PI: Dahlia Nielsen (North Carolina State University) CoPIs: David Bird (North Carolina State University), Mark Melton (St. Augustines College),Jennifer Schaff (North Carolina State University and Valerie Williamson (University of California-Davis) Key Collaborator: Christopher Smith (North Carolina State University)

Root knot nematodes are parasites of most plants, including vegetables, field crops, trees, turf grass, and ornamentals. During an infection, the nematodes penetrate the roots and establish permanent feeding sites that compromise normal root function, including moisture and nutrient uptake by the plant. Infected plants suffer restricted growth, reduced yield and premature death. The goal of this project is to examine the plant-nematode relationship on a genetic level. The overall question addressed is: How does the genetic makeup of the nematode influence gene expression in its host plant? This question will be answered using a modification of a genetic analysis tool called expression quantitative trait locus (eQTL) mapping. Advanced DNA sequencing technology will be used to measure both gene expression levels in the plant and to identify genetic markers in the DNA of the nematode. Connections between the DNA of the nematode and the gene expression of the plant will be made using eQTL mapping strategies. Additionally, various traits related to pathogenicity will be described during the course of the project. Ultimately, genetic markers in the nematode, gene expression levels in the host plant and in the nematode, and pathogenicity trait measurements will be used to infer entire plant-nematode genomic networks.

It is estimated that global losses due to plant-parasitic nematodes exceed $125 billion annually, placing nematodes among the top most economically damaging plant pathogens. Developing new control methods will require a more thorough understanding of the nematode-plant interactions, which is a major goal of this project. All of the sequence data produced by the project will be released to the NCBI Sequence Read Archive for immediate access and long term storage. Processed data, including genotypes and summarized transcript abundances, will be made accessible for graphical visualization and download at the Legume Information System (http://comparative-legumes.org/) and on Nematode.net (www.nematode.net/). A key component of the project is the inclusion of undergraduate students from St. Augustines College in Raleigh, a college that historically serves minority students. Selected students will join NCSU research labs and computational efforts as Kelman Scholars and form the nucleus for a broadened interaction between NCSU and St. Augustines.

Project Report

In this project, our goal was to dissect the genetic basis of the signaling that occurs between a plant host and an infecting parasite. To do this, we used a model system for studying the plant-parasite interaction: the plant Medicago truncatula infected by the root knot nematode (RKN) Meloidogyne hapla. This project was a proof-of-principle to establish a general strategy to investigate the genetic basis of host-parasite interactions, including those that affect human and animal health as well as crop loss. To accomplish our goals, we first produced a set of over 100 lines of RKN derived by crossing two parental nematode strains that differed genetically and differed in the changes that they produced in the host plant. These RKN lines were used to infect a set of genetically identical plants. We then asked the question: can any differences that we found in the response of these identical plants to infection be traced back to genetic differences between the parental nematode strains? We were able to identify approximately 150 plant genes that responded differently depending on the genome complement of the infecting nematode. We were able to connect these variable plant responses to specific regions of the RKN genome. A number of genes that we identified in this project have not previously been described as being involved in the infection process, indicating that they could provide novel directions for developing methods for parasite control. During the course of the project, we trained a number of students in molecular genetics techniques, plant and RKN maintenance and infection protocols, and basic bioinformatics skills. Six graduate students were involved in various aspects of the project. We were particularly interested in training these students in areas outside their main fields of expertise. For example, the bioinformatics students, whose emphases involved computational and statistical aspects of the project all contributed to the plant-based experimental components. The plant pathology and molecular genetics students all helped analyze data. One of the Ph.D. students involved in the project has now graduated and has moved on to a postdoctoral research position. A second Ph.D. student will graduate within six months of the project completion, and has already accepted a research position. Two postdoctoral scholars were also trained during the course of the project. This project also provided summer research experience to three undergraduate students from St. Augustine’s University, a historically black university in downtown Raleigh, all three of which have now graduate from St. Aug’s and have entered graduate programs or scientific professions. Our first summer intern student has nearly completed an M.S. degree in biology with a concentration in microbiology at North Carolina Central University. The second summer intern student has started her second year in the Immunology and Molecular Pathogenesis Ph.D. program at Emory University. The final summer intern student has received a commission as Second Lieutenant in the US Army with an assignment in forensic intelligence. After having completed her summer project, this student continued on part time at NCSU, doing work towards her senior undergraduate project. Two undergraduate students from the University of California at Davis were also trained in maintenance of plants and nematode cultures as well as molecular biology lab procedures. One is working for a local agricultural biotechnology company and the other has entered graduate school. As part of their training, the graduate students supported by this project have had responsibilities in supervising the undergraduate summer internship students. This project has also supported one high school student working at NCSU. She is learning about scientific research practices, and is carrying out a small independent project that she herself identified and designed.

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Diane Jofuku Okamuro
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North Carolina State University Raleigh
United States
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