PFI:AIR-RA: Commercializing of a Molecular Analysis Platform for Plant Genomics in an Industry/University Ecosystem

University Of California-Irvine, Irvine CA

Investigators

Abstract

This PFI: AIR Research Alliance project focuses on the translation and transfer of an integrated microfluidic based screening and testing analysis platform that has the potential to dramatically improve the efficiency and effectiveness of breeding plants. In the current agriculture biotech industry, genetic analyses of complex communities of plant cells are typically carried out in a homogenized, whole community fashion where the output is global information on the average state of the population of cells. This can mask the true extent of cellular heterogeneity that is present by averaging properties and potentially missing intriguing outliers. Molecular analysis at the single cell level would lead to better capability to develop enhanced strains of plant cells that thrive under various conditions. Thus there is a need for a tool that can provide single cell-molecular analysis in large populations, capable of high throughput while preserving heterogeneity information, and tailored to the agriculture genetics industry. The goal of this project is to develop such a tool by applying microfluidic lab-on-a-chip technologies for molecular and single cell analyses derived from the NSF I/UCRC "Center for Advanced Design and Manufacturing of Integrated Microfluidics" (CADMIM) where expertise and discoveries in the design, microfabrication, and manufacturing of microfluidic devices for cellular and molecular processing and detection are utilized. Not only will the proposed technology enable the single cell analysis, it also has the potential to lower the cost per molecular test by an order of magnitude over current methodologies. Current technology used in the agriculture biotech industry relies on discrete, bulky robotic systems that are time and labor intensive and require larger amounts of power, sample, and reagents resulting in much higher cost per test to analyze large numbers of samples. The innovation ecosystem that will be enhanced includes CADMIM, UC Irvine, Johns Hopkins University, and DuPont Pioneer. The UC Irvine site of CADMIM brings microfluidic cellular manipulation, lysing, and micro-scale fluidic handling expertise. Johns Hopkins University brings microfluidic molecular processing and detection expertise. DuPont Pioneer, a leading developer and supplier of plant genetics to farmers worldwide, brings the plant genomic expertise and agriculture biotech business knowledge. Students and post-doctoral fellows from both universities will gain entrepreneurial and technology translation experience through their frequent interactions with DuPont Pioneer's technical team in understanding the current limitations in plant genotyping biotechnology, how a multi-continent international company works to solve large-scale problems, what is required for disruptive technology to displace current working technology paradigms, and how interdisciplinary teams communicate to develop cutting edge solutions. This project addresses several technology gaps as it translates from research discovery toward commercial application. Plant cell genotype screening requires millions of cell-level verification tests and subsequent further massive molecular analyses of specific cell types. The current plant cell processing and molecular analysis platforms consist of multiple cumbersome and expensive cell processing machines that are time consuming and rely on skilled lab workers operating them in sequence. This greatly limits the throughput of cells being analyzed and makes it cost prohibitive for applications that require field-based plant seed sampling and testing. With the integrated microfluidic technologies developed in this project, the multiple steps will be integrated on a compact and potentially portable platform, using smaller liquid volumes to obtain faster results.