IDBR: TYPE A: High-Throughput, Large-Scale Plant Phenotyping Platform

爱荷华州立大学因开发高通量、大规模植物表型仪器，用于植物表型学领域的知识发现而获奖。由于基因组中有大量的基因，并且多变的环境条件会影响植物表型，因此对植物表型的完整表征提出了一个困难的挑战。因此，以足够的通量和分辨率在大尺度和多尺度水平上分析植物表型是困难和昂贵的。该项目将导致基于植物表型仪器的微系统技术的发展，因此将构成现有表型分析的吞吐量和信息内容的变革性飞跃。该仪器的核心是一个集成的植物生长系统，由一系列微型温室、微流控植物芯片和微流控控制逻辑组成。植物生长系统为植物与环境相互作用的大尺度和多尺度研究提供了最大的环境灵活性。微型温室将灵活调节相对湿度、二氧化碳水平和光照强度。微流控植物芯片将被设计成像芯片一样的滑动一次性组件，用于温室内部。每个植物芯片不仅可以让许多植物同时生长所需的时间，而且能够自动捕获单个种子，改变生长温度，调节化学浓度，并将生物物种引入植物生长区域。一个可编程成像系统将被设计用于收集植物种子、根、芽和细胞的图像。为了以高通量的方式量化形态特征和确定表型差异，将开发一种自动化算法来提取和分析植物生长发育过程中获得的图像。拟南芥将作为模式植物进行仪器的生物学验证。该项目将有助于植物表型的系统分析，在基因鉴定、功能基因组学和基因型-表型相关性方面具有广泛的应用。植物的大尺度和多尺度表型与变化的生长环境影响相一致，在应用和基础植物生物学中具有广泛的意义。提出的仪器将在解决表型组学领域的重大挑战方面取得突破性进展，将为植物生物学研究人员提供资源，并通过将强大的数据分析能力交给研究人员，将在植物表型组学领域创造范式转变。教育计划包括为三名博士生和四名本科生提供跨学科的机会，其中包括两名女性和少数民族学生，为本科生生物工程副修课程开设一学分的研讨会课程，并在爱荷华州立大学现有的本科生和研究生课程基础上增加一个新的实验室。传播计划包括通过广泛的合作为爱荷华州立大学及其他地区的植物生物学家提供表型服务，组织植物表型学研讨会，与国家实验室合作传播表型服务，并通过小企业创新研究或小企业技术转让机制将仪器商业化。

An award is made to Iowa State University to develop a high-throughput, large-scale plant phenotyping instrumentation for knowledge discovery in plant phenomics area. Characterization of the complete plant phenome has posed a difficult challenge due to the large number of genes in the genomes, and changeable environmental conditions that influence plant phenotypes. Analyzing plant phenotypes on a large and multi-scale level with sufficient throughput and resolution has thus been difficult and expensive. This project will lead to the development of microsystem technology based plant phenotyping instrumentation, and therefore will constitute a transformative leap in throughput and information content over existing phenotype assays. The core of the instrumentation is an integrated plant growth system consisting of an array of miniature greenhouses, microfluidic plant chips, and microfluidic control logic. The plant growth system can provide maximal environmental flexibility in large- and multi-scale study of plant-environment interactions. The miniature greenhouses will flexibly regulate relative humidity, carbon dioxide level, and light intensity. The microfluidic plant chips will be designed to be sliding chip-like disposable components for use inside the greenhouses. Each plant chip will not only allow a number of plants to simultaneously grow for a desired period of time, but be able to automatically trap individual seeds, change growth temperature, regulate chemical concentration, and introduce biological species to the plant growth regions. A programmable imaging system will be designed to collect images of plant seeds, roots, shoots, and cells. To quantify morphological traits and determine phenotypic differences in a high throughput manner, an automated algorithm will be developed to extract and analyze images acquired during plant growth and development. Arabidopsis thaliana will be used as a model plant for biological verification of the instrumentation. The project will contribute to systematic analysis of plant phenotypes with a wide range of applications in gene identification, functional genomics, and genotype-to-phenotype correlations. Large and multi-scale phenotyping of plants, in concert with changeable growth environmental influences, has broad implications in applied and basic plant biology. The proposed instrumentation will make breakthrough toward solving grand challenging large-scale problems in the field of phenomics, will build resources to benefit plant biology researchers, and will create a paradigm shift in the plant phenomics area by placing powerful data analysis capability in the hands of researchers. The education plans include providing an interdisciplinary opportunity to three doctoral students and four undergraduate students including two female and minority students, creating a one-credit seminar course for the Undergraduate Bioengineering Minor Program, and adding a new lab to existing undergraduate and graduate courses at Iowa State. The dissemination plan includes providing phenotying services to plant biologists at Iowa State and beyond through extensive collaborations, organizing Plant Phenomics workshop, partnering with national laboratories to disseminate phenotying services, and commercializing the instrumentation through the small business innovation research or small business technology transfer mechanism.