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),
the University of Southern California,
CBBC-Tunisia and the
Briefly, 384 predominantly inbred lines spanning the range of Medicago diversity are being resequenced using Illumina/Solexa next generation technology. This will provide a foundation for discovering single nucleotide polymorphisms (SNPs), insertion/deletions (INDELs) and copy number variants (CNV) at very high resolution among the Medicago lines. Thirty of these lines will be deeply resequenced (20X coverage or more), while the remainder will be sequenced at least 5X coverage. The resulting database of sequence variants will establish a basis for describing population structure and identifying genome segments with shared ancestry (haplotypes) – and thereby create a long-term, community-accessible GWAS resource.
Whole-genome association studies (GWAS) 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.