Projects and Faculty

As world leaders in plant genome research, Cornell University, Boyce Thompson Institute (BTI), the USDA-ARS, and the U.S. Plant, Soil, and Nutrition Laboratory are host to many outstanding research labs. These research facilities have built on Cornell’s long tradition of research in plant genetics and breeding to develop novel technologies, the application of which has sought to improve the scientific understanding of many aspects of plant biology. The research interests of the labs are quite varied, ranging from identifying disease resistance in crop plants to understanding how plants sense and respond to light. Please click the following text to learn more about the faculty members associated with the research projects in the various summer internship opportunities at BTI.

Internship Projects

To learn more about available projects and their faculty sponsors, click on the topics below.

TAL effector biology for durable plant disease prevention and DNA targeting applications - Bogdanove Lab, Cornell

Project description:

TAL effector illustration - Jon Bogdanove

TAL effector PthXo1 bound to its target. Illustration by Jon Bogdanove

Research in the Bogdanove laboratory is directed at understanding mechanisms of bacterial plant pathogenesis and plant defense to develop better means of disease control. We focus on the interactions of the globally important staple crop rice with Xanthomonas oryzae, in which transcription activator-like (TAL) effector proteins of the bacterium play an important role. TAL effectors are injected into plant cells by the bacterium, enter the nucleus, and activate specific plant “susceptibility” (S) genes that contribute to disease development. TAL effectors recognize their DNA targets in a modular way: tandem, variable structural repeats in these proteins independently specify single contiguous bases in the DNA. This correspondence makes it possible to rapidly identify TAL effector targets, to engineer novel TAL effectors with custom assortments of repeats to bind DNA sequences of choice, and even to customize genes for TAL effector activation (or prevent it!). Major areas of activity in our lab include 1) identification and characterization of Sgenes, 2) genomic analyses to identify the diversity of TAL effectors in pathogen populations and understand their evolution, and 3) structural and biochemical studies to better harness the unique properties of these proteins for applications such as targeted gene regulation and genome editing. REU opportunities in the lab are available in each of these areas.

Faculty advisor: Adam Bogdanove

More about the Bogdanove Lab

Bioinformatics and genomics to understand important traits of agricultural crops - Fei Lab, BTI

Using integrated bioinformatics and genomics approaches to understand important traits of agricultural crops.

Project description:

The development of high throughput technologies has given rise to a wealth of information at system level including genome, transcriptome, proteome and metabolome. However, it remains a major challenge to digest the massive amounts of information and use it in an intelligent and comprehensive manner. To address this question, Dr. Fei’s group has focused on developing computational tools and resources to analyze and integrate large scale “omics” datasets”, which help researchers to understand how genes work together to comprise functioning cells and organisms.

Faculty advisor: Zhangjun Fei

More about the Fei Lab

Molecular and genetic analysis of fruit ripening - Giovannoni Lab, BTI

Molecular and genetic analysis of fruit ripening and related signal transduction systems, using tomato as the model system

Project description:

Ripening is a process by which the texture, color, flavor, and nutritional content of fruit is enhanced. These traits contribute to the healthfulness and desirability of the fruit as a food source. Clearly, understanding the processes behind fruit ripening are important in terms of nutrition, but also for commercial applications such as transportation and shelf-life. Thus, the focus of research in the Giovannoni lab is molecular and genetic analysis of fruit ripening and related signal transduction systems, using tomato as the model system. Recently, researchers in the lab isolated two genes, RIN and NOR, that are part of the master switch to induce ripening in tomatoes. In addition to identifying important regulatory components of ripening, the lab also investigates lycopene production. Lycopene is the pigment that gives tomatoes their red coloring and which is also suggested to inhibit degenerative diseases such as cancer and heart disease. Using a genomics approach, the lab is investigating the regulatory mechanisms behind accumulation of this important compound in different tomato varieties.

