RESEARCH-PGR: Functional genomics of beneficial legume-microbe interactions

豆科作物是人类食物、牲畜饲料和工业原料的主要来源。豆科植物是可持续农业系统不可或缺的一部分，因为它与一种叫做根瘤菌的细菌共生固氮，每年向这种系统注入5000万吨固定氮。豆科植物还与土壤真菌形成有益的丛枝菌根共生，促进土壤磷和其他养分的获取。这两种共生体可以用较少的肥料进行多产的植物种植，从而减少农业对环境的影响。以豆科植物为重点，该项目将确定与细菌和/或真菌共生所需的关键植物基因，并推进我们对农业中最重要的两种植物-微生物共生关系的理解。该项目汇集了来自五个州六个研究和教学机构的七个研究小组，形成了一个世界级的豆类共生研究虚拟中心，将产生巨大的协同作用，并在基因组学、生物信息学和其他学科提供优秀的跨学科培训机会。培训将在职业水平上提供，从博士后研究人员、研究生到本科生，目的是培养成功的科学事业所需的技能。这个项目的扩展部分将吸引高中生和中学生，普通公众中的成年人和儿童参与教育和有趣的科学体验。拟议的活动将通过帮助培训下一代科学家和通过帮助使农业更加可持续和环境友好来使社会受益。豆科植物是可持续农业系统不可或缺的一部分，因为它与根瘤菌共生固氮（SNF），并与土壤真菌有益的丛枝菌根（AM）共生，促进土壤磷和其他营养物质的获取。尽管通过转录组研究已经发现数千个植物基因与这些共生关系有关，但大多数这些基因的共生作用和重要性仍不清楚。该项目以豆科植物Medicago truncatula为重点，将利用现有的非常大的Tnt1转座子插入突变种群进行SNF和AM共生的功能基因组学研究。在全基因组无偏正向遗传筛选中，已经鉴定出190个具有新颖Nod+Fix或调节性表型的Tnt1插入突变体。新的序列捕获技术将加速因果突变的鉴定，从而鉴定参与固氮和结瘤自动调节的新基因。通过大量Tnt1突变体和索引侧翼序列标签资源，功能基因组学活动将集中在根瘤菌和AM共生过程中参与营养运输的转运蛋白上。Tnt1突变体和通过CRISPR-Cas9基因组编辑产生的突变体的组合将用于研究先前通过比较系统基因组学方法鉴定的AM共生保守的138个基因。总之，这些活动将确定关键的共生基因，并促进我们对可持续农业至关重要的两种植物-微生物共生关系的理解。

Legume crops are a primary source of food for humans, feed for livestock, and raw materials for industry. Legumes are integral to sustainable agricultural systems by virtue of symbiotic nitrogen fixation with bacteria called rhizobia, which injects 50 million tons of fixed-nitrogen into such systems annually. Legumes also form beneficial arbuscular mycorrhizal symbioses with soil fungi, which enhance the acquisition of soil phosphorous and other nutrients. These two symbioses enable productive plant cultivation with less fertilizer, which reduces the environmental impact of agriculture. Focusing on the legume species, Medicago truncatula this project will identify key plant genes required for symbiosis with bacteria and/or fungi and advance our understanding of what are arguably the two most important plant-microbe symbioses in agriculture. This project brings together seven research groups from six research and teaching institutions in five states to form a world-class, virtual center for legume symbiosis research that will generate great synergy and provide outstanding trans-disciplinary training opportunities in genomics, bioinformatics and other disciplines. Training will be provided at career levels ranging from postdoctoral researchers, graduate students, to undergraduate students with the aim of developing skillsets necessary for successful scientific careers. Outreach components of this project will engage high & middle school students, adults in the general public and children in educational and fun scientific experiences. The proposed activities will benefit society by helping to train the next generation of scientists and by helping to make agriculture more sustainable and environmentally-friendly.Legumes are integral to sustainable agricultural systems by virtue of symbiotic nitrogen fixation (SNF) with bacteria called rhizobia, and beneficial arbuscular mycorrhizal (AM) symbioses with soil fungi that enhance the acquisition of soil phosphorous and other nutrients. Although thousands of plant genes have been associated with these symbioses via transcriptome studies, the symbiotic role and importance of most of these genes remain unclear. Focusing on the legume, Medicago truncatula this project will take advantage of a very large existing Tnt1 transposon-insertion mutant population for functional genomics of SNF and AM symbiosis. One hundred and ninety Tnt1 insertion mutants with novel Nod+Fix- or regulatory phenotypes have already been identified in a genome-wide non-biased forward genetic screen. New sequence-capture technologies will accelerate the identification of the causal mutations enabling the identification of new genes involved in nitrogen fixation and autoregulation of nodulation. Functional genomics activities, enabled by a large Tnt1 mutant population and indexed flanking sequence tag resource will focus on transporter proteins involved in nutrient transport during rhizobial and AM symbioses. A combination of Tnt1 mutants and mutants generated through CRISPR-Cas9 genome editing will be used to investigate a set of 138 genes conserved for AM symbiosis identified previously through a comparative phylogenomics approach. Together, these activities will identify key symbiotic genes and advance our understanding of two plant-microbe symbioses that are crucial for sustainable agriculture.