PHYSICAL MAPPING OF THE AEGILOPS TAUSCHII GENOME

 

Ming-Cheng Luo1, Karin R Deal1, Carolyn Thomas1, Patrick E. McGuire2,

Wanloyng Li3, Vasu Kuraparthy3, Bikram S. Gill3, Frank M. You4,

Yong-Qiang Gu4, Olin D. Anderson4 and Jan Dvorak1*

1 Department of Plant Sciences, University of California, Davis, CA 95616, USA

2 Genetic Resources Conservation Program, University of California, Davis, CA 95616, USA

3 Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA

4 USDA/ARS, 800 Buchanan St, Albany, CA 94710, USA

*Corresponding Author: PH: (530) 752-6549; E-mail: jdvorak@ucdavis.edu

 

The large size of wheat genomes will almost certainly preclude the use of whole-genome shotgun sequencing strategy for wheat genome sequencing. Physical maps of wheat chromosomes will be critical for the BAC-by-BAC sequencing strategy or for targeted sequencing of gene-rich regions. Wheat physical maps will also be an invaluable resource for positional gene cloning and elucidation of genome structure. To construct physical maps of hexaploid wheat will require fingerprinting a minimum of 1.5 million BAC clones. Although it is possible to fingerprint this many clones with the SNaPshot fingerprinting technique in a span of one to two years, it is currently unknown if biological limits will permit contig assembly from such a large number of clones. We are assessing techniques for contig assembly and physical mapping of wheat by using the genome of Aegilops tauschii, the ancestor of the wheat D genome, as a model using BAC and BiBAC libraries of Ae. tauschii ssp. strangulata, accession AL8/78, that showed a close genetic proximity to the D genome of Chinese Spring wheat. Total of 270,720 BAC and BiBAC clones, which included the entire BamHI, EcoRI, HindIII BAC libraries, the entire HindIII BiBAC library, and a portion of the BamHI BiBAC library, were fingerprinted and edited with Genoprofiler, a computer program for automated editing of fingerprints. 199,190 clones were used for contig assembly. A total of eight assemblies were performed and the most recent assembly (assembly #1.1 on the project databases) resulted in 7,447 contigs and 5,304 singletons. The fingerprints, contigs, and BAC clone anchoring can be accessed in the project databases (http://wheatdb.ucdavis.edu:8080/wheatdb/).