Novel sources of disease resistance and effector detection from genetic and genomic analysis of Solanum americanum diversity

马铃薯晚疫病是由马铃薯晚疫病菌（Phytophthora infestans，Pi）引起的一种毁灭性病害，曾导致19世纪40年代爱尔兰马铃薯饥荒。大多数马铃薯品种易受枯萎病的影响，在英国，其防治成本约为6000万英镑，在全球范围内约为70亿美元。对枯萎病的遗传抗性将大大减少对农用化学品喷洒的需求，并节省排放二氧化碳和压实土壤的拖拉机行程。植物有强大的防御机制，但抵抗的关键是识别。枯萎病是一种快速进化的病原体，有许多不同的种族。与抗生素一样，依赖一种作用模式或一种耐药性来源是有风险的，与COVID一样，病原体可以迅速进化以科普耐药性机制。我们已经在一个潜在的新品种中部署了3个抗Pi（Rpi）基因我们的主要目标是了解马铃薯相对的美洲茄（Solanumamericanum）（“Sam”）对晚疫病的近免疫性，广泛分布的英国本土植物龙葵的二倍体祖先（S。nigrum）。我们有来自世界各地的54个不同的种质，但所有这些种质在田间都是完全抗性的，尽管有些在促进疾病的实验室条件下表现出易感性，这使我们能够利用遗传学克隆两个抗晚疫病（Rpi）基因，Rpi-amr 1和Rpi-amr 3。（Avramr 1和Avramr 3）被Rpi-amr 1和Rpi-amr 3识别，我们可以在我们的集合中鉴定出许多额外的“非amr 1，3”抗性。我们拥有广泛的Sam基因组序列数据，这极大地有助于分析遗传变异，以检测和抵抗Pi。该提案的一个中心目标是克隆多种额外的抗性，并验证它们对多个Pi种族的功效。我们相信我们的材料中至少有两个额外的抗性基因;来自Sam材料SP2275的Rpi-amr 5（可能但不一定与来自SP3370的Rpi-amr 12相同），以及来自SP2300的Rpi-amr 13（可能但不一定与来自SP2298的Rpi-amr 15相同）和来自SP1101的Rpi-amr 14。鉴定这些新Rpi基因的遗传图谱已经很先进，将在拨款期间完成并发表，并在转基因马铃薯植物中验证功能。我们已经从Pi中鉴定出另外7种毒力组分，这些组分在至少一个Sam登录中被识别，并且正在鉴定支持这些识别能力的Sam基因。其中一个已经被克隆了。我们假设这些多重识别能力有助于抵抗。我们将以两种方式测试这一点：（i）我们将测试这些额外的识别能力单独或组合地转移到马铃薯中是否可以提高对Pi的抗性。(ii)我们将使用最近的“CrispR”技术进行定向诱变，使保藏号为SP2271的这些基因中的三个发生突变，并测试识别能力的降低是否会损害抗性并提高易感性病原体效应物已经进化为当在其宿主上生长时促进其繁殖成功。效应子通过干扰作为植物防御反应的一部分的植物机制来促进病原体毒力。通过识别病原体效应器的宿主靶标，我们确定了植物防御机制的关键组成部分。因此，每一个新的抗性基因的分离不仅有助于实现持久的抗病性，而且还提供了一种途径，以确定公认的分子，这是一个关键的病原体毒力成分，因此也是他们的植物目标，使我们能够大大提高我们对植物免疫的理解。

Potato late blight, caused by Phytophthora infestans (Pi), is a devastating disease of potato crops and led to the Irish potato famine of the 1840s. Most potato varieties are susceptible to blight, and its control costs ~£60M in fungicide applications in the UK, and ~$7B world-wide.Genetic resistance to blight would greatly reduce the need for agrichemical sprays and save on tractor journeys that emit CO2 and compact the soil. Plants have powerful defence mechanisms, but the key to resistance is recognition. Blight is a rapidly evolving pathogen, with many different races. As with antibiotics, reliance on one mode of action or one source of resistance is risky, and as with COVID, pathogens can rapidly evolve to cope with resistance mechanisms. We have deployed a stack of 3 Resistance to Pi (Rpi) genes in a potential new variety ("PiperPlus"), but more Rpi genes are needed in anticipation of pathogen evolution, and also to enhance our understanding of plant/pathogen coevolution, and pathogen virulence mechanisms.Our primary objective is to understand the near-immunity to late blight of the potato relative Solanum americanum ("Sam"), the diploid ancestor of the widespread UK native plant black nightshade (S. nigrum). We have 54 different accessions from around the world, but all are fully resistant in the field, though some show susceptibility under disease-promoting lab conditions, which enabled us to use genetics to clone two Resistance to P. infestans (Rpi) genes, Rpi-amr1 and Rpi-amr3.Because we have cloned the Pi molecules (Avramr1 and Avramr3) that are recognized by Rpi-amr1 and Rpi-amr3, we could identify many additional "non-amr1,3" resistances in our collection. We have extensive Sam genome sequence data that greatly helps analysis of genetic variation for detection of and resistance to Pi. A central goal of this proposal is to clone multiple additional resistances and to verify their efficacy against multiple races of Pi. We are confident there at least two additional resistance genes in our set of accessions; Rpi-amr5 from Sam accession SP2275 (perhaps but not necessarily the same as Rpi-amr12 from SP3370), and Rpi-amr13 from SP2300 (perhaps but not necessarily the same as Rpi-amr15 from SP2298) and Rpi-amr14 from SP1101. Genetic mapping to identify these new Rpi genes is well advanced and will be completed and published during the grant period, with function verified in transgenic potato plants Since Sam is so resistant, it is likely to have many different ways of recognising Pi. We have identified another 7 virulence components from Pi that are recognised in at least one Sam accession, and are well on the way to identifying the Sam gene that underpins each of these recognition capacities. One is already cloned. We hypothesise that these multiple recognition capacities contribute to resistance. We will test this in two ways(i) we will test if transfer of these additional recognition capacities into potato, alone or in combination, can elevate resistance tp Pi.(ii) we will use the recent "CrispR" technology for targeted mutagenesis to mutate three of these genes in accession SP2271, and test if reduction in recognition capacity compromises resistance and elevates susceptibilityPathogen effectors have evolved to promote their reproductive success when growing on their hosts. Effectors contribute to pathogen virulence by interfering with plant mechanisms that are part of the plant defence response. By identifying the host target of a pathogen effector, we identify key components of plant defence mechanisms. Thus, every new resistance gene isolated not only helps enable durable disease resistance, but also provides a route to identifying the recognised molecule that is a key pathogen virulence component, and therefore also their plant targets, enabling us to greatly enhance our understanding of plant immunity.