For more information about the Giovannoni lab, please visit the Plant Biology website. Additionally, the Giovannoni lab, in conjunction with other labs on campus has developed a resource for tomato genomics, the Tomato EST Database. Additional resources and information resulting from tomato genomics activities on the Cornell campus can be found at the Solanaceae Genomics Network site.

Faculty advisor: Jim Giovannoni

Genomic analysis of leaf cuticle development and functional diversity in maize - Gore Lab, Cornell

Project Description:

Protecting crop plants from diseases and adverse growing conditions is key to achieving sustainable food production. The cuticle is a waxy, water-proof layer on the outer surfaces of plant leaves and stems that plays a vital role in preventing water loss. It is also where plants first interact with most insects and diseases. Therefore, the cuticle is important to keep plants healthy while preventing them from drying out in the breeze. While many prior projects have contributed insights into cuticle composition, development and function, very few have focused on the adult leaves of cereal crops, whose cuticle has a significant impact on the agricultural performance of these key crops. This project will discover genes that control cuticle development and function in corn, evaluate the potential for improvement of the leaf cuticle to help produce crops with increased drought tolerance and resistance to diseases, and generate tools to guide these efforts.

Faculty Advisor: Michael Gore

More about the Gore Lab

RNA editing in chloroplasts - Hanson Lab, Cornell

Project description:

Life on earth is dependent on the process of photosynthesis, which captures light energy and carbon dioxide to create essential molecules. The efficiency of carbon fixation in land plants is limited by the properties of the enzyme Rubisco, which is relatively slow and also sometimes reacts with oxygen instead of carbon dioxide.  The properties of Rubisco may potentially be improved by observing natural variation in its amino acid sequence and biochemical properties, or by performing mutational analysis.  We are using transgenic plants to probe ways to improve Rubisco.   Another way to enhance photosynthesis is to increase the concentration of carbon dioxide surrounding the enzyme.  We are using a synthetic biology approach to incorporate microcompartments into chloroplasts that will increase carbon dioxide near Rubisco.

Scientist advisor: Stephane Bentolila

More about the Hanson Lab

Molecular analyses of arbuscular mycorrhizal (AM) symbiosis - Harrison Lab, BTI

Project description:

Phosphorus is a critical macronutrient for proper plant growth. While phosphorus deficiencies can be improved by the application of phosphate fertilizers, it is costly, both to the farmer and to the environment. Furthermore, the crops only take up a small percentage of the applied fertilizer; the remainder is either immobilized in the soil, or carried into ground water and rivers, often resulting in pollution.

Interns in the  Harrison lab investigate two aspects of plant phosphorus nutrition. The first aspect seeks to understand the basis for the symbiotic relationships between vascular flowering plants and arbuscular mycorrhizal (AM) fungi. The fungi colonize root cells, gaining access to carbon supplied by the plant, while at the same time mobilizing mineral nutrients from the soil, including phosphorus, to be used by the plant. For this work, the lab uses the model legume, Medicago truncatula and the fungus Glomus versiforme. The Harrison lab also studies how plants find and take up phosphorus from the soil when they do not have these symbiotic relationships with fungi. This work toward understanding the mechanisms of perception and acquisition of phosphorus by plants may eventually lead to a more effective usage of fertilizers.

Faculty advisor: Maria Harrison

Genetic and biochemical mechanisms of plant defense against insects - Jander Lab, BTI

Project description:

Plants in nature are subject to attack by wide variety of caterpillars, beetles, aphids, and other insect herbivores. Although there are a million or more species of herbivorous insects, any individual plant species is resistant to the vast majority of these. Insect feeding is inhibited by an array of chemical defenses that exhibits great variability both within and among different plant species. However, although it is known that any plant leaf contains several thousand different metabolites, most of these remain unidentified. In the Jander lab we are investigating natural variation in the herbivore resistance of maize, tomato, and potato to elucidate the molecular basis of plant defense traits. Through a combination of genetic crosses, gene expression assays, metabolite profiling, and insect growth experiments, we are able to identify specific plant genes, biosynthetic pathways, and metabolites that are required to mount an effective anti-herbivore defense.

