"PathoScout” - portable DNA analysis for Precision Agriculture

高价值园艺作物和大面积大田作物的农民面临着控制真菌和卵菌病原体的挑战，因为疾病流行会大大降低产品的适销性和产量。早期发现导致重要疾病的病原体将使作物保护产品仅在需要时使用，这将最大限度地提高控制效果并减少不必要的应用，从而降低成本并降低生产的碳足迹。该项目将与项目合作伙伴一起，使用洛桑研究所的培养收集和存档的孢子样本，研究为特定病原体创建诊断LAMP检测试剂盒的可行性，开发和测试从孢子中释放DNA的通用方法，包括将孢子捕获在轮虫孢子陷阱的取样杆上，测试纯化DNA的测试方法，并测试工程流体系统，以自动处理样品以释放DNA，纯化DNA并进行LAMP检测。重点防治设施作物和室外作物的重要病原菌；灰霉菌（许多园艺作物的灰霉菌）、马铃薯疫病菌（马铃薯枯萎病）、葡萄白粉病（葡萄白粉病）和小麦黄锈病（小麦黄锈病）。稳定的LAMP测定试剂将由Polygenyn Ltd生产，并由Rothamsted进行测试。诊断测试本身将被设计用于一种轻便、便携、电池供电的设备，该设备将由agri - sampler有限公司生产，使用Microbritt有限公司开发的流体盒。该设备将兼容于对磨碎的叶子或水果样本进行的测试，以及使用孢子捕集器在空气中捕获的空气微粒样本。总体目标是探索创建一种便携式用户友好且低成本的诊断工具的可行性，以支持作物保护，基于LAMP技术的新型真菌孢子检测，用户可以使用捕获的空气传播孢子或叶子或水果样本进行当日检测。一个成功的可行性结果将提供一个自动化的DNA分析平台，具有广泛的应用范围，超出农业。它将改变作物保护做法，提高英国农业对因气候变化而变得更加零星的疾病的抵御能力。

Farmers of high value horticultural crops and large acre field crops face challenges to control fungal and oomycete pathogens in conditions where disease epidemics can substantially reduce marketability of produce and yield. Early detection of pathogens that cause important diseases will allow crop protection products to be applied only when needed, which will maximise control efficacy and reduce unnecessary applications thereby reducing costs and lowering the carbon footprint of production.This project will use Rothamsted's culture collection and archived spore samples, along with project partners, to research the feasibility of creating kits of diagnostic LAMP assays for specific pathogens, develop and test generic methods to release DNA from spores, including spores trapped onto sampling rods of rotorod spore traps, test methods to purify the DNA and test an engineered fluidic system to automate the handling of samples to release DNA, purify it and perform a LAMP assay. We will focus on important pathogens of protected and outdoor crops; Botrytis cinerea (grey mould of many horticultural crops), Phytophthora infestans (potato blight), Erysiphe necator (grape powdery mildew) and Puccinia striiformis (wheat yellow rust).Stabilised LAMP assay reagents will be produced by Polygenyn Ltd and tested by Rothamsted. The diagnostic test itself will be designed for use in a lightweight, portable, battery-powered device, which will be produced by Agri-Samplers Ltd using a fluidic cassette developed by Microbritt Ltd. The device will be compatible with tests performed on ground-up leaf or fruit samples and also samples of airborne particulates captured in air using a spore trap.The overall aim is to explore the feasibility of creating a portable user-friendly and low-cost diagnostics tool to support crop protection, based on novel fungal spore detection by LAMP technology for same-day testing by the user with samples of either captured airborne spores or leaf or fruit samples.A successful feasibility outcome will deliver an automated DNA analysis platform with broad applications beyond agriculture. It will transform crop protection practices and improve the resilience of UK agriculture to diseases made more sporadic by climate change.