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

大米在撒哈拉以南非洲的国民经济中发挥着举足轻重的作用，其生产增长速度比任何其他谷物都快；它被认为是实现粮食安全和减贫的关键战略作物。非洲水稻迅速扩张的原因之一是引进了18个被称为NERICA的旱稻品种。这些种间品种是由非洲稻种(O.angberrima)与亚洲稻种(O.sativa)杂交而成，产量高，抗旱性和抗病性能优异。因此，在这些旱地生产环境中工作的自给自足的农民越来越多地用NERICA水稻取代玉米，甚至高粱。然而，这些谷物种植区的土壤受到有害寄生杂草的侵扰，这日益限制了水稻产量；开发新的管理策略至关重要。作为综合防治计划的一部分，使用抗稻瘟病品种被认为是可持续的和具有成本效益的，但我们仍然不知道使一些谷物品种比其他品种更抗这些寄生虫的基因的身份，也没有足够的不同类型或抗源来进行育种计划。这一点很重要，因为Striga种子库的遗传多样性如此之大，以至于抗病作物品种的耐久性受到寄生虫毒力快速进化的可能性的影响。因此，寄主品种对稻瘟病菌的长期抗性控制需要鉴定和利用寄主抗性基因的多个来源，并更好地了解不同地点稻瘟病菌种群内和种群间的毒力遗传变异。这些知识将使我们能够在适合不同农业生态区的品种中结合适当的抗性基因，并更有效地管理品种的使用，从而延缓毒力进化。本项目的目的是鉴定水稻对不同稻瘟病菌和不同生态型的抗性的多个数量性状基因座(QTL)和候选抗性基因，并首次鉴定能够使稻瘟病菌克服特定寄主抗性的稻瘟病菌基因座。为了实现我们的目标，我们将利用分子/遗传和群体基因组方法结合对稻瘟病菌材料的广泛田间检测。我们将通过对水稻植株群体进行表型鉴定来鉴定水稻对稻瘟病菌的多个抗性来源，在这些群体中，栽培稻的野生祖先或栽培稻的小片段基因组已导入热带水稻背景(染色体片段置换系群体)，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(已知包含抗性基因)，以确定责任人，并使用基于发根农杆菌诱导的水稻品种毛状根的新的、高通量的基因筛选来验证它们的功能。我们将使用种群基因组学方法来确定使寄生虫能够克服寄主抗性的STRGA基因座(S)，并分析它们在不同寄生虫种群内和之间的空间变异。我们精选的材料将在肯尼亚、坦桑尼亚和乌干达的田间地点进行筛选，以确定他们在田间表现出的抗性以及他们在不同季节的耐受性和产量水平，并向农民和种子公司展示我们的材料，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强的品种，可供在稻瘟病肆虐地区工作的农民立即使用和育种材料，并提供有价值的见解，以加强水稻育种者的工作，进一步提高农民偏爱的品种的抗性。

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.