Medicago Hapmap

We are building a hapmap based on short-read sequencing of approximately 330 inbred Medicago truncatula accessions. This provides a foundation for discovering single nucleotide polymorphisms (SNPs), insertions/ deletions (INDELs) and copy number variants (CNV's) at very high resolution among the Medicago lines. The resulting database of sequence variants establishes a basis for describing population structure and identifying genome segments with shared ancestry (haplotypes) - and thereby creates a long-term, community resource for genome-wide association studies.

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.

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News

July 2014

7th International Conference on Legume Genetics and Genomics Congress in combination with the International Food Legumes Research Conference (Saskatoon, Canada)

January 2014

Blast search now available against draft R108 sequence.

August 2013

Mt4.0 released by J. Craig Venter Institute.

May 2013

Genome-wide association analysis of Medicago Hapmap published in PLoS ONE

October 2012

6th International Conference on Legume Genetics and Genomics (Hyderabad, India)

August 2012

medicagohapmap.org website upgrade

November 2011

Medicago genome sequence published in Nature

October 2011

Medicago sequence diversity published in PNAS

New R108 Blast Available

Site hosted by: Nevin Young's Lab at University of Minnesota. Managed By: Joseph Guhlin

Primary Collaborators: INRA - Montpellier | ENSAT - Toulouse | Noble Foundation | University of Southern California

Co-Principal Investigators: University of Minnesota N. Young, P. Tiffin, M. Sadowsky, B. Stupar, K. Silverstein | NCGR J. Mudge, A. Farmer

Boyce Thompson Institute M. Harrison | Hamline University B. Martinez-Vaz