Faculty advisor: Georg Jander

Seed-free plant genomics and symbioses– Li Lab, BTI

Project description:

The Li lab uses genomic tools to investigate the evolution and biology of seed-free plants: ferns, fern allies, and bryophytes (mosses, liverworts, and hornworts). We are particularly interested in their symbioses with N2-fixing cyanobacteria, which provide plants with their own source of nitrogen fertilizer. We aim to understand the evolution and mechanisms of plant-cyanobacteria symbioses, and the results of which will lay the foundation for future engineering of “self-fertilizing” crops with less reliance on synthetic nitrogen fertilizers. To this end, we are surveying the diversity of cyanobacterial symbionts in hornworts, and using RNA-sequencing to uncover putative symbiosis-related genes.

Faculty advisor: Fay-Wei Li

More about the Li Lab

Investigating pathogen virulence mechanisms - Martin Lab, BTI

Investigating pathogen virulence mechanisms using novel isolates of Pseudomonas syringae pv. tomato collected during a recent outbreak of bacterial speck disease in New York.  Identifying and characterizing immunity-associated genes from wild relatives of tomato.


Bacterial speck disease creates unattractive black spots on a ripe tomato, making it unmarketable. The disease is caused by the bacterium Pseudomonas syringae pv. tomato. (Photo by Gregory Martin)

Project description:

The Martin laboratory studies the molecular basis of plant immunity and bacterial pathogenesis. Our focus is on the infection of tomato by Pseudomonas syringae pv. tomato as this process results in bacterial speck, an economically important disease, and also serves as a powerful model system for understanding fundamental mechanisms involved in plant-pathogen interactions. On the plant side, we identify and characterize genes, proteins and molecular mechanisms that play a role in host immunity and susceptibility. This work relies on natural variation for these traits that is present in cultivated tomato and in the 12 wild relatives of tomato that occur in South America. On the bacterial side, we study the proteins and associated mechanisms that the pathogen uses to interfere with the plant immune response. For the characterization of both plant and bacterial genes and proteins, we use a variety of experimental approaches including biochemistry, bioinformatics, genetics, genomics, molecular biology, and structural biology.

Examples of research projects for undergraduates in my laboratory include: 1) molecular characterization of novel isolates of Pseudomonas syringae pv. tomato collected during a recent outbreak of bacterial speck disease in New York; and 2) Identifying and characterizing immunity-associated genes from wild relatives of tomato.

Faculty advisor: Greg Martin

Understanding how pesticide and pathogen stress influence bee behavior and delivery of pollination services to agriculturally important crops - McArt Lab, Cornell

Project description:

Research in our lab is focused on pollinator health. Major current projects include 1) Evaluating pesticide exposure and risk to wild bees and managed honey bees in different landscapes, 2) Combining empirical data with network modeling to understand pathogen transmission in complex plant-pollinator networks, and 3) Understanding how pesticide and pathogen stress influence bee behavior and delivery of pollination services to agriculturally important crops.

Dissecting the molecular basis of aluminum tolerance in rice - McCouch Lab, Cornell

Project Description:

The McCouch Lab investigates natural variation in rice, focusing on how it evolved, how it is distributed in both domesticated and wild species of Oryza, how it conditions complex phenotypes, and how it can be efficiently utilized in rice improvement.

We have pioneered studies demonstrating that low-yielding wild and exotic Oryza species harbor genes and quantitative trait loci (QTL) that can be used to enhance the performance of modern, high-yielding rice cultivars. This work is done in collaboration with scientists and breeders in Asia, Africa, North and South America.

