequencing to pinpoint candidate biosynthetic genes enriched in RG-producing tissues. By integrating anatomical, metabolomic, and transcriptomic data, this research will generate valuable tools—including molecular markers and tissue maps—to guide breeding efforts for pest-resistant sweet potato cultivars. The results will offer sustainable alternatives to chemical pest control and provide a framework for understanding the spatial regulation of specialized metabolites in root crops more broadly, with implications for food security and crop resilience.
Farmer-Led Innovation and Climate Resilience: Exploring On-Farm Experimentation and Knowledge Networks in New York Agriculture
Katie Rohrbaugh is a 1st year integrated Master’s and PhD student working with Louis Longchamps in Soil and Crop Sciences. Her research focus emphasizes interdisciplinary methodologies to study how farmers experiment on their farms and produce agroecological knowledge to grow crops more sustainably.
Emily Fratz is a first year PhD student in Plant Breeding and Genetics at Cornell with the Moore Lab and Hale Tufan’s EQUAL Lab. She’s interested in dry bean breeding for the Northeastern US and has a particular interest in participatory methods and engaging growers in the research process
Limiting global warming to 2 °C before the end of this century demands transformative shifts in crop management, yet a persistent gap between agronomic innovation and on farm implementation undermines progress toward more sustainable food systems. Traditional research paradigms—randomized replicated trials and statistical analyses—often exclude farmers’ practical knowledge and networks, leaving their insights underutilized. On farm experimentation (OFE) bridges this divide by positioning farmers as co creators of knowledge, with researchers employing digital tools to standardize and contextualize observations. Although literature supports OFE’s potential, little is known about how farmers conduct experiments, exchange insights, or wish to engage with researchers. This study investigates the experiment sharing behaviors and collaboration preferences of New York State farmers, with special attention to underrepresented communities. We predict that frequent experimenters maintain denser social networks and exhibit stronger interest in OFE participation. To test this, we will recruit thirty farmers in the spring and summer of 2025 and conduct in person, semi structured interviews during planting and harvest seasons. Interviews will explore: (1) the design, evaluation, benefits, and challenges of on farm experiments; (2) the structure and dynamics of knowledge exchange networks, eliciting contacts, relationship roles, communication modes, and influence; and (3) farmers’ desired terms of participation in OFE initiatives. We will establish a baseline understanding of farmer led innovation processes and inform the design of future OFE networks. By elucidating how farmers experiment and collaborate, this research will guide the development of participatory frameworks that forefront farmer expertise, accelerate sustainable practice adoption, and strengthen climate resilience in agricultural systems.
Engineering Superior Rubisco from Hornwort to Enhance Photosynthesis and Crop Yield in C3 Plants
Dan Hong Loh is a second-year Plant Biology PhD student in Laura Gunn’s lab. She studies E. coli and tobacco SynBio systems for Rubisco expression and assembly, with a focus on the diversity of bryophyte (hornworts, mosses, liverworts) Rubiscos.
To safeguard food security in the face of climate change and population growth, efforts to improve crop yields must focus on increasing photosynthetic efficiency. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the crucial gateway enzyme for carbon dioxide (CO2)-fixation in photosynthesis; yet its performance is also one of the major limiting factors for photosynthetic efficiency. Rubisco engineering thus presents an opportunity to improve photosynthesis and crop productivity, such as by introducing a kinetically superior Rubisco into crop plants. One such Rubisco includes that of the hornwort Anthoceros agrestis (AaRubisco), which was recently found to have a catalytic rate twice that of Arabidopsis thaliana without sacrificing its affinity for CO2. AaRubisco’s ideal kinetics make it a promising candidate to improve photosynthesis in crop plants. Here, I aim to introduce AaRubisco into tobacco- a C3 plant and a model organism for chloroplast transformation- and evaluate any changes to the growth and photosynthesis of tobacco. This will serve as a proof-of-concept to determine if such a strategy to improve crop yields is feasible, and if successful, will lay the foundation for future research in Rubisco engineering. Given Rubisco’s crucial role in photosynthesis, it has far-reaching impacts on plant physiology and should be part of a holistic approach to improve crop productivity.
Calcium Signaling and Pathogen Evasion: Unraveling Plant–SRP Interactions Under Climate-Driven Flooding Stress
Fatemeh Ekbataniamiri is a second year PhD student in the Swingle Lab in Plant Pathology and Plant Microbe Biology. Her research explores stress responses, gene regulation, and community assembly in Soft rot Pectobacteriaceae, aiming to better understand pathogen–environment interactions and develop innovative strategies for disease management.
Peiqiao Xie is a second-year PhD student in Jian Hua’s lab in Plant Biology. Her research focuses on understanding the physiological responses and molecular mechanisms that underlie calcium homeostasis in Arabidopsis.
Climate change driven flooding events are intensifying the threat of Soft rot Pectobacteriaceae (SRP), necrotrophic bacterial pathogens that favor waterlogged environments and macerate plant tissues. While plants have evolved adaptive mechanisms to cope with flood-induced hypoxia such as calcium (Ca²⁺)-mediated signaling, the role of these responses in modulating disease outcomes remains poorly understood. Emerging evidence shows that loss of function mutations in several Ca²⁺ transporters elevate cytosolic Ca²⁺ levels, potentially priming plants for hypoxia tolerance and enhancing immune responses to pathogen attack. SRP, however, may circumvent these defenses by secreting exopolysaccharides (EPS), which chelate apoplastic Ca²⁺, inhibit Ca²⁺ influx, and suppress Ca²⁺-dependent immune signaling. This study aims to investigate the interplay between plant cytosolic Ca²⁺ homeostasis and SRP virulence under hypoxic conditions. Specifically, we
will determine whether elevated basal cytosolic Ca²⁺ enhances resistance to SRP infection and explore how EPS-mediated Ca²⁺ chelation enables SRP to evade host immunity. By dissecting the role of Ca²⁺ signaling in plant pathogen interactions during flooding stress, this work will provide new insights into the molecular basis of disease susceptibility in flood-prone agricultural systems and inform strategies for climate-resilient crop protection.
