Towards understanding Duckweed evolution - genomic and experimental approaches.

人类和动物食品生产以及合成生物学应用迫切需要简化的植物系统。因此，人们对浮萍的兴趣越来越大，浮萍是一种非常容易处理的系统，其生物量在短短30小时内翻了一番，具有大量的全球多样性收集，并且具有明显的合成生物学潜力，因为它们的基因组很小，测序了150mb，并且易于遗传操作。此外，浮萍已被证明具有修复污水的能力，并显示出作为饲料资源的巨大潜力，特别是在最需要这种资源的发展中国家。最近的证据也支持将其用于控制蚊子和藻类。浮萍水产养殖很容易融入许多由小农或商业规模管理的作物/动物系统。浮萍养殖不需要耕地和肥沃的土地，并且可以方便地提高富营养化废水的质量，最大限度地减少施肥的需要。这使得这些植物成为一种新颖而令人兴奋的水生农业系统，具有很高的潜力。事实上，当有效管理时，浮萍产量为10-30吨重/公顷/年，含有高达43%的粗蛋白质，5%的脂质和高度可消化的干物质。此外，在营养丰富的水中生长的浮萍含有高浓度的微量矿物质、钾、磷和色素，尤其是胡萝卜素和叶黄素，这使得浮萍粉对家禽和其他动物来说是一种特别有价值的补充剂，它为人类提供了丰富的维生素a和B。然而，现在可以做很多事情来优化浮萍的使用，以及利用这个系统进行适应进化基因组学的基础研究。该项目将种群基因组重测序扫描和表型优先元素积累（~20个元素的“离子学”）结合起来，探索浮萍种群适应的基因组基础，并表征这些植物的潜力。该项目将包括在英国范围内收集新的浮萍，并分析水离子和光环境。我们将根据需要使用并进一步开发我们已建立的管道和技术来研究浮萍的多样性，以了解其适应各种环境的基因组基础。这项工作将Yant实验室最近的成功研究扩展到这个有前途的系统。目的1。描述浮萍对极端环境条件的适应性。这将包括表型多达700个加入（200英国，200伊比利亚半岛和300 ‘Landolt’线提供给我们）在一个新的高通量表型平台。分析包括使用自动化高科技表型平台在不同生长条件下的多元素“离子学”和生长参数。改变光环境和媒介操作是实验技术，将用于探索不同浮萍物种之间的生理、生物学和生长差异。这些数据将直接用于目标2。目标2。浮萍适应的种群基因组学研究。我们观察到的基因组学、生理学、形态学和其他特征的基因组基础是什么？是什么位点介导了这些适应？在这个系统中，局部适应的精确基因组特征是什么？我们拥有多根螺旋体的质量参考，并建立了最先进的群体基因组分析管道，以及机器人系统中的高通量Illumina文库制备协议，可轻松对数百个基因组进行重测序。我们首先对最极端的400个基因组进行测序，进行深入的人口统计分析和选择扫描（包括高密度GWAS），并对基因流动和杂交进行分析，这是Yant实验室目前的主要兴趣。这将产生丰富的基因组学信息的基础上，不同的适应，以及候选等位基因介导相应的适应。

There is an urgent need for simplified plant systems for human and animal food production and synthetic biology applications. Accordingly, there has been growing interest in duckweeds, an eminently tractable system, with biomass doubling times of as little as 30 hours, massive worldwide diversity collections, and obvious synthetic biology potential, given their small, sequenced 150mb genome and amenability to genetic manipulation. Further, duckweed has the proven capacity to remediate polluted water and shows great potential as a feed resource, especially in developing nations where this is most needed. Recent evidence also supports its use in controlling mosquitoes and algae. Duckweed aquaculture fits easily into many crop/animal systems managed either by small farmers or on commercial scales. Duckweed farming does not require arable, fertile land and has the convenient ability to improve the quality of the nutrient-rich wastewater, minimizing the need for fertilization. This makes these plants a novel and exciting system of aquatic agriculture with high potential. Indeed, when effectively managed duckweeds yield 10-30 ton DW/ha/year containing up to 43% crude protein, 5% lipids and highly digestible dry matter. Additionally, duckweed grown on nutrient-rich water has a high concentration of trace minerals, K, P and pigments, particularly carotene and xanthophyll, that make duckweed meal an especially valuable supplement for poultry and other animals, and it provides a rich source of vitamins A and B for humans. However, much can be done now optimize the use of duckweed, as well as to leverage this system for fundamental studies in the evolutionary genomics of adaptation. This project merges population genomic resequencing scans and phenotype-first elemental accumulation (~20-element 'ionomics') to explore the genomic basis of adaptation in duckweed populations and to characterise the potential of these plants. The project will involve collection of new duckweed accessions UK-wide and analysis of water ionomes and light environments. We will use and further develop as needed our established pipelines and techniques to duckweed diversity in order to understand the genomic basis of its adaptations to various environments. This work expands recent successful studies from the Yant Lab to this promising system. Aim 1. Characterise the adaptation of duckweeds to extreme environmental conditions. This will include phenotyping up to 700 accessions (200 UK, 200 Iberian Peninsula and 300 'Landolt' lines available to us) in a novel high throughput phenotyping platform. Assays include multi-elemental 'ionomics' and growth parameters in diverse growth conditions using automated high-tech phenotyping platforms. Altered light environments and media manipulation are experimental techniques which will be used to explore physiological, ionomic and growth differences between different duckweed species. These data will feed directly into aim 2.Aim 2. Population Genomics of adaptation in duckweeds. What is the genomic basis for the ionomic, physiological, morphological, and other traits we observe? What loci mediate these adaptations and what are the precise genomic signatures of local adaptation in this system? We have a quality reference for Spirodela polyrhiza and established pipelines for state-of-the-art population genomic analysis, as well as high throughput Illumina library preparation protocols in robotics systems for easy resequencing of hundreds of genomes. We begin by sequencing the most phenotypically extreme 400 genomes for in depth demographic analysis and selection scans (including high density GWAS) and assays for gene flow and hybridisation, a current major interest in the Yant Lab. This will produce a wealth of information on the genomics basis of diverse adaptations, as well as candidate alleles mediating consequential adaptations.