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

艾奥瓦州立大学被授予开发一种高通量、大规模的植物表型仪器，用于植物表型组学领域的知识发现。由于基因组中有大量的基因，以及影响植物表型的多变的环境条件，对完整的植物表型进行表征是一个困难的挑战。因此，在具有足够的吞吐量和分辨率的大范围和多尺度水平上分析植物表型一直是困难和昂贵的。该项目将导致基于微系统技术的植物表型分析仪器的发展，因此将在产量和信息含量方面比现有的表型分析方法产生革命性的飞跃。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逻辑组成。在大规模和多尺度的植物-环境相互作用研究中，植物生长系统可以提供最大的环境灵活性。微型温室将灵活地调节相对湿度、二氧化碳水平和光照强度。微流控植物芯片将被设计为滑动芯片状的一次性组件，用于温室内。每个植物芯片不仅可以让多个植物同时生长一段所需的时间，还可以自动捕获单个种子，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。将设计一个可编程的成像系统来收集植物种子、根、芽和细胞的图像。为了以高通量的方式量化形态特征并确定表型差异，将开发一种自动算法来提取和分析植物生长发育期间获得的图像。拟南芥将被用作该仪器的生物验证的模式植物。该项目将有助于对植物表型的系统分析，在基因鉴定、功能基因组学和基因与表型的相关性方面有广泛的应用。大规模和多尺度的植物表型，与多变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。拟议的仪器将在解决表型组学领域具有重大挑战性的大规模问题方面取得突破，将建立有利于植物生物学研究人员的资源，并将通过将强大的数据分析能力交到研究人员手中，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族裔学生，为本科生生物工程辅修课程创建一学分的研讨会课程，以及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向爱荷华州及其他地区的植物生物学家提供表型鉴定服务，组织植物表型组学研讨会，与国家实验室合作传播表型鉴定服务，并通过小企业创新研究或小企业技术转移机制将仪器商业化。

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.