PAG-XV  Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA


W40 : Barley

An Integrated Genotyping Platform For Barley

Timothy J Close1 , Nils Rostoks2 , Luke Ramsay2 , Jan T Svensson1 , Prasanna Bhat1 , Mikeal L Roose1 , Robbie Waugh2 , Nils Stein3 , Patrick Hayes4 , Peter Szucs4 , Gary J Muehlbauer5 , Barley CAP 5 , AGOUEB consortium2

1  Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
2  Genetics, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA Scotland
3  Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
4  Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331 USA
5  Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA

An international collaboration has been established to develop a high-density SNP map of barley and utilize the SNP markers to genotype barley germplasm. The US barley coordinated agricultural project (CAP) and UK Association Genetics in Elite UK Barley (AGOUEB) project, with input from IPK, have co-developed an integrated genotyping platform for barley. A 1,153 locus SNP map has been developed and the next task is to extend this map to contain ~3,000 loci. SNPs for this project were derived from an EST database and amplicon re-sequencing. We are using Illumina’s GoldenGate Assay, which involves the BeadArray™ platform for SNP detection. The genetic map will be the foundation for a variety of studies ranging from haplotype and association analysis of breeding germplasm, integration with the emerging barley physical map, and a scaffold for genome sequencing. The barley CAP will determine the allele at each of approximately 3,000 SNP loci and assess over 40 traits in 3,840 barley genotypes that are pertinent to US barley breeding programs. In parallel, AGOUEB will examine 3,000 SNP alleles on 1,500 breeding lines of importance to North Western Europe. Haplotype-trait associations will be identified using a whole genome LD-scanning approach that we have previously shown to be possible in elite barley cultivars using this order of bi-allelic SNPs. In both projects, data will be stored in a ‘Germinate’ database with access in the US through a web portal called The Hordeum Toolbox. Current progress on these international projects will be described.