Systems genetics of symbiotic quality in legume-rhizobium mutualism

豆科植物-根瘤菌互利共生质量的系统遗传学

• 批准号: 1645875
• 负责人: Katy Heath
• 金额: $ 71.76万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-04-15 至 2023-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1645875&HistoricalAwards=false
• 关键词: Systems; genetics; symbiotic; quality; legume

Non-technical:Mutually-beneficial interactions between plants and microbes are integral aspects of Earth's ecosystems. These mutualisms are important for stabilizing pristine natural communities, restoring degraded environments, and plant productivity in agricultural systems. Rhizobial bacteria (rhizobia) benefit leguminous host plants (peas, beans, soybean) by fixing atmospheric nitrogen into usable forms, essentially fertilizing their plant hosts. As a result, legumes are high in nitrogen and provide an abundant source of plant-derived protein. Rhizobial strains, however, are diverse in nature and vary quite a bit in partner quality, or the level of benefits they provide to the plant host. This project focuses on a genetic model system (the legume Medicago truncatula and its partner bacterium Sinorhizobium meliloti) to investigate the range of partner quality variation and its underlying molecular basis in rhizobia, integrating various approaches including whole-genome DNA sequencing, gene expression, and metabolomics. These techniques provide insight into the genetic determinants and cellular-level metabolism that characterizes highly-beneficial interactions, versus low-quality interactions that are less beneficial for plant hosts. Understanding what determines partner quality at a mechanistic level is critical foundational knowledge that informs efforts to engineer the plant microbiome as part of plant improvement programs and sustainable crop production. Moreover a basic understanding of what determines partner quality is important for understanding how mutualisms evolve through time and how crucial mutualisms persist in current environments. This project provides biological and computational training at the undergraduate and graduate level, provides internships for local community college students, and generates online outreach and analysis tools.Technical:Mutualists in nature vary widely in partner quality, often with important implications for natural and managed systems, yet the molecular basis of mutualist partner quality variation is not well-understood. Recently studies have demonstrated mutualism decline in response to environmental changes, resulting from dis-association of partners, ecological shifts towards less-mutualistic species, or evolutionary decreases in mean partner quality. A predictive understanding of mutualisms is needed to understand their coevolution, persistence, and potential decline. This project will integrate natural genetic variation with physiological and molecular traits into symbiosis networks to uncover the genetic and molecular architecture underlying the mutualism between the rhizobium Ensifer (Sinorhizobium) meliloti and its host plant Medicago truncatula. The central hypothesis is that naturally-occurring variation can be used to better resolve the genetic regulation of plant and rhizobium metabolic pathways that contribute to high-quality symbiosis. This project integrates rhizobium genome-wide nucleotide variation with both rhizobia and host plant phenotypic and molecular traits to address the molecular basis of rhizobium partner quality (how much rhizobia benefit their plant hosts), a trait relevant to both natural and managed ecosystems. Network analysis of transcriptomic and metabolomic data will result in comparative models of high and low quality symbiosis, enabling gene-to-trait predictions for the ecologically- and evolutionarily- important symbiosis between leguminous plants and nitrogen-fixing rhizobium bacteria. Hypotheses generated by network analysis will be validated in both rhizobia and host plant systems for physiological and molecular phenotypes underlying important partner quality traits.

非技术性：植物和微生物之间的互利互动是地球生态系统不可分割的一部分。这些互惠关系对于稳定原始自然群落、恢复退化环境和农业系统中的植物生产力非常重要。根瘤菌（根瘤菌）通过将大气中的氮固定为可利用的形式，使豆科宿主植物（豌豆，豆类，大豆）受益，基本上是使其植物宿主受益。因此，豆类含氮量高，提供了丰富的植物源蛋白质来源。然而，根瘤菌菌株在性质上是多种多样的，并且在伴侣质量或它们提供给植物宿主的益处水平上变化很大。本项目以豆科植物蒺藜苜蓿及其共生菌苜蓿中华根瘤菌为研究对象，通过全基因组DNA测序、基因表达和代谢组学等方法，研究根瘤菌共生菌质量变异的范围及其潜在的分子基础。这些技术提供了深入了解的遗传决定因素和细胞水平的代谢，其特点是高度有益的相互作用，而低质量的相互作用，是有益的植物宿主。了解在机械水平上决定合作伙伴质量的因素是至关重要的基础知识，可以为植物微生物组的工程设计提供信息，作为植物改良计划和可持续作物生产的一部分。此外，对决定伴侣质量的因素有一个基本的了解，对于理解互惠关系如何随着时间的推移而演变以及至关重要的互惠关系如何在当前环境中持续存在是很重要的。该项目提供生物和计算培训在本科生和研究生水平，为当地社区学院的学生提供实习，并产生在线推广和分析tools.Technical：互利主义者在性质上有很大的不同，在合作伙伴的质量，往往与自然和管理系统的重要影响，但互利主义者的合作伙伴质量变化的分子基础还没有得到很好的理解。最近的研究表明，互惠下降，在应对环境的变化，导致解散的合作伙伴，生态转向少互惠物种，或平均合作伙伴质量的进化下降。我们需要对共生现象有一个预测性的理解，以了解它们的共同进化、持久性和潜在的衰退。本项目将把自然遗传变异与生理和分子性状整合到共生网络中，以揭示苜蓿根瘤菌（Sinorhizobium meliloti）与其宿主植物蒺藜苜蓿（Medicago truncatula）之间互利共生的遗传和分子结构。核心假设是，自然发生的变异可以用来更好地解决植物和根瘤菌代谢途径的遗传调控，有助于高质量的共生。该项目将根瘤菌全基因组核苷酸变异与根瘤菌和宿主植物的表型和分子性状相结合，以解决根瘤菌伴侣质量的分子基础（根瘤菌对其植物宿主有多大益处），这是一种与自然和管理生态系统相关的性状。转录组和代谢组学数据的网络分析将导致高质量和低质量共生的比较模型，使基因性状的预测生态和进化重要的豆科植物和固氮根瘤菌之间的共生。网络分析产生的假设将在根瘤菌和宿主植物系统的重要合作伙伴质量性状的生理和分子表型进行验证。

项目成果

Discordant population structure among rhizobium divided genomes and their legume hosts

• DOI: 10.1111/mec.16704
• 发表时间: 2022-10-05
• 期刊: MOLECULAR ECOLOGY
• 影响因子: 4.9
• 作者: Riley，Alex B.;Grillo，Michael A.;Heath，Katy D.
• 通讯作者: Heath，Katy D.

Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis

结合 GWAS 和群体基因组分析来表征豆科植物与根瘤菌共生的共同进化

• DOI: 10.1111/mec.16602
• 发表时间: 2022
• 期刊: Molecular Ecology
• 影响因子: 4.9
• 作者: Epstein, Brendan;Burghardt, Liana T.;Heath, Katy D.;Grillo, Michael A.;Kostanecki, Adam;Hämälä, Tuomas;Young, Nevin D.;Tiffin, Peter
• 通讯作者: Tiffin, Peter