CAREER: Searching for the Fungal Domestication Syndrome

驯化是过去13000年来最具影响力的技术创新之一。这个项目将研究真菌的驯化。由于种群生物学、生态学和人类对所需性状的人工选择的潜在差异，研究人员假设驯化对真菌的影响不同于植物和动物的驯化。研究人员最近开发了米曲霉作为真菌驯化的模型。这是一种丝状霉菌，几千年来一直用于生产亚洲传统的发酵食品和饮料。在使用这些真菌作为食品加工和生产的一部分时，人类已经改变了这些真菌物种的特征和DNA蓝图。本项目将探索这些变化。这项研究有可能提高食品发酵的安全性，并阐明发酵食品的健康益处。重要的是，该项目将通过公民科学项目让公众参与科学发现。我们鼓励市民提供自制或商业发酵食品的样品。本科生通过直接的研究经验或通过实践课程，将从食品样品中分离和鉴定微生物。学生将获得微生物学、分子生物学、基因组学和生物信息学方面的实践经验。这个项目的成果将被改编成电影与教师和本科生在艺术合作。在驯化植物和动物的同时，真菌（如酵母和霉菌）也因其在食物保存、调味、香气和质地方面的用途而被驯化。然而，通过驯化植物和动物的研究形成的概括是否可以扩展到驯化真菌，这在很大程度上仍未得到探索。为了解决真菌之间以及植物、动物和真菌之间的驯化模式和影响是否相似，研究人员将分析数百株米曲霉及其祖先黄曲霉的基因组和表型变异模式，并将这些结果与两种现有的真菌驯化模型（酿酒酵母菌和盘古青霉）进行比较。它将确定人工选择的目标基因组区域，并确定驯化对弧菌的表型效应。该项目将测量A. oryzae和A. flavus菌株在不同条件下的生长速度、对社区食物微生物的抑制作用、挥发性化合物谱和基因表达谱。这项研究的结果将阐明驯化过程及其对真菌的影响，并将增加我们对适应的基因组和进化过程的了解。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Domestication was one of the most influential technological innovations of the last 13,000 years. This project will study the domestication of fungi. Because of underlying differences in population biology, ecology, and artificial selection by humans for desired traits, the researchers hypothesize that the effect of domestication on fungi is distinct from plant and animal domestication. The researchers have recently developed Aspergillus oryzae as a model of fungal domestication. This species is a filamentous mold used for millennia in the production of traditional fermented Asian foods and beverages. In using these fungi as part of food processing and production, humans have changed the traits and DNA blueprint of these fungal species. This project will explore those changes. This research has the potential to improve the safety of food fermentation and to shed light on the health benefits of fermented foods. Importantly, this project will involve the public in scientific discovery through a citizen-science project. Members of the public will be encouraged to contribute samples of homemade or commercial fermented foods. Undergraduates, through direct research experiences or through hands-on coursework, will isolate and identify microorganisms from food samples. Students will gain practical experience in microbiology, molecular biology, genomics and bioinformatics. The results of this project will be adapted into a film in partnership with faculty and undergraduate students in the arts.In parallel with the domestication of plants and animals, fungi (e.g. yeasts and molds) were also domesticated for their utility in food preservation, flavoring, aroma, and texture. However, it remains largely unexplored whether the generalizations formed through the study of domesticated plants and animals can be extended to domesticated fungi. To address whether the patterns and effects of domestication are similar between fungi and across plants, animals, and fungi, the researchers will analyze patterns of genomic and phenotypic variation across hundreds of isolates of A. oryzae and its progenitor A. flavus, and compare these results to two existing models of fungal domestication (Saccharomyces cerevisiae and Penicillium roqueforti). It will identify the genomic regions that were targeted by artificial selection and determine the phenotypic effect of domestication on A. oyzae. The project will measure growth rate, inhibitory effects on community food microbes, volatile compound profiles, and gene expression profiles of A. oryzae and A. flavus strains under diverse conditions. The outcomes of this research will shed light on the process of domestication and its effect on fungi and will increase our knowledge of the genomic and evolutionary processes underlying adaptation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.