BREAD ABRDC: Development of Essential Genetic and

小米是一种对东非粮食安全具有战略重要性的粮食作物。 这种谷物营养价值高，可以在干旱环境中生长，因此对小农的生计很重要。 该地区的一个主要农业目标是通过减少或消除影响植物生长的疾病来开发高产的手指粟品种。 稻瘟病菌是谷子的主要病害之一，可使谷子减产80%以上。为了了解如何控制疾病爆发，该项目使用基因组测序作为一种强有力的方法来识别真菌的精确菌株，并研究真菌如何在植物中引起疾病症状。对在肯尼亚、坦桑尼亚、乌干达和埃塞俄比亚收集的稻瘟病菌株的序列分析将提供东非病原体遗传多样性的信息，并为确定导致手指粟感染的因素提供资源。从这种方法中获得的知识对于制定有效的疾病管理策略至关重要。此外，手指粟主机的序列分析将澄清为什么有些品种比其他品种更抗稻瘟病。所产生的资源也将被用作培训东非本科生和研究生生物信息学的工具，这是一种将信息转化为改进育种战略所必不可少的专门知识。 本项目的具体目标是：（1）获得异源四倍体小米基因组的80倍PacBio序列（1C=1.8 Gb）以产生高质量的基因组组装体（1C=1.8 Gb）;（2）对200个东非指状粟瘟病菌Magnaporthe bastum分离株进行重测序，其中包括10年前收集的24个分离株，以确定随着时间的推移和地理区域的变化，这种指粟病原体的多样性和进化。将使用效应子预测管道来挖掘胚粒基因组序列以鉴定候选效应子基因，所述效应子预测管道结合了已知效应子的共同特征（分泌和高多态性水平）;（3）使用RNA-Seq分析胚粒-指粟相互作用转录组以鉴定在感染的早期阶段诱导的基因。将从RNA-Seq实验中鉴定编码分泌蛋白的基因，并与使用效应子预测管道鉴定的基因交叉引用。将在亲和和不亲和互作中差异表达的宿主基因与稻瘟病感染早期差异表达的基因进行比较;（4）采用双循环设计，建立了一个由来自21个不同亲本的约4000个RIL组成的巢式关联作图组。该种群将代表第一个捕获指粟种质中存在的大量多样性并具有高数量性状基因座检测能力的绘图资源。

Finger millet is a grain crop of strategic importance to food security in Eastern Africa. The grain has high nutritional value, can grow in arid environments and thus is important to the livelihood of smallholder farmers. A major agricultural goal in the region is to develop higher yielding varieties of finger millet through reducing or eliminating diseases that impact growth of the plant. Blast fungus is a pathogen that reduces yield up to 80% and is one of the main diseases affecting finger millet. To understand how to control disease outbreaks, this project uses genomic sequencing as a powerful approach to identify precise strains of the fungus and to study how the fungus causes disease symptoms in the plant. Sequence analyses of blast strains collected in Kenya, Tanzania, Uganda and Ethiopia will provide information on the genetic diversity of the pathogen in Eastern Africa, and provide a resource to identify the factors that are responsible for infection of finger millet. The knowledge from this approach is essential to develop efficient disease management strategies. Furthermore, sequence analyses of the finger millet host will clarify why some cultivars are more resistant to blast than others. The generated resources will also be used as a vehicle to train undergraduate and graduate students in Eastern Africa in bioinformatics, an expertise that is essential to translate the information to improve breeding strategies. The specific aims of the project are to (1) Generate 80X PacBio sequence for the allotetraploid finger millet genome (1C=1.8 Gb) to generate a high quality genome assembly (1C=1.8 Gb); (2) Resequence 200 Eastern African isolates of the finger millet blast fungus Magnaporthe oryzae, including 24 that were collected 10 years ago, to determine the diversity and evolution of this finger millet pathogen both over time and across geographic regions. The blast genome sequences will be mined to identify candidate effector genes using an effector prediction pipeline that incorporates common characteristics of known effectors (secretion and high polymorphism levels;(3) Analyze the blast-finger millet interaction transcriptome using RNA-Seq to identify genes that are induced at early stages of infection. Genes encoding secreted proteins will be identified from the RNA-Seq experiment and cross-referenced to those identified using the effector prediction pipeline. Host genes that are differentially expressed will be compared between compatible and incompatible interactions, and with genes that are differentially expressed during early stages of blast infection in rice, and(4) Develop a nested association mapping panel of some 4000 RILs derived from 21 diverse parents using a double round robin design. This population will represent the first mapping resource that captures substantial diversity present in finger millet germplasm and has a high quantitative trait loci detection power.