A Medicago Truncatula HapMap as a Platform for Exploring the Genetics of Legume Symbioses

PI：NIVIN D.Young(明尼苏达大学)Copis：Michael J.Sadowsky和Peter L.Tiffin(明尼苏达大学)，Maria J.Harrison(博伊斯·汤普森植物研究所)，Betsy M.Martinez-Vaz(哈姆林大学)和Joann Mdge(国家基因组资源中心)合作者：Gregory D.May(国家基因组资源中心)豆类，第三大开花植物家族，以其与根瘤菌形成共生关系的能力而闻名。这种共生关系在全球范围内产生了大量的生物氮，为人类和动物提供了有机肥料和植物蛋白的主要来源。圆叶紫花苜蓿是豆科植物基因组学研究的模式种，其中一个重要的问题是控制豆科植物共生变异的自然发生基因的识别。该项目将使用关联映射技术来创建Medicago“HapMap”。简而言之，从INRA-Montpellier、Ecole National Superieur Agronomique de Toulouse(ENSAT)和Noble Foundation的合作者那里获得的384个不同的遗传系将使用下一代测序技术对不同Medicago系之间的序列多态(SNP)进行重新测序。通过基因组重测序发现SNP是可能的，因为通过之前的NSF资助已经创建了Medicago富含基因的常染色质的参考序列。紫花苜蓿品系之间庞大的SNPs数据库使具有共同祖先(单倍型)的基因组片段的预测成为可能，然后这些基因组片段可以在统计上与共生中的性状变异相关联。由于SNP密度非常高，关联图谱可以接近单基因的分辨率。更广泛的科学家社区将通过一个直观的网络界面(将建立)访问Medicago HapMap平台，该界面将在人类HapMap网站(www.hapmap.org)上建模。Hapmap中包含的所有线路的种子将通过联系项目人员或直接通过INRA-Montpellier、ENSAT和诺布尔基金会(通过GRIN设施)获得。有了这些数据和种质，科学家将能够进行他们自己的关联图谱实验，包括共生以外的其他特征。由于应用于豆类共生研究的HapMap平台的开发自然是一个跨学科的项目，高中、本科生和研究生将发现许多项目整合了他们在植物生物学、微生物学、种群遗传学和生物信息学方面的知识。该项目将与哈姆莱恩大学合作开发新的本科课程，还将接触来自哈姆莱恩大学和波多黎各大学的本科生，以及来自新墨西哥州各地机构的高中生，作为暑期实习生参加直接参与Medicago HapMap和共生项目的项目。这些研究实习生将由一群跨越多个研究生项目的研究生组成，他们由从生物统计学到植物病理学和土壤学的所有学术部门的联合PI教员共同提供建议。

PI: Nevin D. Young (University of Minnesota)CoPIs: Michael J. Sadowsky and Peter L. Tiffin (University of Minnesota), Maria J. Harrison (Boyce Thompson Institute for Plant Research), Betsy M. Martinez-Vaz (Hamline University), and Joann Mudge (National Center for Genome Resources)Collaborators: Gregory D. May (National Center for Genome Resources)Legumes, the third largest family of flowering plants, are notable for their ability to form symbiotic relationships with rhizobia bacteria. This symbiosis leads to massive amounts of biological nitrogen worldwide, providing a major source of organic fertilizer and vegetable protein for humans and animals. Medicago truncatula is a widely studied model species for legume genomics and one important question focuses on the identity of naturally occurring genes that control variation in symbiosis in legumes. This project will use association mapping techniques to create a Medicago "HapMap". In brief, 384 diverse genetic lines obtained from collaborators at INRA-Montpellier, Ecole National Superieur Agronomique de Toulouse (ENSAT) and the Noble Foundation will be resequenced using next generation sequencing technology for sequence polymorphisms (SNPs) between the different Medicago lines. SNP discovery through genome resequencing is possible because a reference sequence for the gene-rich euchromatin of Medicago has already been created through previous NSF funding. The massive database of SNPs between Medicago lines enables the prediction of genome segments with shared ancestry (haplotypes), which can then be associated statistically with trait variation in symbiosis. Because of the exceedingly high level of SNP density, association mapping can approach the resolution of a single gene.The broader community of scientists will access the Medicago hapmap platform through an intuitive web interface (to be established) that will be modeled on the human hapmap website (www.hapmap.org). Seed for all lines included in the hapmap will be available by contacting project personnel or directly through INRA-Montpellier, ENSAT and the Noble Foundation (through the GRIN facility). With access to the data and germplasms, scientists will be able to carry out their own association mapping experiments, including traits other than symbiosis. Because the development of a hapmap platform applied to the study of symbiosis in legumes is a naturally cross-disciplinary project, high school, undergraduate and graduate students will find numerous projects that integrate their knowledge of plant biology, microbiology, population genetics and bioinformatics. This project will partner with Hamline University to develop new undergraduate curriculum and will also reach out to undergraduates coming from Hamline University and the University of Puerto Rico, as well as high school students coming from institutions throughout the state of New Mexico to participate as summer interns in projects directly involved in the Medicago hapmap and symbiosis project. These research interns will be complemented by an integrated group of graduate students spanning multiple graduate programs who are co-advised by a co-PI faculty in academic departments all the way from biostatistics to plant pathology and soil science.