Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Connecting The Barley Genetic And Physical Maps For 1000 Abiotic Stress Genes

Jan T. Svensson¹ , Kavitha Madishetty¹ , Jie Zheng² , Jin Xu³ , Pascal Condamine¹ , Rehana Ashgar¹ , Steve Wanamaker¹ , Prasanna Bhat¹ , Matt Moscou¹ , Edmundo Rodriguez¹ , Harkamal Walia¹ , Josh Resnik¹ , Hung Le¹ , Serdar Bozdag² , Heather Witt⁴ , Frank You⁵ , Nils Rostoks⁶ , Robbie Waugh⁶ , Nils Stein⁷ , Rajeev Varshney⁷ , Andreas Graner⁷ , Ming-Chen Luo⁴ , Xinping Cui³ , Tao Jiang² , Stefano Lonardi² , Timothy J. Close¹

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

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

³  Dept. of Statistics, University of California, Riverside, CA, 92521, USA

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

⁵  USDA-ARS, Albany, CA 94710, USA

⁶  Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK

⁷  Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Germany.

We have an objective to genetically and physically map 1000 abiotic stress-related genes of barley. We conducted microarray analyses on ABA-, drought-, salt- and low temperature-treated barley to create an extended list of abiotic stress responsive genes. A total of 7,735 abiotic stress probe sets were found, representing 7,422 unigenes. The Morex BAC library was probed with overgos designed from most of these genes by our UC Riverside group and by collaborator G Muehlbauer (U Minnesota). BAC fingerprinting and contig assembly is in progress. From the assembled contigs we will derive a minimal tiling path. These BACs will be used to deconvulate overgo:BAC relationships. To genetically map 1,000 stress-related genes we made use of single nucleotide polymorphisms (SNPs) evident in EST sequences, we discovered a total of 12,615 SNPs in 3,509 unigenes. This was supplemented by SNP information provided by co-authors at SCRI (565 unigenes) and IPK (217 unigenes) from PCR amplicon sequences. The SNPs were used for design of a high-throughput bead-array representing 1524 barley loci. Genotyping was done using three doubled haploid (DH) mapping populations (Steptoe x Morex, Morex x Barke, and Oregon Wolfe Barleys), genotyping data is currently being analyzed and some results will be presented. We also explored single feature polymorphism (SFP) in gene expression data for these same three mapping population parents. Several thousand SFP markers seem to be satisfactory. This work was supported by grants from NSF and USDA.