Plant & Animal Genome IX Conference

Poster: Sequencing & EST
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SURVEYING THE SOYBEAN GENOME: BAC CONTIGS AND BAC-END SEQUENCES NEAR RFLP AND SSR MARKERS

¹ Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, 55108, USA

² Department of Agronomy, Iowa State University, Ames, Iowa, 50011, USA

³ USDA, Corn Insect and Crop Genetics Research Unit, Iowa State University, Ames, Iowa, 50011, USA

⁴Computational Biology Centers, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA

Because of the highly duplicated nature and large size of the soybean genome, physical mapping is difficult. To facilitate physical mapping efforts, we are developing a scaffold of BAC contigs identified using mapped RFLP and SSR markers and are obtaining BAC-end sequence information for each contig. Because the BAC contigs were identified with mapped molecular markers, the physical scaffold is linked to the soybean genetic map. This set of genetically-anchored contigs and the BAC-end sequences derived from them have given insight into the structure and organization of the soybean genome. BLAST analysis predicted that the SSR-identified BACs have a higher percentage of coding regions then do the RFLP-identified BACs. This difference, however, was largely accounted for by a higher percentage of hits to repetitive coding regions in the SSR-identified BAC-end sequences. Indeed, both library screens had a similar percentage of BAC-end sequences with significant hits to experimentally-defined genes. The BAC-end sequences have also allowed us to explore microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. In addition, probing the BAC libraries with RFLP probes has yielded information on duplicated regions within the soybean genome. This map-based approach to genome sampling provides a means to assay soybean genome structure and organization.

We thank the National Science Foundation for providing funding for this work.