Tuesday, November 14, 2006 - 10:00 AM

Developing a high-density single nucleotide polymorphism (SNP) map of barley.

Timothy Close1, Nils Rostoks2, Luke Ramsay2, Jan Svensson1, Prasanna Bhat1, Mikeal Roose1, Robbie Waugh2, Patrick Hayes3, Peter Szucs3, and Gary Muehlbauer4. (1) University of California-Riverside, Department of Botany and Plant Sciences, Riverside, CA 92521, (2) Scottish Crop Research Institute, Genetics, Invergowrie, United Kingdom, (3) Oregon State University, OSU-Dept. Crop Science, 30th & Campus Way CS Bldg.107, Corvallis, OR 97331-8506, (4) University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN 55108

The barley Coordinated Agricultural Project (CAP), in collaboration with the Scottish Crop Research Institute, is extending the current 1,100 locus barley SNP map to include nearly 3,000 loci.  These SNP-marked loci will become the centerpiece of a genotyping activity located at the USDA genotyping facility in Fargo, North Dakota and will be used for a variety of applications including: haplotype and association genetics analysis of barley germplasm; marker assisted selection, map-based cloning, and as a scaffold for physical map development and genome sequencing.  SNPs for this project were drawn from a database of more than 15,000 SNPs defined using a combination of EST and amplicon sequences.  We are using Illumina’s GoldenGate Assay, which involves the BeadArray™ platform.  In this project, we will use two oligonucleotide pool assays (OPAs), each containing 1,536 SNPs.  Currently, these OPAs are proceeding through design and testing.  This design and testing phase of the project includes the placement of new loci on the barley genetic linkage map using three barley doubled haploid mapping populations: the Morex x Barke, Oregon Wolfe Barley, and Steptoe x Morex populations. Ultimately, during the four year USDA-funded barley CAP we will determine the allele at each of approximately 3000 loci in 3840 barley genotypes that are pertinent to US barley breeding programs.