Plant & Animal Genomes XV Conference

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

Progress On Physical Mapping Of The Gene-Space Of Barley

Kavitha Madishetty¹ , Pascal Condamine¹ , Matthew Moscou¹ , Jan T Svensson¹ , Jie Zheng² , Steve Wanamaker¹ , Prasanna Bhat¹ , Edmundo Rodriguez¹ , Harkamal Walia¹ , Serdar Bozdag² , Josh Resnik¹ , Hung Le¹ , Shane Heinen³ , Gary H Muehlbauer³ , Ming-Cheng Luo⁴ , Tao Jiang² , Stefano Lonardi² , Heather Witt⁴ , Frank You⁵ , Timothy J Close¹

¹  Dept. of Botany & Plant Sciences, University of California, Riverside, CA, 92521

²  Dept. of Computer Sciences, University of California, Riverside, CA, 92521

³  Dept. of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, 55108

⁴  Dept. of Agronomy & Range Science, University of California, Davis, CA, 95616

⁵  USDA-ARS, Albany, CA 94710

Barley is a diploid member of the tribe Triticeae with a genome size of 5,300 Mb, including more than 80% repetitive DNA. An objective of NSF Plant Genome Research Program project DBI-0321756 has been to enable map-based cloning and set up for genome sequencing by finding gene-bearing BACs in a Morex barley library and creating a physical map of this portion of the genome. We used EST unigene sequences from HarvEST:Barley (harvest.ucr.edu) to design 36-mer overgo probes using OligoSpawn (oligospawn.ucr.edu). We hybridized using pools of generally 192 overgos, increasing the gene-positive BACs from approximately 15,000 previously identified to 83,592. We probed with 12,467 overgos using an improved labeling method with an initial cocktail containing four radiactive nucleotides followed by a cold nucleotide chase. About 35% of the BACs were identified by more than one pool and 3.5% by five or more pools. We derived a function to estimate the number of gene-positive BACs in the Morex library, indicating that 76% of all gene-bearing BACs that can be found, (using the methods that have been employed) have been found. Four-dye fingerprinting and FPC assembly provided 6,579 contigs containing 43,094 clones and 4,355 singletons. The contigs comprise 1,300 Mb of gene-enriched BACs, available online at http://phymap.ucdavis.edu:8080/barley. Through a coupled objective in this NSF project, more than 1000 abiotic-stress-regulated genes have been placed on the barley genetic linkage map. Probes for these genes were included in our BAC hybridization, and work is underway to relate specific BACs to each of these loci.