About this 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, the University of Southern California, 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.
Primary funding for the Medicago Hapmap project comes from the Plant Genome Program of the National Science Foundation.
News
August 2017
Reference quality sequence for R108 published in BMC-Genomics
March 2017
Medicago de novo assemblies published in BMC-Genomics.
January 2017
GWAS candidate validation published in Plant Physiology.
June 2016
Genome sequence for CADL, “Cultivated Alfalfa at the Diploid Level” (v. 0.95P)
March 2016
Blast search against de novo assemblies
May 2015
ALLPATH de novo assemblies for 20 M. truncatula accessions
April 2014
Updated SNPs against Mt4.0 now available.
May 2013
Genome-wide association analysis of Medicago Hapmap published in PLoS ONE
November 2011
Medicago genome sequence published in Nature and PNAS
