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

真菌，被称为丛枝菌根，与许多植物的根形成重要的共生关系，并在从土壤中吸收养分方面发挥重要作用。尽管这种联系对于为许多植物提供营养至关重要，并且在提高作物产量方面起着重要作用，但我们对这种联系的了解仍然少得惊人。西红柿提供了一个很好的系统，在这个系统中，人们可以通过实验操纵西红柿，它自然具有菌根菌，而突变株可以在没有菌根菌的情况下生长。该项目将侧重于使用基因组工具来了解菌根真菌和根之间的相互作用如何改变根在有局部营养斑块的土壤中的功能方式，这在大多数土壤中都是典型的，通过在土壤中使用番茄来富集和不富集几种重要营养物质：硝酸盐、铵、锌和磷。pi将使用稳定同位素，将菌根和非菌根番茄根系中的基因表达谱与向土壤中添加营养斑块（模仿自然斑块和农业斑块）进行比较。最初的分析将包括一个番茄微阵列，它允许对数千个基因进行研究，同时检查在田间和温室实验中对复杂和更受控制的环境的基因组和生理反应。pi还将使用超高通量测序方法，为发现新基因和比较处理和番茄基因型之间的基因表达提供全面的数据集。这项工作的结果将使人们更好地了解可用于农业管理和作物育种的策略，以便从菌根共生中获得更大的利益并提高养分利用效率。了解根系和共生真菌之间的相互作用将有可能导致减少肥料使用和提高土壤养分捕获的策略。通过这个项目，研究生和本科生将在多个学科中得到培训，包括生态学、微生物学、生理学、基因组学、生物信息学和统计学，而pi将特别注意招募代表性不足的群体。本科学生将被招募为丹佛斯REU项目的一部分，并将在夏季为期11周的项目中接受多学科培训。在加州大学戴维斯分校，来自代表性不足群体的学生助理将参与今年的暑期实地和实验室工作。

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.