With funding for over a decade from the NSF and the USDA, the Rice Diversity Project supports QTL mapping, Genome Wide Association Studies (GWAS), and gene discovery using a suite of open-source genetic, genomic and bioinformatic resources developed in the McCouch lab.  These resources comprise a ‘rice diversity research platform’ that is widely used the international rice research community to understand the genetic basis of complex traits, to investigate molecular mechanisms involved in key forms of stress tolerance, and to efficiently utilize natural variation to breed highly productive rice varieties for the future that are more nutritious, resource-use efficient, and stress tolerant than those we currently grow.

SUMMER INTERNSHIPS:  Summer interns will have a chance to participate in one of our flagship projects aimed at investigating the molecular basis of stress tolerance in rice.  For 2016, the focus will be on ‘Dissecting the molecular basis of aluminum tolerance in rice’ and the intern will help characterize a key protein involved in rice aluminum tolerance using a variety of molecular tools and strategies. This project involves a collaboration between the McCouch and Kochian labs, and the intern will work closely with postdocs and graduate students involved in the project.

Under a grant from the Global Diversity Trust, we are using genomic tools to develop inter-specific introgression lines, novel genetic resources that are derived from crosses between diverse wild relatives and elite, high yielding varieties of both indica and japonica rice. This is a collaboration with the International Rice Research Institute (IRRI ) in the Philippines, and the objective is to use pre-breeding strategies to explore the genetic potential of wild and unadapted rice germplasm and to enlarge the gene pool that is utilized for routine plant improvement.

As a collaborator on two Bill & Melinda Gates-funded projects, one with the University of York in the UK and the Central Rice Research Institute (CRRI) in India, and the other with AfricaRice in Nigeria, we are evaluating diverse genetic materials, including the Rice Diversity Panel (part of the Rice Diversity Project, described above) and a library of interspecific chromosome segment substitution lines (CSSLs), for tolerance to two major forms of stress: drought and iron toxicity.  In our trials in India, our collaborators at the Central Rice Research Instistute are evaluating CSSLs for ‘yield-under-drought’ in multi-location field trials, and in our trials in West Africa, our collaborators at AfricaRice are evaluating the Rice Diversity Panel for iron toxicity in multiple sites in the region.  We are also developing  cost-effective SNP genotyping platforms for use in the breeding programs  in India and Nigeria to enable geneticists and breeders to efficiently transfer favourable alleles from diverse sources into native rice varieties adapted to the ecosystems in which they will be grown.

The Genomics & Open-source Breeding Informatics Initiative (GOBII) is a project funded by the Bill & Melinda Gates Foundation that brings together software engineers, quantitative geneticists and plant breeders at three institutions in Ithaca, Cornell, the Boyce Thomson Institute, and the USDA-ARS, and three international crop improvement centers in Mexico, India and the Philippines to develop modular, open-source breeding software resources and get them into the hands of plant breeders in the developing world. Focusing initially on five staple crops – wheat, rice, maize, sorghum and chickpea— the project seeks to empower public plant breeders to use genome-wide approaches to model plant performance in real time using tools that can be shared across diverse species and regions of the world.

Understanding the evolution of plant metabolic pathways using comparative genomics - Moghe Lab, Cornell

Project Description:

Metabolic pathways in plants are quite dynamic, resulting in production of over a million metabolites across ~300,000 estimated plant species. These metabolic pathways are in a constant state of innovation due to gene duplication, transcriptional divergence, enzyme promiscuity etc. How have specific metabolic pathways originated and diversified? What is the role of positive selection and genetic drift in shaping metabolic diversity? How does enzyme promiscuity influence evolution of specialized metabolic pathways? We are investigating these and other allied questions using evolutionary genomic approaches, by performing comparative analyses of plant genomes, transcriptomes and proteomes. Research in the Moghe lab is highly integrative and comprised of both computational and wet-lab approaches.

Faculty Advisor: Gaurav Moghe

More about the Moghe Lab

Bioinformatics and genomics - Mueller Lab, BTI

Project Description:

Interns in the Mueller lab work on a variety of bioinformatics and genomics projects and gain experience in the following areas: genome assembly, structural and functional annotation, biochemical pathways, comparative genomics, ontology development and data presentation and visualization.

