100 years of plant breeding - what have we done to the seed microbiome?

人类驯化植物已经有几千年的历史了，大约公元前9000年左右，人类在肥沃的中东新月地区首次驯化了谷物。植物传统上被认为是一个单一的实体，基于表型的选择导致植物基因组的修改，更晚些时候，对基因组的理解被用来加速关键表型的选择。然而，随着下一代测序技术的到来，人们对植物微生物组及其元基因组在植物表现中的作用有了更大的认识。种子生物库对于保护因栖息地丧失和环境变化而在野外丧失的植物多样性至关重要，但我们对长期储存对微生物群的影响一无所知。我们将检验驯化、育种和储存改变植物微生物组组成的假设，从而影响植物在产量、弹性和质量方面的表现。种子微生物组是这项研究的理想目标，因为它代表了植物招募的、潜在地适应内生存在的群落。我们将分析三种不同历史和农业用途的作物的细菌微生物群：1)燕麦(燕麦)：在公元前1000年被驯化为人类食物的粮食作物。2)多年生黑麦草：一种畜牧业(肉和奶)生产的牧草，已有近100年的历史。3)芒属：最近从野外挑选出来的一种高大的草，用作生物能源和工业产品以及营养食品(如益生菌和甜味剂)的原料，代表着一种正在进行的新的驯化。AU的种子生物库保存着这三个物种的收藏，包括野生近亲和繁育系，分别可以追溯到大约40年、100年和15年前。我们将利用这一资源：1.测量收集(Y1)中不同年龄的三个物种的种子萌发和植物适合性，并调查它们与存在的细菌组成(通过快速和经济有效的16S rDNA图谱)和收集时为种子提供的气候数据(Y1/2)的关系。B.通过育种品系(Y1)的世代比较燕麦和黑麦草的微生物组，并将现有的种群与这些品系可获得的广泛特性数据相关联，包括分别包括谷物和饲料质量(Y1/2)。C.对于芒属，i)将野生采集种子的微生物组组成与采集来源进行比较，ii)将其与最近产生的杂交种进行比较，以确定种群在世代之间的保存程度(Y1/2)。2.将最近一批种子置于不同的条件下模拟长期储存(Y1/2)，并确定这些处理对种子萌发、微生物群组成以及在最佳条件和非生物胁迫(Y2/3/4)下对后续植物表现的影响。3.从不同年龄和来源的燕麦、黑麦草和芒属植物中分离出细菌内生菌(Y1)，并在适宜的条件和非生物胁迫下进行植物生长促进实验，以筛选出有益的菌株(Y2/3/4)。我们将比较历史上驯化的粮食作物、较新培育的饲料作物和第一次接受选择的野生物种的微生物群。我们将把采集点的气候和其他环境数据与种子微生物群联系起来，并代代相传。最终，我们将确定选择和育种是否无意中导致了植物微生物组内多样性的减少，从而减少了潜在的植物效益，或者它们是否导致了优化的元基因组。这将为微生物群对植物适合性的影响提供新的理解，对未来的种子储存和育种战略产生影响，并提高英国农业对未来气候的可持续性和弹性。

Humans have domesticated plants for millennia, with cereals first domesticated in the Fertile Crescent of the Middle East around 9000 BCE. The plant has traditionally been considered as a single entity, with selection based on phenotype resulting in modification of the plant genome, and more latterly, understanding of the genome being used to accelerate selection of key phenotypes. However, with the advent of next generation sequencing technology, there has been greater appreciation of the role of the plant microbiome and its metagenome in plant performance. Seed biobanks are critically important for preserving plant diversity which may be lost in the wild due to habitat loss and the changing environment, but we know nothing about the effect of long-term storage on the microbiome. We will test the hypothesis that domestication, breeding and storage alter the composition of the plant microbiome, with impacts on plant performance in terms of yield, resilience and quality. The seed microbiome is the ideal target for this study as this represents the community recruited by the plant and potentially adapted to endophytic existence. We will analyse the bacterial microbiomes of 3 crops with contrasting histories and agricultural uses: 1) Avena sativa (oats): domesticated as a grain crop for human food during the first millennium BC. 2) Lolium perenne: a forage grass for livestock (meat and milk) production that has been bred for ~100 years. 3) Miscanthus: a tall grass recently selected from the wild as a feedstock for bioenergy and industrial products, as well as nutraceuticals (e.g. prebiotics and sweeteners) and represents a novel domestication in progress. The seed biobank at AU holds collections, including wild relatives and breeding lines, of all three species, going back approximately 40 years, 100 years, and 15 years respectively. We will use this resource to: 1. A. Measure seed germination and plant fitness of the three species of different ages in the collection (Y1) and investigate their relationship to both the bacterial composition present (via rapid and cost-effective 16S rDNA profiling) and the climatic data provided for the seed at collection (Y1/2). B. Compare the microbiome of oats and Lolium through the generations of breeding lines (Y1), and correlate the populations present with the extensive trait data available for these lines, including grain and forage quality respectively (Y1/2). C. For Miscanthus, i) compare microbiome composition of wild collected seed with origin of collection and ii) compare these with recently generated hybrids to determine the extent to which the populations are conserved across generations (Y1/2). 2. Subject a recent batch of seed to various conditions to simulate long-term storage (Y1/2), and determine the effect of these treatments on seed germination, microbiome composition, and on subsequent plant performance under optimal conditions and abiotic stresses (Y2/3/4). 3. Isolate bacterial endophytes from oats, Lolium and Miscanthus of different ages and origins (Y1) and conduct plant growth promotion experiments, under optimal conditions and abiotic stresses, to identify beneficial strains (Y2/3/4). We will compare the microbiomes of a historically domesticated grain crop, a more-recently bred forage crop, and a wild species undergoing selection for the first time. We will correlate climatic and other environmental data from the collection site with the seed microbiome, and trace this through generations. Ultimately we will determine whether selection and breeding have inadvertently resulted in reduced diversity within the plant microbiome with reductions to the potential plant benefits, or whether they have resulted in an optimised metagenome. This will provide novel understanding about the impact of the microbiome on plant fitness, with implications for future seed storage and breeding strategies, and for improving sustainability and resilience of UK agriculture to future climates.