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Expanding the Medicago truncatula Hapmap as a Platform for Exploring the Genetics of Legume Symbioses

扩展蒺藜苜蓿单体型图作为探索豆科植物共生遗传学的平台

基本信息

批准号：
1237993
负责人：
Nevin Young
金额：
$ 499.69万
依托单位：
University of Minnesota-Twin Cities
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2013
资助国家：
美国
起止时间：
2013-02-15 至 2018-01-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1237993&HistoricalAwards=false
关键词：
Expanding Medicago truncatula Hapmap Platform

项目摘要

PI: Nevin Young (University of Minnesota)Co-PIs: Michael Sadowsky, Robert Stupar, and Peter Tiffin (University of Minnesota), Maria Harrison (Boyce Thompson Institute for Plant Research), Betsy Martinez-Vaz (Hamline University), Jason Rafe Miller (J. Craig Venter Institute), Joann Mudge (National Center for Genome Resources) This project uses functional assays, de novo genome assembly and bioinformatic data-mining to characterize symbiosis genes in the model legume Medicago truncatula. Legumes are noteworthy for the sophisticated symbioses they form with rhizobial bacteria and arbuscular mycorrhizal (AM) fungi. However, existing knowledge about symbioses comes primarily from knockout mutants, an approach that often misses genes of subtle yet significant effect, especially genes likely to be important in contemporary evolution. In earlier work, several strongly supported candidate symbiosis loci were discovered through genome-wide association analysis (GWAS) and support for candidate genes often included independent evidence like expression profile, correlation with multiple traits or co-localization with known symbiotic phenotypes. The current project will test ~100 of these candidate loci through reverse genetic experiments involving Tnt1 insertion and RNAi "knockdown" plant lines. Promising genes will be examined through interaction assays involving previously defined Sinorhizobium and AM strains and tested for "gene-for-gene" relationships using a panel of 48 sequenced Sinorhizobium strains. Earlier GWAS mapping only targeted SNP variation, even though structural variants (SVs) and copy number variants (CNVs) are known to have major impacts on genome variation. This is especially relevant to the genomics of symbiosis because the large gene families such as the NB-ARC domain-containing genes and nodule cysteine rich peptides (NCRs) play critical roles in symbiosis. This project will deeply sequence and de novo assemble 30 nodal M. truncatula accessions, in order to discover SVs and CNVs. SVs and CNVs will be imputed genome-wide, leading to a new round of GWAS to discover symbiotic loci missed in the earlier phase of mapping. The primary outcomes of this project will be the identification of genes associated with the contemporary evolution of symbiosis as well as the architecture of M. truncatula genomic diversity. This research effort will be extended by involving undergraduates from Hamline University, a four year institution located near the University of Minnesota, and from the University of Puerto Rico (UPR). Students at Hamline will work throughout the academic year and then together with UPR students during the summer as part of Minnesota's Life Sciences Summer Undergraduate Research Program (LSSURP) program. Their work will target the important but largely uncharacterized Sinorhizobial enzyme, ACC deaminase, and students will also participate in the screening of reverse genetic mutants. These experiences will provide the students the opportunity to develop their own hypothesis-driven projects. Through joint mentoring by project PIs, student training will also assist the undergraduate research program at Hamline to become more competitive for its own future external research initiatives. Genomic sequence resources will be available for public through medicagohapmap.org, and the Short Read Archive, dbSNP and FTP sites at Genbank. Importantly, the underlying Medicago Hapmap GWAS platform, available at medicagohapmap.org, will provide a long-term resource for the broader research community to discover legume genes controlling quantitative variation of agricultural and biological interest, especially trait variation in alfalfa (Medicago sativa), the fourth most widely cultivated crop in the U.S.

主要研究者：内文·扬（明尼苏达大学）Co-PI：迈克尔·萨多夫斯基、罗伯特·斯图帕尔和彼得·蒂芬（明尼苏达大学），玛丽亚·哈里森（博伊斯汤普森植物研究所），贝特西·马丁内斯-瓦兹（哈姆林大学），贾森雷夫米勒（J.克雷格文特尔研究所），乔安·马吉（国家基因组资源中心）该项目使用功能分析，从头基因组组装和生物信息学数据挖掘来表征模式豆科植物蒺藜苜蓿中的共生基因。豆科植物与根瘤菌和丛枝菌根（AM）真菌形成复杂的共生关系。然而，关于共生的现有知识主要来自敲除突变体，这种方法往往会遗漏那些具有微妙但重要影响的基因，特别是那些可能在当代进化中很重要的基因。在早期的工作中，通过全基因组关联分析（GWAS）发现了几个强有力的候选共生位点，候选基因的支持通常包括独立的证据，如表达谱，与多个性状的相关性或与已知共生表型的共定位。目前的项目将通过涉及Tnt 1插入和RNAi“敲低”植物系的反向遗传实验来测试这些候选基因座中的约100个。有前途的基因将通过相互作用试验，涉及以前定义的中华根瘤菌和AM菌株进行检查，并使用一组48个测序的中华根瘤菌菌株测试的“基因对基因”的关系。早期的GWAS作图仅针对SNP变异，尽管已知结构变异（SV）和拷贝数变异（CNV）对基因组变异具有重大影响。这与共生的基因组学特别相关，因为大的基因家族如含NB-ARC结构域的基因和结节富含半胱氨酸的肽（NCR）在共生中起关键作用。该项目将对30个节点M进行深度测序和重新组装。为了发现SV和CNV。SV和CNV将在全基因组范围内进行估算，从而导致新一轮的GWAS，以发现在早期定位阶段遗漏的共生基因座。该项目的主要成果将是鉴定与共生的当代进化相关的基因以及M。蒺藜基因组多样性这项研究工作将通过涉及来自Hamline大学（位于明尼苏达大学附近的一所四年制大学）和波多黎各大学（UPR）的本科生来扩展。学生在哈姆林将在整个学年工作，然后在夏季与UPR学生一起作为明尼苏达州生命科学夏季本科生研究计划（LSSURP）计划的一部分。他们的工作将针对重要但基本上没有特征的Sinorhizobial酶ACC脱氨酶，学生还将参与反向遗传突变体的筛选。这些经验将为学生提供发展自己的假设驱动项目的机会。通过项目PI的联合指导，学生培训还将帮助Hamline的本科研究项目，使其未来的外部研究计划更具竞争力。基因组序列资源将通过medicagohapmap.org以及Genbank的Short Read Archive、dbSNP和FTP网站向公众提供。重要的是，可在medicagohapmap.org上获得的基础Medicago Hapmap GWAS平台将为更广泛的研究社区提供长期资源，以发现控制农业和生物学兴趣的数量变异的豆类基因，特别是苜蓿（Medicago sativa）的性状变异，苜蓿是美国第四大种植作物。