Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

A High-Density Linkage Map Of Brachypodium distachyon

John P. Vogel¹ , Naxin Huo^1,2 , David F. Garvin³ , Yong Q. Gu¹ , Frank M. You² , Stephanie McMahon¹ , Gerard R. Lazo¹ , Olin D. Anderson¹ , Mingcheng Luo²

¹  Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA

²  Department of Plant Sciences, University of California, Davis, CA 95616, USA

³  USDA-ARS Plant Science Research Unit, 411 Borlaug Hall, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA

A high-density genetic linkage map is necessary to fully realize the potential of the small grass Brachypodium distachyon as a model system. To fulfill this need, we developed a genetic linkage map using SNP markers and an F₂ mapping population derived from parental inbred lines Bd21 and Bd3-1. SNPs were identified by targeted resequencing of Bd3-1 and comparison to Bd21 BAC end and genomic sequences. We identified 3,337 SNPs at 968 loci. SNPs at 667 of those loci were predicted to be suitable for use as genetic markers using the Illumina GoldenGate Genotyping platform. Genotyping of 476 F₂ individuals was completed and acceptable data was obtained for 562 markers. All 562 markers were placed into 5 linkage groups corresponding to the 5 chromosomes of Brachypodium. The first use of the genetic map was to aid and verify the final assembly of the 8x shotgun sequence produced by JGI. The development and analysis of the map, including an overview of recombination frequency across the genome, will be presented.