Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Coupling Expressed Sequences And Bacterial Artificial Chromosome Resources To Access The Barley Genome

Timothy J Close¹ , Jan T Svensson¹ , Jie Zheng² , Stefano Lonardi² , Tao Jiang² , Steve Wanamaker¹ , Frank M You³ , Heather N Witt³ , Ming-Cheng Luo³

¹  Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521,USA

²  Department of Computer Sciences, University of California, Riverside, CA, 92521,USA

³  Department of Agronomy & Range Science, University of California, Davis, CA, 95616,USA

Barley genomic resources now include BAC and cDNA libraries, several widely used mapping populations, about 400,000 ESTs representing about 70% of all barley genes, and a 22K microarray. In work supported by North American Barley Genome Project and National Science Foundation Plant Genome Research Program, we aim to couple these resources to facilitate access of US and worldwide researchers to the barley genome. The unifying objective is to accelerate a transition to comprehensive physical mapping and sequencing of the “gene-space”. We utilize knowledge of unigene sequences to create 36-mer “overgo” probes to identify Morex BAC clones that carry expressed genes. We then apply a genetic fingerprinting technique to create thousands of contigs of these BAC clones, from which a minimal set can be identified. Special emphasis is given to 1000 genes related to abiotic stress, including drought, low temperature, heat, and salinity, such that these genes and their corresponding BACs will be anchored to the genetic linkage map. The “OligoSpawn” website http://oligospawn.ucr.edu provides access to elements of our oligo design algorithms. The “HarvEST” website http://harvest.ucr.edu provides access to sequence assemblies, unigene sequences and function annotations. The “Barley Genome” website http://phymap.ucdavis.edu:8080/barley/ provides access to BAC contig data. About 50% of the Morex barley gene-bearing BACs seem to have been found so far, based on compilation of results from our own work and that of collaborators Andris Kleinhofs, Gary Muehlbauer, Roger Wise, Patrick Hayes, Kulvinder Gill, Nils Stein, MA Saghai Maroof and their co-workers.