Research Training Fellowship Program Translational Genomics Foci

Description of the research opportunity: Use of disease resistant cultivars has been the major method for controlling a majority of the plant pathogens worldwide. Development of cultivars carrying resistance to multiple pathogens through many breeding steps is, however, both time-consuming and expensive. In the proposed investigation a translational genomics approach will be applied in creating broad-spectrum resistance against many serious pathogens in soybean. Such an approach, if successful, will reduce the cost and time required to develop soybean cultivars with disease resistance against many pathogens.

Nonhost resistance mechanism makes Arabidopsis immune to all soybean pathogens. Therefore, identification and transfer of the nonhost resistance mechanism from Arabidopsis to soybean could lead to creation of broad-spectrum resistance against many pathogens in soybean. Several genes encoding nonhost resistance of Arabidopsis have already been isolated. Bhattacharyya lab is in the process of cloning the Arabidopsis genes that encode nonhost resistance against the soybean pathogen, Phytophthora sojae. These genes could be ideal in improving soybean for broad-spectrum disease resistance. However, little knowledge is available regarding the nonhost resistance mechanism and how Arabidopsis defends P. sojae attack. This study will contribute significantly towards better understanding of Arabidopsis nonhost resistance mechanism against this pathogen and also towards possible improvement of soybean for Phytophthora resistance.

In the proposed research the student will be able to investigate the following aspects in order to reach the goal of the proposed research. Initially the candidate will conduct virus-induced gene silencing (VIGS) experiments in Hill and Whitham Laboratories for determining the roles of the soybean genes, similar to Arabidopsis nonhost resistance genes, in the expression of Phytophthora resistance. Based on the results of the initial VIGS experiments, the student will select those soybean genes that are important for Phytophthora resistance. He or she will then learn soybean transformation procedures in Wang Laboratory and overexpress these genes in transgenic soybean plants. The transgenic plants will be evaluated in Bhattacharyya Laboratory. The yield potentiality of the Phytophthora resistant transgenic lines will then be evaluated. The student will work with Cianzio group in determining the yield potentialities of the selected transgenic lines.

Description of the training opportunity: The student will be able to get training in plant molecular biology, VIGS, plant pathology, bioinformatics, plant transformation, and field data collection and analyses.

Desired skill set: Strong background in biology, biochemistry, mathematics is desired. Some lab experience is preferred, but not essential.

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Research Focus: Security and nutritional value of grain.

Primary advisor: Dr. Lance Gibson lgibson@iastate.edu

Description of the research opportunity: Participants in this project will enhance the security and nutritional value of grain consumed in the United States by 1) contributing to the genomic and methodological knowledge base needed to efficiently improve grain for functional food attributes, 2) devising, refining, and disseminating efficient breeding methods that optimally use data conferred by cutting-edge biotechnologies, and 3) developing educational materials and programs to stimulate the curiosity and invite the next generation of plant breeders to become involved in this profession. Participants will do this through the enhancement of beta-glucan content of oat using new marker-assisted selection methods and creating materials for recruiting and educating the next generation of plant breeders. The importance of beta-glucan to the health impact of oat has long been appreciated. Beta-glucans are classified as a water-soluble dietary fiber. Significant potential exists for beta-glucan from oat to help avert or mitigate a number of diseases of Western civilization associated with a highly refined diet. A diet high in soluble fiber from whole oats (oat bran, oatmeal and oat flour) and low in saturated fat and cholesterol may reduce the risk of heart disease by decreasing total serum cholesterol concentration. In addition to lowering cholesterol, beta-glucan consumption has other benefits. 1) It can slow the release of glucose into the blood stream, 2) can assist with weight loss by increasing satiety after food consumption, and 3) has anti-tumor and immune stimulating properties.

Description of the training opportunity: Students participating in this research and education program will work in partnership with scientists in genetics, plant breeding, food science and human nutrition, resident and distance education. They will have access to excellent field, greenhouse, laboratory, and teaching facilities through the Departments of Agronomy and Food Science and Human Nutrition. The project will involve significant interaction with USDA research geneticists at Iowa State University and the US Nutrition Lab at Cornell University. The students will interact with a diverse set of faculty in a multi-disciplinary environment. Skills will be developed in areas crucial to future success in research and academic settings. Taken as a whole, the plant breeding, genetics, human nutrition, and educational components of this program will provide all the necessary elements to prepare students to excel as scientists and educators.

Desired skill set: Proven aptitude in the biological and physical sciences, including biology, genetics, chemistry, agronomy, food science and/or human nutrition. Excellent written communication skills and the capacity to work both independently and within a team environment are essential. Demonstrated skill in problem solving, data collection, hypothesis testing, and data analysis.