Uncovering Sex Determination in Hechtia texensis: A Genomic Approach to Understanding Dioecy in Bromeliaceae
Josh Felton is a second year PhD student in Chelsea Specht’s lab in Plant Biology. His research explores how reproductive strategies influence genetic diversity, population structure, and diversification within the family Bromeliaceae.
Sex determination in flowering plants has evolved through a wide variety of genetic mechanisms, offering a system to understand the evolutionary pressures and genomic rearrangements that drive sex chromosome evolution. While sex determination is well-studied in some plant lineages, the genetic basis of sex determination in Bromeliaceae remains a mystery. This undergrad-led project aims to fill the gap by generating the first chromosome-scale reference genome for Hechtia texensis, a dioecious, limestone endemic species native to the Trans-Pecos region of Texas. Using a combination of sequencing approaches, we will identify and characterize the sex-determining region using a recently developed k-mer based approach. This study will lay a crucial foundation for understanding the genomic underpinnings of dioecy in Bromeliaceae and will contribute to broader questions about the repeated evolution of separate sexes in flowering plants. As part of this study, we will carry out targeted fieldwork to expand botanical collections, assess natural population sex ratios, and document intraspecific variation in morphology and habitat. Specimens will be deposited at the L.H. Bailey Hortorium and the Botanical Research Institute of Texas, providing valuable resources for future genomic, ecological, and conservation research in Hechtia. By integrating biodiversity genomics with collections-based research, this project will help shed light on how sex chromosomes evolve in a diverse and understudied lineage of terrestrial bromeliads.
Decoding Rhizosphere Dynamics: Investigating Root Exudate Impacts on Soil Microbiomes and Carbon Persistence
Gillian Gomer is a fourth-year PhD Candidate in Taryn Bauerle’s lab. Her research focuses on the development of new plant root rhizospheres within soil over space and time. She is interested in identifying root traits that promote organic carbon input and increase soil moisture retention to improve drought tolerance.
Roots exude water and metabolites into the soil to condition their environment and foster symbiotic relationships with soil microorganisms which, in exchange, provide essential nutrients otherwise inaccessible to the plant. Plants can alter the composition of their root exudates according to abiotic and biotic conditions to dynamically engineer their environment. The initial development of a rhizosphere remains unresolved spatially and temporally: it is important to clarify these dynamics to identify traits that promote persistent carbon-hotspots for beneficial microbes and soil moisture retention. With the support of this grant, I will finely resolve the spatial (sub-mm) and temporal (hour) development of a realistic rhizosphere as it relates to root-derived carbon. By using medical microdialysis probes to mimic root exudation, this research considers the relative impact of exudate composition, concentration, and soil microbial activity on rhizosphere size and lifespan.
Understanding Species Interactions in Traditional Grain Mixtures: Integrating Farmer Knowledge and Root Dynamics for Climate-Resilient Intercropping
Leah Treffer is a second year Plant Breeding PhD student in the Jannink and Moore labs. She is evaluating cereal-legume intercrops (alfalfa-intermediate wheatgrass and spring oat-pea) with the goal of contributing to varieties that perform well in intercrop systems.
Adele Woodmansee is a PhD candidate in Soil and Crop Science and she is a member of Andrew McDonald’s research group. Her research looks at changing cropping systems and cereal diversity, including barley landrace diversity and cereal species mixtures, in the High Atlas Mountains of Morocco.
Intercropping supports diverse diets and ecosystem functions worldwide. In some smallholder systems, grains of multiple species are planted together, producing mixed grains used for food or fodder. These mixtures include cereal species mixtures and cereal-legume mixtures. Grain mixtures are particularly understudied but could have value for nutrition, risk management, and sustainable yield intensification. Contemporary grain mixtures have been documented in Ethiopia, Georgia, Lebanon, and Morocco. Mixtures can serve as an insurance strategy for drought – mixing desirable and drought tolerant reliable varieties can ensure that at least one will be productive under a range of conditions. Despite growing interest in mixed cropping systems, the mechanisms of interaction between species in mixtures remain poorly understood, especially below-ground. We will conduct greenhouse experiments to evaluate durum-bread wheat and barley-grass pea mixtures, using landraces sourced directly from farmers in Lebanon and Morocco. These landrace mixtures likely show complementarity and may have co-evolved under farmer selection as mixtures. We will evaluate the above- and below-ground dynamics of these mixtures and their monocultures under varying water treatments. In addition, we will carry out interviews with Moroccan farmers about their perceptions of competition and complementarity in mixtures that they plant to incorporate farmer knowledge into our understanding of species interactions. Finally, we will use the Agricultural Production Systems Simulator (APSIM) to simulate the performance of these mixtures under diverse drought scenarios, focusing on the role of phenology and root architecture. Our work will provide insight into the mechanics of interaction in these mixtures.