About the Project
We are developing a Medicago Hapmap as part of an international consortium consisting of the University of Minnesota, the National Center for Genome Resources (NCGR), Boyce Thompson Institute (BTI), J. Craig Venter Institute (JCVI) Hamline University, INRA-Montpellier, ENSAT-Toulouse, and the Noble Foundation.
Briefly, 384 inbred lines spanning the range of Medicago diversity are being resequenced using Illumina next generation technology. This provides a foundation for discovering single nucleotide polymorphisms (SNPs), insertions/deletions (INDELs) and copy number variants (CNV) at very high resolution among the Medicago lines. Thirty of these lines have been deeply resequenced (20X coverage or more), while the remainder are sequenced at least 5X coverage. The resulting database of sequence variants establishes a basis for describing population structure and identifying genome segments with shared ancestry (haplotypes) - and thereby creating a long-term, community-accessible genome-wide association (GWA) mapping resource.
GWA studies in the model legume Medicago truncatula will enable the exploration of genes and gene-systems that play a role in the contemporary evolution of symbiosis with rhizobia and mycorrhizal fungi. With this goal in mind, we are assaying these same line for symbiosis-related phenotypes through greenhouse experiments involving several Sinorhizobium isolates and Glomus species. Together, the Medicago hapmap and corresponding phenotype data will help to uncover genotype/phenotype associations related to symbiotic success.
All Hapmap resources will be available to enable studies into the genetic basis of other evolutionarily important traits in Medicago.
Primary funding for the Medicago Hapmap project comes from the Plant Genome Program of the National Science Foundation.