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Research Focus: Functional relationships between gene expression and seed composition

Primary advisor: Dr. Mark E. Westgate westgate@iastate.edu

Description of the research opportunity: Soybean seeds provide about 25% of the world’s supply of oils and 66% of the world’s supply of vegetable proteins. Spurred by dramatic increases in federal support to develop plant-based raw-materials for bioenergy and biobased products, a number of major research initiatives are being developed on campus (e.g., creating soybeans to produce ‘ready made’ oils for biodiesel and improved lubricants). These initiatives provide an ideal and timely environment to support a graduate student training program in soybean translational genomics. The ultimate goal of our research team is to determine the molecular basis for shifts in cellular metabolism that alter the capacity for protein and oil accumulation in soybeans seeds. The central hypothesis guiding the activities of our training program is that functional relationships between gene expression and seed composition are defined primarily by their impacts on metabolic flux into desired storage products. The knowledge gained in these studies will guide genetic engineering approaches to develop novel soybean germplasm with unique and valuable compositional qualities. The primary research team brings together scientific expertise in germplasm development, physiology, biochemistry, gene expression profiling, metabolic flux analysis, and bioinformatics. Through its collaborators, this training program is linked to a large network of research activities across the ISU campus utilizing state-of-the-art technologies in translational genomics. Integrating these resources provides a stimulating environment for generating fundamental discoveries on molecular regulation of seed composition and for training the next generation of graduate students in this exciting area of agronomic research.

Description of the training opportunity: The specific research objectives of this training program are (1) to utilize 13C metabolic flux mapping technology to quantify carbon and nitrogen fluxes through metabolic pathways leading to protein, oil, and starch synthesis in seeds varying significantly in final seed composition, and (2) to identify potential regulatory determinants of metabolic partitioning into protein, oil, and starch in seeds of these lines. Dr. Shanks’ lab conducts the flux analysis utilizing a metabolic flux map uniquely designed for soybean seeds. Dr. Cannon’s lab coordinates the bioinformatics analysis of deep sequencing profiles targeted to structural and regulatory genes related to primary metabolism. Dr. Westgate’s lab conducts the gene expression and physiology studies, oversees germplasm development, and provides overall coordination for the training program. In addition, students will have the opportunity to work closely with ISU faculty in the Plant Science Institute Center for Designer Crops and its Initiative on Biorenewables. Students will receive training in molecular biology techniques, gene expression profiling, metabolic flux analysis, bioinformatics, genomics and physiology -- depending on their primary area of interest. Active participation in research group meetings, presentations at local, regional and international scientific meetings and publishing in leading research journals are central to the training program. Graduate training in this program is expected to lead to a Ph.D. in agronomy, genetics, plant physiology, biochemistry, chemical engineering, or bioinformatics depending on student interests and capabilities.

Desired skill set: Excellent biological science background with emphasis in genomics, biochemistry, molecular biology and/or physiology. Excellent communication skills, demonstrated ability to work independently; and ability to integrate across layers of biological complexity (i.e. molecular, biochemical, physiological). Willingness to work as a team member with a wide range of scientific expertise.

Selected References: Iyer, V., G. Sriram, D.B. Fulton, R. Zhou, M.E. Westgate, and J.V. Shanks. 2007. Metabolic flux maps: A comparative tool for studying the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons (Submitted to Plant, Cell, and Environment).

Zhou, R.L., and M.E. Westgate. 2007. Maternal and embryonic control of protein and oil accumulation in developing soybean cotyledons. (Submitted to Journal of Agronomy and Crop Science).

Febrer, M., Cheung, F., Town, C.D., Cannon, S.B., Young, N.D., Abberton, M., Jenkins, G., Milbourne, D. 2007. Construction, characterization and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.). Genome 50:412-421.

Cannon, S.B., L. Sterck, S. Rombauts, et al. 2006. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proceedings National Academy Sciences. 103:14959-14964.

Shanks, J. V. 2005. Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science. AIChE Journal 51: 2-7.

Sriram, G., D.B. Fulton, R. Zhou, M.E. Westgate, M.H. Spalding, and J.V. Shanks. 2004. Quantification of Metabolic Fluxes in Developing Soybean (Glycine max) Embryos Using Biosynthetically Directed Fractional 13C Labeling, 2-D [13C, 1H] NMR and Rigorous Isotopomer Balancing. Plant Physiol. 136: 3043-3057

Sriram, G., and J.V. Shanks. 2004. Improvements in Metabolic Flux Analysis using Carbon Bond Labeling Experiments: Bondomer Balancing and Boolean Function Mapping. Metabol. Eng. 6: 116-132.

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