RESEARH-PGR: Genomics of strain- and host-specific performance in the legume-rhizobia symbiosis

RESEARH-PGR：豆科植物-根瘤菌共生中菌株和宿主特异性表现的基因组学

• 批准号: 1856744
• 负责人: Peter Tiffin
• 金额: $ 176.83万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1856744&HistoricalAwards=false
• 关键词: RESEARH; PGR; Genomics; strain; host

The plants and animals we see around us, including agriculturally important crop plants, live in close association with millions of microorganisms (microbes). Some of these microbes cause disease but others are beneficial. Identifying the genes and genetic pathways that determine the outcome of host-microbe associations provides targets for manipulating them for human benefit. This project uses an innovative approach based on high-throughput genome sequencing to efficiently identify bacterial and host genes that shape the outcome of host-microbe associations. The new methods are being deployed on one of the most important plant-microbe associations, that between leguminous plants (soybeans, beans, peas, alfalfa) and rhizobial bacteria. When rhizobia grow in association with these plants, they convert atmospheric nitrogen into a plant useable form, thereby "feeding" the plant and lessening the need for nitrogen fertilizer. The results will provide new empirical tools that advance how we study these systems and the identification of genes and bacterial strains that can be exploited to increase the benefits rhizobial bacteria provide in agricultural systems. Teams of student writers and designers, as well as local high school teachers, will be actively involved in the project to communicate the results using print, graphics, and animation.The symbiosis between leguminous plants and rhizobial bacteria is a classic system for understanding how plant and microbial genomes function in a coordinated manner. The benefits of host-rhizobia interactions depend on genomic variation found in both partners (i.e. inter-genome or genome-by-genome variation). Neither the reasons for nor the consequences of this inter-genome variation are well understood. Moreover, very little is known about the genetic basis of genome by genome variation in this, or any other, host-microbe system. The research under this award will fill this void through a novel two-species genotype-phenotype association study, two-species co-expression networks, and functional validation of candidate genes. A similar approach will be used to evaluate the inter-genome variation between Medicago and Aphanomyces, an economically important pathogen. The data and code used for analyses will be made available in a timely manner through public data repositories. Analyses of these data will uncover, in unprecedented detail, the genetic basis and mechanisms responsible for variation in inter-genome effects on phenotype in host-symbiont and host-pathogen systems. To extend the reach of the project and actively disseminate the results, students from other disciplines (such as writers and graphic designers) will develop new communication materials that will be used in local high school curricula.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

我们周围看到的植物和动物，包括农业上重要的作物，都与数百万种微生物（微生物）密切相关。其中一些微生物会导致疾病，但其他微生物是有益的。确定决定宿主-微生物关联结果的基因和遗传途径为操纵它们以造福人类提供了目标。该项目使用基于高通量基因组测序的创新方法，有效地识别塑造宿主-微生物关联结果的细菌和宿主基因。这些新方法正被用于最重要的植物-微生物关系之一，即豆科植物（大豆、菜豆、豌豆、苜蓿）和根瘤菌之间的关系。当根瘤菌与这些植物一起生长时，它们将大气中的氮转化为植物可用的形式，从而“喂养”植物并减少对氮肥的需求。这些结果将提供新的经验工具，推动我们如何研究这些系统，并确定可用于增加根瘤菌在农业系统中提供的益处的基因和菌株。学生作家和设计师团队以及当地高中教师将积极参与该项目，使用印刷，图形和动画传达结果。豆科植物和根瘤菌之间的共生关系是理解植物和微生物基因组如何以协调方式发挥作用的经典系统。宿主-根瘤菌相互作用的益处取决于在双方中发现的基因组变异（即基因组间或基因组间变异）。这种基因组间变异的原因和后果都还不清楚。此外，在这个或任何其他宿主-微生物系统中，对基因组变异的遗传基础知之甚少。该奖项下的研究将通过新的两种基因型-表型关联研究，两种共表达网络和候选基因的功能验证来填补这一空白。一个类似的方法将被用来评估苜蓿和丝囊霉，一个经济上重要的病原体之间的基因组间的变化。用于分析的数据和代码将通过公共数据储存库及时提供。这些数据的分析将揭示，在前所未有的细节，在宿主共生体和宿主-病原体系统的表型基因组间的影响的变化负责的遗传基础和机制。为了扩大该项目的影响范围并积极传播成果，来自其他学科的学生（如作家和平面设计师）将开发新的沟通材料，这些材料将用于当地高中课程。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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

Comparison of nodule endophyte composition, diversity, and gene content between Medicago truncatula genotypes

蒺藜苜蓿基因型间根瘤内生菌组成、多样性及基因含量比较

• DOI: 10.1094/pbiomes-10-20-0077-r
• 发表时间: 2021
• 期刊: Phytobiomes Journal
• 影响因子: 4.4
• 作者: Burns, Mannix;Epstein, Brendan;Burghardt, Liana
• 通讯作者: Burghardt, Liana

Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

• DOI: 10.1098/rspb.2020.1804
• 发表时间: 2021-01-13
• 期刊: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
• 影响因子: 4.7
• 作者: Epstein，Brendan;Tiffin，Peter
• 通讯作者: Tiffin，Peter