En-Gen: A Genomic and Physiology Approach to Understanding the Impact of Fungal Colonization on Root Metabolism and Nutrient Acquisition

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Fungi, called arbuscular mycorrhizae, form an important symbiosis with the roots of many plants and play an important role in nutrient uptake from soils. Although this association is vital for providing nutrients for many plants, and plays an important role in increasing crop yields, we still know surprisingly little about this association. Tomatoes provide an excellent system in which to ask questions about this association as one can experimentally manipulate tomatoes, which naturally have mycorryzae, and mutant strains that can grow without mycorrhizal associations. This project will focus on using genomic tools to understand how the interaction between mycorrhizal fungi and roots alters the way in which roots function in soils where there are localized patches of nutrients, as is typical in most soils, by using tomatoes in soil with and without enrichment with several important nutrients: nitrate, ammonium, zinc and phosphorus. The PIs will compare the gene expression profiles in mycorrhizal and in non-mycorrhizal tomato roots to the addition of nutrient patches to the soil (mimicking natural and agricultural patchiness), using stable isotopes. Initial analyses will include a tomato microarray, which allows for the study of thousands of genes to simultaneously examine genomic and physiological responses to complex and more controlled environments in the field and in the greenhouse experiments. The PIs will also use an ultra-high throughput sequencing method, which provides comprehensive data sets for both the discovery of new genes and for comparative gene expression between treatments and tomato genotypes. The results of this work will yield a better understanding of strategies that may be used for agricultural management and crop breeding to achieve greater benefits from mycorrhizal symbiosis and to increase nutrient use efficiency. An understanding of the interaction between roots and symbiotic fungi will potentially lead to strategies for decreased fertilizer usage and enhanced nutrient capture from soils. Through this project, graduate students and undergraduates will be trained in multiple disciplines, including ecology, microbiology, physiology, genomics, bioinformatics and statistics, and the PIs will pay special attention to recruiting under-represented groups. Undergraduate students will be recruited as part of the Danforth REU program and will gain multidisciplinary training during the eleven week program in the summer. At UC Davis, student assistants from under-represented groups will be involved in the summer field and lab work during the year.