New tools for predicting spread of Fusarium wilt in banana

香蕉（Musa spp）是全球第五大最重要的主食，但由于其无性系性质，香蕉生产受到病原体的严重影响。在上一次香蕉大灾难中，尖孢镰刀菌变种cubense 1种（Foc1）摧毁了“大米歇尔”香蕉的全球生产。印度是世界上最大的香蕉生产国（约占全球产量的25%），几乎消耗了所有的香蕉。高毒力的枯萎病热带变种4 （Foc4）于2018年抵达印度，并于2019年在南美洲被发现，威胁到粮食安全（印度是世界上最大的香蕉生产国）和香蕉商品贸易。这个项目有两个主要目标。(i)产生可靠的分子标记，可在现场用于识别TR4并为管理策略提供信息。将发展基于卫星的遥感方法，用于香蕉种植园的自动划界和确定植物的压力。方法：新一代测序技术、大数据分析技术、卫星雷达技术、高光谱成像技术、诊断分子标记技术等。田间镰刀菌LAMP检测方法的建立。这将涉及处理大型数据集的培训，包括基因组（镰刀菌；跨不同种族和地理/人口结构的比较基因组学）和地球卫星。开发可用于跟踪单个病原体基因型跨空间和时间传播的特异性基因组标记。这些tr4特异性序列将用于开发基于PCR和lamp的诊断分析，后者可以使用电池供电的便携式设备在现场部署。遥感研究（从本月18日开始）将使用欧洲航天局的哨兵合成孔径雷达（SAR）来开发香蕉种植园的雷达特征，使用谷歌地球图像和来自合作组织的种植园地图。首先，哥斯达黎加的数据将用于训练和统计聚类算法，如用于分类的随机森林。开放获取的LANDSAT光谱数据将用于开发人工林植被指数，以了解植物健康的时空变化。更高分辨率的图像将使用带有多光谱扫描仪的无人机获取，既可以验证卫星图像，也可以避免由于云层覆盖而导致的图像获取问题。对于地面实况无人机数据收集，我们的目标是包括一些温室实验，以监测疾病对反射率的影响，由于叶片化学或形态的变化。

Banana (Musa spp) is the 5th most important global food staple, but as a consequence of its clonal nature, banana production suffers significantly from pathogens. In the last banana apocalypse, Fusarium oxysporum var. cubense Race 1 (Foc1) destroyed global production of "Gros Michel". India, the biggest producer of bananas in the world (~25% global production), consumes nearly all its production. The highly virulent Fusarium Wilt Tropical Race 4 (Foc4) arrived in India in 2018 and in 2019 it was found in South America, threatening both food security (India is the world's largest banana producer) and the trade in banana commodities. This project has two key objectives. (i) Generating robust molecular markers that can be used in field for identification of TR4 and inform management strategies. (ii) Developing satellite-based remote sensing approaches will be developed for automatic demarcation of banana plantations, and identification of plant stress.Methods:Next generation sequencingBig data analysis - satellite radarHyperspectral imagingDevelopment of diagnostic molecular markers.Development of LAMP assays for in field detection of Fusarium.This will involve training in handling large datasets, both genomic (Fusarium; comparative genomics across different races and geographical/population structures) and geo-sattelite. to develop intra-specific genomic markers that can be used to track spread of individual pathogen genotypes across space and time. These TR4-specific sequences, will be used to develop PCR- and LAMP-based diagnostic assays, the latter of which could be deployed in the field using a battery-powered portable device.The remote sensing studies (from month 18) will use the European Space Agency's Sentinel Synthetic Aperature Radar (SAR) to develop radar signatures for banana plantations, using Google Earth imagery and plantation maps from partner organizations. In the first instance Costa Rica data will be used for training and statistical clustering algorithms such as Random Forest used for classification. Open-access, spectral data from LANDSAT will be used to develop vegetation indices for plantations, to understand spatial and temporal variation in plant health. Higher resolution imagery will be acquired using UAVs with multispectral scanners, both to validate satellite imagery and to avoid problems with image acquisition due to cloud cover. For ground truthing drone data collection, we aim to include some glasshouse experimentation to monitor effects of diseases on reflectance, due to changes in leaf chemistry or morphology.