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

PI：Nevin D. Young（明尼苏达大学）CoPI：Michael J. Sadowsky和Peter L.蒂芬（明尼苏达大学），玛丽亚J哈里森（博伊斯汤普森植物研究所），贝特西M。Martinez-Vaz（Hamline大学）和Joann Mudge（国家基因组资源中心）合作者：Gregory D.豆科植物是开花植物的第三大家族，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。蒺藜苜蓿是豆科植物基因组学研究的一个重要模式物种，其重要问题之一是控制豆科植物共生关系变异的天然基因的身份。本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 Agronomieur Agronomique de图卢兹（ENSAT）和Noble Foundation的合作者处获得的384个不同的遗传品系将使用下一代测序技术对不同苜蓿品系之间的序列多态性（SNP）进行重新测序。通过基因组重测序发现SNP是可能的，因为苜蓿基因丰富的常染色质的参考序列已经通过先前的NSF资助创建。苜蓿品系之间的大量SNP数据库使得能够预测具有共同祖先（单倍型）的基因组片段，然后可以将其与共生中的性状变异统计学关联。由于SNP密度极高，关联作图可以接近单个基因的分辨率。更广泛的科学家社区将通过一个直观的网络界面（有待建立）访问Medicago hapmap平台，该界面将模仿人类hapmap网站（www.hapmap.org）。 hapmap中包含的所有品系的种子将通过联系项目人员或直接通过INRA-蒙彼利埃，ENSAT和Noble基金会（通过GRIN设施）获得。 有了这些数据和胚芽，科学家们将能够进行自己的关联映射实验，包括共生以外的性状。由于应用于豆科植物共生研究的hapmap平台的开发是一个自然的跨学科项目，高中生，本科生和研究生会发现许多项目整合了他们的植物生物学，微生物学，群体遗传学和生物信息学的知识。该项目将与哈姆林大学合作开发新的本科课程，并将接触来自哈姆林大学和波多黎各大学的本科生，以及来自整个新墨西哥州的高中生，作为暑期实习生参加直接参与Medicago hapmap和共生项目的项目。这些研究实习生将得到一个综合的研究生群体的补充，该群体跨越多个研究生课程，由学术部门的共同PI教师共同提供建议，从生物统计学到植物病理学和土壤科学。

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.