erumpent yellow rust pustules seen on wheat leaves in Ethiopia. Photography by Matt Heaton, John Innes Centre.

植物害虫和疾病是对全球粮食安全的主要威胁，如果不加以治疗，有可能破坏整个农作物。据估计，仅在前五名粮食作物中停止真菌疾病的传播就可以喂养超过6亿人。小麦 - 这五个前五种农作物之一 - 正受到威胁越来越大，真菌病原体引起小麦锈病，这是最大的担忧。

如今,这些在gr在欠发达国家eatest risk of large-scale crop losses due to inaccessibility of effective diagnostic tests and control measures. Just like with human disease, if you see visible symptoms but aren’t sure of the causal agent, then how can you action the correct treatment? This is where genome-based diagnostics and disease surveillance comes into play. Identifying the precise strain of a pathogen ensures the most appropriate control measures are actioned and, particularly for less-resourced countries, limited resources used wisely.

revolutionary portable genome sequencing devices aid disease diagnostics
在clinical labs, the full genetic code of human disease agents is frequently unravelled to assist with disease diagnostics. Since the release of the first portable genome sequencer by牛津纳米孔在2015年，无论环境多么荒凉，这种基因组水平的诊断和监测现在都可以准确地进行疾病爆发的地方。这彻底改变了诊断的速度，建立了有关病原体菌株的发展速度和的实时基因组信息帮助绘制其传输路线。

这些最初的研究集中在病毒病原体上。但是，对实时基因组水平诊断的需求对于真菌疾病也至关重要。但是，将这种策略用于真菌并不直接。真菌基因组通常比病毒大数十千倍，并且经常与宿主植物分离。因此，我们不能仅仅对含有真菌和（相当大的）宿主植物基因组的感染叶子进行序列，目前它的价格昂贵。我们需要一种不同的方法。

Implementing portable genomic-based diagnostics for fungal pathogens
我们决定使用一种经常用于测试特定人类疾病的方法，该方法经常被采用。这种方法着重于分析较小的基因子集的遗传密码，这些基因的遗传代码对特定条件具有丰富的信息。这种目标方法大大减少了每个样本生成的数据量，从而相关成本。

在our studypublished inBMC生物学，，，，we focused on the wheat yellow rust fungal pathogen (Puccinia striiformisf.sp。Tritici）。We first identified genes that showed high variability in their DNA code between pathogen strains and then used this small subset of genes for targeted re-sequencing. This allowed us to rapidly determine which particular strain is in our infected leaf sample. This new system termed – MARPLE (mobileAndrEAL时间plant disease) diagnostics – is also highly suited to disease emergencies as it can generate detailed data on which strain of the yellow rust pathogen is in a farmer’s field within just 48 hours of collecting a sample.

MARPLE：埃塞俄比亚小麦生锈预警系统中的缺失作品
埃塞俄比亚是撒哈拉以南非洲最大的小麦生产商，但也是gateway for new wheat yellow rust pathogen strains entering Africaand hence the highest priority country for rapid diagnostics. Wheat yellow rust continues to plague wheat production in Ethiopia causing large-scale epidemics e.g. in 2010, 600,000 hectares of wheat were affected, with losses estimated in excess of $250 million, and new pathogen strains present a very high risk for recurring large-scale disease epidemics.

Following such wide-scale devastation, Ethiopia developed an integrated wheat rust early warning system to prevent future catastrophic losses. Yet, the ability to define the precise strain of the pathogen in a farmer’s field in real-time was just not possible with prevailing methods. MARPLE was designed precisely to fill this void.

Working with the Ethiopian Institute for Agricultural Research (EIAR) we developed a mobile lab system housed in a single hard-case, removing the need for additional infrastructure or high-level specialist expertise. We successfully trialed an optimized MARPLE pipeline in Ethiopia in September 2018. As the ultimate demonstration of its robust nature and mobility, we also ran the pipeline in the back of a Landcruiser directly in the field, demonstrating feasibility without continuous mains electricity or access to any additional laboratory equipment (seehttps://acaciaafrica.org/marple-diagnostics/）。

Our partnership between the John Innes Centre and CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo) also allowed data generated through this method to feed directly into early-warning systems and control recommendations. This project integration is now positioning Ethiopia as a world leader in pathogen diagnostics and forecasting for wheat rust diseases.

Marple Diagnostics的下一步是什么？
我们开发用于靶向重新测量的基因面板也非常灵活，并且可以根据需要轻松适应其他基因。我们目前正在合并编码在真菌病原体中鉴定为保守杀菌剂靶标的蛋白质的基因。这将允许对突变进行实时监控，这些突变可能会提醒我们为黄色锈病病原体中的杀真菌剂实用程序故障。Marple Diagnostics为基于基因组的移动性菌株诊断提供了路线图，该路线图可以容易地应用于其他不断威胁全球粮食安全的复杂真菌病原体。