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.