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

真菌，称为丛枝菌根，与许多植物的根形成重要的共生关系，在从土壤中吸收养分方面发挥着重要作用。尽管这种联系对为许多植物提供养分至关重要，并在提高作物产量方面发挥着重要作用，但令人惊讶的是，我们仍然对这种联系知之甚少。西红柿提供了一个很好的系统，可以在其中询问关于这种联系的问题，因为人们可以实验性地操纵西红柿，因为西红柿天生就有真菌，以及可以在没有菌根联系的情况下生长的突变菌株。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在有局部营养块的土壤中的根的功能方式，这在大多数土壤中是典型的，通过在土壤中使用番茄来增加和不增加几种重要的营养物质：硝酸盐、铵、锌和磷。PI将使用稳定的同位素，将菌根和非菌根番茄根中的基因表达谱与向土壤中添加营养斑块(模仿自然和农业斑块)进行比较。初步分析将包括番茄微阵列，它允许研究数千个基因，以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。PIS还将使用超高通量测序方法，为发现新基因以及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理解可用于农业管理和作物育种的战略，以从菌根共生中获得更大的好处，并提高养分的利用效率。了解根系和共生真菌之间的相互作用可能会导致减少化肥使用和加强从土壤中获取养分的策略。通过这个项目，研究生和本科生将接受多学科的培训，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，私营部门将特别注意招聘代表性不足的群体。本科生将被招为丹福斯REU项目的一部分，并将在夏季的11周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在这一年参与暑期实地考察和实验室工作。

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.