Mapping of genetic host compatibility loci that promote the colonization of bacterial endophytes in maize

**人类、动物和植物都有繁荣的细菌生态系统，这些细菌生活在它们体内而不会引起疾病。值得注意的是，人类拥有的来自微生物栖息地的基因比来自人类基因组本身的基因要多，植物的情况可能也类似。栖息在植物体内而不引起疾病的微生物被称为内生菌。我们最近进行了最全面的地理和进化研究不同类型的玉米（玉米）横跨中美洲到加拿大。玉米是世界上重要的作物之一，为人类提供了15%的卡路里，然而人们对这种作物上的微生物的了解有限，即使其中一些微生物，例如，可能会产生毒素。因此，了解导致特定内生菌在植物内茁壮成长或不茁壮成长的因素是很重要的。**在我们之前的研究中，我们发现一些细菌内生菌在数千年的作物育种和跨美洲的迁移中持续存在于玉米中，而其他内生菌只在单一玉米品种中定植。这些结果表明，玉米能够识别并接受或拒绝特定的内生菌菌株。不幸的是，科学家们对特定植物如何接受或拒绝特定的内生菌知之甚少。内生菌可能被宿主植物的不同遗传因素识别，然后被接受或拒绝，并且/或者可能或多或少地与宿主的内部环境兼容（例如，一些植物可能有适当的营养物质来喂养内生菌株）。这一建议试图了解玉米如何在遗传水平上接受或拒绝特定的内生菌。我们将测量玉米遗传学家使用的两种玉米（B73和Mo17）中存在或不存在哪些内生菌，然后利用这些差异绘制负责接受或拒绝选定内生菌的玉米基因（qtl）。**为什么这个建议很重要？与内生菌等中性或友好的微生物相比，了解作物如何能够区分导致重要作物病害的微生物敌人是很重要的——这类信息可能有助于科学家更好地了解作物病害的爆发以及如何预防它们。第二个原因是，几十年来，人们一直对使用内生菌覆盖在种子上（称为接种剂）或喷洒在作物上感兴趣，因为一些微生物可以抑制作物疾病或减少对肥料的需求。不管安全与否，有机农民已经在推广使用微生物作为合成农药和化肥的天然替代品。现在，主要的农业生物技术公司已经把它们未来增长的一部分押在了内生菌等“生物制剂”的销售上。不幸的是，在过去，内生菌常常不成功，因为它们不能在接种后在植物中持续存在；这些失败的一个原因可能是来自田间其他微生物的竞争，但另一个主要原因似乎是特定内生菌与特定作物品种的兼容性差。如果研究人员能够绘制出作物的内生菌亲和性基因图谱，他们就可以利用传统育种方法培育出能够接受有益内生菌的作物。事实上，这项基础研究计划之所以选择玉米，而不是一种更简单的植物，其中一个原因是，获得的信息可以立即转化为玉米种植者在现实世界中的应用。我的实验室在全球范围内处于进行这项研究的绝佳位置。首先，我们有一个独特的内生菌集合，我们已经描述了它们在13种玉米中的定植。其次，我的实验室在内生菌生物学和玉米遗传学方面都有专长，这是一个不寻常的组合。

PLAIN LANGUAGE SUMMARY (GENERAL PUBLIC)**Humans, animals and plants have thriving ecosystems of bacteria that live inside them without causing disease. Remarkably, humans possess more genes from their microbial inhabits than from the human genome itself, and the situation is likely similar in plants. Microbes that inhabit plants without causing disease are called endophytes. We recently conducted the most comprehensive geographic and evolutionary study of bacterial endophytes of diverse types of corn (maize) spanning Central America to Canada. Corn is one of the world's important crops, supplying 15% of human calories, yet there is limited knowledge about the microbes that inhabit this crop, even though some of these microbes, for example, may be producing toxins. Thus it is important to understand factors that cause particular endophytes to thrive or not within a plant. **In our previous study, we discovered that some bacterial endophytes persisted in corn across thousands of years of crop breeding and migration across the Americas, whereas other endophytes colonized only a single corn variety. These results suggested that corn is able to recognize, and either accept or reject, specific strains of endophytes. Unfortunately, scientists have very little knowledge as to how specific plants accept or reject specific endophytes. Endophytes may be recognized, then accepted or rejected, by different genetic factors in the host plant and/or may be more or less compatible with the host's internal environment (e.g. some plants may have the appropriate nutrients to feed an endophytic strain). This proposal attempts to understand how corn accepts or rejects specific endophytes at the genetic level. We will measure which endophytes are present or absent in two types of corn used by corn geneticists (B73 and Mo17), then use these differences to map the corn genes (QTLs) responsible for accepting or rejecting a selected endophyte.**Why is this proposal important? It is important to understand how crops are able to distinguish between microbial enemies that cause important crop diseases, compared to neutral or friendly microbes such as endophytes - such information may help scientists better understand crop disease outbreaks and how to prevent them. The second reason, is that for decades, there has been interest in using endophytes to coat onto seeds (termed inoculants) or spray onto crops, since some microbes can suppress crop disease or reduce the need for fertilizers. Whether safe or not, organic farmers already promote the use of microbes as natural alternatives to synthetic pesticides and fertilizers. Now major agbiotech companies have staked part of their future growth on the sale of "biologicals" including endophytes. Unfortunately, in the past, endophytes have often not succeeded because they fail to persist in the plant after inoculation; one reason for these failures may be competition from other microbes in the field, but another major reason appears to be poor compatibility of a specific endophyte with a specific crop variety. If researchers can map the endophyte compatibility genes in crops, they can use traditional breeding to breed crops that will accept beneficial endophytes. In fact, one reason why corn was selected for this basic research proposal, as opposed to a simpler plant, is that the information gained can immediately translate into real world applications for corn farmers. My lab is in an excellent position globally to conduct this research. First, we have a unique collection of endophytes, and we have already characterized their colonization across 13 types of corn. Second, my Lab has expertise in both endophyte biology and corn genetics, which is an unusual combination.