BREAD: Determining the Pan-African Sweet Potato Virome: Understanding Virus Diversity, Distribution and Evolution and their Impacts on Sweet Potato Production in Africa

主要合作者：Martin Chiona(赞比亚国家农业研究组织)、Paul Demo(CIP-马拉维)、Britta Kosalski(CIP-安哥拉)、Douglas Miano(肯尼亚农业研究所，肯尼亚)、Settomba Mukasa(乌干达Makerere大学)、Joseph Ndunguru(坦桑尼亚Mikocheni农业研究所)、Ian Robertson和Elizabeth Ngadze(津巴布韦大学)、Steffen Schulz(CIP-埃塞俄比亚)和MarTachin(Abomey-Calavi大学)甘薯是世界上最重要的粮食作物之一，也是撒哈拉以南非洲(SSA)自给自足农民极为重要的粮食作物。它在整个非洲大陆都有种植，目前全球大约34.5%的甘薯种植面积在非洲。甘薯产量的一个主要限制是品种下降，主要是由于病毒感染对这种无性繁殖作物的累积影响。因此，病毒病被认为是全世界甘薯生产的主要限制因素，特别是在南沙地区。该项目的目的是评估一种新的方法，即从非洲各地采集的田间种植的甘薯样本中对小RNA进行深度测序，以系统和有效地识别已知和新的病毒基因组序列。总共将从非洲十多个国家收集大约1750个地理参考的田间种植的红薯样本。这些样本的小RNA种群将使用高通量的下一代测序技术进行准备和测序，然后组装起来识别已知和新的甘薯病毒。广泛的影响：粮食安全对数百万非洲人来说仍然是一个巨大的挑战，特别是对于那些依赖农业为生的撒哈拉以南地区的人。新出现和再次出现的病原体，包括许多病毒，继续给非洲的粮食生产造成毁灭性的损失。目前对非洲作物病毒的了解有限，充其量也只能是零星的。通过对小RNA群体进行深度测序的新的病毒基因组识别技术在大陆调查中具有潜在的应用价值，因为它在病毒识别方面的有效性已经在温室和田间种植的样本中得到证明。然后，这项技术可以用于系统地确定非洲其他一些主要农作物，如玉米、水稻、西红柿、豆类和木薯的总病毒基因组序列(病毒组)。公开这些信息将为科学界和政府提供前所未有的可能性，以了解作物病毒在非洲的分布，指导植物检疫要求，预测未来流行的风险，并建议区域疾病管理战略。在该项目下产生的数据将通过项目网站传播(可通过http://bti.cornell.edu/ZhangjunFei.php)获取)，原始和加工的小核糖核酸序列也将分别通过EBI Sequence Read Archive和NCBI gene Expression Omnibus获得。新的病毒基因组序列将被存入GenBank。

PI: Zhangjun Fei (Boyce Thompson Institute for Plant Research)Co-PIs: Jan Kreuze [International Potato Center (CIP), Peru]Key Collaborators: Martin Chiona (National Agricultural Research Organization, Zambia), Paul Demo (CIP-Malawi), Britta Kowalski (CIP-Angola), Douglas Miano (Kenya Agricultural Research Institute, Kenya), Settumba Mukasa (Makerere University, Uganda), Joseph Ndunguru (Mikocheni Agricultural Research Institute, Tanzania), Ian Robertson and Elizabeth Ngadze (University of Zimbabwe), Steffen Schulz (CIP-Ethiopia) and Martine Tachin (Université d'Abomey-Calavi, Rép. BéninSweet potato is among the most important food crops in the world and an extremely important food crop for subsistence farmers in sub-Saharan Africa (SSA). It is grown throughout the African continent and currently around 34.5% of global sweet potato area is in Africa. One major limitation in sweet potato production is cultivar decline, mostly due to the cumulative effect of virus infection on this vegetatively propagated crop. Thus, viral diseases are considered a major limiting factor in sweet potato production worldwide, and particularly in SSA. The objective of this project is to evaluate a novel approach, deep sequencing of small RNAs from field-grown sweet potato samples collected throughout Africa, to systematically and efficiently identify known and novel virus genome sequences. A total of around 1750 geo-referenced field-grown samples of sweet potato will be collected from more than ten countries in Africa. Small RNA populations of these samples will be prepared and sequenced using high throughput next-generation sequencing technology, and then assembled to identify known and novel sweet potatoviruses.Broader Impacts: Food security remains a huge challenge for millions of Africans, particularly for those in sub-Saharan regions, who depend on agriculture for their subsistence. Emerging and reemerging pathogens, including many viruses, continue to cause devastating losses of food production in Africa. Current knowledge of crop viruses in Africa is limited and sporadic at best. Novel virus genome identification technology through deep sequencing of small RNA population is potentially applicable to continental surveys as its efficiency in virus identification has been proven with both greenhouse and field grown samples. This technology can then be applied to systematically determine the total virus genome sequences (virome) on a number of other major crop plants in Africa such as maize, rice, tomato, bean, and cassava. Public availability of such information will provide the scientific community and government unprecedented possibilities to understand crop virus distribution in Africa, guide phytosanitary requirements, predict risks of future epidemics, and suggest regional disease management strategies. Data generated under this project will be disseminated through the project website (accessible via http://bti.cornell.edu/ZhangjunFei.php) and raw and processed small RNA sequences will also be available through EBI Sequence Read Archive and NCBI Gene Expression Omnibus, respectively. Novel virus genome sequences will be deposited into GenBank.