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

主要研究者：费章军（博伊斯汤普森植物研究所）合作研究者：Jan Kreuze [国际马铃薯中心（CIP），秘鲁]主要合作者：马丁·基奥纳（赞比亚国家农业研究组织），Paul Demo（CIP-Malawi），Britta Kowalski（CIP-Angola），道格拉斯米亚诺（肯尼亚农业研究所，肯尼亚），Settumba 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（埃塞俄比亚投资促进局）和Martine Tachin（阿波美-卡拉维大学，Rép.贝宁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）自给农民极其重要的粮食作物。它生长在整个非洲大陆，目前全球甘薯面积的34.5%在非洲。甘薯生产的一个主要限制是品种下降，主要是由于病毒感染对这种蔬菜繁殖作物的累积效应。因此，病毒性疾病被认为是世界范围内甘薯生产的主要限制因素，特别是在SSA。该项目的目的是评估一种新的方法，对从非洲各地收集的田间种植的甘薯样品中的小RNA进行深度测序，以系统有效地鉴定已知和新型病毒基因组序列。将从非洲10多个国家收集约1750个具有地理参考的甘薯田间生长样本。这些样本的小RNA群体将被制备并使用高通量下一代测序技术进行测序，然后组装以鉴定已知的和新的甘薯病毒。更广泛的影响：粮食安全仍然是数百万非洲人面临的巨大挑战，特别是对撒哈拉以南地区的人们来说，他们依靠农业为生。新出现和重新出现的病原体，包括许多病毒，继续对非洲粮食生产造成毁灭性损失。目前对非洲作物病毒的了解是有限的，充其量也只是零星的。通过对小RNA群体进行深度测序的新型病毒基因组鉴定技术可能适用于大陆调查，因为其在病毒鉴定方面的效率已被温室和田间生长的样品所证明。然后，该技术可用于系统地确定非洲许多其他主要作物植物（如玉米、水稻、番茄、豆类和木薯）上的总病毒基因组序列（病毒组）。这些信息的公开将为科学界和政府提供前所未有的可能性，以了解非洲作物病毒的分布，指导植物检疫要求，预测未来流行病的风险，并提出区域疾病管理战略。本项目产生的数据将通过项目网站（可通过http：//bti.cornell.edu/ZhangjunFei.php访问）传播，原始和加工的小RNA序列也将分别通过EBI序列读取档案和NCBI基因表达综合数据库提供。新的病毒基因组序列将存入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.