Facilitating smart crop breeding through understanding the genetics of resistance and virulence in the Striga-rice interaction

摘要(4000字)水稻是世界上最重要的农作物之一，在撒哈拉以南非洲(SSA)的国民经济中发挥着举足轻重的作用，但产量受到称为Striga的专性根寄生杂草的限制，这种杂草导致20%-100%的产量损失。Striga是极其难以控制的，因为个体产生数百万个小的、长寿的、遗传多样化的种子，这些种子只有在对宿主根分泌物中存在的萌发刺激剂做出反应时才能萌发。由于稻瘟病在寄主根部附着后立即严重损害作物的发育，因此必须在生活史的早期采取控制措施，以防止产量损失。抗病品种应该在防治策略中发挥关键作用，但目前还没有关于抗病基因的身份或作用机制的已发表信息。Striga迅速进化以克服寄主抗性，强烈影响以抗性育种为基础的作物改良战略的可持续性。在一个变种中堆积许多抗性基因对于减少寄生虫进化克服抗性的可能性至关重要，但这需要了解宿主抗性和寄生虫毒力基因的身份。该项目旨在发现新的抗性基因，并将其与了解寄生虫毒力基因的分子遗传学基础相联系，以培育持久防御。我们最近在水稻12号染色体上发现了第一组抗性基因(受体类蛋白(RLP))，它们对几个生态型(遗传变种)的水稻提供了抗性，并表明在一个抗性品种中同时下调其中许多基因可以恢复感病。然而，为了有效地培育品种，我们需要知道是否有一个或多个基因提供抗性，或者是否有不同的基因组合对寄生虫的不同遗传生态型起作用。我们将通过在抗性品种中单独和联合使用CRISPR/Cas9来灭活RLP基因，用不同的Striga生态型感染，并确定其对敏感性的影响，来研究这一点。最近，我们比较了在敏感和抗性寄主上生长的Striga，并采用群体基因组学的方法来鉴定一组候选毒力基因。为了确定它们是否与RLP抗性基因相互作用，我们将收集来自SSA的多个寄主物种/品种的Striga生态型。这些病毒将用中性标记(SNPs)进行基因分型，以观察种群结构(对解释和管理毒力至关重要)，然后用候选毒力基因中的SNPs测试与已知抗药性形式的特定关联。这将为今后研究抗病基因和毒力基因之间的功能相互作用以及检测与其他抗病基因相关的毒力基因提供基础。为了发现新的抗性基因，我们将利用一个普通野生稻亲本(cv.IR64)，有十个不同的父母。对2000个NAM品系进行了基因分型，为10个群体中的每个群体制作了非常详细的遗传图谱，有助于快速发现新的抗稻瘟病基因。我们将首先对10个具有现有和新的striga生态型的亲本进行表型鉴定，形成一个毒力/抗性矩阵，以便我们在为期2年的项目中选择感兴趣的生态型和NAM种群进行表型，同时为将来在野外和实验室进行更广泛的表型鉴定提供数据。

Summary (4000 characters)Rice is one of the most important crops worldwide and plays a pivotal role in the national economies of sub-Saharan Africa (SSA) yet yields are constrained by species of obligate root parasitic weeds called Striga that cause yield losses of 20-100%. Striga is extremely difficult to control as individuals produce millions of small, long-lived, genetically diverse seeds that only germinate in response to germination stimulants present in host root exudates. As Striga severely damages the development of the crop immediately after attaching to the host root, control measures must act early in the life cycle to prevent losses in yield. Resistant varieties should play a key role in control strategies yet there is no published information about the identity or mechanism of action of Striga-resistance genes. Striga evolves rapidly to overcome host resistance, strongly influencing the sustainability of crop improvement strategies based on breeding for resistance. Stacking many resistance genes in a variety is essential to reduce the likelihood of resistance being overcome by the evolution of the parasite but this requires knowledge about the identity of host resistance and parasite virulence genes. This project aims to discover new resistance genes and to link this with an understanding the molecular genetic basis of parasite virulence genes for breeding of durable defence. We have recently identified the first cluster of resistance genes (Receptor-Like-Proteins (RLP)) on chromosome 12 of rice that provide resistance against several ecotypes (genetic variants) of S. hermonthica and S. asiatica and shown that simultaneous down-regulation of many of these genes in a resistant cultivar (by RNAi) restores susceptibility. However, for effective breeding of varieties, we need to know whether one, or more of the genes, acts to provide resistance, or whether different combinations of genes act against different genetic ecotypes of the parasite. We will investigate this by inactivating RLP genes, singly and in combination using CRISPR/Cas9 in resistant varieties, infecting with different ecotypes of Striga, and determining the effect on susceptibility. Recently we have compared Striga growing on susceptible and resistant hosts and taken a population genomics approach to identify a set of candidate virulence genes. To determine whether they interact with the RLP resistance genes we will collect Striga ecotypes from multiple host species/varieties across SSA. These will be genotyped with 'neutral' markers (SNPs) to look at the structure of the populations, (critical for interpretation and management of virulence) and then with SNPs in candidate virulence genes to test for specific associations with known forms of resistance. This will provide a foundation for future studies on the functional interaction between resistance and virulence genes and for association analyses to detect virulence genes relevance to other sets of resistance genes. To discover new resistance genes we will use a rice (Nested Association Mapping (NAM)) population derived from crossing one common O. sativa ssp indica parent (cv. IR64) with ten diverse parents. Two thousand NAM lines have been genotyped to produce highly detailed genetic maps for each of the 10 populations, facilitating the rapid discovery of new Striga resistance genes. We will first phenotype the 10 parents with existing and new Striga ecotypes to form a matrix of virulence/resistance to allow us to select interesting ecotypes and NAM populations to phenotype during the 2-year project whilst providing data for more extensive phenotyping in the field and laboratory in the future.