Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

The Medicago truncatula HapMap Project: Deep Coverage Sequencing Of 30 Inbred Lines Using Illumina’s Solexa Technology

Antoine Branca¹ , Tim Paape¹ , Roman Briskine² , Peng Zhou² , Shelley Wang² , Roxanne Denny² , Joann Mudge³ , Arvind K. Bharti³ , Andrew Farmer³ , Gregory D. May³ , Peter L. Tiffin¹ , Nevin D. Young²

¹  Department of Plant Biology--University of Minnesota, St Paul, MN, 55108, USA

²  Department of Plant Pathology--University of Minnesota, St Paul, MN, 55108, USA

³  National Center for Genome Resources, Santa Fe, New Mexico 87505, USA

Medicago truncatula is a model legume that is also central to the study of mutualist interactions with Sinorhizobium bacteria and the process of biological nitrogen fixation. The Medicago HapMap Project initially consists of sequencing the whole-genomes of 30 inbred lines (eventually 384 lines) with deep coverage through an Illumina Solexa sequencing pipeline. In parallel, multiple plant phenotypes revealing symbiotic success are being monitored in greenhouse experiments on the Medicago lines. The two main objectives are to explore genetic basis of symbiosis and to create a robust platform for genome-scale association mapping. Here we present a preliminary study about the performance of Solexa sequencing to detect single nucleotide polymorphism (SNP) and insertions and deletions (INDEL) in the Medicago truncatula genome. Small regions of DNA were sequenced by Solexa and the classic Sänger method and followed by alignment to the reference genome using GSNAP software. The fragments for Sänger sequencing were chosen randomly throughout the genome among exons, introns and intergenic space. Three inbred lines were used for validation data with a mean total length per line of ~20kB. This step allowed us to choose the best parameters to use in GSNAP alignment and in filtering SNPs and INDELs (i.e. those providing the best balance between Type-I and Type-II error). We also introduce here the preliminary results on patterns of polymorphism in Medicago truncatula across the lines completed so far.