Faculty Advisor: Lukas Mueller

Identifying factors that control distribution of recombination events along chromosomes - Pawlowski Lab, Cornell

Project description:

The goal of the research in the Pawlowski lab is to understand the basis of inheritance in plants by studying the mechanisms governing chromosome behavior and genetic recombination in meiosis.  Meiosis is a specialized type of cell division that leads to the production of gametes.  During meiosis, homologous chromosomes, one from the mother and the other one from the father, pair with each other and exchange parts (recombine).  These processes are essential for accurate transmission of genetic material from parents to progeny and for generating genetic variation.  Our research combines genetics, molecular biology, and cutting-edge microscopy to identify genes, and pathways that regulate meiosis.  These basic studies will provide means to investigating how meiotic processes can be modified to improve plant breeding methods.  We use two model plant systems, maize, one of the most important crop plants in the world, and a common weed, Arabidopsis thaliana.

Faculty advisor: Wojtek Pawlowski

More about the Pawlowski Lab

The interface between epigenetics and nuclear cell biology in plants - Richards Lab, BTI

Project description:

Nuclei from normal and mutant root cells

Nuclei (green) from normal (wild type, left) and mutant (crwn1, right) root cells of Arabidopsis thaliana. Image source: Travis Dittmer.

The three-dimensional structure of the nucleus affects gene expression and other activities of the eukaryotic genome. We apply genetics, genomics, cell biology and biochemical approaches to study how the organization and dynamics of the nuclear organelle affect genome function.

Faculty advisor: Eric Richards

Cell size and sepal size in Arabidopsis - Roeder Lab, Cornell

Project Description:

Size is a critical property of plants, yet we know little about how it is controlled. In the Roeder laboratory, we ask how does a cell know how big to be and how does the whole organ (e.g. leaf, sepal or petal) made up of many cells know how big to be. To answer these questions we image living plants on a confocal microscope and measure the growth of cells, examine the cell division pattern, and quantify fluorescent proteins expressed.

Faculty Advisor: Adrienne Roeder

More about the Roeder Lab

Polymers and matrices of the cell wall and cuticle of tomato fruit - Rose Lab, Cornell

Characterization of key structural polymers and matrices of the cell wall and cuticle of tomato fruit, and mechanisms of their synthesis and modification.

Project Description:

Research in the Rose lab is focused on understanding the biological importance of the structural polymers that form plant cell walls, as well as the water resistant barrier, called the cuticle (the plant ‘skin’), which covers the above ground surfaces of land plants. We look at how those polymers are synthesized and assembled into complex polymer matrices, and how they contribute to factors such as plant architecture, resistance to pathogens and limiting drought stress. This involves a wide range of analytical approaches, including genomics, proteomics and imaging techniques. Much of the research uses tomato as a model system and the research aims to bridge basic science and practical applications geared towards enhancing fruit quality traits and food security.

Faculty Advisor: Jocelyn Rose

More about the Rose Lab

Dorsiventrality in Tomato Leaves: the Role of the STA Gene - Scanlon Lab, Cornell

Project description:

Research in the Scanlon lab focuses on mechanisms of plant development and evolution of plant morphology. Utilizing comparative developmental genetics and functional genomics, we are especially interested in the processes whereby meristems make leaves and embryos make meristems. Our lab exploits leaf and embryo mutants of maize, Arabidopsis and tomato as the foundation in comparative studies of these fundamental processes in plant development.

