Genomic approaches to understanding resistance and virulence in the cereal-Striga interaction for targeted breeding of durable defence.

稻米在撒哈拉以南非洲的国民经济中发挥着关键作用，产量增长速度超过任何其他谷物;稻米被视为实现粮食安全和减贫的关键战略作物。水稻在非洲迅速发展的原因之一是引进了18种称为非洲新稻的高地品种。这些种间栽培品种是由非洲稻（O. glaberrima）与亚洲稻（O. sativa），具有优异的耐旱性和抗病性。因此，在这些高地生产环境中工作的自给农民越来越多地用非洲新稻取代玉米，甚至高粱。然而，这些谷物种植区的土壤被有害的寄生杂草S侵染。asiatica或S. hermonthica，这越来越限制水稻生产;制定新的管理战略至关重要。抗独脚金品种的使用，作为一个综合控制计划的一部分，被认为是可持续的和具有成本效益的，但我们仍然不知道的基因，使一些谷物品种比其他人更能抵抗这些寄生虫的身份，我们也没有足够的不同类型或抗性育种计划的来源。这一点很重要，因为独脚金种子库的遗传多样性如此之大，以至于抗虫作物品种的持久性受到寄生虫毒力快速进化潜力的影响。因此，长期成功的控制独脚金的宿主品种抗性需要鉴定和利用多种来源的宿主抗性基因，以及更好地了解来自不同地点的独脚金种群内和种群之间的毒力遗传变异。这些知识将使我们能够将联合收割机适当的抗性基因结合到适合不同农业生态区的品种中，并更有效地管理品种的使用，从而延缓毒力进化。本研究的目的是通过分子/遗传学和群体基因组学方法，结合田间试验，鉴定水稻对不同种和生态型的独脚金抗性的多个QTL和候选抗性基因，并首次发现能够使寄生虫克服特定寄主抗性的独脚金基因座。我们将通过对含有O. glaberrima或O. rufipogon（栽培稻的野生祖先）已经渗入到热带O. sativa背景（染色体片段代换系群体），以确定抗性QTL/基因在这些水稻基因组上的位置。我们将精细定位水稻12号染色体的一个现有区域（已知含有抗性基因），以确定那些负责和验证其功能，使用一种新的，高通量的“基因筛选”的基础上发根农杆菌诱导的“毛状根”在水稻品种。我们将使用人口基因组学的方法，以确定Striga位点，使寄生虫克服寄主抗性（S）在特定的品种，并分析其空间变异内和不同的寄生虫种群之间。我们的材料将在肯尼亚、坦桑尼亚和乌干达的田间进行筛选，以表征其田间抗性表达以及不同季节的耐受性和产量水平，并将我们的材料展示给农民和种子公司，并从他们那里获得宝贵的反馈。该项目将产生抗性和适应性品种，可供在Striga出没地区工作的农民立即使用，并产生育种材料和宝贵的见解，以加强水稻育种工作，进一步提高农民首选品种的抗性。

Rice plays a pivotal role in the national economies of sub-Saharan Africa and production is expanding faster than any other cereal; it is considered a key strategic crop for attaining food security and poverty alleviation. One of the reasons for the rapid expansion of rice in Africa has been the introduction of 18 upland rice cultivars known as NERICA. These interspecific cultivars, generated by crossing the African rice species (O. glaberrima) with the Asian rice species (O. sativa), are high yielding and have excellent drought tolerance and disease resistance. Thus, subsistence farmers working in these upland production environments are increasingly replacing maize, and even sorghum, with NERICA rice. However, the soils of these cereal growing areas are infested by the pernicious parasitic weeds S. asiatica or S. hermonthica, which increasingly limits rice production; the development of new management strategies is essential. The use of Striga-resistant cultivars, as part of an integrated control programme, is recognized as sustainable and cost effective yet we still do not know the identity of genes that make some cereal cultivars more resistant to these parasites than others, nor do we have enough different types or sources of resistance for breeding programmes. This is important because the Striga seed bank is so genetically diverse that the durability of resistant crop varieties is compromised by the potential for rapid evolution of parasite virulence. Thus, the long-term success of host cultivar resistance for the control of Striga requires the identification and exploitation of multiple sources of host resistance genes together with a greater understanding of the genetic variation for virulence within and among Striga populations from different locations. Such knowledge will allow us to combine appropriate resistance genes in cultivars that are suitable for different agro-ecological zones and to manage the use of cultivars more effectively such that virulence evolution is delayed. The aim of this project is to identify multiple Quantitative Trait Loci (QTL) and candidate resistance genes underlying resistance in rice to different Striga species and ecotypes and characterise, for the first time, Striga loci that enable parasites to overcome specific host resistances.To achieve our aims, we will utilise molecular/genetic and population genomic approaches combined with extensive field testing of materials for resistance to Striga. We will identify multiple sources of resistance in rice to Striga species by phenotyping populations of rice plants in which small segments of the genomes of either O. glaberrima or O. rufipogon (wild ancestor of cultivated rice) have been introgressed into a tropical O. sativa background (Chromosome Segment Substitution Line populations) to determine the location of the resistance QTL/genes on these rice genomes. We will fine map an existing region of rice chromosome 12 (known to contain resistance genes) to identify those responsible and validate their function using a novel, high throughput, 'gene screen' based on Agrobacterium rhizogenes -induced 'hairy roots' in rice cultivars. We will use a population genomics approach to identify Striga loci that enable parasites to overcome host resistance(s) in specific cultivars and analyse their spatial variation within and amongst different parasite populations. A selection of our material will be screened at field sites in Kenya, Tanzania and Uganda to characterize their field expression of resistance as well as their levels of tolerance and yield across seasons and to expose our material to farmers and seed companies and get valuable feed-back from them. The project will generate resistant and adapted cultivars that can be used immediately by farmers working in Striga-infested areas and breeding material and valuable insights to enhance the work of rice breeders to further improve the resistance of farmer preferred cultivars.