Faculty Advisor: Mike Scanlon

More about the Scanlon Lab

Evolution of floral traits in a California native plant lineage (Calochortus) - Specht Lab, Cornell

Project description:

Calochortus (Liliaceae) is a large genus (75 spp.) of bulbous herbs with flowers of kaleidoscopic vari­ety and exquisite complexity. It has a center of diversity in California and ranges north to British Colum­bia, west to the Dakotas, and south to Mexico and Guatemala. Calochortus has undergone strik­ing radiations in flower morphology, habitat, and substrate preference, and most taxa have narrow ranges. Floral syndromes include Mariposas with large, brightly colored, tulip-like blossoms with an erect perianth (tepals); Cat’s Ears with a smaller, spread­ing perianth densely covered with trichomes; Star Tulips with spreading, mostly glabrous tepals; and Fairy Lanterns with closed, globular nodding flowers. Calo­chortus petals are marked by unique, often brightly colored glands. Species inhabit deserts, grass­lands, chaparral, mead­ows, vernal pools, springs, montane woodlands, and forest under­stories. One quarter of all species occur on or are limited to serpentine; nearly as many are federally endang­ered or extinct. Several species are visited by a wide range of pollinators, while others attract a narrow range of visitors.

Given the diversity of habitats, geographic ranges, and floral forms seen in Calochortus, a well-resolved and densely sampled phylo­geny would provide the opportunity to address many questions at the interface of ecology, evolution, and biogeography: Are species with similar floral syndromes each other’s closest rela­tives, or have such syndromes arisen multiple times independently? What is the adaptive significance and developmental origin of each floral syndrome? Has the ability to tolerate serpentine evolved more than once within and among clades? What has been the historical pattern of geographic spread within the genus? Do closely related species occupy similar ecological distributions?

The selected student will work with graduate student Adriana Hernandez to develop a phylogeny for Calochortus and to investigate gene flow and diversification in floral form among various species native to California and Mexico.

Faculty Advisor: Chelsea Specht

Chloroplast biology - Stern Lab, BTI

Project Description:

The underlying research themes in the Stern laboratory are chloroplast biology, bioenergy and nuclear-cytoplasmic interactions. Within this framework, we study how chloroplast genes and metabolic activities are regulated by the products of nuclear genes, usually acting at the transcriptional or post-transcriptional level. Areas of emphasis include the roles of ribonucleases and RNA-binding proteins and assembly of the carbon-fixing enzyme Rubisco. We are also using molecular and genetic techniques to adjust chloroplast metabolism for the production of useful hydrocarbons.

Faculty Advisor: David Stern

Comparing leaf development and cellular differentiation - Van Wijk Lab, Cornell

Comparing leaf development and cellular differentiation in the C3 species rice to that in the C4 species maize mainly using large scale comparative protein (proteome) analysis.

Project Description:

Grasses such as rice, wheat, maize and sorghum are important cereal crops grown in different parts of the world. Plants are classified as C3 or C4 species based on the primary product of carbon fixation in photosynthesis. C4-type plants, such as maize, sorghum and sugarcane, have traits that greatly increase their efficiency of carbon-fixation especially when water or nitrogen are limiting and temperatures are higher; this makes C4 crop species particularly successful in warmer parts of the earth. The van Wijk lab is comparing leaf development and cellular differentiation in the C3 species rice to that in the C4 species maize mainly using large scale comparative protein (proteome) analysis. Since chloroplasts play such a key role in C3 and C4 photosynthesis and plant growth, we pay particular attention to chloroplasts. We focus on proteins, since most cellular functions are carried out by proteins. Proteome analysis relies on modern mass spectrometers, as well as the availability of sequenced genomes and bioinformatics tools. Therefore to facilitate our biological research, the van Wijk lab also tries to develop and implement proteomics tools. Together with our Cornell colleague Dr Qi Sun, we also developed the Plant Proteomics Database PPDB to provide an integrated resource for experimentally identified proteins in the plant species Arabidopsis, maize and rice.

Faculty Advisor: Klaas Van Wijk

More about the Van Wijk Lab

Internships are funded by the National Science Foundation, Research Experiences for Undergraduates Award #1358843, individual faculty grants, and the generosity of local donors including the Ithaca Garden Club, the Legacy Foundation of Tompkins County, and the Tompkins Charitable Gift Fund.